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Martín M, Yoder R, Salgado R, Del Monte-Millán M, Alvarez EL, Echavarría I, Staley JM, O'Dea AP, Nye LE, Stecklein SR, Bueno Muiño C, Jerez-Gilarranz Y, Cebollero M, Bueno O, Garcia-Saenz JÁ, Moreno F, Bohn U, Gomez H, Massarrah T, Khan QJ, Godwin AK, López-Tarruella S, Sharma P. Tumor-infiltrating lymphocytes refine outcomes in triple-negative breast cancer treated with anthracycline-free neoadjuvant chemotherapy. Clin Cancer Res 2024:735115. [PMID: 38466643 DOI: 10.1158/1078-0432.ccr-24-0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Stromal tumor-infiltrating lymphocytes (sTILs) are associated with pathologic complete response (pCR) and long-term outcomes for triple-negative breast cancer (TNBC) in setting of anthracycline-based chemotherapy. Impact of sTILs on refining outcomes beyond prognostic information provided by pCR in anthracycline-free neoadjuvant chemotherapy (NAC) is not known. PATIENTS & METHODS This is pooled analysis of two studies where patients with stage I(T>1cm)-III TNBC received carboplatin(AUC 6) plus docetaxel(75mg/m2) (CbD) NAC. sTILs were evaluated centrally on pre-treatment H&E slides using standard criteria. Cox regression analysis was used to examine effect on event-free survival (EFS) and overall survival (OS). RESULTS Among 474 patients, 44% had node-positive disease. Median sTILs were 5% (range 1%-95%), and 32% of patients had ≥30% sTILs. pCR rate was 51%. On multivariable analysis, T stage (OR=2.08,p=0.007), nodal status (OR=1.64,p=0.035), and sTILs (OR=1.10,p=0.011) were associated with pCR. On multivariate analysis, nodal status (HR=0.46,p=0.008), pCR(HR=0.20,p<0.001), and sTILs(HR=0.95,p=0.049) were associated with OS. At 30% cut-point, sTILs stratified outcomes in stage III disease, 5-year OS 86% vs 57% in ≥30% vs <30% sTILs (HR=0.29,p=0.014), and numeric trend in stage II, 5-year OS 93% vs 89% in ≥30% vs <30% sTILs (HR=0.55,p=0.179). Among stage II-III patients with pCR, EFS was better in those with ≥30% sTILs (HR=0.16,p=0.047). CONCLUSIONS sTILs density was independent predictor of OS beyond clinicopathologic features and pathologic response in TNBC patients treated with anthracycline-free CbD chemotherapy. Notably, sTILs density stratified outcomes beyond TNM stage and pathologic response. These findings highlight role of sTILs in patient selection/stratification for neo/adjuvant escalation and de-escalation strategies.
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Affiliation(s)
- Miguel Martín
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón Instituto de Investigacion Sanitaria Gregorio Marañon, CIBERONC, Universidad Complutense, Madrid., Madrid, Spain
| | - Rachel Yoder
- University of Kansas Cancer Center, Westwood, KS, United States
| | | | - Maria Del Monte-Millán
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón Instituto de Investigación Sanitaria Gregorio Marañón, CIBERONC, Madrid, Spain, Madrid, Spain
| | | | - Isabel Echavarría
- Instituto de Investigación Sanitaria Gregorio Marañon (IiSGM), Madrid, Spain
| | - Joshua M Staley
- University of Kansas Medical Center, Westwood, KS, United States
| | - Anne P O'Dea
- University of Kansas Medical Center, Westwood, KS, United States
| | - Lauren E Nye
- University of Kansas, Westwood, KS, United States
| | | | | | | | - María Cebollero
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Oscar Bueno
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | | | - Uriel Bohn
- Hospital de Gran Canaria Dr. Negrín, Las Palmas, Spain
| | - Henry Gomez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | - Qamar J Khan
- University of Kansas Medical Center, Westwood, KS, United States
| | - Andrew K Godwin
- University of Kansas Medical Center, Kansas City, KS, United States
| | - Sara López-Tarruella
- Medical Oncology Service, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Universidad Complutense,, Madrid, Spain
| | - Priyanka Sharma
- University of Kansas Medical Center, Westwood, KS, United States
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Barnes DR, Tyrer JP, Dennis J, Leslie G, Bolla MK, Lush M, Aeilts AM, Aittomäki K, Andrieu N, Andrulis IL, Anton-Culver H, Arason A, Arun BK, Balmaña J, Bandera EV, Barkardottir RB, Berger LP, de Gonzalez AB, Berthet P, Białkowska K, Bjørge L, Blanco AM, Blok MJ, Bobolis KA, Bogdanova NV, Brenton JD, Butz H, Buys SS, Caligo MA, Campbell I, Castillo C, Claes KB, Colonna SV, Cook LS, Daly MB, Dansonka-Mieszkowska A, de la Hoya M, deFazio A, DePersia A, Ding YC, Domchek SM, Dörk T, Einbeigi Z, Engel C, Evans DG, Foretova L, Fortner RT, Fostira F, Foti MC, Friedman E, Frone MN, Ganz PA, Gentry-Maharaj A, Glendon G, Godwin AK, González-Neira A, Greene MH, Gronwald J, Guerrieri-Gonzaga A, Hamann U, Hansen TV, Harris HR, Hauke J, Heitz F, Hogervorst FB, Hooning MJ, Hopper JL, Huff CD, Huntsman DG, Imyanitov EN, Izatt L, Jakubowska A, James PA, Janavicius R, John EM, Kar S, Karlan BY, Kennedy CJ, Kiemeney LA, Konstantopoulou I, Kupryjanczyk J, Laitman Y, Lavie O, Lawrenson K, Lester J, Lesueur F, Lopez-Pleguezuelos C, Mai PL, Manoukian S, May T, McNeish IA, Menon U, Milne RL, Modugno F, Mongiovi JM, Montagna M, Moysich KB, Neuhausen SL, Nielsen FC, Noguès C, Oláh E, Olopade OI, Osorio A, Papi L, Pathak H, Pearce CL, Pedersen IS, Peixoto A, Pejovic T, Peng PC, Peshkin BN, Peterlongo P, Powell CB, Prokofyeva D, Pujana MA, Radice P, Rashid MU, Rennert G, Richenberg G, Sandler DP, Sasamoto N, Setiawan VW, Sharma P, Sieh W, Singer CF, Snape K, Sokolenko AP, Soucy P, Southey MC, Stoppa-Lyonnet D, Sutphen R, Sutter C, Teixeira MR, Terry KL, Thomsen LCV, Tischkowitz M, Toland AE, Van Gorp T, Vega A, Velez Edwards DR, Webb PM, Weitzel JN, Wentzensen N, Whittemore AS, Winham SJ, Wu AH, Yadav S, Yu Y, Ziogas A, Berchuck A, Couch FJ, Goode EL, Goodman MT, Monteiro AN, Offit K, Ramus SJ, Risch HA, Schildkraut JM, Thomassen M, Simard J, Easton DF, Jones MR, Chenevix-Trench G, Gayther SA, Antoniou AC, Pharoah PD. Large-scale genome-wide association study of 398,238 women unveils seven novel loci associated with high-grade serous epithelial ovarian cancer risk. medRxiv 2024:2024.02.29.24303243. [PMID: 38496424 PMCID: PMC10942532 DOI: 10.1101/2024.02.29.24303243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Nineteen genomic regions have been associated with high-grade serous ovarian cancer (HGSOC). We used data from the Ovarian Cancer Association Consortium (OCAC), Consortium of Investigators of Modifiers of BRCA1/BRCA2 (CIMBA), UK Biobank (UKBB), and FinnGen to identify novel HGSOC susceptibility loci and develop polygenic scores (PGS). Methods We analyzed >22 million variants for 398,238 women. Associations were assessed separately by consortium and meta-analysed. OCAC and CIMBA data were used to develop PGS which were trained on FinnGen data and validated in UKBB and BioBank Japan. Results Eight novel variants were associated with HGSOC risk. An interesting discovery biologically was finding that TP53 3'-UTR SNP rs78378222 was associated with HGSOC (per T allele relative risk (RR)=1.44, 95%CI:1.28-1.62, P=1.76×10-9). The optimal PGS included 64,518 variants and was associated with an odds ratio of 1.46 (95%CI:1.37-1.54) per standard deviation in the UKBB validation (AUROC curve=0.61, 95%CI:0.59-0.62). Conclusions This study represents the largest GWAS for HGSOC to date. The results highlight that improvements in imputation reference panels and increased sample sizes can identify HGSOC associated variants that previously went undetected, resulting in improved PGS. The use of updated PGS in cancer risk prediction algorithms will then improve personalized risk prediction for HGSOC.
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Affiliation(s)
- Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Amber M. Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Nadine Andrieu
- Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Irene L. Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Adalgeir Arason
- Department of Pathology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Department of Medical Oncology, University Hospital of Vall d’Hebron, Barcelona, Spain
| | - Elisa V. Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lieke P.V. Berger
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, The Netherlands
| | | | - Pascaline Berthet
- Département de Biopathologie, Centre François Baclesse, Caen, France
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amie M. Blanco
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, USA
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kristie A. Bobolis
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - James D. Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- National Tumour Biology Laboratory, National Institute of Oncology, Budapest, Hungary
- Department of Oncology Biobank, National Institute of Oncology, Budapest, Hungary
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, USA
| | | | - Ian Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Carmen Castillo
- Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Barcelona, Spain
| | - Kathleen B.M. Claes
- Centre for Medical Genetics, Ghent University, Gent, Belgium
- Department of Biomolecular Medicine, University of Ghent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | | | - EMBRACE Collaborators
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Sarah V. Colonna
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, UT, USA
| | - Linda S. Cook
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Medicine, Institute of Oncology and Maria Sklodowska-Curie Cancer Center, Warsaw, Poland
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - Allison DePersia
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Zakaria Einbeigi
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - D. Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St. Mary’s Hospital, Manchester, UK
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St. Mary’s Hospital, Manchester, UK
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Renée T. Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | | | - Eitan Friedman
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Assuta Medical Center, Tel-Aviv, Israel
| | - Megan N. Frone
- National Cancer Institute, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Patricia A. Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Centre, UCLA, Los Angeles, CA, USA
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre, Madrid, Spain
- Spanish Network on Rare Diseases, Madrid, Spain
| | - Mark H. Greene
- National Cancer Institute, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Aliana Guerrieri-Gonzaga
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas v.O. Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Holly R. Harris
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | - Frans B.L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David G. Huntsman
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - kConFab Investigators
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Louise Izatt
- Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center and the Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ramunas Janavicius
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
- Hematology, Oncology and Transfusion Medicine Center, Oncogenetics Unit, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Esther M. John
- Department of Epidemiology & Population Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Catherine J. Kennedy
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Medicine, Institute of Oncology and Maria Sklodowska-Curie Cancer Center, Warsaw, Poland
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ofer Lavie
- Technion-Israel Institute of Technology, Haifa, Israel
- Carmel Medical Center, Haifa, Israel
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women’s Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Carlos Lopez-Pleguezuelos
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Escola de Doutoramento Internacional, Universidade de Santiago, Santiago de Compostela, Spain
| | - Phuong L. Mai
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Taymaa May
- Princess Margaret Cancer Center, Toronto, Canada
| | - Iain A. McNeish
- Division of Cancer and Ovarian Cancer Action Research Centre, Department Surgery & Cancer, Imperial College London, London, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Roger L. Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Francesmary Modugno
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jennifer M. Mongiovi
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | | | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Catherine Noguès
- Département d’Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes, Marseille, France
- Aix Marseille Université, INSERM, IRD, SESSTIM, Marseille, France
| | - Edit Oláh
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Ana Osorio
- Spanish Network on Rare Diseases, Madrid, Spain
- Familial Cancer Clinical Unit, Human Cancer Genetics Programme, Madrid, Spain
| | - Laura Papi
- Department of Experimental and Clinical Biomedical Sciences ‘Mario Serio’, Medical Genetics Unit, University of Florence, Florence, Italy
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Celeste L. Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Inge S. Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Ana Peixoto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Tanja Pejovic
- Department of Obstetrics & Gynecology, Providence Medical Center, Medford, OR, USA
- Providence Cancer Center, Medford, OR, USA
| | - Pei-Chen Peng
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Beth N. Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Jess and Mildred Fisher Center for Hereditary Cancer and Clinical Genomics Research, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - C. Bethan Powell
- Hereditary Cancer Program, Kaiser Permanente Northern California, San Francisco, CA, USA
| | | | - Miquel Angel Pujana
- ProCURE, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Barcelona, Spain
- ProCURE, IDIBGI (Girona Biomedical Research Institute), Catalan Institute of Oncology, Girona, Spain
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Gad Rennert
- Technion-Israel Institute of Technology, Haifa, Israel
- The Association for Promotion of Research in Precision Medicine, Haifa, Israel
| | - George Richenberg
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Rockville, MD, USA
| | - Naoko Sasamoto
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Veronica W. Setiawan
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Weiva Sieh
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian F. Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Katie Snape
- Medical Genetics Unit, St George’s, University of London, London, UK
| | - Anna P. Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, QC, Canada
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Parkville, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, East Melbourne, Victoria, Australia
| | - Dominique Stoppa-Lyonnet
- Genetics Department, Institut Curie, Paris, France
- Unité INSERM U830, Paris, France
- Université Paris Cité, Paris, France
| | - Rebecca Sutphen
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Kathryn L. Terry
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Liv Cecilie V. Thomsen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Norway
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Amanda E. Toland
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Toon Van Gorp
- Division of Gynecologic Oncology, University Hospital Leuven, Leuven, Belgium
- Leuven Cancer Institute, University of Leuven, Leuven, Belgium
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Digna R. Velez Edwards
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Penelope M. Webb
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alice S. Whittemore
- Department of Epidemiology & Population Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Anna H. Wu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Marc T. Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- AnaNeo Therapeutics, New York, NY, USA
| | - Susan J. Ramus
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW Sydney, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia
| | - Harvey A. Risch
- Chronic Disease Epidemiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec – Université Laval Research Center, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Michelle R. Jones
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul D.P. Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Saeed A, Park R, Pathak H, Al-Bzour AN, Dai J, Phadnis M, Al-Rajabi R, Kasi A, Baranda J, Sun W, Williamson S, Chiu YC, Osmanbeyoglu HU, Madan R, Abushukair H, Mulvaney K, Godwin AK, Saeed A. Clinical and biomarker results from a phase II trial of combined cabozantinib and durvalumab in patients with chemotherapy-refractory colorectal cancer (CRC): CAMILLA CRC cohort. Nat Commun 2024; 15:1533. [PMID: 38378868 PMCID: PMC10879200 DOI: 10.1038/s41467-024-45960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
CAMILLA is a basket trial (NCT03539822) evaluating cabozantinib plus the ICI durvalumab in chemorefractory gastrointestinal cancer. Herein, are the phase II colorectal cohort results. 29 patients were evaluable. 100% had confirmed pMMR/MSS tumors. Primary endpoint was met with ORR of 27.6% (95% CI 12.7-47.2%). Secondary endpoints of 4-month PFS rate was 44.83% (95% CI 26.5-64.3%); and median OS was 9.1 months (95% CI 5.8-20.2). Grade≥3 TRAE occurred in 39%. In post-hoc analysis of patients with RAS wild type tumors, ORR was 50% and median PFS and OS were 6.3 and 21.5 months respectively. Exploratory spatial transcriptomic profiling of pretreatment tumors showed upregulation of VEGF and MET signaling, increased extracellular matrix activity and preexisting anti-tumor immune responses coexisting with immune suppressive features like T cell migration barriers in responders versus non-responders. Cabozantinib plus durvalumab demonstrated anti-tumor activity, manageable toxicity, and have led to the activation of the phase III STELLAR-303 trial.
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Affiliation(s)
- Anwaar Saeed
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Robin Park
- Division of Hematology and Medical Oncology, Moffitt Cancer Cente, Tampa, FL, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ayah Nedal Al-Bzour
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Junqiang Dai
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Milind Phadnis
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Raed Al-Rajabi
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Anup Kasi
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Joaquina Baranda
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Weijing Sun
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Stephen Williamson
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, Ks, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
| | | | | | - Rashna Madan
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Hassan Abushukair
- Department of Medicine, Division of Hematology & Oncology, University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, USA
| | - Kelly Mulvaney
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Azhar Saeed
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, USA
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4
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Sharma P, Stecklein SR, Yoder R, Staley JM, Schwensen K, O’Dea A, Nye L, Satelli D, Crane G, Madan R, O’Neil MF, Wagner J, Larson KE, Balanoff C, Kilgore L, Phadnis MA, Godwin AK, Salgado R, Khan QJ, O’Shaughnessy J. Clinical and Biomarker Findings of Neoadjuvant Pembrolizumab and Carboplatin Plus Docetaxel in Triple-Negative Breast Cancer: NeoPACT Phase 2 Clinical Trial. JAMA Oncol 2024; 10:227-235. [PMID: 37991778 PMCID: PMC10666040 DOI: 10.1001/jamaoncol.2023.5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 11/23/2023]
Abstract
Importance Addition of pembrolizumab to anthracycline-based chemotherapy improves pathologic complete response (pCR) and event-free survival (EFS) in triple-negative breast cancer (TNBC). The efficacy of anthracycline-free chemoimmunotherapy in TNBC has not been assessed. Objective To assess the efficacy of the anthracycline-free neoadjuvant regimen of carboplatin and docetaxel plus pembrolizumab in TNBC. Design, Setting, and Participants This was an open-label phase 2 clinical trial including a single group of patients with stage I to III TNBC enrolled at 2 sites who received neoadjuvant carboplatin and docetaxel plus pembrolizumab every 21 days for 6 cycles. Participants were enrolled from 2018 to 2022. Intervention or Exposure Carboplatin (with an area under the free carboplatin plasma concentration vs time curve of 6) and docetaxel (75 mg/m2) plus pembrolizumab (200 mg) every 21 days for 6 cycles. Myeloid growth factor support was administered with all cycles. Main Outcomes and Measures Primary end point was pathologic complete response (pCR) defined as no evidence of invasive tumor in breast and axilla. The secondary end points were residual cancer burden, EFS, toxicity, and immune biomarkers. RNA isolated from pretreatment tumor tissue was subjected to next-generation sequencing. Specimens were classified as positive or negative for the 44-gene DNA damage immune response (DDIR) signature and for the 27-gene tumor immune microenvironment (TIM; DetermaIO) signature using predefined cutoffs. Stromal tumor-infiltrating lymphocytes (sTILs) were evaluated using standard criteria. Programmed cell death-ligand 1 (PD-L1) testing was performed using a standard immunohistochemical assay. Results Among the eligible study population of 115 female patients (median [range] age, 50 [27-70] years) who enrolled from September 2018 to January 2022, 39% had node-positive disease. pCR and residual cancer burden 0 + 1 rates were 58% (95% CI, 48%-67%) and 69% (95% CI, 60%-78%), respectively. Grade 3 or higher immune-mediated adverse events were observed in 3.5% of patients. sTILs, PD-L1, DDIR, and TIM were each predictive of pCR in multivariable analyses. The areas under curve for pCR were 0.719, 0.740, 0.699, and 0.715 for sTILs, PD-L1, DDIR, and TIM, respectively. Estimated 3-year EFS was 86% in all patients; 98% in pCR group and 68% in no-pCR group. Conclusions and Relevance The findings of the phase 2 clinical trial indicate that neoadjuvant carboplatin and docetaxel plus pembrolizumab shows encouraging pCR and 3-year EFS. The regimen was well tolerated, and immune enrichment as identified by various biomarkers was independently predictive of pCR. These results provide data on an alternative anthracycline-free chemoimmunotherapy regimen for patients who are not eligible for anthracycline-based regimens and support further evaluation of this regimen as a chemotherapy de-escalation strategy in randomized studies for TNBC. Trial Registration ClinicalTrials.gov Identifier: NCT03639948.
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Affiliation(s)
- Priyanka Sharma
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Shane R. Stecklein
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City
| | - Rachel Yoder
- The University of Kansas Cancer Center, Kansas City
| | | | - Kelsey Schwensen
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Anne O’Dea
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Lauren Nye
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Deepti Satelli
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Gregory Crane
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Rashna Madan
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Maura F. O’Neil
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Jamie Wagner
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Kelsey E. Larson
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Christa Balanoff
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Lyndsey Kilgore
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Milind A. Phadnis
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City
| | - Andrew K. Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
- The University of Kansas Cancer Center, Kansas City
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter Mac Callum Canter Centre, Melbourne, Australia
| | - Qamar J. Khan
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
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5
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Rayamajhi S, Sipes J, Tetlow AL, Saha S, Bansal A, Godwin AK. Extracellular Vesicles as Liquid Biopsy Biomarkers across the Cancer Journey: From Early Detection to Recurrence. Clin Chem 2024; 70:206-219. [PMID: 38175602 DOI: 10.1093/clinchem/hvad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/26/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer is a dynamic process and thus requires highly informative and reliable biomarkers to help guide patient care. Liquid-based biopsies have emerged as a clinical tool for tracking cancer dynamics. Extracellular vesicles (EVs), lipid bilayer delimited particles secreted by cells, are a new class of liquid-based biomarkers. EVs are rich in selectively sorted biomolecule cargos, which provide a spatiotemporal fingerprint of the cell of origin, including cancer cells. CONTENT This review summarizes the performance characteristics of EV-based biomarkers at different stages of cancer progression, from early malignancy to recurrence, while emphasizing their potential as diagnostic, prognostic, and screening biomarkers. We discuss the characteristics of effective biomarkers, consider challenges associated with the EV biomarker field, and report guidelines based on the biomarker discovery pipeline. SUMMARY Basic science and clinical trial studies have shown the potential of EVs as precision-based biomarkers for tracking cancer status, with promising applications for diagnosing disease, predicting response to therapy, and tracking disease burden. The multi-analyte cargos of EVs enhance the performance characteristics of biomarkers. Recent technological advances in ultrasensitive detection of EVs have shown promise with high specificity and sensitivity to differentiate early-cancer cases vs healthy individuals, potentially outperforming current gold-standard imaging-based cancer diagnosis. Ultimately, clinical translation will be dictated by how these new EV biomarker-based platforms perform in larger sample cohorts. Applying ultrasensitive, scalable, and reproducible EV detection platforms with better design considerations based upon the biomarker discovery pipeline should guide the field towards clinically useful liquid biopsy biomarkers.
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Affiliation(s)
- Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jared Sipes
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Ashley L Tetlow
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Souvik Saha
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
| | - Ajay Bansal
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
- Division of Genomic Diagnostics, University of Kansas Health System, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, United States
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Tatarian J, Tupper N, Li P, Feusier J, Abdo M, Hyter S, Gonzales PR, Zhang D, Woodroof J, Kelting S, Godwin AK, Cui W. Morphologic, immunophenotypic, molecular genetic, and clinical characterization in patients with SRSF2-mutated acute myeloid leukemia. Am J Clin Pathol 2023; 160:490-499. [PMID: 37458189 PMCID: PMC10629464 DOI: 10.1093/ajcp/aqad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 09/21/2023] Open
Abstract
OBJECTIVES SRSF2 mutations are known to be associated with poor outcomes in myelodysplastic neoplasm, but studies on their prognostic impact on acute myeloid leukemia (AML) remain limited. In this retrospective study, we analyzed clinical and pathologic characteristics of patients with AML and correlated the outcomes with SRSF2 mutations. METHODS We characterized the morphologic, immunophenotypic, molecular, and clinical findings in AML with mutated SRSF2 and compared them with SRSF2 wild-type (WT) myeloid neoplasms (MNs). RESULTS Using next-generation sequencing, we identified 134 patients with MNs and SRSF2 mutations (85 with AML and 49 with MNs) in addition to 342 SRSF2-WT AMLs. Fifty-two (62%) patients with altered SRSF2 demonstrated a variable degree of morphologic dysplasia. The most frequent immunophenotypic aberrancies in SRSF2-mutant AML included diminished CD33 expression and overexpression of CD7, CD56, or CD123, similar to WT AML. More IDH1/2 (P = .015) and NPM1 (P = .002) mutations were seen in SRSF2-mutant AML than in SRSF2-mutant non-AML. Further, more IDH1/2, ASXL1, RUNX1, and STAG2 mutations were observed in SRSF2-mutant AML than in SRSF2-WT AML (P < .0001 to P = .001). Finally, patients with SRSF2-mutant AML showed a significantly worse overall survival (OS) than patients with SRSF2-WT AML (P < .0001), but this worse OS appeared to be rescued by allogeneic stem cell transplant (allo-SCT). CONCLUSIONS Acute myeloid leukemia with altered SRSF2 shows a variable degree of morphologic dysplasia without uniform immunophenotypic aberrancies. SRSF2 mutations appear to be independent poor prognostic factors, but allo-SCT has improved the clinical outcomes in patients with SRSF2-mutant AML.
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Affiliation(s)
- Joshua Tatarian
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Natalie Tupper
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Peng Li
- Division of Hematopathology, Department of Pathology, University of Utah, Salt Lake City, UT, US
| | - Julie Feusier
- Division of Hematopathology, Department of Pathology, University of Utah, Salt Lake City, UT, US
| | - Maryam Abdo
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Stephen Hyter
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Patrick R Gonzales
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Da Zhang
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Janet Woodroof
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Sarah Kelting
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Andrew K Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Wei Cui
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
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7
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Chen CS, Zirpoli G, Barlow WE, Budd GT, McKiver B, Pusztai L, Hortobagyi GN, Albain KS, Damaj MI, Godwin AK, Thompson A, Henry NL, Ambrosone CB, Stringer KA, Hertz DL. Vitamin D Insufficiency as a Risk Factor for Paclitaxel-Induced Peripheral Neuropathy in SWOG S0221. J Natl Compr Canc Netw 2023; 21:1172-1180.e3. [PMID: 37935109 DOI: 10.6004/jnccn.2023.7062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/24/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Prior work suggests that patients with vitamin D insufficiency may have a higher risk of chemotherapy-induced peripheral neuropathy (CIPN) from paclitaxel. The objective of this study was to validate vitamin D insufficiency as a CIPN risk factor. METHODS We used data and samples from the prospective phase III SWOG S0221 (ClinicalTrials.gov identifier: NCT00070564) trial that compared paclitaxel-containing chemotherapy regimens for early-stage breast cancer. We quantified pretreatment 25-hydroxy-vitamin D in banked serum samples using a liquid chromatography-tandem mass spectrometry targeted assay. We tested the association between vitamin D insufficiency (≤20 ng/mL) and grade ≥3 sensory CIPN via multiple logistic regression and then adjusted for self-reported race, age, body mass index, and paclitaxel schedule (randomization to weekly or every-2-week dosing). We also tested the direct effect of vitamin D deficiency on mechanical hypersensitivity in mice randomized to a regular or vitamin D-deficient diet. RESULTS Of the 1,191 female patients in the analysis, 397 (33.3%) had pretreatment vitamin D insufficiency, and 195 (16.4%) developed grade ≥3 CIPN. Patients with vitamin D insufficiency had a higher incidence of grade ≥3 CIPN than those who had sufficient vitamin D (20.7% vs 14.2%; odds ratio [OR], 1.57; 95% CI, 1.14-2.15; P=.005). The association retained significance after adjusting for age and paclitaxel schedule (adjusted OR, 1.65; 95% CI, 1.18-2.30; P=.003) but not race (adjusted OR, 1.39; 95% CI, 0.98-1.97; P=.066). In the mouse experiments, the vitamin D-deficient diet caused mechanical hypersensitivity and sensitized mice to paclitaxel (both P<.05). CONCLUSIONS Pretreatment vitamin D insufficiency is the first validated potentially modifiable predictive biomarker of CIPN from paclitaxel. Prospective trials are needed to determine whether vitamin D supplementation prevents CIPN and improves treatment outcomes in patients with breast and other cancer types.
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Affiliation(s)
- Ciao-Sin Chen
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | | | - G Thomas Budd
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Bryan McKiver
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, Virginia
| | | | - Gabriel N Hortobagyi
- Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - M Imad Damaj
- Department of Pharmacology and Toxicology and Translational Research Initiative for Pain and Neuropathy, Virginia Commonwealth University, Richmond, Virginia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | | | - N Lynn Henry
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kathleen A Stringer
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan
- NMR Metabolomics Laboratory, University of Michigan College of Pharmacy, Ann Arbor, Michigan
| | - Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
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8
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Subham S, Jeppson JD, Gibbs BK, Babai J, Alker R, Godwin AK, Akhavan D. Rapid In Vitro Cytotoxicity Evaluation of Jurkat Expressing Chimeric Antigen Receptor using Fluorescent Imaging. J Vis Exp 2023. [PMID: 37955379 DOI: 10.3791/65560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cells are at the forefront of oncology. A CAR is constructed of a targeting domain (usually a single chain variable fragment, scFv), with an accompanying intra-chain linker, followed by a hinge, transmembrane, and costimulatory domain. Modification of the intra-chain linker and hinge domain can have a significant effect on CAR-mediated killing. Considering the many different options for each part of a CAR construct, there are large numbers of permutations. Making CAR-T cells is a time-consuming and expensive process, and making and testing many constructs is a heavy time and material investment. This protocol describes a platform to rapidly evaluate hinge-optimized CAR constructs in Jurkat cells (CAR-J). Jurkat cells are an immortalized T cell line with high lentivirus uptake, allowing for efficient CAR transduction. Here, we present a platform to rapidly evaluate CAR-J using a fluorescent imager, followed by confirmation of cytolysis in PBMC-derived T cells.
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Affiliation(s)
- Siddharth Subham
- Department of Radiation Oncology, University of Kansas Cancer Center; Department of Cancer Biology, University of Kansas Cancer Center; BioEngineering Program, University of Kansas
| | - John D Jeppson
- Department of Radiation Oncology, University of Kansas Cancer Center
| | - Benjamin K Gibbs
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center
| | - Jacqueline Babai
- Department of Cancer Biology, University of Kansas Cancer Center
| | - Riza Alker
- Department of Radiation Oncology, University of Kansas Cancer Center
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center; University of Kansas Cancer Center; Kansas Institute for Precision Medicine, University of Kansas Medical Center
| | - David Akhavan
- Department of Radiation Oncology, University of Kansas Cancer Center; Department of Cancer Biology, University of Kansas Cancer Center; BioEngineering Program, University of Kansas;
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9
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Trinidad CV, Pathak HB, Cheng S, Tzeng SC, Madan R, Sardiu ME, Bantis LE, Deighan C, Jewell A, Rayamajhi S, Zeng Y, Godwin AK. Lineage specific extracellular vesicle-associated protein biomarkers for the early detection of high grade serous ovarian cancer. Sci Rep 2023; 13:18341. [PMID: 37884576 PMCID: PMC10603107 DOI: 10.1038/s41598-023-44050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
High grade serous ovarian carcinoma (HGSOC) accounts for ~ 70% of ovarian cancer cases. Non-invasive, highly specific blood-based tests for pre-symptomatic screening in women are crucial to reducing the mortality associated with this disease. Since most HGSOCs typically arise from the fallopian tubes (FT), our biomarker search focused on proteins found on the surface of extracellular vesicles (EVs) released by both FT and HGSOC tissue explants and representative cell lines. Using mass spectrometry, 985 EV proteins (exo-proteins) were identified that comprised the FT/HGSOC EV core proteome. Transmembrane exo-proteins were prioritized because these could serve as antigens for capture and/or detection. With a nano-engineered microfluidic platform, six newly discovered exo-proteins (ACSL4, IGSF8, ITGA2, ITGA5, ITGB3, MYOF) plus a known HGSOC associated protein, FOLR1 exhibited classification performance ranging from 85 to 98% in a case-control study using plasma samples representative of early (including stage IA/B) and late stage (stage III) HGSOCs. Furthermore, by a linear combination of IGSF8 and ITGA5 based on logistic regression analysis, we achieved a sensitivity of 80% with 99.8% specificity and a positive predictive value of 13.8%. Importantly, these exo-proteins also can accurately discriminate between ovarian and 12 types of cancers commonly diagnosed in women. Our studies demonstrate that these lineage-associated exo-biomarkers can detect ovarian cancer with high specificity and sensitivity early and potentially while localized to the FT when patient outcomes are more favorable.
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Affiliation(s)
- Camille V Trinidad
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Harsh B Pathak
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 3040, Kansas City, KS, 66160, USA
- University of Kansas Cancer Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Shibo Cheng
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | - Rashna Madan
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 3040, Kansas City, KS, 66160, USA
| | - Mihaela E Sardiu
- University of Kansas Cancer Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Leonidas E Bantis
- University of Kansas Cancer Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Andrea Jewell
- University of Kansas Cancer Center, Kansas City, KS, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 3040, Kansas City, KS, 66160, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Andrew K Godwin
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 3040, Kansas City, KS, 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS, USA.
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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10
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Turaga SM, Vishwakarma V, Hembruff SL, Gibbs BK, Sabu P, Puri RV, Pathak HB, Samuel G, Godwin AK. Inducing Mitotic Catastrophe as a Therapeutic Approach to Improve Outcomes in Ewing Sarcoma. Cancers (Basel) 2023; 15:4911. [PMID: 37894278 PMCID: PMC10605681 DOI: 10.3390/cancers15204911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Ewing sarcoma (EWS) is an aggressive pediatric malignancy of the bone and soft tissues in need of novel therapeutic options. To identify potential therapeutic targets, we focused on essential biological pathways that are upregulated by EWS-FLI1, the primary oncogenic driver of EWS, including mitotic proteins such as Aurora kinase A (AURKA) and kinesin family member 15 (KIF15) and its binding partner, targeting protein for Xklp2 (TPX2). KIF15/TPX2 cooperates with KIF11, a key mitotic kinesin essential for mitotic spindle orientation. Given the lack of clinical-grade KIF15/TPX2 inhibitors, we chose to target KIF11 (using SB-743921) in combination with AURKA (using VIC-1911) given that phosphorylation of KIF15S1169 by Aurora A is required for its targeting to the spindle. In vitro, the drug combination demonstrated strong synergy (Bliss score ≥ 10) at nanomolar doses. Colony formation assay revealed significant reduction in plating efficiency (1-3%) and increased percentage accumulation of cells in the G2/M phase with the combination treatment (45-52%) upon cell cycle analysis, indicating mitotic arrest. In vivo studies in EWS xenograft mouse models showed significant tumor reduction and overall effectiveness: drug combination vs. vehicle control (p ≤ 0.01), SB-743921 (p ≤ 0.01) and VIC-1911 (p ≤ 0.05). Kaplan-Meier curves demonstrated superior overall survival with the combination compared to vehicle or monotherapy arms (p ≤ 0.0001).
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Affiliation(s)
- Soumya M. Turaga
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (S.M.T.); (V.V.); (B.K.G.); (R.V.P.); (H.B.P.)
| | - Vikalp Vishwakarma
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (S.M.T.); (V.V.); (B.K.G.); (R.V.P.); (H.B.P.)
| | - Stacey L. Hembruff
- University of Kansas Cancer Center, Kansas City, KS 66160, USA; (S.L.H.); (P.S.)
| | - Benjamin K. Gibbs
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (S.M.T.); (V.V.); (B.K.G.); (R.V.P.); (H.B.P.)
| | - Priya Sabu
- University of Kansas Cancer Center, Kansas City, KS 66160, USA; (S.L.H.); (P.S.)
- Division of Gynecologic Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Rajni V. Puri
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (S.M.T.); (V.V.); (B.K.G.); (R.V.P.); (H.B.P.)
| | - Harsh B. Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (S.M.T.); (V.V.); (B.K.G.); (R.V.P.); (H.B.P.)
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Glenson Samuel
- Division of Pediatric Hematology Oncology and Bone Marrow Transplantation, Children’s Mercy Hospital, Kansas City, MO 64108, USA;
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (S.M.T.); (V.V.); (B.K.G.); (R.V.P.); (H.B.P.)
- University of Kansas Cancer Center, Kansas City, KS 66160, USA; (S.L.H.); (P.S.)
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 3040, Kansas City, KS 66160, USA
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11
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Vikramdeo KS, Anand S, Sudan SK, Pramanik P, Singh S, Godwin AK, Singh AP, Dasgupta S. Profiling mitochondrial DNA mutations in tumors and circulating extracellular vesicles of triple-negative breast cancer patients for potential biomarker development. FASEB Bioadv 2023; 5:412-426. [PMID: 37810173 PMCID: PMC10551276 DOI: 10.1096/fba.2023-00070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Early detection and recurrence prediction are challenging in triple-negative breast cancer (TNBC) patients. We aimed to develop mitochondrial DNA (mtDNA)-based liquid biomarkers to improve TNBC management. Mitochondrial genome (MG) enrichment and next-generation sequencing mapped the entire MG in 73 samples (64 tissues and 9 extracellular vesicles [EV] samples) from 32 metastatic TNBCs. We measured mtDNA and cardiolipin (CL) contents, NDUFB8, and SDHB protein expression in tumors and in corresponding circulating EVs. We identified 168 nonsynonymous mtDNA mutations, with 73% (123/186) coding and 27% (45/168) noncoding in nature. Twenty percent of mutations were nucleotide transversions. Respiratory complex I (RCI) was the key target, which harbored 44% (74/168) of the overall mtDNA mutations. A panel of 11 hotspot mtDNA mutations was identified among 19%-38% TNBCs, which were detectable in the serum-derived EVs with 82% specificity. Overall, 38% of the metastatic tumor-signature mtDNA mutations were traceable in the EVs. An appreciable number of mtDNA mutations were homoplasmic (18%, 31/168), novel (14%, 23/168), and potentially pathogenic (9%, 15/168). The overall and RCI-specific mtDNA mutational load was higher in women with African compared to European ancestry accompanied by an exclusive abundance of respiratory complex (RC) protein NDUFB8 (RCI) and SDHB (RCII) therein. Increased mtDNA (p < 0.0001) content was recorded in both tumors and EVs along with an abundance of CL (p = 0.0001) content in the EVs. Aggressive tumor-signature mtDNA mutation detection and measurement of mtDNA and CL contents in the EVs bear the potential to formulate noninvasive early detection and recurrence prediction strategies.
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Affiliation(s)
- Kunwar Somesh Vikramdeo
- Mitchell Cancer Institute, University of South AlabamaMobileAlabamaUSA
- Department of Pathology, College of MedicineUniversity of South AlabamaMobileAlabamaUSA
| | - Shashi Anand
- Mitchell Cancer Institute, University of South AlabamaMobileAlabamaUSA
- Department of Pathology, College of MedicineUniversity of South AlabamaMobileAlabamaUSA
| | - Sarabjeet Kour Sudan
- Mitchell Cancer Institute, University of South AlabamaMobileAlabamaUSA
- Department of Pathology, College of MedicineUniversity of South AlabamaMobileAlabamaUSA
| | - Paramahansa Pramanik
- Department of Mathematics and StatisticsUniversity of South AlabamaMobileAlabamaUSA
| | - Seema Singh
- Mitchell Cancer Institute, University of South AlabamaMobileAlabamaUSA
- Department of Pathology, College of MedicineUniversity of South AlabamaMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Andrew K. Godwin
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKansasUSA
- The University of Kansas Cancer Center, University of Kansas Medical CenterKansas CityKansasUSA
- Kansas Institute for Precision Medicine, University of Kansas Medical CenterKansas CityKansasUSA
| | - Ajay Pratap Singh
- Mitchell Cancer Institute, University of South AlabamaMobileAlabamaUSA
- Department of Pathology, College of MedicineUniversity of South AlabamaMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Santanu Dasgupta
- Mitchell Cancer Institute, University of South AlabamaMobileAlabamaUSA
- Department of Pathology, College of MedicineUniversity of South AlabamaMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
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12
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Freed IM, Kasi A, Fateru O, Hu M, Gonzalez P, Weatherington N, Pathak H, Hyter S, Sun W, Al-Rajabi R, Baranda J, Hupert ML, Chalise P, Godwin AK, A. Witek M, Soper SA. Circulating Tumor Cell Subpopulations Predict Treatment Outcome in Pancreatic Ductal Adenocarcinoma (PDAC) Patients. Cells 2023; 12:2266. [PMID: 37759489 PMCID: PMC10526802 DOI: 10.3390/cells12182266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
There is a high clinical unmet need to improve outcomes for pancreatic ductal adenocarcinoma (PDAC) patients, either with the discovery of new therapies or biomarkers that can track response to treatment more efficiently than imaging. We report an innovative approach that will generate renewed interest in using circulating tumor cells (CTCs) to monitor treatment efficacy, which, in this case, used PDAC patients receiving an exploratory new therapy, poly ADP-ribose polymerase inhibitor (PARPi)-niraparib-as a case study. CTCs were enumerated from whole blood using a microfluidic approach that affinity captures epithelial and mesenchymal CTCs using anti-EpCAM and anti-FAPα monoclonal antibodies, respectively. These antibodies were poised on the surface of two separate microfluidic devices to discretely capture each subpopulation for interrogation. The isolated CTCs were enumerated using immunophenotyping to produce a numerical ratio consisting of the number of mesenchymal to epithelial CTCs (denoted "Φ"), which was used as an indicator of response to therapy, as determined using computed tomography (CT). A decreasing value of Φ during treatment was indicative of tumor response to the PARPi and was observed in 88% of the enrolled patients (n = 31). Changes in Φ during longitudinal testing were a better predictor of treatment response than the current standard CA19-9. We were able to differentiate between responders and non-responders using ΔΦ (p = 0.0093) with higher confidence than CA19-9 (p = 0.033). For CA19-9 non-producers, ΔΦ correctly predicted the outcome in 72% of the PDAC patients. Sequencing of the gDNA extracted from affinity-selected CTC subpopulations provided information that could be used for patient enrollment into the clinical trial based on their tumor mutational status in DNA repair genes.
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Affiliation(s)
- Ian M. Freed
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
| | - Anup Kasi
- Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (W.S.); (R.A.-R.); (J.B.); (P.C.)
| | - Oluwadamilola Fateru
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
| | - Mengjia Hu
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (H.P.); (S.H.)
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, KS 66160, USA
| | - Phasin Gonzalez
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
| | - Nyla Weatherington
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
| | - Harsh Pathak
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (H.P.); (S.H.)
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Stephen Hyter
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (H.P.); (S.H.)
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Weijing Sun
- Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (W.S.); (R.A.-R.); (J.B.); (P.C.)
| | - Raed Al-Rajabi
- Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (W.S.); (R.A.-R.); (J.B.); (P.C.)
| | - Joaquina Baranda
- Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (W.S.); (R.A.-R.); (J.B.); (P.C.)
| | | | - Prabhakar Chalise
- Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (W.S.); (R.A.-R.); (J.B.); (P.C.)
| | - Andrew K. Godwin
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (H.P.); (S.H.)
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (H.P.); (S.H.)
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (I.M.F.); (O.F.); (M.H.); (P.G.); (N.W.); (M.A.W.)
- Center of Bio-Modular Multiscale Systems for Precision Medicine (CBM), The University of Kansas, Lawrence, KS 66047, USA;
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA; (H.P.); (S.H.)
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, KS 66160, USA
- BioFluidica, Inc., San Diego, CA 92121, USA;
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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13
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Stecklein SR, Barlow W, Pusztai L, Timms K, Kennedy R, Logan GE, Seitz R, Badve S, Gökmen-Polar Y, Porter P, Linden H, Tripathy D, Hortobagyi GN, Godwin AK, Thompson A, Hayes DF, Sharma P. Dual Prognostic Classification of Triple-Negative Breast Cancer by DNA Damage Immune Response and Homologous Recombination Deficiency. JCO Precis Oncol 2023; 7:e2300197. [PMID: 37972336 PMCID: PMC10681491 DOI: 10.1200/po.23.00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/12/2023] [Accepted: 09/11/2023] [Indexed: 11/19/2023] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is a heterogeneous disease. We previously showed that homologous recombination deficiency (HRD) and the DNA damage immune response (DDIR) signature are prognostic in TNBC. We hypothesized that these biomarkers reflect related but not completely interdependent biological processes, that their combined use would be prognostic, and that simultaneous assessment of the immunologic microenvironment and susceptibility to DNA damaging therapies might be able to identify subgroups with distinct therapeutic vulnerabilities. METHODS We analyzed the dual DDIR/HRD classification in 341 patients with TNBC treated with adjuvant anthracycline-based chemotherapy on the SWOG S9313 trial and corroborated our findings in The Cancer Genome Atlas breast cancer data set. RESULTS DDIR/HRD classification is highly prognostic in TNBC and identifies biologically and immunologically distinct subgroups. Immune-enriched DDIR+/HRD+ TNBCs have the most favorable prognosis, and DDIR+/HRD- and DDIR-/HRD+ TNBCs have favorable intermediate prognosis, despite the latter being immune-depleted. DDIR-/HRD- TNBCs have the worst prognosis and represent an internally heterogeneous group of immune-depleted chemoresistant tumors. CONCLUSION Our findings propose DDIR/HRD classification as a potentially clinically relevant approach to categorize tumors on the basis of therapeutic vulnerabilities.
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Affiliation(s)
| | | | | | | | - Richard Kennedy
- Almac Diagnostic Services, Craigavon, Northern Ireland, United Kingdom
- Patrick G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, United Kingdom
| | - Gemma E Logan
- Almac Diagnostic Services, Craigavon, Northern Ireland, United Kingdom
| | | | - Sunil Badve
- Emory University School of Medicine, Atlanta, GA
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14
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Chen CS, Zirpoli G, Thomas Budd G, Barlow WE, Pusztai L, Hortobagyi GN, Albain KS, Godwin AK, Thompson A, Lynn Henry N, Ambrosone CB, Stringer KA, Hertz DL. Pre-treatment Amino Acids and Risk of Paclitaxel-induced Peripheral Neuropathy in SWOG S0221. Res Sq 2023:rs.3.rs-3242513. [PMID: 37693586 PMCID: PMC10491324 DOI: 10.21203/rs.3.rs-3242513/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Chemotherapy-induced peripheral neuropathy (CIPN) is a treatment-limiting and debilitating neurotoxicity of many commonly used anti-cancer agents, including paclitaxel. The objective of this study was to confirm the previously found inverse association between pre-treatment blood concentrations of histidine and CIPN occurrence and examine relationships of other amino acids with CIPN severity. Methods Pre-treatment levels of 20 amino acid concentrations were measured via a targeted mass spectrometry assay in banked serum from the SWOG S0221 (NCT00070564) trial of patients with early-stage breast cancer receiving paclitaxel. The associations between amino acid levels and CIPN occurrence or severity were tested in regression analysis adjusted for paclitaxel schedule, age, self-reported race, and body mass index with Bonferroni correction for multiple comparisons. The network of metabolic pathways of amino acids was analyzed using over-representation analysis in MetaboAnalyst. The partial correlation network of amino acids was evaluated using a debiased sparse partial correlation algorithm and Cytoscape. Results In the primary analysis, histidine concentration was not associated with CIPN occurrence (odds ratio (OR) = 0.97 [0.83, 1.13], p = 0.72). In a secondary analysis, no amino acid was associated with CIPN occurrence (all p > 0.0025). Higher concentrations of four amino acids, glutamate (β = 0.58 [0.23, 0.93], p = 0.001), phenylalanine (β = 0.54 [0.19, 0.89], p = 0.002), tyrosine (β = 0.57 [0.23, 0.91], p = 0.001), and valine (β = 0.58 [0.24, 0.92], p = 0.001) were associated with more severe CIPN, but none of these associations retained significance after adjustment. In the over-representation analysis, no amino acid metabolic pathways were significantly enriched (all FDR > 0.05). In the network of enriched pathways, glutamate metabolism had the highest centrality. Conclusions This analysis showed that pre-treatment serum amino acid concentrations are not strongly predictive of CIPN severity. Future prospectively designed studies that assess non-amino acid metabolomics predictors are encouraged.
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15
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Sun W, Veeramachaneni N, Al-Rajabi R, Madan R, Kasi A, Al-Kasspooles M, Baranda J, Saeed A, Phadnis MA, Godwin AK, Olyaee M, Streeter N, Nagji A, Dai J, Williamson S. A phase II study of perioperative pembrolizumab plus mFOLFOX in patients with potentially resectable esophagus, gastroesophageal junction (GEJ), and stomach adenocarcinoma. Cancer Med 2023; 12:16098-16107. [PMID: 37326317 PMCID: PMC10469814 DOI: 10.1002/cam4.6263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Perioperative chemotherapy/chemoradiation is standard in esophageal/gastric/gastroesophageal junction (GEJ) adenocarcinoma, immune checkpoint inhibitors (ICI) effect in setting of metastatic and postoperatively. This study is to assess ICI + chemotherapy perioperatively. METHODS Patients with locally advanced (T1N1-3M0 or T2-3NanyM0) potentially resectable esophageal/gastric/GEJ adenocarcinoma by PET/EUS/CT and staging-laparoscopy, were treated preoperative 4 cycles mFOLFOX6 (Oxaliplatin 85 mg/m2 /Leucovorin 400 mg/m2 /5-FU bolus 400 mg/m2 then infusion 2400 mg/m2 for 46 h q2weeks) and 3 cycles pembrolizumab (200 mg q3week). Those without distal disease post-neoadjuvant and eligible for resection underwent surgery. Postoperative treatment was initiated at 4-8 weeks with 4 cycles mFOLFOX and 12 cycles pembrolizumab. The primary objective is pathological response (ypRR with tumor regression score, TRS ≤2). The expression of ICI-related markers PD-L1 (CPS), CD8, and CD20 were analyzed before and after preoperative therapy. RESULTS Thirty-seven patients completed the preoperative treatment. Twenty-nine patients had curative R0 resection. 6/29 (21%; 95% CI: 0.08-0.40) achieved ypCR with TRS 0 in resected patients. 26/29 (90%; 95% CI: 0.73-0.98) had ypRR with TRS ≤2. Twenty-six patients finished adjuvant therapy with a median 36.3-month follow-up. Three patients had recurrence/metastatic disease (at 9-, 10-, 22 months enrollment) with one dead at 23 months, and two are still alive at 28 and 36.5 months. The remaining (23/26) are free of disease with 3 years DFS of 88.5% and 3 years OS of 92.3%. There were no unexpected toxicities. Preoperative ICI + chemotherapy enhanced immune responses significantly with increasing expression of PD-L1 (CPS ≥10, p = 0.0078) and CD8 (>5%, p = 0.0059). CONCLUSIONS The perioperative pembrolizumab and mFOLFOX combination in resectable esophageal/gastric/GEJ adenocarcinoma is very effective with 90% ypRR, 21% ypCR, and impressive long-time survival benefits.
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Affiliation(s)
- Weijing Sun
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Nirmal Veeramachaneni
- Cardiothoracic Surgery Division, Department of Surgery, Saint Louis University School of Medicine, Saint Louis, Missouri, USA
| | - Raed Al-Rajabi
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Rashna Madan
- Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Anup Kasi
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Mazin Al-Kasspooles
- University of Kansas Cancer Center, Kansas City, Kansas, USA
- Division of Surgical Oncology, Department of Surgery, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Joaquina Baranda
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Anwaar Saeed
- Hematology-Oncology Division, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Milind A Phadnis
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Andrew K Godwin
- University of Kansas Cancer Center, Kansas City, Kansas, USA
- Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mojtaba Olyaee
- Division of Gastroenterology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | | | - Alykhan Nagji
- University of Kansas Cancer Center, Kansas City, Kansas, USA
- Department of Cardiothoracic Surgery, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Junqiang Dai
- Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Stephen Williamson
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- University of Kansas Cancer Center, Kansas City, Kansas, USA
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16
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Vaidyanathan S, Wijerathne H, Gamage SST, Shiri F, Zhao Z, Choi J, Park S, Witek MA, McKinney C, Verber M, Hall AR, Childers K, McNickle T, Mog S, Yeh E, Godwin AK, Soper SA. High Sensitivity Extended Nano-Coulter Counter for Detection of Viral Particles and Extracellular Vesicles. Anal Chem 2023; 95:9892-9900. [PMID: 37336762 DOI: 10.1021/acs.analchem.3c00855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
We present a chip-based extended nano-Coulter counter (XnCC) that can detect nanoparticles affinity-selected from biological samples with low concentration limit-of-detection that surpasses existing resistive pulse sensors by 2-3 orders of magnitude. The XnCC was engineered to contain 5 in-plane pores each with an effective diameter of 350 nm placed in parallel and can provide high detection efficiency for single particles translocating both hydrodynamically and electrokinetically through these pores. The XnCC was fabricated in cyclic olefin polymer (COP) via nanoinjection molding to allow for high-scale production. The concentration limit-of-detection of the XnCC was 5.5 × 103 particles/mL, which was a 1,100-fold improvement compared to a single in-plane pore device. The application examples of the XnCC included counting affinity selected SARS-CoV-2 viral particles from saliva samples using an aptamer and pillared microchip; the selection/XnCC assay could distinguish the COVID-19(+) saliva samples from those that were COVID-19(-). In the second example, ovarian cancer extracellular vesicles (EVs) were affinity selected using a pillared chip modified with a MUC16 monoclonal antibody. The affinity selection chip coupled with the XnCC was successful in discriminating between patients with high grade serous ovarian cancer and healthy donors using blood plasma as the input sample.
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Affiliation(s)
- Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Sachindra S T Gamage
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Zheng Zhao
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Małgorzata A Witek
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, North Carolina 27101, United States
| | - Katie Childers
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Taryn McNickle
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Shalee Mog
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Elaine Yeh
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew K Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Comprehensive Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Comprehensive Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
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17
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Luu GT, Ge C, Tang Y, Li K, Cologna SM, Godwin AK, Burdette JE, Su J, Sanchez LM. An Integrated Approach to Protein Discovery and Detection From Complex Biofluids. Mol Cell Proteomics 2023; 22:100590. [PMID: 37301378 PMCID: PMC10388710 DOI: 10.1016/j.mcpro.2023.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/22/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023] Open
Abstract
Ovarian cancer, a leading cause of cancer-related deaths among women, has been notoriously difficult to screen for and diagnose early, as early detection significantly improves survival. Researchers and clinicians seek routinely usable and noninvasive screening methods; however, available methods (i.e., biomarker screening) lack desirable sensitivity/specificity. The most fatal form, high-grade serous ovarian cancer, often originate in the fallopian tube; therefore, sampling from the vaginal environment provides more proximal sources for tumor detection. To address these shortcomings and leverage proximal sampling, we developed an untargeted mass spectrometry microprotein profiling method and identified cystatin A, which was validated in an animal model. To overcome the limits of detection inherent to mass spectrometry, we demonstrated that cystatin A is present at 100 pM concentrations using a label-free microtoroid resonator and translated our workflow to patient-derived clinical samples, highlighting the potential utility of early stage detection where biomarker levels would be low.
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Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chang Ge
- Wyant College of Optical Sciences, University of Arizona, Tucson, Arizona, USA
| | - Yisha Tang
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | - Kailiang Li
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA; Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA; The University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Judith Su
- Wyant College of Optical Sciences, University of Arizona, Tucson, Arizona, USA; Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA.
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18
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O'Mahony DG, Ramus SJ, Southey MC, Meagher NS, Hadjisavvas A, John EM, Hamann U, Imyanitov EN, Andrulis IL, Sharma P, Daly MB, Hake CR, Weitzel JN, Jakubowska A, Godwin AK, Arason A, Bane A, Simard J, Soucy P, Caligo MA, Mai PL, Claes KBM, Teixeira MR, Chung WK, Lazaro C, Hulick PJ, Toland AE, Pedersen IS, Neuhausen SL, Vega A, de la Hoya M, Nevanlinna H, Dhawan M, Zampiga V, Danesi R, Varesco L, Gismondi V, Vellone VG, James PA, Janavicius R, Nikitina-Zake L, Nielsen FC, van Overeem Hansen T, Pejovic T, Borg A, Rantala J, Offit K, Montagna M, Nathanson KL, Domchek SM, Osorio A, García MJ, Karlan BY, De Fazio A, Bowtell D, McGuffog L, Leslie G, Parsons MT, Dörk T, Speith LM, Dos Santos ES, da Costa AABA, Radice P, Peterlongo P, Papi L, Engel C, Hahnen E, Schmutzler RK, Wappenschmidt B, Easton DF, Tischkowitz M, Singer CF, Tan YY, Whittemore AS, Sieh W, Brenton JD, Yannoukakos D, Fostira F, Konstantopoulou I, Soukupova J, Vocka M, Chenevix-Trench G, Pharoah PDP, Antoniou AC, Goldgar DE, Spurdle AB, Michailidou K. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2. Br J Cancer 2023; 128:2283-2294. [PMID: 37076566 PMCID: PMC10241792 DOI: 10.1038/s41416-023-02263-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/22/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system. METHODS Data for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong). RESULTS No histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis. CONCLUSIONS We provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.
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Affiliation(s)
- Denise G O'Mahony
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus
| | - Susan J Ramus
- School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - Nicola S Meagher
- School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | | | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1×5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, 66205, USA
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, 171-252, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, 171-252, Poland
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavik, 101, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Anita Bane
- Department of Pathology & Molecular Medicine, Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, L8V 1C3, Canada
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, G1V 4G2, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, G1V 4G2, Canada
| | - Maria A Caligo
- SOD Genetica Molecolare, University Hospital, Pisa, 56126, Italy
| | - Phuong L Mai
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | | | - Manuel R Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Comprehensive Cancer Center, Porto, 4200-072, Portugal
- School of Medicine and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, 4050-013, Portugal
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, 10032, USA
| | - Conxi Lazaro
- Hereditary Cancer Program, ONCOBELL-IDIBELL-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, 08908, Spain
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, 60201, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, 60637, USA
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, 9000, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, 9000, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, 9000, Denmark
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, 28029, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, 15706, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, 15706, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, 28040, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, 00290, Finland
| | - Mallika Dhawan
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, 94143-1714, USA
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Rita Danesi
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, 47014, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, 16132, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, 16132, Italy
| | | | - Paul A James
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, 14049-900, Brazil
| | - Ramunas Janavicius
- Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius University, Vilnius, LT-03101, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, 8410, Lithuania
| | | | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, DK-2100, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, DK-2100, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, , University of Copenhagen, Copenhagen, 2200, Denmark
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, 222 41, Sweden
| | - Johanna Rantala
- Clinical Genetics, Karolinska Institutet, Stockholm, 171 76, Sweden
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, 35128, Italy
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19066, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19066, USA
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, 28029, Spain
- Genetics Service, Fundación Jiménez Díaz, Madrid, 28040, Spain
| | - María J García
- Computational Oncology Group, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Anna De Fazio
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, 2145, Australia
- The University of Sydney, Sydney, NSW, 2145, Australia
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, 30625, Germany
| | - Lisa-Marie Speith
- Gynaecology Research Unit, Hannover Medical School, Hannover, 30625, Germany
| | - Elizabeth Santana Dos Santos
- Service de Génétique, Institut Curie, Paris, 75005, France
- Oncology Center, Hospital Sirio-Libanes, São Paulo, 01308-050, Brazil
- Department of Clinical Oncology, A.C.Camargo Cancer Center, São Paulo, 1509900, Brazil
| | - Alexandre André B A da Costa
- Department of Clinical Oncology, A.C.Camargo Cancer Center, São Paulo, 1509900, Brazil
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 2215, USA
| | - Paolo Radice
- Unit of Preventive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, 20133, Italy
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, 20139, Italy
| | - Laura Papi
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics Unit, University of Florence, Florence, 27571, Italy
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, 04107, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, H4A 3J1, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christian F Singer
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
| | - Yen Yen Tan
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
| | - Alice S Whittemore
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12000, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, 12000, Czech Republic
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, 2371, Cyprus.
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
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19
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Fanucci KA, Bai Y, Pelekanou V, Nahleh ZA, Shafi S, Burela S, Barlow WE, Sharma P, Thompson AM, Godwin AK, Rimm DL, Hortobagyi GN, Liu Y, Wang L, Wei W, Pusztai L, Blenman KRM. Image analysis-based tumor infiltrating lymphocytes measurement predicts breast cancer pathologic complete response in SWOG S0800 neoadjuvant chemotherapy trial. NPJ Breast Cancer 2023; 9:38. [PMID: 37179362 PMCID: PMC10182981 DOI: 10.1038/s41523-023-00535-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
We assessed the predictive value of an image analysis-based tumor-infiltrating lymphocytes (TILs) score for pathologic complete response (pCR) and event-free survival in breast cancer (BC). About 113 pretreatment samples were analyzed from patients with stage IIB-IIIC HER-2-negative BC randomized to neoadjuvant chemotherapy ± bevacizumab. TILs quantification was performed on full sections using QuPath open-source software with a convolutional neural network cell classifier (CNN11). We used easTILs% as a digital metric of TILs score defined as [sum of lymphocytes area (mm2)/stromal area(mm2)] × 100. Pathologist-read stromal TILs score (sTILs%) was determined following published guidelines. Mean pretreatment easTILs% was significantly higher in cases with pCR compared to residual disease (median 36.1 vs.14.8%, p < 0.001). We observed a strong positive correlation (r = 0.606, p < 0.0001) between easTILs% and sTILs%. The area under the prediction curve (AUC) was higher for easTILs% than sTILs%, 0.709 and 0.627, respectively. Image analysis-based TILs quantification is predictive of pCR in BC and had better response discrimination than pathologist-read sTILs%.
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Affiliation(s)
- Kristina A Fanucci
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06520, USA
| | - Yalai Bai
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
| | - Vasiliki Pelekanou
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
- Bayer Pharmaceuticals, 245 First St Cambridge Science Center 100 and 200 Floors 1 and 2, Cambridge, MA, 02142, USA
| | - Zeina A Nahleh
- Department of Hematology/Oncology, Cleveland Clinic Florida, Maroone Cancer Center, 2950 Cleveland Clinic Blvd, Weston, FL, 33331, USA
| | - Saba Shafi
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
- Department of Pathology, Ohio State University, 6100 Optometry Clinic & Health Sciences Faculty Office Building, 1664 Neil Avenue, Columbus, OH, 43210, USA
| | - Sneha Burela
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
| | - William E Barlow
- SWOG Statistics and Data Management Center, 1730 Minor Avenue Suite 1900, Seattle, WA, 98101, USA
| | - Priyanka Sharma
- Department of Medical Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Alastair M Thompson
- Section of Breast Surgery, 1 Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Andrew K Godwin
- Department of Medical Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT, 06520, USA
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Yihan Liu
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Leona Wang
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Wei Wei
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Lajos Pusztai
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06520, USA
| | - Kim R M Blenman
- Department of Internal Medicine Section of Medical Oncology and Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06520, USA.
- Department of Computer Science, Yale School of Engineering and Applied Science, 17 Hillhouse Avenue, New Haven, CT, 06520, USA.
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20
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Bergqvist M, Nordmark A, Williams A, Paoletti C, Barlow W, Cobain EF, Mehta RS, Gralow JR, Hortobagyi GN, Albain KS, Pusztai L, Sharma P, Godwin AK, Thompson AM, Hayes DF, Rae JM. Thymidine kinase activity levels in serum can identify HR+ metastatic breast cancer patients with a low risk of early progression (SWOG S0226). Biomarkers 2023; 28:313-322. [PMID: 36647745 PMCID: PMC10681159 DOI: 10.1080/1354750x.2023.2168063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/07/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND Some patients with metastatic breast cancer (MBC) stay on endocrine therapy (ET) for years and others progress quickly. Serum thymidine kinase activity (TKa), an indicator of cell-proliferation, is a potential biomarker for monitoring ET and predicting MBC outcome. We have previously reported TKa as being prognostic in MBC in SWOG S0226. Here, new data on progression within 30/60 days post sampling, with a new, FDA approved version of DiviTum®TKa highlighting differences vs. a Research Use Only version is reported. METHODS 1,546 serum samples from 454 patients were assessed, collected at baseline and at 4 subsequent timepoints during treatment. A new predefined cut-off tested the ability to predict disease progression. A new measuring unit, DuA (DiviTum® unit of Activity) is adopted. RESULTS A DiviTum®TKa score <250 DuA provides a much lower risk of progression within 30/60 days after blood draw, the negative predictive value (NPV) was 96.7% and 93.5%, respectively. Patients <250 DuA experienced significantly longer progression-free survival and overall survival, demonstrated at baseline and for all time intervals. CONCLUSIONS DiviTum®TKa provides clinically meaningful information for patients with HR+ MBC. Low TKa levels provide such a high NPV for rapid progression that such patients might forego additional therapy added to single agent ET.Trial registration: NCT00075764.
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Affiliation(s)
| | | | | | | | | | - Erin F. Cobain
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Rita S. Mehta
- Chao Family Comprehensive Cancer Center, University of California Irvine Medical Center, Orange, CA, USA
| | - Julie R. Gralow
- Seattle Cancer Care Alliance and University of Washington Medical Center, Seattle, WA, USA
| | - Gabriel N. Hortobagyi
- Department of Breast Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kathy S. Albain
- Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Lajos Pusztai
- Breast Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Priyanka Sharma
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Alastair M. Thompson
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel F. Hayes
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - James M. Rae
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
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21
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Karki S, Sun W, Madan R, Lamsal K, Schmitt S, Godwin AK, Kasi A. Microsatellite Instability with BRAF V600E Associated with Delayed Presentation but Poor Survival in Stage III Colorectal Cancer. Fortune J Health Sci 2023; 6:167-173. [PMID: 37736078 PMCID: PMC10512748 DOI: 10.26502/fjhs.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Colorectal cancer (CRC) has tremendous molecular and genetic heterogeneity, making it a difficult cancer to treat. Two of the key prognostic indicators of CRC include microsatellite instability (MSI) and BRAF V600E mutation. Here, we performed a retrospective survival analysis on 145 stage II and III CRC patients treated at the University of Kansas Cancer Center between 2009 and 2020. Of the 145 patients, BRAF V600E was observed in 15% patients and MSI in 28% patients. Median survival was not reached for stage II. For stage III, patients with BRAF V600E showed poor overall survival, which worsened with concurrent presence of MSI [χ2=6.4, p=0.01]. Eighty-five percent of this group was found to have right-sided CRC. For stage III, overall survival (OS) was 27 months, 37 months, 87 months and not reached for MSI-H/BRAF V600E, MSS/BRAF V600E, MSS/BRAF WT and MSI-H/BRAF WT, respectively. Although associated with poor prognosis, presence of MSI in BRAF V600E patients was associated with delayed disease presentation (mean age 77) compared to those with stable microsatellite (mean age 63) [p=0.01]. Although median survival between the groups could not be assessed for stage II due to very few deaths and/or inadequate length of study, comparison of survival trend suggests that BRAF V600E, rather than MSI, is what drives prognosis in stage II CRC. Our findings suggest that prognostic value of MSI is more relevant for stage III than stage II CRC. Patients with MSI-H and BRAF V600E have advantage of late presentation, although at the cost of poor overall prognosis.
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Affiliation(s)
- Sophiya Karki
- University of Kansas School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Weijing Sun
- Division of Medical Oncology, University of Kansas University Cancer Center, Kansas City, KS, USA
| | - Rashna Madan
- Department of Pathology Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kamal Lamsal
- KU School of Business, University of Kansas, Kansas City, KS, USA
| | - Sarah Schmitt
- Department of Pathology Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Pathology Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anup Kasi
- Division of Medical Oncology, University of Kansas University Cancer Center, Kansas City, KS, USA
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22
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Hu M, Brown V, Jackson JM, Wijerathne H, Pathak H, Koestler DC, Nissen E, Hupert ML, Muller R, Godwin AK, Witek MA, Soper SA. Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles' mRNA. Anal Chem 2023; 95:7665-7675. [PMID: 37071799 DOI: 10.1021/acs.analchem.3c00624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Extracellular vesicles (EVs) carry RNA cargo that is believed to be associated with the cell-of-origin and thus have the potential to serve as a minimally invasive liquid biopsy marker for supplying molecular information to guide treatment decisions (i.e., precision medicine). We report the affinity isolation of EV subpopulations with monoclonal antibodies attached to the surface of a microfluidic chip that is made from a plastic to allow for high-scale production. The EV microfluidic affinity purification (EV-MAP) chip was used for the isolation of EVs sourced from two-orthogonal cell types and was demonstrated for its utility in a proof-of-concept application to provide molecular subtyping information for breast cancer patients. The orthogonal selection process better recapitulated the epithelial tumor microenvironment by isolating two subpopulations of EVs: EVEpCAM (epithelial cell adhesion molecule, epithelial origin) and EVFAPα (fibroblast activation protein α, mesenchymal origin). The EV-MAP provided recovery >80% with a specificity of 99 ± 1% based on exosomal mRNA (exo-mRNA) and real time-droplet digital polymerase chain reaction results. When selected from the plasma of healthy donors and breast cancer patients, EVs did not differ in size or total RNA mass for both markers. On average, 0.5 mL of plasma from breast cancer patients yielded ∼2.25 ng of total RNA for both EVEpCAM and EVFAPα, while in the case of cancer-free individuals, it yielded 0.8 and 1.25 ng of total RNA from EVEpCAM and EVFAPα, respectively. To assess the potential of these two EV subpopulations to provide molecular information for prognostication, we performed the PAM50 test (Prosigna) on exo-mRNA harvested from each EV subpopulation. Results suggested that EVEpCAM and EVFAPα exo-mRNA profiling using subsets of the PAM50 genes and a novel algorithm (i.e., exo-PAM50) generated 100% concordance with the tumor tissue.
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Affiliation(s)
- Mengjia Hu
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, Kansas 66160, United States
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Virginia Brown
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Joshua M Jackson
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harshani Wijerathne
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Devin C Koestler
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Emily Nissen
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | | | - Rolf Muller
- BioFluidica, Inc., San Diego, California 92121, United States
| | - Andrew K Godwin
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Malgorzata A Witek
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Steven A Soper
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, Kansas 66160, United States
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- BioFluidica, Inc., San Diego, California 92121, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
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23
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Turaga SM, Sardiu ME, Vishwakarma V, Mitra A, Bantis LE, Madan R, Merchant ML, Klein JB, Samuel G, Godwin AK. Identification of small extracellular vesicle protein biomarkers for pediatric Ewing Sarcoma. Front Mol Biosci 2023; 10:1138594. [PMID: 37122563 PMCID: PMC10140755 DOI: 10.3389/fmolb.2023.1138594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Ewing Sarcoma (EWS) is the second most common osseous malignancy in children and young adults after osteosarcoma, while it is the fifth common osseous malignancy within adult age population. The clinical presentation of EWS is quite often non-specific, with the most common symptoms at presentation consisting of pain, swelling or general discomfort. The dearth of clinically relevant diagnostic or predictive biomarkers continues to remain a pressing clinical challenge. Identification of tumor specific biomarkers can lend towards an early diagnosis, expedited initiation of therapy, monitoring of therapeutic response, and early detection of recurrence of disease. We carried-out a complex analysis of cell lines and cell line derived small extracellular vesicles (sEVs) using label-free-based Quantitative Proteomic Profiling with an intent to determine shared and distinct features of these tumor cells and their respective sEVs. We analyzed EWS cells with different EWS-ETS fusions (EWS-FLI1 type I, II, and III and EWS-ERG) and their corresponding sEVs. Non-EWS controls included osteosarcoma, rhabdomyosarcoma, and benign cells, i.e., osteoid osteoma and mesenchymal stem cells. Proteomic profiling identified new shared markers between cells and their corresponding cell-derived sEVs and markers which were exclusively enriched in EWS-derived sEVs. These exo-biomarkers identified were validated by in silico approaches of publicly available protein databases and by capillary electrophoresis based western analysis (Wes). Here, we identified a protein biomarker named UGT3A2 and found its expression highly specific to EWS cells and their sEVs compared to control samples. Clinical validation of UGT3A2 expression in patient tumor tissues and plasma derived sEV samples demonstrated its specificity to EWS, indicating its potential as a EWS biomarker.
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Affiliation(s)
- Soumya M. Turaga
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Mihaela E. Sardiu
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Vikalp Vishwakarma
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Amrita Mitra
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Leonidas E. Bantis
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Rashna Madan
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Michael L. Merchant
- Clinical Proteomics Laboratory, Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Jon B. Klein
- Robley Rex Veterans Administration Medical Center, Louisville, KY, United States
| | - Glenson Samuel
- University of Kansas Cancer Center, Kansas City, KS, United States
- Division of Pediatric Hematology Oncology and Bone Marrow Transplantation, Children’s Mercy-Kansas City, Kansas City, MO, United States
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
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24
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Turaga SM, Vishwakarma V, Hembruff S, Puri R, Sabu P, Samuel G, Godwin AK. Abstract 1565: Targeting of KIF11 and AURKA to improve outcomes in Ewing sarcoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Ewing Sarcoma (EWS) is a rare and aggressive pediatric malignancy of the bone and soft tissues. Despite intensive systemic combination chemotherapy and surgery/radiotherapy for local control, patients with metastatic disease have dismal prognosis (<30% overall survival rate). To identify better therapies for patients with refractory, recurrent and metastatic disease, we previously conducted in silico and drug re-purposing screens (PMID: 27863422; 31025088) that identified proteins essential for mitotic spindle formation and cell cycle progression such as Aurora Kinase A (AURKA), Kinesin Family Member 11 (KIF11), Kinesin Family Member 15 (KIF15) and its binding partner; targeting protein for Xklp2 (TPX2) that are upregulated by EWS-FLI1, the primary oncogenic driver of EWS, indicating their potential as therapeutic targets. KIF11 and KIF15 are mitotic motor kinesins essential for bipolar spindle formation, whereas AURKA is a mitotic kinase essential for centrosome maturation and mitotic spindle assembly. Though KIF11 and AURKA inhibitors have been extensively used in clinical trials before but have not been tested together in combination for any type of cancer. We hypothesized that targeting these two key proteins essential for mitotic progression provides a therapeutic vulnerability for Ewing Sarcoma by inducing G2/M arrest and mitotic catastrophe. Specific KIF11 (SB-743921) and AURKA (VIC-1911, VITRAC Therapeutics) inhibitors were used for targeting these proteins. We evaluated the in vitro activity of VIC-1911 and SB-743921 and synergy was measured by percentage inhibition of growth via SynergyFinder, that employs reference models (Bliss) to score synergy (scores >10 is synergistic). EWS showed strong synergistic interaction at physiologically relevant doses compared to control cell lines (e.g., mesenchymal stem cells and non-EWS tumor cells). This drug combination was effective in refractory EWS cells established post-chemotherapy (synergy score >24) and at much lower doses in cells established from pre-treatment tumor tissue (synergy score >27) indicating effectiveness at various clinical stages of EWS disease. Importantly, this therapy appeared preferential to EWS cells with an EWS-ETS fusion as compared to non-EWS cells. We observed zero colony formation in vitro with the combination treatment and increased percentage accumulation of cells in G2/M phase upon cell-cycle analysis indicating mitotic arrest. In vivo studies in EWS xenograft mouse models showed sustained tumor regression (NED at 30 days after ending therapy). The combination arm showed significant survival versus control (p≤ 0.001, HR=0.42, 95% CI=0.14-1.25), VIC-1911 (p≤ 0.001, HR=0.48, 95% CI=0.16-1.42) or SB-743921 (p ≤ 0.01, p≤ HR=0.71, 95% CI=0.21-2.34) alone. Efforts are underway to translate these preclinical studies into an early phase clinical trial of patients with histologically proven EWS who have failed standard of care therapy.
Citation Format: Soumya M. Turaga, Vikalp Vishwakarma, Stacey Hembruff, Rajni Puri, Priya Sabu, Glenson Samuel, Andrew K. Godwin. Targeting of KIF11 and AURKA to improve outcomes in Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1565.
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Affiliation(s)
| | | | | | - Rajni Puri
- 1University of Kansas Medical Center, Kansas City, KS
| | - Priya Sabu
- 1University of Kansas Medical Center, Kansas City, KS
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25
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Trinidad CV, Pathak HB, Cheng S, Madan R, Sardiu ME, Bantis LE, Zeng Y, Godwin AK. Abstract 3351: Identification of novel biomarkers for high grade serous ovarian cancer screening via extracellular vesicle proteomic profiling. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Ovarian cancer is a silent killer that rarely shows symptoms and therefore is detected at later stages when treatments are less effective. Developing non-invasive blood tests for pre-symptomatic screening and early detection is crucial. Recent studies support the paradigm that high grade serous carcinomas (HGSOCs), the most common and deadliest form of ovarian cancers, arise from the epithelial cells within the fimbriated end of the fallopian tubes (FT). The goal of this study was to uncover novel protein biomarkers associated with tumor-derived extracellular vesicles (EVs) originating from the FT epithelial cells to advance liquid-based assays for the early detection of HGSOC. We hypothesize that EV-associated proteins (exo-proteins), i.e., lineage biomarkers, shared between the progenitor cells residing in the FT and tumor cells residing in cancerous tissue will allow for detection of the earliest forms of HGSOC.
Methods: Differential ultracentrifugation was used to enrich EVs from FT and HGSOC cell lines (n=3 & n=5) and healthy FT and HGSOC tissue explants (n=6 & n=15), respectively. Unbiased proteomic profiling of EVs was performed by LC-MS/MS.
Results: We report for the first time 985 proteins that compose the FT/HGSOC EV core proteome. We used bioinformatic pipelines to identify high-quality candidate exo-biomarkers for further validation. We selected exo-proteins that were predicted to have at least one transmembrane domain which could serve as an antigen for immunoaffinity capture. We prioritized proteins that showed a log2 fold-change ≥ -0.58 to identify potential biomarkers present in FT-associated EVs which were elevated as the disease progresses to HGSOC. A ranked list of 45 predicted transmembrane exo-proteins was screened using Simple Western assays for expression in FT and HGSOC cell line-derived EVs. Expression of the top 6 candidate biomarkers (i.e., ACSL4, IGSF8, ITGA2, ITGA5, ITGB3 and MYOF) were confirmed in FT and HGSOC tissue sample by immunohistochemistry using tissue microarray (n=100). Next, we analyzed plasma samples from a small case-control study using our ExoProfile chip (e.g., PMID 31293733) and found these 6 exo-biomarkers, plus folate receptor alpha exhibited higher levels in the HGSOC plasma relative to matched healthy controls. We performed receiver operating characteristic (ROC) analyses and found that all 6 FT/HGSOC shared exo-biomarkers exhibit an overall classification performance ranging from 0.85-0.98 as reflected by the area under the curve (AUC). Furthermore, when we used a linear combination of IGSF8 and ITGA5 based on logistic regression analysis, we achieved a sensitivity of 80% at 99.8% specificity.
Conclusion: Validated lineage-associated exo-protein biomarkers can be used in liquid-based assays to detect ovarian cancer while localized to the FT/ovary and when patient outcomes are more favorable.
Citation Format: Camille V. Trinidad, Harsh B. Pathak, Shibo Cheng, Rashna Madan, Mihaela E. Sardiu, Leonidas E. Bantis, Yong Zeng, Andrew K. Godwin. Identification of novel biomarkers for high grade serous ovarian cancer screening via extracellular vesicle proteomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3351.
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Affiliation(s)
| | | | | | - Rashna Madan
- 1University of Kansas Medical Center, Kansas, KS
| | | | | | - Yong Zeng
- 2University of Florida, Gainesville, FL
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Gibbs BK, Douglas JT, Wates RJ, McDonald PR, Whitaker AM, Ndi CN, Pathak HB, Harned LA, Neuenswander SA, Broward MA, Freudenthal BD, Roy A, Schoenen FJ, Godwin AK. Abstract 5334: Targeting the KIF15-TPX2 PPI to overcome KIF11 inhibitor resistance in epithelial ovarian cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Most cases of epithelial ovarian cancer (EOC) exhibit extensive molecular heterogeneity, presenting challenges in developing targeted therapies. Despite extensive efforts and incremental successes in developing targeted drugs and immunotherapies for other cancers, chemotherapies continue to be the most used treatment of ovarian cancer. Although seemingly simplistic, identification of drugs targeting cellular machinery independent of genomic and genetic status continues to be a strong clinical need. Previously, we performed an RNAi-based screen of the druggable genome across a diverse histological panel of EOC cell line representing both platinum-sensitive and -resistant tumors (PMID: 23056589). This screen elucidated KIF11 as essential in maintaining EOC cell viability. KIF11, a mitotic spindle assembly motor protein, has been targeted clinically. Although drugs are well tolerated, potent, and specific, the objective response rates to KIF11 inhibitors in clinical trials were commonly less than 10%. The efficacy of KIF11 inhibitors is blunted via a compensatory motor kinesin, KIF15. The overexpression of KIF15 has been shown to compensate for absent KIF11 in the formation of the bipolar spindle apparatus during mitosis. Silencing KIF15 significantly sensitizes cells to KIF11 inhibitors and resensitizes resistant cells to KIF11 inhibitors. We developed a high throughput screening approach using Alpha technology to identify compounds that inhibit the protein-protein interaction (PPI) between KIF15 and TPX2, a unique approach to inhibiting KIF15 from previous efforts. Of the nearly 200,000 compounds screened, 177 compounds were selected to be further characterized based on assay performance and chemical properties. These compounds were screened for TPX2 or KIF15 binding by STD-NMR and waterLOGSY. Three compounds across two chemotypes were confirmed to bind KIF15. No compounds were found to bind TPX2. Additionally, 168 of the 177 compounds were screened for drug synergism in vitro. The synergism assay yielded 32 strongly and 8 weakly synergistic hits. The lead compound in each of the two chemotypes revealed by NMR were classified as strongly synergistic (max. bliss score of 8.0 and 29.9). To expand the potential lead compounds identified for further development, an antibody-free cellular thermal shift assay (CETSA) is being completed with 168 compounds. Preliminarily, CETSA has shown that the two lead compounds significantly stabilize KIF15 (ΔTm = 5.6 °C and 9.6 °C). These two lead compounds behaved in a dose-dependent manner in the AlphaScreen (IC50= 2 µM and 6 µM), a favorable characteristic for further development. To date, two chemotypes have been identified as KIF15 inhibitors uniquely targeting the KIF15-TPX2 PPI. The data indicates KIF15 inhibition in combination with KIF11 inhibition is synergistic, thus demonstrating a potential novel treatment approach for people with EOCs.
Citation Format: Benjamin K. Gibbs, Justin T. Douglas, Rebecca J. Wates, Peter R. McDonald, Amy M. Whitaker, Cornelius N. Ndi, Harsh B. Pathak, Laurie A. Harned, Sarah A. Neuenswander, Melinda A. Broward, Bret D. Freudenthal, Anuradha Roy, Frank J. Schoenen, Andrew K. Godwin. Targeting the KIF15-TPX2 PPI to overcome KIF11 inhibitor resistance in epithelial ovarian cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5334.
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Wen Y, Vishwakarma V, Godwin AK, Zeng Y. Abstract 3301: Ultrasensitive compartment-free digital phenotyping of circulating extracellular vesicles for diagnosis of Ewing sarcoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Ewing sarcoma (EWS) is the second most common pediatric osseous malignancy in the US. Vague symptoms and high prevalence of metastasis and recurrence present serious obstacles to its clinical management. Current diagnostic and monitoring modalities for EWS, including tissue biopsy, imaging, and cytogenetics have limitations in the early diagnosis and disease monitoring. Thus, EWS patients, as do other solid pediatric cancers, face unique challenges in the lack of non-invasive tests to aid with patient management. Extracellular vesicles (EVs), including exosomes, are emerging as a new paradigm of liquid biopsy for non-invasive cancer diagnosis and monitoring owing to their informative cargoes and imperative biological functions. However, limited progresses have been reported in the field of EWS-related EV diagnostics. To address this gap, we developed a new microfluidics-based digital immunoassay platform, termed μTUNER (microfluidic Topographic modUlation and iNtensification of Enzymatic Reaction), for ultrasensitive single-molecular analysis of EV protein biomarkers and liquid biopsy-based diagnosis of EWS. Through constructing nanoconfinements with tunable sizes, this technology affords programmable patterning and modulation of surface enzymatic reactions in a non-contact manner. Such unique capacity enables us to develop a compartment-free digital immunoassay platform which is conceptually distinct from the existing digital assays. As a proof-of-concept for clinical applications, we adapted the μTUNER digital immunoassay platform to quantitatively evaluate four exo-protein biomarkers (CD99, ENO-2, NGFR, and Ezrin) that we identified by extensive proteomics analysis of EWS cell line-derived EVs (PMID: 32821345). Using protein standards and EWS cell line-derived EVs, we demonstrated that our technology affords sensitive and quantitative detection of exo-protein biomarkers with LODs at the fg/mL level, which warrants subsequent assessment of its adaptability to clinical EWS diagnosis. EV profiling of plasma samples from adult and pediatric EWS patients (n = 16) and matched healthy controls (n = 17) reveals unique expression patterns of the four markers. These exo-protein biomarkers individually afforded excellent diagnostic performance (AUC, CD99: 0.992; ENO-2: 0.985; NGFR: 0.996; Ezrin: 0.978) to differentiate the EWS and control groups. The unweighted SUM signature of the four proteins further improves the diagnostic power to yield an AUC of 1.00. Meanwhile, the distinctive EV signature obtained from the machine learning-based analysis permits further classification of control, adult, and pediatric patients with an overall accuracy of 97%. Based on these results, we envision that our technology combined with the novel exo-protein biomarker signature can be useful clinically to improve the diagnosis of patients with Ewing sarcoma.
Citation Format: Yunjie Wen, Vikalp Vishwakarma, Andrew K. Godwin, Yong Zeng. Ultrasensitive compartment-free digital phenotyping of circulating extracellular vesicles for diagnosis of Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3301.
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Affiliation(s)
| | | | | | - Yong Zeng
- 1University of Florida, Gainesville, FL
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Lumpkins CY, Nelson R, Twizele Z, Ramírez M, Kimminau KS, Philp A, Mustafa RA, Godwin AK. Communicating risk and the landscape of cancer prevention - an exploratory study that examines perceptions of cancer-related genetic counseling and testing among African Americans and Latinos in the Midwest. J Community Genet 2023; 14:121-133. [PMID: 36930422 PMCID: PMC10021032 DOI: 10.1007/s12687-022-00629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/21/2022] [Indexed: 03/18/2023] Open
Abstract
African American (AA) and Latino populations are impacted disproportionately by cancer incidence and mortality compared to the general US population. Contributing to these rates are multiple inheritable cancers that impact both men and women. Some of these diseases may be detected through genetic counseling and germline DNA testing; however, AA and Latinos are unaware and have limited knowledge and thus significantly underutilize these services and technologies. Research to detect influencing factors to testing uptake has also been slow due to multiple factors. The research team followed a community-based participatory research (CBPR) approach and worked with a Community Advisory Board composed of cancer survivors and co-survivors to design the exploratory study. Six focus groups were held with a pilot sample of African Americans and Latinos who self-reported to be at-risk for cancer (N = 53). The study was held over a 2-month period where attitudes, perceptions, and beliefs about cancer risk and preference regarding cancer-related genetic counseling and testing risk communication were explored. Themes that emerged included (1) the lack of knowledge about cancer-related genetic counseling and testing; (2) cancer is feared often; (3) cancer-related genetic testing was perceived as something that could help but was also perceived as unnecessary testing that exposed individuals to medical harm; and (4) benefits to test were perceived as favorable for medical personnel but not for the patient. Implications of the study provide a unique lens to explore how lived experiences among AA and Latinos may inform strategic risk communication about cancer-related genetic counseling and testing and help advance cancer health equity. Participants viewed cancer genetic testing as important cancer risk prevention strategies. Identification of perceptions of cancer risk and cancer-related genetic counseling and testing in collaboration with members of the community is needed to bolster communication efforts among these populations.
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Affiliation(s)
- Crystal Y Lumpkins
- Department of Communication, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Rafaela Nelson
- Pediatrics Department, University of Kansas Medical Center, Kansas City, KS, USA
| | - Zawadi Twizele
- University of Kansas Medical Center, Kansas City, KS, USA
| | - Mariana Ramírez
- Department of Population Health, JUNTOS Center for Advancing Latino Health, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kim S Kimminau
- Department of Family and Community Medicine, University of Missouri, Columbia, MO, USA
| | | | - Reem A Mustafa
- Department of Internal Medicine, University of Kansas Health System, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
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Zha D, Rayamajhi S, Sipes J, Russo A, Pathak HB, Li K, Sardiu ME, Bantis LE, Mitra A, Puri RV, Trinidad CV, Cain BP, Isenberg BC, Coppeta J, MacLaughlan S, Godwin AK, Burdette JE. Proteomic Profiling of Fallopian Tube-Derived Extracellular Vesicles Using a Microfluidic Tissue-on-Chip System. Bioengineering (Basel) 2023; 10:423. [PMID: 37106610 PMCID: PMC10135590 DOI: 10.3390/bioengineering10040423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The human fallopian tube epithelium (hFTE) is the site of fertilization, early embryo development, and the origin of most high-grade serous ovarian cancers (HGSOCs). Little is known about the content and functions of hFTE-derived small extracellular vesicles (sEVs) due to the limitations of biomaterials and proper culture methods. We have established a microfluidic platform to culture hFTE for EV collection with adequate yield for mass spectrometry-based proteomic profiling, and reported 295 common hFTE sEV proteins for the first time. These proteins are associated with exocytosis, neutrophil degranulation, and wound healing, and some are crucial for fertilization processes. In addition, by correlating sEV protein profiles with hFTE tissue transcripts characterized using GeoMx® Cancer Transcriptome Atlas, spatial transcriptomics analysis revealed cell-type-specific transcripts of hFTE that encode sEVs proteins, among which, FLNA, TUBB, JUP, and FLNC were differentially expressed in secretory cells, the precursor cells for HGSOC. Our study provides insights into the establishment of the baseline proteomic profile of sEVs derived from hFTE tissue, and its correlation with hFTE lineage-specific transcripts, which can be used to evaluate whether the fallopian tube shifts its sEV cargo during ovarian cancer carcinogenesis and the role of sEV proteins in fallopian tube reproductive functions.
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Affiliation(s)
- Didi Zha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jared Sipes
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Angela Russo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Harsh B. Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Kailiang Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mihaela E. Sardiu
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Leonidas E. Bantis
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Amrita Mitra
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Rajni V. Puri
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Camille V. Trinidad
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Brian P. Cain
- Charles Stark Draper Laboratory, Cambridge, MA 02139, USA
| | | | | | - Shannon MacLaughlan
- Department of Obstetrics and Gynecology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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Tabak C, Hyter S, Yacoub A, Byrd K, McGuirk J, Godwin AK, Abdelhakim H. Case report: Invasive fungal infection in a patient with a rare CVID-causing gene (TNFRSF13B) mutation undergoing AML treatment. Front Oncol 2023; 13:1017230. [PMID: 37007115 PMCID: PMC10050568 DOI: 10.3389/fonc.2023.1017230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
Acute myeloid leukemia (AML) is a complex diagnosis that puts patients at a higher risk for developing infections, particularly invasive fungal infections (IFI). Mutations in TNFRSF13B have been shown to cause dysfunction in B-cell homeostasis and differentiation, making it a risk factor for developing immunodeficiency syndromes. In this case, a male patient in his 40s presented to our emergency department (ED) with symptoms leading to a diagnosis of AML with concurrent mucormycosis of the lungs and sinuses. Targeted next generation sequencing (NGS) of the patient’s bone marrow showed, among other variants, a loss of function mutation in the TNFRSF13B gene. While most patients present with fungal infections after prolonged periods of neutropenia associated with AML treatment, this case presented with IFI at diagnosis without neutropenia suggesting an immunodeficiency syndrome. The concurrent IFI and AML diagnoses create a delicate balance between treatment of the infection and the malignancy. This case highlights the risk of infection in patients receiving chemotherapy, especially those with unrecognized immunodeficiency syndromes, and emphasizes the importance of NGS for prognosis and treatment.
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Stecklein SR, Kimler BF, Yoder R, Schwensen K, Staley JM, Khan QJ, O'Dea AP, Nye LE, Elia M, Heldstab J, Home T, Hyter S, Isakova K, Pathak HB, Godwin AK, Sharma P. ctDNA and residual cancer burden are prognostic in triple-negative breast cancer patients with residual disease. NPJ Breast Cancer 2023; 9:10. [PMID: 36878909 PMCID: PMC9988835 DOI: 10.1038/s41523-023-00512-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) patients with residual disease (RD) after neoadjuvant systemic therapy (NAST) are at high risk for recurrence. Biomarkers to risk-stratify patients with RD could help individualize adjuvant therapy and inform future adjuvant therapy trials. We aim to investigate the impact of circulating tumor DNA (ctDNA) status and residual cancer burden (RCB) class on outcomes in TNBC patients with RD. We analyze end-of-treatment ctDNA status in 80 TNBC patients with residual disease who are enrolled in a prospective multisite registry. Among 80 patients, 33% are ctDNA positive (ctDNA+) and RCB class distribution is RCB-I = 26%, RCB-II = 49%, RCB-III = 18% and 7% unknown. ctDNA status is associated with RCB status, with 14%, 31%, and 57% of patients within RCB-I, -II, and -III classes demonstrating ctDNA+ status (P = 0.028). ctDNA+ status is associated with inferior 3-year EFS (48% vs. 82%, P < 0.001) and OS (50% vs. 86%, P = 0.002). ctDNA+ status predicts inferior 3-year EFS among RCB-II patients (65% vs. 87%, P = 0.044) and shows a trend for inferior EFS among RCB-III patients (13% vs. 40%, P = 0.081). On multivariate analysis accounting for T stage and nodal status, RCB class and ctDNA status independently predict EFS (HR = 5.16, P = 0.016 for RCB class; HR = 3.71, P = 0.020 for ctDNA status). End-of-treatment ctDNA is detectable in one-third of TNBC patients with residual disease after NAST. ctDNA status and RCB are independently prognostic in this setting.
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Affiliation(s)
- Shane R Stecklein
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Bruce F Kimler
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rachel Yoder
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kelsey Schwensen
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Joshua M Staley
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Qamar J Khan
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anne P O'Dea
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Lauren E Nye
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Manana Elia
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jaimie Heldstab
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Trisha Home
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Stephen Hyter
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kamilla Isakova
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Harsh B Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Priyanka Sharma
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA.
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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Stecklein SR, Yoder R, Salgado R, Staley JM, O’Dea A, Nye L, Elia M, Satelli D, Crane G, McKittrick R, Godwin AK, Khan Q, Sharma P. Abstract PD1-06: Black patients with triple negative breast cancer (TNBC) have enriched stromal tumor infiltrating lymphocytes (sTILs) and receive preferential benefit from neoadjuvant immunotherapy. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd1-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Introduction TNBC is overrepresented in Black women, and Black patients with TNBC have worse clinical outcomes compared to non-Black patients. This disparity likely results from racial differences in clinical, biological, and demographic features of TNBC and social determinants of health. Neoadjuvant chemoimmunotherapy is current standard of care for high-risk TNBC. However, Black patients have been poorly represented in immunotherapy TNBC trials, making it difficult to assess comparative efficacy of immunotherapy in Black patients. Methods We utilized two TNBC neoadjuvant trials to assess racial differences in the tumor immune microenvironment composition and evaluate impact of race on response to chemotherapy vs chemoimmunotherapy. NeoSTOP trial (NCT02413320) randomized 100 stage I-III TNBC patients to receive neoadjuvant carboplatin/paclitaxel + doxorubicin/cyclophosphamide (CbP+AC) or carboplatin/docetaxel (CbD). NeoPACT trial (NCT03639948) enrolled 120 patients with stage I-III TNBC who received neoadjuvant CbD + pembrolizumab (CbD+P). sTILs were centrally quantified, and RNA extracted from pretreatment tissue was subjected to next-generation sequencing. Relative leukocyte fractions were computed by CIBERSORTx. Factors were tested as predictors of pathologic complete response (pCR) using logistic regression analysis. Event-free survival (EFS) was estimated by the Kaplan-Meier method and compared between groups by log-rank test, followed by Cox regression analysis. Results The study population includes 197 patients with known race, sTILs, and gene expression data (84 patients from NeoSTOP, 113 from NeoPACT). 15/84 (18%) patients in NeoSTOP and 20/113 (18%) patients in NeoPACT self-reported Black race. There was no significant difference in age, T or N stage, or germline BRCA1/2 mutation status by race in either study. Black patients had significantly higher sTILs than non-Black patients (median 40% vs 15%, P=0.048) and were more likely to have ≥20% sTILs than non-Black patients (66% vs 44%, P=0.026). There was no significant difference in pCR by race in NeoSTOP (OR=0.60, 95% CI 0.19-1.84, P=0.37; pCR 47% for Black vs 59% for non-Black). In contrast, in NeoPACT, Black patients had a significantly higher pCR compared to non-Black patients (OR=3.27, 95% CI 1.01-10.64, P=0.049; pCR 79% for Black vs 53% for non-Black). In NeoSTOP, EFS was similar for Black and non-Black patients (3-year EFS 92% and 94%, respectively, HR=0.88, 95% CI 0.11-7.28, P=0.90). In NeoPACT, EFS was numerically higher in Black vs non-Black patients (3-year EFS 93% and 81%, respectively, HR=0.43, 95% CI 0.05-3.36, P=0.40); NeoPACT survival follow-up is ongoing at the time of this report. On CIBERSORTx analysis, Black patients had relative depletion of immunosuppressive pro-tumorigenic M2 macrophages (P=0.005) and CD4+ memory resting T cells (P=0.021) compared to non-Black patients. Conclusions Compared to non-Black patients, Black patients with TNBC are more likely to have immune-enriched tumors with lower relative abundance of immunosuppressive leukocytes. These findings suggest potential for higher relative magnitude of benefit from checkpoint inhibitor therapy in Black compared to non-Black patients. Supporting this biological hypothesis, we noted that Black and non-Black patients had equivalent rates of pCR with neoadjuvant chemotherapy; however, pCR rate among Black patients was significantly higher than in non-Black patients when treated with neoadjuvant chemoimmunotherapy. These findings should be confirmed in other studies and can optimize utilization of neoadjuvant chemoimmunotherapy. Our findings also underscore the importance of efforts to address disparity in access and use of immunotherapy in Black patients.
Citation Format: Shane R. Stecklein, Rachel Yoder, Roberto Salgado, Joshua M. Staley, Anne O’Dea, Lauren Nye, Manana Elia, Deepti Satelli, Gregory Crane, Richard McKittrick, Andrew K. Godwin, Qamar Khan, Priyanka Sharma. Black patients with triple negative breast cancer (TNBC) have enriched stromal tumor infiltrating lymphocytes (sTILs) and receive preferential benefit from neoadjuvant immunotherapy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD1-06.
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Affiliation(s)
- Shane R. Stecklein
- 1University of Kansas Medical Center; Kansas Institute for Precision Medicine
| | | | - Roberto Salgado
- 3GZA-ZNA-Hospitals, Antwerp, Belgium; Peter Mac Callum Cancer Centre, Melbourne, Australia
| | | | | | | | | | | | | | | | - Andrew K. Godwin
- 11University of Kansas Medical Center; Kansas Institute for Precision Medicine; The University of Kansas Cancer Center
| | | | - Priyanka Sharma
- 13University of Kansas Medical Center Westwood, Westwood, KS, USA
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Sharma P, Stecklein SR, Yoder R, Staley JM, Salgado R, Paré L, Conte B, Brasó-Maristany F, O’Dea A, Nye L, Elia M, Satelli D, Crane G, McKittrick R, Khan Q, Godwin AK, Prat A. Abstract PD11-07: PD11-07 Association of TNBC-DX scores with outcomes in triple-negative breast cancer (TNBC) treated with neoadjuvant pembrolizumab and chemotherapy: a correlative analysis from NeoPACT and NeoSTOP trials. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd11-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Introduction: The TNBC-DX risk score includes the 14-gene immunoglobulin (IGG) immune signature, tumor size, and nodal status and has shown prognostic value for survival in early-stage TNBC (B. Conte et al., ESMO Breast 2021). However, currently unknown are the value of the TNBC-DX risk score and IGG immune signature in 1) predicting pathologic complete response (pCR) following neoadjuvant therapy, and 2) predicting outcomes the context of neoadjuvant anti-PD1 treatment. Here, we assessed the IGG signature and the TNBC-DX risk score in patients with TNBC treated with neoadjuvant chemoimmunotherapy (NeoPACT; NCT03639948) and neoadjuvant chemotherapy without immunotherapy (NeoSTOP; NCT02413320). Methods: NeoPACT trial enrolled 120 patients with stage I-III TNBC who received carboplatin (AUC 6) + docetaxel (75 mg/m2) + pembrolizumab (200 mg) every 21 days x 6 cycles. NeoSTOP randomized 100 patients with stage I-III TNBC to two chemotherapy regimens; Arm B of NeoSTOP was included in this correlative study as the chemotherapy regimen was identical to NeoPACT. RNA isolated from pretreatment tumor tissue was subjected to next-generation sequencing. The 14-gene IGG immune signature and TNBC-DX risk score were calculated in silico as previously described. Evaluation of stromal tumor-infiltrating lymphocytes (sTILs) was performed as previously described. Markers were tested for prediction of pCR. Logistic regression analysis was used to examine the effect of multiple variables. Event-free survival (EFS) curves were assessed by the Kaplan-Meier method and groups compared by the log-rank test, followed by Cox regression analysis. Results: In this analysis, 112 patients were treated with chemoimmunotherapy on NeoPACT (node-positive = 38%, pCR rate = 58%). In the NeoPACT trial, the 14-gene IGG signature (as a continuous variable) was significantly associated with improved pCR (odds ratio [OR]=1.105, 95% CI 1.019-1.197, P=0.015 for every 0.2 increment). The pCR rates in IGG-high (≥ median) and IGG-low (< median) groups were 71% and 44%, respectively (OR=3.152, 95% CI 1.420-6.996, P=0.005). In terms of EFS, the 14-gene IGG signature was not prognostic (hazard ratio [HR]=0.507, 95% CI 0.148-1.735, p=0.269). In contrast, TNBC-DX risk score was strongly associated with EFS (HR=5.684, 95% CI 1.226-26.356, P=0.012), even when adjusted for sTILs and pCR status (HR=8.415, 95% CI 1.054-67.169, P=0.044). Estimated 3-year EFS rates in TNBC-DX high and low risk groups (above and below median) were 77% and 89%, respectively (P=0.012). In 43 NeoSTOP patients treated with neoadjuvant chemotherapy only (node-positive = 33%, pCR rate = 53%), no association of IGG signature with pCR or TNBC-DX score with EFS was observed. Finally, we observed a moderate correlation between IGG signature and sTILs in both trial datasets combined (r=0.642, P< 0.001). Conclusions: High expression of the 14-gene IGG immune signature in baseline pretreatment tumor samples in early-stage TNBC is significantly associated with pCR following pembrolizumab-based neoadjuvant chemotherapy. The combination of this signature with tumor burden as assessed by TNBC-DX is prognostic for long-term outcomes. Availability of biomarkers that can predict both pathological response and survival with chemoimmunotherapy can optimize this therapy, and evaluation of this biomarker in larger studies is warranted.
Citation Format: Priyanka Sharma, Shane R. Stecklein, Rachel Yoder, Joshua M. Staley, Roberto Salgado, Laia Paré, Benedetta Conte, Fara Brasó-Maristany, Anne O’Dea, Lauren Nye, Manana Elia, Deepti Satelli, Gregory Crane, Richard McKittrick, Qamar Khan, Andrew K. Godwin, Aleix Prat. PD11-07 Association of TNBC-DX scores with outcomes in triple-negative breast cancer (TNBC) treated with neoadjuvant pembrolizumab and chemotherapy: a correlative analysis from NeoPACT and NeoSTOP trials [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD11-07.
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Affiliation(s)
- Priyanka Sharma
- 1University of Kansas Medical Center Westwood, Westwood, KS, USA
| | - Shane R. Stecklein
- 2University of Kansas Medical Center; Kansas Institute for Precision Medicine
| | | | | | - Roberto Salgado
- 5GZA-ZNA-Hospitals, Antwerp, Belgium; Peter Mac Callum Cancer Centre, Melbourne, Australia
| | | | - Benedetta Conte
- 7Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Fara Brasó-Maristany
- 8Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS)
| | | | | | | | | | | | | | | | - Andrew K. Godwin
- 16University of Kansas Medical Center; Kansas Institute for Precision Medicine; The University of Kansas Cancer Center
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Chen Y, Barlow WE, Li H, Lu C, Janowczyk A, Corredor G, Ganesan S, Feldman M, Fu P, Gilmore H, Albain KS, Pusztai L, Rae J, Hayes D, Godwin AK, Thompson AM, Madabhushi A. Abstract P2-11-16: Computerized Measurements of Nuclear Morphology Features, Mitosis Rate, and Tubule Formation from H&E Images Predicts Disease-Free Survival in Patients with HR+ & LN+ Invasive Breast Cancer from SWOG S8814. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p2-11-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Lymph node (LN) involvement is a strong indicator of poor prognosis for breast cancer (BC), with adjuvant chemotherapy remaining fundamental to management of these patients. SWOG S8814 was a Phase III randomized trial of postmenopausal patients with pathologic LN-positive BC who were hormone receptor positive (HR+). The objectives of the clinical trial were to compare disease free survival (DFS) and overall survival (OS) of 1) these postoperative patients treated with a combination of cyclophosphamide, doxorubicin, fluorouracil (CAF) plus tamoxifen versus tamoxifen alone; and 2) patients treated with CAF followed by tamoxifen versus CAF plus concurrent tamoxifen. In this study we sought to evaluate the potential of applying computational image analysis on whole slide images (WSI) for predicting DFS and OS in SWOG S8814. Methods: A cohort of 135 patients (N=53 DFS event) diagnosed with HR+ & LN+ BC from clinical trial ECOG 2197 was utilized as training set D1. Validation set D2 comprised 630 patients (N=260 DFS event, N=195 death) with HR+& LN+ BC from SWOG S8814. Three deep learning models were employed to respectively detect nuclei, mitosis, and tubules in WSIs. Subsequently, a total of 1,810 features relating to nuclear morphology (e.g., spatial distribution, shape, texture, orientation), mitotic activity (e.g., mitosis hotspot, mitotic rates) and tubule formation (e.g., tubular nuclei distribution, ratio of tubule to non-tubule area) were extracted from each WSI. A lasso regularized Cox regression model (IbRiS) was trained on D1 to respectively identify four features from each of the feature categories (nuclei morphology, mitotic activity, and tubule formation) most strongly associated with DFS, a continuous risk score based on the selected features was then constructed. An optimal risk threshold was identified on D1 to dichotomize the risk scores into high vs. low risk of recurrence categories. Blinded validation of the machine learning model on SWOG S8814 using Cox regression was performed by SWOG to evaluate its performance in terms of DFS and OS. Results: In D2, patients identified as high risk of recurrence by IbRiS had a significantly worse prognosis in terms of DFS with hazard ratio=1.30 (p=0.039, 95% CI=1.01-1.66). IbRiS was also found to be significantly prognostic of OS with hazard ratio=1.38 (p=0.026, 95% CI=1.04-1.83). IbRiS was however, neither prognostic of DFS (HR = 1.20; 95% CI 0.93-1.54) nor OS (HR = 1.28; 95% CI 0.96-1.71) in multivariable analysis adjusting for treatment, tumor size, and number of positive nodes. IbRiS was also not a significant predictor of chemotherapy benefit (DFS p=0.45; OS p=0.25). Conclusion: We developed a prognostic model (IbRiS) based on the combined features of nuclear morphology, mitosis count, and tubule formation that can help further risk stratify HR+ & LN+ BC patients by only using H&E slides.
Citation Format: Yuli Chen, William E. Barlow, Haojia Li, Cheng Lu, Andrew Janowczyk, German Corredor, Shridar Ganesan, Michael Feldman, Pingfu Fu, Hannah Gilmore, Kathy S. Albain, Lajos Pusztai, James Rae, Daniel Hayes, Andrew K. Godwin, Alastair M. Thompson, Anant Madabhushi. Computerized Measurements of Nuclear Morphology Features, Mitosis Rate, and Tubule Formation from H&E Images Predicts Disease-Free Survival in Patients with HR+ & LN+ Invasive Breast Cancer from SWOG S8814 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-16.
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Affiliation(s)
- Yuli Chen
- 1Shanxi Normal University, School of Computer Science
| | | | - Haojia Li
- 3Case Western Reserve University, Department of Biomedical Engineering
| | - Cheng Lu
- 4Case Western Reserve University, Department of Biomedical Engineering
| | - Andrew Janowczyk
- 5Case Western Reserve University/Lausanne University Hospital, Precision Oncology Center
| | - German Corredor
- 6Case Western Reserve University, Department of Biomedical Engineering
| | | | - Michael Feldman
- 8University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Pingfu Fu
- 9Case Western Reserve University, Department of Population and Quantitative Health Sciences
| | | | - Kathy S. Albain
- 11Loyola University Chicago Stritch School of Medicine, Cardinal Bernardin Cancer Center
| | | | - James Rae
- 13University of Michigan Medical School
| | - Daniel Hayes
- 14University of Michigan Comprehensive Cancer Center
| | - Andrew K. Godwin
- 15University of Kansas Medical Center; Kansas Institute for Precision Medicine; The University of Kansas Cancer Center
| | | | - Anant Madabhushi
- 17Case Western Reserve University, Department of Biomedical Engineering/Louis Stokes, Cleveland Veterans Administration Medical Center
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Rastogi A, Behbod F, Navin N, Lin J, Li L, Li H, Godwin AK, Thompson AM, Fields T, Hong Y. Abstract P6-14-08: Epithelial/stromal cross talks that induce malignant transition of human ductal carcinoma in situ. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-14-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: A large fraction of human DCIS (>50%) may not need the multimodality treatment options currently offered to all patients. More importantly, while we may be overtreating many, we cannot identify those most at risk for invasion/metastasis. Revealing the cellular and molecular mechanisms by which some DCIS remain indolent while others advance to invasive and metastatic breast cancers is currently a clinical unmet need. Methods: To address this gap, we developed the Mouse-INtraDuctal (MIND) model, by which patient-derived (PDX) DCIS epithelial cells are injected intraductally and allowed to progress naturally in mice. Single cell RNA-sequencing (scRNA-seq) was utilized to profile the DCIS epithelial and stroma cells in progressors vs. non-progressors. To distinguish between stromal (diploid) cells and tumor (aneuploid) cells, we calculated Copy Number Aberration (CNA) profiles from RNA using CopyKAT. Cell-type specific differential gene expression analysis of DCIS epithelial cells and microenvironment cell types in progressors and non-progressors was performed. We also predicted putative ligand:receptor interactions between the tumor cells and cell types in the microenvironment by CellPhoneDB. Results: Among 37 PDX DCIS MIND models followed for a median of 9 months, 20 (54%) grafted into 95 glands, showed in vivo invasive progression (progressed) while 17 (46%), injected into 107 glands, remained non-invasive (non-progressed). ScRNA-seq was performed on 13 DCIS samples including 10 progressors and 3 non-progressors. Aneuploid cells were further analyzed to identify deferentially expressed genes that were upregulated in progressors compared to non-progressors (log2 fold=1, FDR p< 0.05).. Notable genes included NEAT1, EIF4EBP1, SCGB2A2, TFF1 and TFF3 that were upregulated in the progressors. NEAT1, the core structural component of the paraspeckles, is frequently overexpressed in human cancers and its expression is correlated with worse survival in cancer patients. NEAT1 drives tumor progression by regulating genes involved in cellular growth, migration, invasion, metastasis, EMT, stemness, radio- and chemoresistance, supporting its role as a potential biomarker and therapeutic target. TFF1/TFF3 mRNAs show increased expression in metastatic breast cancers. EIF4EBP1 is located on chrom 8p11-p12 which is frequently amplified in breast cancer and is associated with poor clinical prognosis. Further analysis using Cancer Hallmarks identified mitotic spindle, interferon signaling, DNA repair, oxidative phosphorylation and P53 pathway among the top signatures that were upregulated in the progressors. CellPhoneDB identified expression of several receptor/ligand interactions including CD74/MIF involved in epithelial/stromal and stromal/stromal cross talks that may play a role in DCIS invasive progression. Conclusions: Future studies will validate our findings using patient DCIS samples with known long-term outcome and in vivo MIND models to further refine risk associated biomarkers for invasion/metastasis and to identify more effective treatments.
Citation Format: Aditi Rastogi, Fariba Behbod, Nicholas Navin, Jerome Lin, Linheng Li, Hua Li, Andrew K. Godwin, Alastair M. Thompson, Timothy Fields, Yan Hong. Epithelial/stromal cross talks that induce malignant transition of human ductal carcinoma in situ. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-14-08.
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Affiliation(s)
| | | | | | - Jerome Lin
- 4The University of Texaxs MD Anderson Cancer Center
| | - Linheng Li
- 5The University of Kansas Medical Center/Stowers Institute for Medical Research
| | - Hua Li
- 6Stowers Institute for Medical Research
| | - Andrew K. Godwin
- 7University of Kansas Medical Center; Kansas Institute for Precision Medicine; The University of Kansas Cancer Center
| | | | | | - Yan Hong
- 10The University of Kansas Medicla Center
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Saeed A, Park R, Dai J, Al-Rajabi R, Kasi A, Baranda J, Williamson S, Saeed A, Ripp J, Collins Z, Mulvaney K, Shugrue M, Firth-Braun J, Godwin AK, Madan R, Phadnis M, Sun W. Cabozantinib plus durvalumab in advanced gastroesophageal cancer and other gastrointestinal malignancies: Phase Ib CAMILLA trial results. Cell Rep Med 2023; 4:100916. [PMID: 36702123 PMCID: PMC9975105 DOI: 10.1016/j.xcrm.2023.100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023]
Abstract
This is the phase Ib part of the phase I/II CAMILLA trial evaluating cabozantinib plus durvalumab in advanced chemo-refractory proficient mismatch repair or microsatellite stable (pMMR/MSS) gastrointestinal malignancies including gastric/gastroesophageal junction/esophageal (G/GEJ/E) adenocarcinoma, colorectal cancer (CRC), and hepatocellular carcinoma (HCC). Thirty-five patients are enrolled. There are no observed dose-limiting toxicities during dose escalation. The overall grade 3/4 treatment-related adverse event rate is 34%. Among evaluable patients (n = 30), the objective response rate (ORR) is 30%, disease control rate (DCR) 83.3%, 6-month progression-free survival (PFS) 36.7%, median PFS 4.5 months, and median overall survival (OS) 8.7 months. Responses are seen in 4 of 17, 3 of 10, and 2 of 3 patients with CRC, G/GEJ/E adenocarcinoma, and HCC, respectively. Participants with a PD-L1 combined positive score (CPS) ≥5 have numerically higher ORR, PFS, and OS. Cabozantinib plus durvalumab demonstrates a tolerable safety profile and potential efficacy in previously treated advanced pMMR/MSS gastrointestinal malignancies.
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Affiliation(s)
- Anwaar Saeed
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA; Kansas University Cancer Center, Kansas City, KS 66205, USA; Department of Medicine, Division of Hematology and Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Robin Park
- Division of Hematology and Medical Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Junqiang Dai
- Department of Biostatistics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Raed Al-Rajabi
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA; Kansas University Cancer Center, Kansas City, KS 66205, USA
| | - Anup Kasi
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA; Kansas University Cancer Center, Kansas City, KS 66205, USA
| | - Joaquina Baranda
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA; Kansas University Cancer Center, Kansas City, KS 66205, USA
| | - Stephen Williamson
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA; Kansas University Cancer Center, Kansas City, KS 66205, USA
| | - Azhar Saeed
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jacob Ripp
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Zachary Collins
- Department of Radiology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Kelly Mulvaney
- Kansas University Cancer Center, Kansas City, KS 66205, USA
| | - Molly Shugrue
- Kansas University Cancer Center, Kansas City, KS 66205, USA
| | | | - Andrew K Godwin
- Kansas University Cancer Center, Kansas City, KS 66205, USA; Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Rashna Madan
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Milind Phadnis
- Department of Biostatistics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Weijing Sun
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA; Kansas University Cancer Center, Kansas City, KS 66205, USA
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Rodler E, Sharma P, Barlow WE, Gralow JR, Puhalla SL, Anders CK, Goldstein L, Tripathy D, Brown-Glaberman UA, Huynh TT, Szyarto CS, Godwin AK, Pathak HB, Swisher EM, Radke MR, Timms KM, Lew DL, Miao J, Pusztai L, Hayes DF, Hortobagyi GN. Cisplatin with veliparib or placebo in metastatic triple-negative breast cancer and BRCA mutation-associated breast cancer (S1416): a randomised, double-blind, placebo-controlled, phase 2 trial. Lancet Oncol 2023; 24:162-174. [PMID: 36623515 PMCID: PMC9924094 DOI: 10.1016/s1470-2045(22)00739-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Poly(ADP-ribose) polymerase (PARP) inhibitors are effective in germline BRCA1 or BRCA2 (BRCA1/2) mutation-associated metastatic breast cancer. However, studies evaluating PARP inhibitors plus platinum-based chemotherapy in germline BRCA1/2-wildtype triple-negative breast cancer are scarce. A large proportion of germline BRCA1/2-wildtype triple-negative breast cancer shows homologous recombination deficiency (HRD), resulting in a BRCA-like phenotype that might render sensitivity to PARP inhibitors. The S1416 trial assessed the efficacy of cisplatin combined with the PARP inhibitor veliparib in three predefined groups of metastatic breast cancer: germline BRCA1/2-mutated, BRCA-like, and non-BRCA-like. METHODS S1416 was a randomised, double-blind, placebo-controlled, phase 2 trial conducted at 154 community and academic clinical sites across the USA. Eligible patients aged 18 years or older had metastatic or recurrent triple-negative breast cancer or germline BRCA1/2-associated metastatic or recurrent breast cancer, an Eastern Cooperative Oncology Group performance status of 0-2, and had received up to one line of chemotherapy for metastatic disease. Patients were randomly assigned (1:1) via the National Clinical Trials Network open interactive system with dynamic balancing on number of previous cytotoxic regimens for metastatic disease to receive intravenous cisplatin (75 mg/m2, day 1) combined with either veliparib or matching placebo (300 mg orally twice a day, days 1-14) on a 21-day cycle. Investigators, patients, and the sponsors were masked to treatment assignment; the study statisticians were unmasked. Central testing after ran domisation classified patients as having mutated or wildtype germline BRCA1/2. A biomarker panel established a priori was used to classify patients with wildtype germline BRCA1/2 into BRCA-like and non-BRCA-like phenotype groups, with BRCA-like status based on at least one of the biomarkers: genomic instability score (≥42), somatic BRCA1/2 mutations, BRCA1 promoter methylation, or non-BRCA1/2 homologous recombination repair germline mutations. The primary endpoint was investigator-assessed progression-free survival, analysed separately for the three predefined biomarker groups with a prespecified α value for each analysis. Efficacy analyses were done by intention to treat and included all eligible patients. Safety analyses of toxicities attributed to treatment included all patients who received at least one dose of veliparib or placebo. The study is ongoing and registered with ClinicalTrials.gov, NCT02595905. FINDINGS Between July 7, 2016, and June 15, 2019, 335 patients were enrolled and randomly assigned. 320 patients (n=162 to cisplatin plus veliparib, all women; and n=158 to cisplatin plus placebo, 157 women and one man) were eligible for efficacy evaluation. 247 patients were classified into the three biomarker groups: germline BRCA1/2-mutated (n=37), BRCA-like (n=101), and non-BRCA-like (n=109). 73 patients could not be classified due to missing biomarker information. Median follow-up was 11·1 months (IQR 5·6-20·8). In the germline BRCA1/2-mutated group, median progression-free survival was 6·2 months (95% CI 2·3-9·2) in the cisplatin plus veliparib group and 6·4 months (4·3-8·2) in the cisplatin plus placebo group (HR 0·79 [95% CI 0·38-1·67]; log-rank p=0·54). In the BRCA-like group, median progression-free survival was 5·9 months (95% CI 4·3-7·8) in the cisplatin plus veliparib group versus 4·2 months (2·3-5·0) in the cisplatin plus placebo group (HR 0·57 [95% CI 0·37-0·88]; p=0·010). In the non-BRCA-like group, median progression-free survival was 4·0 months (95% CI 2·5-4·7) in the cisplatin plus veliparib group versus 3·0 months (2·2-4·4) in the cisplatin plus placebo group (HR 0·89 [95% CI 0·60-1·33]; p=0·57). The most common grade 3 or worse adverse events attributed to treatment were neutropenia (71 [46%] of 155 patients in the cisplatin plus veliparib group vs 29 [20%] of 147 in the cisplatin plus placebo group), leukopenia (42 [27%] vs 11 [7%]), anaemia (35 [23%] vs 12 [8%]), and thrombocytopenia (29 [19%] vs four [3%]). Serious adverse events attributed to treatment occurred in 48 (31%) patients in the cisplatin plus veliparib group and 53 (36%) patients in the cisplatin plus placebo group. Treatment-related adverse events led to death in one patient in the cisplatin plus veliparib group (sepsis) and one patient in the cisplatin plus placebo group (acute kidney injury due to cisplatin plus heart failure from previous doxorubicin exposure). INTERPRETATION The addition of veliparib to cisplatin significantly improved progression-free survival in patients with BRCA-like metastatic triple-negative breast cancer, but not in patients with non-BRCA-like metastatic breast cancer. PARP inhibitors combined with platinum-based chemotherapy should be explored further in BRCA-like triple-negative breast cancer. FUNDING National Cancer Institute and National Institute of General Medical Sciences (US National Institutes of Health); AbbVie; Myriad Genetics; the Biomarker, Imaging, and Quality of Life Studies Funding Program (awarded by the National Cancer Institute); and The University of Kansas Cancer Center.
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Affiliation(s)
- Eve Rodler
- Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Priyanka Sharma
- Department of Internal Medicine, University of Kansas Medical Center, Westwood, KS, USA.
| | - William E Barlow
- Department of Biostatistics, SWOG Statistical and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie R Gralow
- Department of Breast Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA
| | - Shannon L Puhalla
- Division of Hematology/Oncology, University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, USA
| | - Carey K Anders
- Department of Medicine, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Lori Goldstein
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ursa A Brown-Glaberman
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA; New Mexico MU-NCORP, Albuquerque, NM, USA
| | - Thu-Tam Huynh
- Department of Hematology/Oncology, Kaiser Permanente NCORP, Anaheim, CA, USA; Kaiser Permanente Medical Group, Anaheim, CA, USA
| | - Christopher S Szyarto
- Department of Hematology/Oncology, Genesee Hematology Oncology PC, Flint, MI, USA; Michigan CRC NCORP, Flint, MI, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Harsh B Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - Kirsten M Timms
- Department of Research, Myriad Genetics, Salt Lake City, UT, USA
| | - Danika L Lew
- Department of Biostatistics, SWOG Statistical and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jieling Miao
- Department of Biostatistics, SWOG Statistical and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lajos Pusztai
- Department of Medicine, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Daniel F Hayes
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Nanou A, Miao J, Coumans FA, Dolce EM, Darga E, Barlow W, Smerage JB, Paoletti C, Godwin AK, Pusztai L, Sharma P, Thompson A, Hortobagyi GN, Terstappen LW, Hayes DF. Tumor-Derived Extracellular Vesicles as Complementary Prognostic Factors to Circulating Tumor Cells in Metastatic Breast Cancer. JCO Precis Oncol 2023; 7:e2200372. [PMID: 36634296 PMCID: PMC9928629 DOI: 10.1200/po.22.00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 12/02/2022] [Indexed: 01/13/2023] Open
Abstract
PURPOSE Circulating tumor cells (CTCs) are strongly prognostic for overall survival (OS) in metastatic breast cancer although additional prognostic biomarkers are needed. We evaluated the complementary prognostic value of tumor-derived extracellular vesicles (tdEVs) next to CTCs. METHODS We applied the open-source ACCEPT software to archived CellSearch images from the prospective clinical trial SWOG0500 to enumerate CTCs and tumor-derived extracellular vesicles (tdEVs) before and after one cycle of chemotherapy. RESULTS CTCs enumerated by ACCEPT were strongly correlated with classical ocular enumeration (correlation r = 0.98). OS was worse with elevated tdEVs (median OS for high/medium/low groups: 17.1 v 29.0 v 43.3 months; P < .0001). In patients with longer OS by CTC counts (< 5 CTC/7.5 mL blood), elevated tdEV levels were independently associated with poorer OS (multivariable analysis P < .001). OS was also longer for patients with low tdEVs after one cycle of chemotherapy (median OS for high/medium/low group: 10.8 v 17.8 v 26.7; P < .0001). CONCLUSION This study highlights the complementary prognostic significance of tdEVs in metastatic breast cancer before and after one cycle of chemotherapy.
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Affiliation(s)
- Afroditi Nanou
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, the Netherlands
| | - Jieling Miao
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Frank A.W. Coumans
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, the Netherlands
| | - Emily M. Dolce
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | - William Barlow
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | | | | | | | - Leon W.M.M. Terstappen
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, University of Twente, Enschede, the Netherlands
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Crow J, Samuel G, Farrow E, Gibson M, Johnston J, Guest E, Miller N, Pei D, Koestler D, Pathak H, Liang X, Mangels C, Godwin AK. MicroRNA Content of Ewing Sarcoma Derived Extracellular Vesicles Leads to Biomarker Potential and Identification of a Previously Undocumented EWS-FLI1 Translocation. Biomark Insights 2022; 17:11772719221132693. [PMCID: PMC9629554 DOI: 10.1177/11772719221132693] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Objective: Ewing Sarcoma Family of Tumors (ESFT) are a highly aggressive pediatric bone and soft tissue malignancy with poor outcomes in the refractory and recurrent setting. Over 90% of Ewing Sarcoma (ES) tumors are driven by the pathognomonic EWS-ETS chimeric transcripts and their corresponding oncoproteins. It has been suggested that the EWS-ETS oncogenic action can mediate microRNA (miRNA) processing. Importantly, small extracellular vesicles (sEVs), including those frequently referred to as exosomes have been shown to be highly enriched with tumor-derived small RNAs such as miRNAs. We hypothesized that ESFT-specific sEVs are enriched with certain miRNAs which could be utilized toward an exo-miRNA biomarker signature specific to this disease. Methods: We performed miRNAseq to compare both the exo-derived and cell-derived miRNA content from 8 ESFT, 2 osteosarcoma, 2 non-cancerous cell lines, and pediatric plasma samples. Results: We found that sEVs derived from ESFT cells contained nearly 2-fold more number of unique individual miRNAs as compared to non-ESFT samples. Quantitative analysis of the differential enrichment of sEV miRNAs resulted in the identification of 62 sEV-miRNAs (exo-miRNAs) with significant (P < .05) enrichment variation between ESFT and non-ESFT sEV samples. To determine if we could utilize this miRNA signature to diagnose ESFT patients via a liquid biopsy, we analyzed the RNA content of total circulating sEVs isolated from 500 µL plasma from 5 pediatric ESFT patients, 2 pediatric osteosarcoma patients, 2 pediatric rhabdomyosarcoma patients, and 4 non-cancer pediatric controls. Pearson’s clustering of 60 of the 62 candidate exo-miRNAs correctly identified 80% (4 of 5) of pathology confirmed ESFT patients. Importantly, RNAseq analysis of tumor tissue from the 1 outlier, revealed a previously uncharacterized EWS-FLI1 translocation.Conclusions: Taken together, these findings support the development and validation of an exo-miRNA-based liquid biopsy to aid in the diagnosis and monitoring of ESFT.
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Affiliation(s)
- Jennifer Crow
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Glenson Samuel
- Children’s Mercy Kansas City, Kansas City, MO, USA,The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Emily Farrow
- The Center for Pediatric Genomic Medicine at Children’s Mercy, Kansas City, MO, USA
| | - Margaret Gibson
- The Center for Pediatric Genomic Medicine at Children’s Mercy, Kansas City, MO, USA
| | - Jefferey Johnston
- The Center for Pediatric Genomic Medicine at Children’s Mercy, Kansas City, MO, USA
| | - Erin Guest
- Children’s Mercy Kansas City, Kansas City, MO, USA,The Center for Pediatric Genomic Medicine at Children’s Mercy, Kansas City, MO, USA
| | - Neil Miller
- The Center for Pediatric Genomic Medicine at Children’s Mercy, Kansas City, MO, USA
| | - Dong Pei
- The Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Devin Koestler
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA,The Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA,Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA,Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Xiaobo Liang
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Cooper Mangels
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA,The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA,Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA,Andrew K Godwin, Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 3040, Kansas City, KS 66160, USA.
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40
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Hakkaart C, Pearson JF, Marquart L, Dennis J, Wiggins GAR, Barnes DR, Robinson BA, Mace PD, Aittomäki K, Andrulis IL, Arun BK, Azzollini J, Balmaña J, Barkardottir RB, Belhadj S, Berger L, Blok MJ, Boonen SE, Borde J, Bradbury AR, Brunet J, Buys SS, Caligo MA, Campbell I, Chung WK, Claes KBM, Collonge-Rame MA, Cook J, Cosgrove C, Couch FJ, Daly MB, Dandiker S, Davidson R, de la Hoya M, de Putter R, Delnatte C, Dhawan M, Diez O, Ding YC, Domchek SM, Donaldson A, Eason J, Easton DF, Ehrencrona H, Engel C, Evans DG, Faust U, Feliubadaló L, Fostira F, Friedman E, Frone M, Frost D, Garber J, Gayther SA, Gehrig A, Gesta P, Godwin AK, Goldgar DE, Greene MH, Hahnen E, Hake CR, Hamann U, Hansen TVO, Hauke J, Hentschel J, Herold N, Honisch E, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Izquierdo A, Jakubowska A, James PA, Janavicius R, John EM, Joseph V, Karlan BY, Kemp Z, Kirk J, Konstantopoulou I, Koudijs M, Kwong A, Laitman Y, Lalloo F, Lasset C, Lautrup C, Lazaro C, Legrand C, Leslie G, Lesueur F, Mai PL, Manoukian S, Mari V, Martens JWM, McGuffog L, Mebirouk N, Meindl A, Miller A, Montagna M, Moserle L, Mouret-Fourme E, Musgrave H, Nambot S, Nathanson KL, Neuhausen SL, Nevanlinna H, Yie JNY, Nguyen-Dumont T, Nikitina-Zake L, Offit K, Olah E, Olopade OI, Osorio A, Ott CE, Park SK, Parsons MT, Pedersen IS, Peixoto A, Perez-Segura P, Peterlongo P, Pocza T, Radice P, Ramser J, Rantala J, Rodriguez GC, Rønlund K, Rosenberg EH, Rossing M, Schmutzler RK, Shah PD, Sharif S, Sharma P, Side LE, Simard J, Singer CF, Snape K, Steinemann D, Stoppa-Lyonnet D, Sutter C, Tan YY, Teixeira MR, Teo SH, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Trainer AH, Tripathi V, Tung N, van Engelen K, van Rensburg EJ, Vega A, Viel A, Walker L, Weitzel JN, Wevers MR, Chenevix-Trench G, Spurdle AB, Antoniou AC, Walker LC. Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers. Commun Biol 2022; 5:1061. [PMID: 36203093 PMCID: PMC9537519 DOI: 10.1038/s42003-022-03978-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09-1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.
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Affiliation(s)
- Christopher Hakkaart
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Louise Marquart
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Public Health, University of Queensland, Brisbane, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bridget A Robinson
- Department of Medicine, University of Otago, Christchurch, New Zealand
- Canterbury Regional Cancer and Haematology Service, Canterbury District Health Board, Christchurch Hospital, Christchurch, New Zealand
| | - Peter D Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kristiina Aittomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Judith Balmaña
- Hereditary cancer Genetics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Hospital Campus, Barcelona, Spain
- Department of Medical Oncology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sami Belhadj
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lieke Berger
- Department of Clinical Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Susanne E Boonen
- Department of Clinical Genetics, Odense University Hospital, Odence C, Denmark
| | - Julika Borde
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Angela R Bradbury
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), ONCOBELL-IDIBELL-IGTP, CIBERONC, Barcelona, Spain
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Maria A Caligo
- SOD Genetica Molecolare, University Hospital, Pisa, Italy
| | - Ian Campbell
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | | | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, UK
| | - Casey Cosgrove
- Gynecologic Oncology, Translational Therapeutics, Department of Obstetrics and Gynecology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sita Dandiker
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rosemarie Davidson
- Department of Clinical Genetics, Queen Elizabeth University Hospital, Glasgow, UK
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Robin de Putter
- Centre for Medical Genetics, Ghent University Hospital, Gent, Belgium
| | - Capucine Delnatte
- Oncogénétique, Institut de Cancérologie de l'Ouest siteRené Gauducheau, Saint Herblain, France
| | - Mallika Dhawan
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, USA
| | - Orland Diez
- Hereditary cancer Genetics Group, Vall d'Hebron Institute of Oncology, Vall d'Hebron Hospital Campus, Barcelona, Spain
- Area of Clinical and Molecular Genetics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Alan Donaldson
- Clinical Genetics Department, St Michael's Hospital, Bristol, UK
| | - Jacqueline Eason
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Skåne University Hospital, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), ONCOBELL-IDIBELL-IGTP, CIBERONC, Barcelona, Spain
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Megan Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrea Gehrig
- Department of Human Genetics, University Würzburg, Würzburg, Germany
| | - Paul Gesta
- Service Régional Oncogénétique Poitou-Charentes, CH Niort, Niort, France
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Eric Hahnen
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jan Hauke
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University Hospital Leipzig, Leipzig, Germany
| | - Natalie Herold
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Ellen Honisch
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Louise Izatt
- Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Angel Izquierdo
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), ONCOBELL-IDIBELL-IGTP, CIBERONC, Barcelona, Spain
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - Ramunas Janavicius
- Faculty of Medicine, Institute of Biomedical Sciences, Dept. Of Human and Medical Genetics, Vilnius University, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Esther M John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Zoe Kemp
- Breast and Cancer Genetics Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Judy Kirk
- Familial Cancer Service, Weatmead Hospital, Wentworthville, New South Wales, Australia
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Marco Koudijs
- Department of Medical Genetics, University Medical Center, Utrecht, The Netherlands
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China
- Department of Surgery, The University of Hong Kong, Hong Kong, China
- Department of Surgery and Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Fiona Lalloo
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Christine Lasset
- Unité de Prévention et d'Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
| | - Charlotte Lautrup
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), ONCOBELL-IDIBELL-IGTP, CIBERONC, Barcelona, Spain
| | | | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Phuong L Mai
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Véronique Mari
- Département d'Hématologie-Oncologie Médicale, Centre Antoine Lacassagne, Nice, France
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer team, Inserm U900, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, University of Munich, Campus Großhadern, Munich, Germany
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Lidia Moserle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | | | - Hannah Musgrave
- Department of Clinical Genetics, Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Sophie Nambot
- Unité d'oncogénétique, Centre de Lutte Contre le Cancer, Centre Georges-François Leclerc, Dijon, France
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Joanne Ngeow Yuen Yie
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Ana Osorio
- Familial Cancer Clinical Unit, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO) and Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Claus-Eric Ott
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Pedro Perez-Segura
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Timea Pocza
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | | | - Gustavo C Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, University of Chicago, Evanston, IL, USA
| | - Karina Rønlund
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle Hospital, Vejle, Denmark
| | - Efraim H Rosenberg
- Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rita K Schmutzler
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Payal D Shah
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Saba Sharif
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Birmingham, UK
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | | | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Christian F Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Katie Snape
- Medical Genetics Unit, St George's, University of London, London, UK
| | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Department of Tumour Biology, INSERM U830, Paris, France
- Université Paris Cité, Paris, France
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Yen Yen Tan
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence C, Denmark
| | - Darcy L Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Department of medicine, University Of Melbourne, Melbourne, Victoria, Australia
| | - Vishakha Tripathi
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Klaartje van Engelen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Alessandra Viel
- Division of Functional onco-genomics and genetics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, UK
| | - Jeffrey N Weitzel
- Latin American School of Oncology, Tuxtla Gutiérrez, Chiapas, Mexico
| | | | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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Gamage SST, Pahattuge TN, Wijerathne H, Childers K, Vaidyanathan S, Athapattu US, Zhang L, Zhao Z, Hupert ML, Muller RM, Muller-Cohn J, Dickerson J, Dufek D, Geisbrecht BV, Pathak H, Pessetto Z, Gan GN, Choi J, Park S, Godwin AK, Witek MA, Soper SA. Microfluidic affinity selection of active SARS-CoV-2 virus particles. Sci Adv 2022; 8:eabn9665. [PMID: 36170362 PMCID: PMC9519043 DOI: 10.1126/sciadv.abn9665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/10/2022] [Indexed: 06/07/2023]
Abstract
We report a microfluidic assay to select active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral particles (VPs), which were defined as intact particles with an accessible angiotensin-converting enzyme 2 receptor binding domain (RBD) on the spike (S) protein, from clinical samples. Affinity selection of SARS-CoV-2 particles was carried out using injection molded microfluidic chips, which allow for high-scale production to accommodate large-scale screening. The microfluidic contained a surface-bound aptamer directed against the virus's S protein RBD to affinity select SARS-CoV-2 VPs. Following selection (~94% recovery), the VPs were released from the chip's surface using a blue light light-emitting diode (89% efficiency). Selected SARS-CoV-2 VP enumeration was carried out using reverse transcription quantitative polymerase chain reaction. The VP selection assay successfully identified healthy donors (clinical specificity = 100%) and 19 of 20 patients with coronavirus disease 2019 (COVID-19) (95% sensitivity). In 15 patients with COVID-19, the presence of active SARS-CoV-2 VPs was found. The chip can be reprogrammed for any VP or exosomes by simply changing the affinity agent.
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Affiliation(s)
- Sachindra S. T. Gamage
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Thilanga N. Pahattuge
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Uditha S. Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Lulu Zhang
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Zheng Zhao
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | | | | | | | | | | | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Gregory N. Gan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Andrew K. Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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Yoder R, Kimler BF, Staley JM, Schwensen K, Wang YY, Finke K, O'Dea A, Nye L, Elia M, Crane G, McKittrick R, Pluenneke R, Madhusudhana S, Beck L, Shrestha A, Corum L, Marsico M, Stecklein SR, Godwin AK, Khan QJ, Sharma P. Impact of low versus negative estrogen/progesterone receptor status on clinico-pathologic characteristics and survival outcomes in HER2-negative breast cancer. NPJ Breast Cancer 2022; 8:80. [PMID: 35817765 PMCID: PMC9273627 DOI: 10.1038/s41523-022-00448-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/10/2022] [Indexed: 12/21/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is classically defined by estrogen receptor (ER) and progesterone receptor (PR) immunohistochemistry expression <1% and absence of HER2 amplification/overexpression. HER2-negative breast cancer with low ER/PR expression (1–10%) has a gene expression profile similar to TNBC; however, real-world treatment patterns, chemotherapy response, endocrine therapy benefit, and survival outcomes for the Low-ER group are not well known. 516 patients with stage I-III HER2-negative breast cancer and ER/PR expression ≤10% who were enrolled in a multisite prospective registry between 2011 and 2019 were categorized on the basis of ER/PR expression. TNBC (ER and PR < 1%) and Low-ER (ER and/or PR 1–10%) groups comprised 87.4% (n = 451) and 12.6% (n = 65) of patients, respectively. Demographic, clinical, and treatment characteristics, including prevalence of germline BRCA1/2 mutation, racial and ethnic distribution, and chemotherapy use were not different between TNBC and Low-ER groups. No difference was observed in recurrence-free survival (RFS) and overall survival (OS) between TNBC and Low-ER groups (3-year RFS 82.5% versus 82.4%, respectively, p = 0.728; 3-year OS 88.0% versus 83.4%, respectively, p = 0.632). Among 358 patients receiving neoadjuvant chemotherapy, rates of pathologic complete response were similar for TNBC and Low-ER groups (49.2% vs 51.3%, respectively, p = 0.808). The HER2-negative Low-ER group is often excluded from TNBC clinical trials assessing novel treatments (immunotherapy and antibody-drug conjugates), thus limiting efficacy data for newer effective therapies in this group. Given that HER2-negative Low-ER disease displays clinical characteristics and outcomes similar to TNBC, inclusion of this group in TNBC clinical trials is encouraged.
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Affiliation(s)
- Rachel Yoder
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Bruce F Kimler
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Kelsey Schwensen
- Department of Internal Medicine, University of Kansas Medical Center, Westwood, KS, USA
| | - Yen Y Wang
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Karissa Finke
- Clinical Trials Shared Resource, University of Kansas Medical Center, Westwood, KS, USA
| | - Anne O'Dea
- Department of Internal Medicine, University of Kansas Medical Center, Westwood, KS, USA
| | - Lauren Nye
- Department of Internal Medicine, University of Kansas Medical Center, Westwood, KS, USA
| | - Manana Elia
- Department of Internal Medicine, University of Kansas Medical Center, Lee's Summit, MO, USA
| | - Gregory Crane
- Department of Internal Medicine, University of Kansas Medical Center, Overland Park, KS, USA
| | - Richard McKittrick
- Department of Internal Medicine, University of Kansas Medical Center, Overland Park, KS, USA
| | - Robert Pluenneke
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Sheshadri Madhusudhana
- Department of Internal Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Larry Beck
- Tammy Walker Cancer Center, Salina Regional Health Center, Salina, KS, USA
| | - Anuj Shrestha
- Richard & Annette Bloch Cancer Center, Truman Medical Center, Kansas City, MO, USA
| | - Larry Corum
- Olathe Cancer Care, Olathe Medical Center, Olathe, KS, USA
| | - Mark Marsico
- Department of Pharmacoepidemiology/Oncology, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Shane R Stecklein
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrew K Godwin
- University of Kansas Cancer Center, Kansas City, KS, USA.,Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Qamar J Khan
- Department of Internal Medicine, University of Kansas Medical Center, Westwood, KS, USA
| | - Priyanka Sharma
- Department of Internal Medicine, University of Kansas Medical Center, Westwood, KS, USA.
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He N, Thippabhotla S, Zhong C, Greenberg Z, Xu L, Pessetto Z, Godwin AK, Zeng Y, He M. Nano pom-poms prepared exosomes enable highly specific cancer biomarker detection. Commun Biol 2022; 5:660. [PMID: 35787656 PMCID: PMC9253007 DOI: 10.1038/s42003-022-03598-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/16/2022] [Indexed: 01/27/2023] Open
Abstract
Extracellular vesicles (EVs), particularly nano-sized small EV exosomes, are emerging biomarker sources. However, due to heterogeneous populations secreted from diverse cell types, mapping exosome multi-omic molecular information specifically to their pathogenesis origin for cancer biomarker identification is still extraordinarily challenging. Herein, we introduced a novel 3D-structured nanographene immunomagnetic particles (NanoPoms) with unique flower pom-poms morphology and photo-click chemistry for specific marker-defined capture and release of intact exosome. This specific exosome isolation approach leads to the expanded identification of targetable cancer biomarkers with enhanced specificity and sensitivity, as demonstrated by multi-omic exosome analysis of bladder cancer patient tissue fluids using the next generation sequencing of somatic DNA mutations, miRNAs, and the global proteome (Data are available via ProteomeXchange with identifier PXD034454). The NanoPoms prepared exosomes also exhibit distinctive in vivo biodistribution patterns, highlighting the highly viable and integral quality. The developed method is simple and straightforward, which is applicable to nearly all types of biological fluids and amenable for enrichment, scale up, and high-throughput exosome isolation.
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Affiliation(s)
- Nan He
- grid.266515.30000 0001 2106 0692Department of Chemical and Petroleum Engineering, Bioengineering Program, University of Kansas, Lawrence, KS 66045 USA ,Clara Biotech Inc., Lawrence, KS 66047 USA
| | - Sirisha Thippabhotla
- grid.266515.30000 0001 2106 0692Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045 USA
| | - Cuncong Zhong
- grid.266515.30000 0001 2106 0692Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045 USA
| | - Zachary Greenberg
- grid.15276.370000 0004 1936 8091Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
| | - Liang Xu
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA
| | - Ziyan Pessetto
- grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Andrew K. Godwin
- grid.412016.00000 0001 2177 6375Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160 USA ,grid.468219.00000 0004 0408 2680University of Kansas Cancer Center, Kansas City, KS 66160 USA
| | - Yong Zeng
- grid.15276.370000 0004 1936 8091Department of Chemistry, University of Florida, Gainesville, FL 32603 USA
| | - Mei He
- grid.266515.30000 0001 2106 0692Department of Chemical and Petroleum Engineering, Bioengineering Program, University of Kansas, Lawrence, KS 66045 USA ,grid.15276.370000 0004 1936 8091Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
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Khan QJ, Bivona CR, Martin GA, Zhang J, Liu B, He J, Li KH, Nelson M, Williamson S, Doolittle GC, Sun W, Mudaranthakam DP, Streeter NR, McGuirk JP, Al-Rajabi R, Hoffmann M, Kasi A, Parikh RA, Zhong C, Mitchell L, Pessetto ZY, Pathak H, Ghosh A, LaFaver S, Sharma P, Godwin AK. Evaluation of the Durability of the Immune Humoral Response to COVID-19 Vaccines in Patients With Cancer Undergoing Treatment or Who Received a Stem Cell Transplant. JAMA Oncol 2022; 8:1053-1058. [PMID: 35446353 PMCID: PMC9026224 DOI: 10.1001/jamaoncol.2022.0752] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/07/2022] [Indexed: 01/12/2023]
Abstract
Importance The durability of the antibody response to COVID-19 vaccines in patients with cancer undergoing treatment or who received a stem cell transplant is unknown and may be associated with infection outcomes. Objective To evaluate anti-SARS-CoV-2 spike protein receptor binding domain (anti-RBD) and neutralizing antibody (nAb) responses to COVID-19 vaccines longitudinally over 6 months in patients with cancer undergoing treatment or who received a stem cell transplant (SCT). Design, Setting, and Participants In this prospective, observational, longitudinal cross-sectional study of 453 patients with cancer undergoing treatment or who received an SCT at the University of Kansas Cancer Center in Kansas City, blood samples were obtained before 433 patients received a messenger RNA (mRNA) vaccine (BNT162b2 or mRNA-1273), after the first dose of the mRNA vaccine, and 1 month, 3 months, and 6 months after the second dose. Blood samples were also obtained 2, 4, and 7 months after 17 patients received the JNJ-78436735 vaccine. For patients receiving a third dose of an mRNA vaccine, blood samples were obtained 30 days after the third dose. Interventions Blood samples and BNT162b2, mRNA-1273, or JNJ-78436735 vaccines. Main Outcomes and Measures Geometric mean titers (GMTs) of the anti-RBD; the ratio of GMTs for analysis of demographic, disease, and treatment variables; the percentage of neutralization of anti-RBD antibodies; and the correlation between anti-RBD and nAb responses to the COVID-19 vaccines. Results This study enrolled 453 patients (mean [SD] age, 60.4 [13,1] years; 253 [56%] were female). Of 450 patients, 273 (61%) received the BNT162b2 vaccine (Pfizer), 160 (36%) received the mRNA-1273 vaccine (Moderna), and 17 (4%) received the JNJ-7846735 vaccine (Johnson & Johnson). The GMTs of the anti-RBD for all patients were 1.70 (95% CI, 1.04-2.85) before vaccination, 18.65 (95% CI, 10.19-34.11) after the first dose, 470.38 (95% CI, 322.07-686.99) at 1 month after the second dose, 425.80 (95% CI, 322.24-562.64) at 3 months after the second dose, 447.23 (95% CI, 258.53-773.66) at 6 months after the second dose, and 9224.85 (95% CI, 2423.92-35107.55) after the third dose. The rate of threshold neutralization (≥30%) was observed in 203 of 252 patients (80%) 1 month after the second dose and in 135 of 166 patients (81%) 3 months after the second dose. Anti-RBD and nAb were highly correlated (Spearman correlation coefficient, 0.93 [0.92-0.94]; P < .001). Three months after the second dose, anti-RBD titers were lower in male vs female patients (ratio of GMTs, 0.52 [95% CI, 0.34-0.81]), patients older than 65 years vs patients 50 years or younger (ratio of GMTs, 0.38 [95% CI, 0.25-0.57]), and patients with hematologic malignant tumors vs solid tumors (ratio of GMTs, 0.40 [95% CI, 0.20-0.81]). Conclusions and Relevance In this cross-sectional study, after 2 doses of an mRNA vaccine, anti-RBD titers peaked at 1 month and remained stable over the next 6 months. Patients older than 65 years of age, male patients, and patients with a hematologic malignant tumor had low antibody titers. Compared with the primary vaccine course, a 20-fold increase in titers from a third dose suggests a brisk B-cell anamnestic response in patients with cancer.
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Affiliation(s)
- Qamar J. Khan
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Cory R. Bivona
- Department of Pharmacy, The University of Kansas Health System, Kansas City
| | - Grace A. Martin
- Department of Pharmacy, The University of Kansas Health System, Kansas City
| | - Jun Zhang
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City
| | - Ben Liu
- Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence
| | - Jianghua He
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City
| | - Kevin H. Li
- School of Medicine, The University of Kansas Medical Center, Kansas City
| | - Maggie Nelson
- Department of Pharmacy, The University of Kansas Health System, Kansas City
| | - Stephen Williamson
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Gary C. Doolittle
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Weijing Sun
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Dinesh Pal Mudaranthakam
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City
| | - Natalie R. Streeter
- Clinical Research, Strategy & Operations, The University of Kansas Medical Center, Kansas City
| | - Joseph P. McGuirk
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Raed Al-Rajabi
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Marc Hoffmann
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Anup Kasi
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Rahul A. Parikh
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence
| | - Laura Mitchell
- Clinical Research, Strategy & Operations, The University of Kansas Medical Center, Kansas City
| | - Ziyan Y. Pessetto
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Arnab Ghosh
- Department of Zoology, Rajiv Gandhi University, Arunachal Pradesh, India
| | - Stephanie LaFaver
- Department of Nursing, The University of Kansas Medical Center, Kansas City
| | - Priyanka Sharma
- Department of Internal Medicine, The University of Kansas Medical Center, Kansas City
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City
- The University of Kansas Cancer Center, Kansas City
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Gupta VG, Roby KF, Pathak HB, Godwin AK, Gunewardena S, Khabele D. Abstract 3457: Rebastinib, a TIE2 antagonist improves chemotherapy response in homologous recombination proficient epithelial ovarian cancer murine models. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Objectives: The Angiopoietin (ANGPT)/TIE2 kinase axis plays a critical role in cancer angiogenesis. Rebastinib, an investigational TIE2 inhibitor inhibits Tie2 receptor in endothelial cells and macrophages. M2-like Tie2+ macrophages, being pro-tumorigenic, are an attractive target for cancer therapy. Current clinical trials are testing rebastinib with chemotherapy in platinum-resistant ovarian cancer. However, the mechanism is not fully understood. The objective of this study was to determine the effects of rebastinib alone and combined with chemotherapy in preclinical models of ovarian cancer.
Methods: RNA-Seq was carried out to determine rebastinib-induced gene expression in ID8 cells and PMJ2R murine peritoneal macrophages. To determine the pharmacodynamics of immune cells in ascites, syngeneic ID8 mice were pre-treated with 10 mg/kg/day rebastinib/control for a week, followed by rebastinib with or without 20 mg/kg carboplatin + 12 mg/kg paclitaxel (chemo) for two weeks. Mice were sacrificed 24h after the last treatment to harvest ascites for flow cytometry. Cohorts of mice from syngeneic ID8 murine model and from a patient derived xenograft (PDX) model of ovarian cancer were used for survival analysis.
Results: RNA-Seq showed that in ID8 cells, 1528 genes were upregulated and 3115 genes were downregulated by rebastinib. In macrophages, 2302 genes were upregulated and 2970 genes were downregulated. Several ANGPT-like genes (ANGPTL2, ANGPTL4, ANGPTL6) involved in tumorigenesis, angiogenesis, proliferation were downregulated 2X-10X (p<0.001) in ID8 cells and macrophages. ANGPTL1, an anti-angiogenic and anti-apoptotic gene, was increased 10X in ID8 cells (p<0.001) but not altered in macrophages. ANGPT2, a context-dependent agonist/antagonist of TIE2 pathway, was increased 1.42X in ID8 (P<0.05) cells and 4.6X in macrophages (p<0.001). Flow studies showed that rebastinib significantly increased CD45+ macrophage (p<0.03 vs. chemo; p<0.02 vs. rebastinib+chemo), maintained Th leukocytes (p<0.03, vs. chemo) and significantly increased cytotoxic T cells (p<0.02 vs. control; p<0.0004, p<0.0001 vs. chemo and rebastinib+chemo, respectively). Rebastinib had no significant effect on regulatory T cells, Tie2+ macrophages or Tie2+ M2 macrophages. Rebastinib combined with chemotherapy improved median survival significantly in murine models of ovarian cancer - ID8 (p<0.01) and PDX (p<0.0001).
Conclusions: Rebastinib exerts differential effects on tumor cells and macrophages that could contribute to its mechanism of action. Rebastinib alters immune cells and increases cytotoxic T cells in ascites. Rebastinib combined with chemotherapy extends survival in PDX and syngeneic ID8 murine models of ovarian cancer. Further investigation using rational combinations of rebastinib and chemotherapy are underway.
Citation Format: Vijayalaxmi G. Gupta, Katherine F. Roby, Harsh B. Pathak, Andrew K. Godwin, Sumedha Gunewardena, Dineo Khabele. Rebastinib, a TIE2 antagonist improves chemotherapy response in homologous recombination proficient epithelial ovarian cancer murine models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3457.
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Standing D, Gunewardena S, Sayed AA, Pritchard MT, Pathak HB, Godwin AK, Petersen S, Khabele D, Roy JA, Dandawate P, Weir SJ, Anant S. Abstract 5306: IRAK1: A novel TOLLway to target ovarian cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ovarian cancer (OvCa) is the leading cause of gynecologic cancer-related deaths. While the overall response rate to first line therapy is encouraging (~80%), the majority of women develop recurrent disease that is characterized by resistance to chemotherapy. It is believed that cancer stem cells (CSCs) may contribute, in part, to resistance and recurrence of OvCa. To understand the pathways involved in enhancing this stem-like phenotype, we performed RNA sequencing. We identified that the TLR-ILR1 (TIR) pathways are highly activated in cisplatin resistant OvCa and in CSC-enriched 3-dimensional culture models. To further understand the role of the TIR pathway, we mined the Cancer Genome Atlas database and observed that interleukin receptor-associated kinase 1 (IRAK1), a critical mediator of TIR signaling is upregulated in cancer tissues. In addition, the locus surrounding the IRAK1 gene is amplified in 10% of OvCa patients. We confirmed that IRAK1 expression is upregulated in a majority of OvCa samples by immunohistochemistry of a tumor microarray consisting of 100 patient and paired non-cancerous fallopian tube tissues. Furthermore, this upregulation correlated with early cancer onset and shorter overall survival. To study the specific role of IRAK1 in OvCa, we knocked down its expression using specific shRNA. This significantly impaired cancer growth both in vitro in 2-dimension (2D) and 3-dimensional (3D) spheroid cultures, and in vivo in peritoneal disease models. Moreover, IRAK1 knockdown resulted in decreased expression of CSC marker genes, including MYC, ALDH1A1, DCLK1, and KLF4 suggesting a critical role in maintenance of stemness programming. Since IRAK1 is an upstream kinase that is activated by TIR receptors, we were intrigued by mechanisms driving its activation. In this regard, we have observed that low molecular weight hyaluronic acid (LMW HA) is present at high levels (100-200 ng/ml) in malignant ascites following peritoneal metastasis. Treatment of OVCAR8, A2780 and A1847 cells with LMW HA (50-200 ng/ml) induced IRAK1 phosphorylation at 80 ng/ml that was further enhanced at 200 ng/ml. In addition, LMW HA induced stemness and multidrug resistance genes. With additional studies using specific inhibitors, we identified that the increased spheroid formation occurred via a CD44-PKC-IRAK1-STAT3 signaling axis. Finally, using molecular modeling and in silico screening, coupled with Eurofin’s ScanMAX platform, we identified TCS2210 as a novel highly specific IRAK1 inhibitor. Also, TCS2210 abrogated LMW HA induced activation of IRAK1 and STAT3, and CSC marker genes MYC and DCLK1. Moreover, TCS2210 effectively suppressed OvCa cell growth in in vitro 2D and 3D cultures, and in peritoneal disease models alone and in combination with cisplatin. These data, taken together, strongly suggest that IRAK1 is a valid therapeutic target for OvCa.
Citation Format: David Standing, Sumedha Gunewardena, Afreen A. Sayed, Michele T. Pritchard, Harsh B. Pathak, Andrew K. Godwin, Shariska Petersen, Dineo Khabele, Jensen A. Roy, Prasad Dandawate, Scott J. Weir, Shrikant Anant. IRAK1: A novel TOLLway to target ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5306.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jensen A. Roy
- 1University of Kansas Medical Center, Kansas City, KS
| | | | - Scott J. Weir
- 1University of Kansas Medical Center, Kansas City, KS
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Blenman K, Fanucci K, Bai Y, Pelekanou V, Nahleh ZA, Shafi S, Burela S, Barlow WE, Sharma P, Thompson AM, Godwin AK, Rimm DL, Hortobagyi GN, Pusztai L. Prediction of pathologic complete response to neoadjuvant chemotherapy in breast cancer (SWOG S0800) using image analysis-based tumor infiltrating lymphocyte measurements. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
594 Background: Image analysis-based tumor infiltrating lymphocyte (TIL) quantitation methods are being developed to eliminate reader-to-reader variation in TIL assessment that hinders its clinical adoption as prognostic and chemotherapy response predictive marker. We evaluated the ability of an image analysis-based TIL score to predict pathologic complete response (pCR) and event free survival (EFS) in breast cancer. Methods: 113 pretreatment samples were analyzed from the SWOG S0800 trial that randomized stage IIB-IIIC HER-2-negative breast cancers to neoadjuvant chemotherapy with or without bevacizumab. TIL quantitation was performed on H&E sections using QuPath open-source software and a convolutional neural network cell classifier (CNN11). The digital easTILs% score was calculated as [sum of TIL Area (mm2) / Stromal Area (mm2)] x 100. Pathologist-read stromal TIL score (sTILs%) was defined using international guidelines. A previously validated threshold of easTILs% > 19.9% defined high easTILs% status. Results: Pretreatment easTILs% was significantly higher in cases with pCR compared to residual disease (RD) (means, 31% vs. 17%, p < 0.001). easTILs% high and low cases had pCR rates of 41% and 21% (p = 0.019), respectively. In logistic regression adjusting for other factors, easTILs% was prognostic for pCR as continuous score (p < 0.001) and as high vs low categories (p = 0.035). There was strong positive correlation between easTILs% and sTILs% (r = 0.606, p < 0.0001), and sTILs% was also predictive of pCR. The areas under the prediction curve (AUC) were 0.709 and 0.627 for easTILs% and sTILs%, respectively. There was no statistically significant interaction between easTILs% and bevacizumab benefit (p = 0.26), and higher easTILs% or sTILs were not associated with better EFS. Conclusions: Image analysis-based TIL quantification is predictive of pCR in breast cancer and had better pCR outcome discrimination than pathologist-read sTIL count. [Table: see text]
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Affiliation(s)
| | | | | | | | | | - Saba Shafi
- The Ohio State University Wexner Medical Center, Columbus, OH
| | - Sneha Burela
- Department of Pathology, Yale School of Medicine, New Haven, CT
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Chen CSC, Zirpoli G, McCann S, Barlow WE, Budd GT, Pusztai L, Hortobagyi GN, Godwin AK, Thompson AM, Ambrosone CB, Stringer KA, Hertz DL. Vitamin D insufficiency as a peripheral neuropathy risk factor in white and black patients in SWOG 0221. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.12023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
12023 Background: Peripheral neuropathy (PN) is a treatment-limiting toxicity of paclitaxel. Black patients have higher rates of PN and vitamin D insufficiency, and our prior work suggests vitamin D insufficiency increases risk of paclitaxel-induced PN. The objective of this study was to validate that patients with vitamin D insufficiency have higher risk of paclitaxel-induced PN and investigate whether this explains racial disparities in PN risk. Methods: This retrospective validation study was conducted in the phase III SWOG 0221 (NCT00070564) trial comparing paclitaxel-containing chemotherapy regimens for early-stage breast cancer. Pre-treatment 25-hydroxy-vitamin D was quantified in cryopreserved serum. Males and patients who received less than a third of the paclitaxel treatment were excluded. The association between vitamin D insufficiency (≤20 ng/mL) and grade 3+ sensory PN was tested via logistic regression and then adjusted for self-reported race, age, paclitaxel schedule (QW vs Q2W), and body mass index. Results: Of the 1,116 female patients in the analysis, 169 (15.1%) experienced PN and 376 (33.7%) had vitamin D insufficiency. Vitamin D insufficiency was associated with higher PN risk (19.4% vs 13.0%, OR = 1.62, p = 0.005, Data Table). The association was borderline significant (OR = 1.44, p = 0.056) after adjustment for black race (OR = 2.41, p = 0.001), paclitaxel schedule (OR = 2.22, p < 0.001), and age (OR = 1.03, p = 0.005). Compared with white patients (n = 943), black patients (n = 99) had more prevalent vitamin D insufficiency (77.8% vs 28.6%, OR = 8.72, p < 0.001) and increased PN risk (29.3% vs 13.5%, OR = 2.66, p < 0.001); adjusting for vitamin D insufficiency decreased but did not eliminate the higher PN risk in black patients (OR = 2.23, p = 0.002). Conclusions: Vitamin D insufficiency increases risk of paclitaxel-induced PN and partially explains the higher risk of PN in black patients. Prospective trials are needed to test whether vitamin D supplementation lessens PN and reduces disparities in treatment outcomes. [Table: see text]
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Affiliation(s)
| | - Gary Zirpoli
- Boston University Slone Epidemiology Center, Boston, MA
| | - Susan McCann
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
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Sun W, Saeed A, Al-Rajabi RMT, Kasi A, Veeramachaneni NK, Al-Kasspooles MF, Baranda JC, Phadnis MA, Godwin AK, Olyaee M, Madan R, Streeter N, Nagji A, Williamson SK. A phase II study of perioperative mFOLFOX plus pembrolizumab combination in patients with potentially resectable adenocarcinoma of the esophageal, gastroesophageal junction (GEJ) and stomach. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.4047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4047 Background: Surgical rection is the only potentially curative intervention for locally advanced adenocarcinoma of esophagus, GEJ and stomach. Results from various studies have demonstrated the benefits of perioperative treatment including neoadjuvant and adjuvant chemotherapy or chemoradiation, however, there is lack of universally accepted standard. Recent data demonstrated the benefit of immune checkpoint inhibitor in adjuvant setting in patients who had pre-operative chemoradiation. This single arm phase 2 trial is aimed to evaluate efficacy and safety of pembrolizumab, an immune checkpoint inhibitor, in combination with mFOLFOX in patients with potentially resectable adenocarcinoma of distal esophagus, GEJ and stomach. The primary objective is pathological response rate (ypRR with tumor regression score, TRS ≤ 2). Methods: Newly diagnosed locally advanced (T1N1-3M0 or T2-3NanyM0), potentially resectable adenocarcinoma of distal esophagus, GEJ and stomach by PET, EUS, CT C/A/P and staging laparoscopy were treated with pre-operative mFOLFOX6 (oxaliplatin 85mg/m2, Leucovorin 400mg/m2, 5-FU bolus 400mg/m2, and 5-FU 2400mg/m2 infusion every 2 weeks) for 4 cycles and pembrolizumab (200 mg IV q3week) for 3 cycles. Patients with no evidence of metastatic disease by PET and CT C/A/P who are eligible for resection underwent surgery. Post-operative treatment consisted of 4 cycles of mFOLFOX and 13 cycles of pembrolizumab 4-8 weeks postoperatively. Results: Up to 2/10/2021, all 37 patients eligible for the study finished preoperative treatment. 27 had curative intended operations, and all had R0 resection. 5 of 27 (19%) achieved ypCR and 6/27 (22 %) with regression score of 0 in the primary cancer. All except 2 patients (25/27, 93%) had shown pathologic response to the treatment with TRS ≤ 2. 21 patients completed all planned treatment with an average follow-up of 27 months. 2 patients had recurrence/metastatic disease (at 9 and 10 months from the enrollment) with 1 died at 23 months, and the other is still alive at 20 month. The rest patients (19/21) are all free of disease. G3/4 toxicities were reported in 21 of all 37 treated patients. There were no unexpected toxicities. Conclusions: The combination of mFOLFOX and pembrolizumab as peri-operative (pre- and post-operative) therapy in patients with locally advanced adenocarcinoma of distal esophagus, GEJ and stomach is safe. The preliminary benefit data are very encouraging with ypRR of 93%, ypCR of 19 %, and the long-time survival. The data support the combination of chemotherapy and Immune checkpoint inhibitor at perioperative setting. In addition, the data supports the staging laparoscopy for peritoneal disease assessment as the standard in resctacbility evaluation. Clinical trial information: NCT03488667.
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Affiliation(s)
- Weijing Sun
- University of Kansas Medical Center, Kansas City, KS
| | - Anwaar Saeed
- University of Kansas Cancer Center, Westwood, KS
| | | | - Anup Kasi
- University of Kansas Cancer Center, Westwood, KS
| | | | | | | | | | | | - Mojtaba Olyaee
- University of Kansas Medical Center (KUMC), Kansas City, KS
| | - Rashna Madan
- University of Kansas Cancer Center, Westwood, KS
| | | | - Alykhan Nagji
- University of Kansas Medical Center (KUMC), Kansas City, KS
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Sharma P, Stecklein SR, Yoder R, Staley JM, Schwensen K, O'Dea A, Nye LE, Elia M, Satelli D, Crane G, Madan R, O'Neil MF, Wagner JL, Larson KE, Balanoff C, Phadnis MA, Godwin AK, Salgado R, Khan QJ, O'Shaughnessy J. Clinical and biomarker results of neoadjuvant phase II study of pembrolizumab and carboplatin plus docetaxel in triple-negative breast cancer (TNBC) (NeoPACT). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
513 Background: Addition of pembrolizumab to anthracycline-taxane-platinum chemotherapy improves pathologic complete response (pCR) and event free survival (EFS) in TNBC. Aim of this study was to assess the efficacy of the anthracycline free neoadjuvant regimen of pembrolizumab plus carboplatin plus docetaxel (Cb+D) in TNBC. Methods: In this multicenter study, eligible patients with stage I-III TNBC received carboplatin (AUC 6) + docetaxel (75 mg/m2) + pembrolizumab (200 mg) every 21 days x 6 cycles. The primary endpoint was pCR (no evidence of invasive tumor in breast and axilla). Secondary endpoints were residual cancer burden (RCB), EFS, toxicity, and immune response biomarkers. RNA isolated from pretreatment tumor tissue was subjected to next generation sequencing. Samples were classified as DNA Damage Immune Response (DDIR) signature and DetermaIO signature positive/negative using predefined cutoffs. Evaluation of stromal tumor infiltrating lymphocytes (sTILs) was performed using standard criteria. Results: 117 patients were enrolled from September 2018 to January 2022. 18% were African American, 39% had node positive disease, 88% had stage II/III disease and 15% had ER/PR 1-10%. Pathologic response information is available for 105 patients. pCR and RCB 0+1 rates were 60% (95% CI 51%-70%) and 71% (95% CI 62%-80%), respectively. Treatment related adverse events led to discontinuation of any trial drug in 12% of patients. Immune adverse events were observed in 28% of patients (Grade ≥3=6%). 47% of patients had sTILs ≥30%, 48% were DetermaIO positive, and 61% DDIR positive. The table describes the impact of these biomarkers on pCR and RCB. The areas under the prediction curve (AUC) for pCR were 0.660, 0.709, and 0.719 for DDIR, sTILs, and DetermaIO respectively. At a median follow up of 21 months, 2-year EFS is 88% in all patients; 98% in pCR group and 82% in no pCR group. Conclusions: Neoadjuvant pembrolizumab plus Cb+D regimen yields pCR of 60% and 2-year EFS of 88% in the absence of adjuvant pembrolizumab. The regimen was well tolerated, and no new toxicity signals were noted. Immune enrichment identified by sTILs or DetermaIO signature was associated with high pCR rates approaching or exceeding 80%. PD-L1 and additional biomarker analyses are ongoing. Clinical trial information: NCT03639948. [Table: see text]
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Affiliation(s)
| | | | - Rachel Yoder
- The University of Kansas Cancer Center, Kansas City, KS
| | | | | | - Anne O'Dea
- University of Kansas Medical Center, Westwood, KS
| | | | - Manana Elia
- University of Kansas Medical Center, Westwood, KS
| | | | | | - Rashna Madan
- University of Kansas Medical Center, Kansas City, KS
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