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Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Liu W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep 2024; 43:113063. [PMID: 38578829 DOI: 10.1016/j.celrep.2023.113063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
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Mekahli D, Müller RU, Marlais M, Wlodkowski T, Haeberle S, de Argumedo ML, Bergmann C, Breysem L, Fladrowski C, Henske EP, Janssens P, Jouret F, Kingswood JC, Lattouf JB, Lilien M, Maleux G, Rozenberg M, Siemer S, Devuyst O, Schaefer F, Kwiatkowski DJ, Rouvière O, Bissler J. Clinical practice recommendations for kidney involvement in tuberous sclerosis complex: a consensus statement by the ERKNet Working Group for Autosomal Dominant Structural Kidney Disorders and the ERA Genes & Kidney Working Group. Nat Rev Nephrol 2024:10.1038/s41581-024-00818-0. [PMID: 38443710 DOI: 10.1038/s41581-024-00818-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by the presence of proliferative lesions throughout the body. Management of TSC is challenging because patients have a multifaceted systemic illness with prominent neurological and developmental impact as well as potentially severe kidney, heart and lung phenotypes; however, every organ system can be involved. Adequate care for patients with TSC requires a coordinated effort involving a multidisciplinary team of clinicians and support staff. This clinical practice recommendation was developed by nephrologists, urologists, paediatric radiologists, interventional radiologists, geneticists, pathologists, and patient and family group representatives, with a focus on TSC-associated kidney manifestations. Careful monitoring of kidney function and assessment of kidney structural lesions by imaging enable early interventions that can preserve kidney function through targeted approaches. Here, we summarize the current evidence and present recommendations for the multidisciplinary management of kidney involvement in TSC.
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Affiliation(s)
- Djalila Mekahli
- PKD Research Group, Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
- Department of Paediatric Nephrology, University Hospitals Leuven, Leuven, Belgium.
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Matko Marlais
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Tanja Wlodkowski
- Division of Paediatric Nephrology, Center for Paediatrics and Adolescent Medicine, University Hospital, Heidelberg, Germany
| | - Stefanie Haeberle
- Division of Paediatric Nephrology, Center for Paediatrics and Adolescent Medicine, University Hospital, Heidelberg, Germany
| | - Marta López de Argumedo
- Basque Office for Health Technology Assessment, (OSTEBA), Basque Government, Vitoria-Gasteiz, Spain
| | - Carsten Bergmann
- Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Luc Breysem
- Department of Radiology, University Hospital of Leuven, Leuven, Belgium
| | - Carla Fladrowski
- Associazione Sclerosi Tuberosa ASP, Rome, Italy
- European Tuberous Sclerosis Complex Association (ETSC), Oestrich-Winkel, Germany
| | - Elizabeth P Henske
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter Janssens
- Department of Nephrology and Arterial Hypertension, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel, Brussels, Belgium
| | - François Jouret
- Division of Nephrology, Department of Internal Medicine, University of Liège Hospital, Liège, Belgium
- Interdisciplinary Group of Applied Genoproteomics, Cardiovascular Sciences, University of Liège, Liège, Belgium
| | - John Christopher Kingswood
- Cardiology Clinical Academic Group, Molecular and Clinical Sciences Research Centre, St Georges University of London, London, UK
| | - Jean-Baptiste Lattouf
- Department of Surgery-Urology, CHUM-Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Marc Lilien
- Department of Paediatric Nephrology, Wilhelmina Children´s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geert Maleux
- Department of Radiology, University Hospitals Leuven, Leuven, Belgium
| | - Micaela Rozenberg
- European Tuberous Sclerosis Complex Association (ETSC), Oestrich-Winkel, Germany
- Associação de Esclerose Tuberosa em Portugal, Lisbon, Portugal
| | - Stefan Siemer
- Department of Urology and Paediatric Urology, Saarland University, Homburg, Germany
| | - Olivier Devuyst
- Department of Physiology, Mechanisms of Inherited Kidney Disorders, University of Zurich, Zurich, Switzerland
- Institute for Rare Diseases, Saint-Luc Academic Hospital, UC Louvain, Brussels, Belgium
| | - Franz Schaefer
- Division of Paediatric Nephrology, Center for Paediatrics and Adolescent Medicine, University Hospital, Heidelberg, Germany
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Olivier Rouvière
- Department of Radiology, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon, France
- Université Lyon 1, Lyon, France, Faculté de médecine Lyon Est, Lyon, France
| | - John Bissler
- Department of Paediatrics, University of Tennessee Health Science Center and Le Bonheur Children's Hospital, Memphis, TN, USA.
- Children's Foundation Research Institute (CFRI), Le Bonheur Children's Hospital, Memphis, TN, USA.
- Paediatric Medicine Department, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Wagner AJ, Ravi V, Riedel RF, Ganjoo K, Van Tine BA, Chugh R, Cranmer L, Gordon EM, Hornick JL, Du H, Ding L, Schmid AN, Navarro WH, Kwiatkowski DJ, Dickson MA. Phase II Trial of nab-Sirolimus in Patients With Advanced Malignant Perivascular Epithelioid Cell Tumors (AMPECT): Long-Term Efficacy and Safety Update. J Clin Oncol 2024:JCO2302266. [PMID: 38427923 DOI: 10.1200/jco.23.02266] [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: 10/18/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 03/03/2024] Open
Abstract
Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.nab-Sirolimus is approved in the United States for the treatment of metastatic or locally advanced malignant perivascular epithelioid cell tumor (PEComa) on the basis of the primary analysis results of the phase II Advanced Malignant Perivascular Epithelioid Cell Tumors (AMPECT) trial (ClinicalTrials.gov identifier: NCT02494570). Results from the primary analysis were previously published; however, the median duration of response (mDOR) had not been reached at that time. Here, 3 years after the primary analysis, we report final efficacy and safety data (data cutoff: April 29, 2022). At study completion, the confirmed overall response rate (by independent radiologist review using RECIST v1.1) was 38.7% (95% CI, 21.8 to 57.8), with an additional converted confirmed complete response (n = 2). Median progression-free survival remained the same at 10.6 months (95% CI, 5.5 to 41.2). The mDOR was reached at 39.7 months (95% CI, 6.5 to not reached [NR]), and the median overall survival at completion was 53.1 months (95% CI, 22.2 to NR). The most common treatment-related adverse events (TRAEs) were stomatitis (82.4%) and fatigue and rash (each 61.8%). No new or unexpected adverse events occurred, and no grade ≥4 TRAEs were reported. These results highlight the long-term clinical benefit of nab-sirolimus in patients with advanced malignant PEComa, with a DOR of >3 years.
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Affiliation(s)
- Andrew J Wagner
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | | | | | | | | | | | - Lee Cranmer
- University of Washington/Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Heng Du
- Brigham and Women's Hospital, Boston, MA
| | - Li Ding
- Aadi Bioscience Inc, Pacific Palisades, CA
| | | | | | | | - Mark A Dickson
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
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Bou Farhat E, Adib E, Daou M, Naqash AR, Matulonis U, Ng K, Kwiatkowski DJ, Sholl LM, Nassar AH. Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy. Cancer Cell 2024; 42:323. [PMID: 38350424 DOI: 10.1016/j.ccell.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
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Naqash AR, Floudas CS, Aber E, Maoz A, Nassar AH, Adib E, Choucair K, Xiu J, Baca Y, Ricciuti B, Alessi JV, Awad MM, Kim C, Judd J, Raez LE, Lopes G, Nieva JJ, Borghaei H, Takebe N, Ma PC, Halmos B, Kwiatkowski DJ, Liu SV, Mamdani H. Influence of TP53 Comutation on the Tumor Immune Microenvironment and Clinical Outcomes With Immune Checkpoint Inhibitors in STK11-Mutant Non-Small-Cell Lung Cancer. JCO Precis Oncol 2024; 8:e2300371. [PMID: 38330261 PMCID: PMC10860998 DOI: 10.1200/po.23.00371] [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: 07/26/2023] [Revised: 11/05/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Abstract
PURPOSE Non-small-cell lung cancer (NSCLC) with STK11mut has inferior outcomes to immune checkpoint inhibitors (ICIs). Using multiomics, we evaluated whether a subtype of STK11mut NSCLC with a uniquely inflamed tumor immune microenvironment (TIME) harboring TP53 comutations could have favorable outcomes to ICIs. PATIENTS AND METHODS NSCLC tumors (N = 16,896) were analyzed by next-generation sequencing (DNA-Seq/592 genes). A subset (n = 5,034) underwent gene expression profiling (RNA-Seq/whole transcriptome). Exome-level neoantigen load for STK11mut NSCLC was obtained from published pan-immune analysis. Tumor immune cell content was obtained from transcriptome profiles using the microenvironment cell population (MCP) counter. ICI data from POPLAR/OAK (n = 34) and the study by Rizvi et al (n = 49) were used to model progression-free survival (PFS), and a separate ICI-treated cohort (n = 53) from Dana-Farber Cancer Institute (DFCI) was used to assess time to treatment failure (TTF) and tumor RECIST response for STK11mutTP53mut versus STK11mutTP53wt NSCLC. RESULTS Overall, 12.6% of NSCLC tumors had a STK11mut with the proportions of tumor mutational burden (TMB)-high (≥10 mut/Mb), PD-L1 ≥50%, and microsatellite instability-high being 38.3%, 11.8%, and 0.72%, respectively. Unsupervised hierarchical clustering of STK11mut (n = 463) for stimulator of interferon-gamma (STING) pathway genes identified a STING-high cluster, which was significantly enriched in TP53mut NSCLC (P < .01). Compared with STK11mutTP53wt, tumors with STK11mutTP53mut had higher CD8+T cells and natural killer cells (P < .01), higher TMB (P < .001) and neoantigen load (P < .001), and increased expression of MYC and HIF-1A (P < .01), along with higher expression (P < .01) of glycolysis/glutamine metabolism genes. Meta-analysis of data from OAK/POPLAR and the study by Rizvi et al showed a trend toward improved PFS in patients with STK11mutTP53mut. In the DFCI cohort, compared with the STK11mut TP53wt cohort, the STK11mutTP53mut tumors had higher objective response rates (42.9% v 16.7%; P = .04) and also had longer TTF (14.5 v 4.5 months, P adj = .054) with ICI. CONCLUSION STK11mut NSCLC with TP53 comutation is a distinct subgroup with an immunologically active TIME and metabolic reprogramming. These properties should be exploited to guide patient selection for novel ICI-based combination approaches.
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Affiliation(s)
- Abdul Rafeh Naqash
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | - Etan Aber
- Center for Immuno-Oncology, National Cancer Institute, NIH, Bethesda, MD
| | - Asaf Maoz
- Dana Farber Cancer Institute, Boston, MA
| | - Amin H. Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT
| | - Elio Adib
- Dana Farber Cancer Institute, Boston, MA
| | - Khalil Choucair
- Department of Oncology, Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI
| | | | | | | | | | | | - Chul Kim
- Department of Hematology and Oncology, Georgetown University, Washington, DC
| | - Julia Judd
- Fox Chase Cancer Center, Philadelphia, PA
| | - Luis E. Raez
- Memorial Cancer Institute//Florida Atlantic University (FAU), Miami, FL
| | - Gilberto Lopes
- University of Miami Miller School of Medicine, Miami, FL
| | | | | | - Naoko Takebe
- Developmental Therapeutics Clinic, National Cancer Institute, Bethesda, MD
| | - Patrick C. Ma
- Department of Hematology/ Oncology, Penn State Cancer Institute, Hershey, PA
| | - Balazs Halmos
- Medical Oncology, Albert Einstein College of Medicine, NY
| | | | - Stephen V. Liu
- Department of Hematology and Oncology, Georgetown University, Washington, DC
| | - Hirva Mamdani
- Department of Oncology, Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI
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Nassar AH, Kim SY, Aredo JV, Feng J, Shepherd F, Xu C, Kaldas D, Gray JE, Dilling TJ, Neal JW, Wakelee HA, Liu Y, Lin SH, Abuali T, Amini A, Nie Y, Patil T, Lobachov A, Bar J, Fitzgerald B, Fujiwara Y, Marron TU, Thummalapalli R, Yu H, Owen DH, Sharp J, Farid S, Rocha P, Arriola E, D'Aiello A, Cheng H, Whitaker R, Parikh K, Ashara Y, Chen L, Sankar K, Harris JP, Nagasaka M, Ayanambakkam A, Velazquez AI, Ragavan M, Lin JJ, Piotrowska Z, Wilgucki M, Reuss J, Luders H, Grohe C, Baena Espinar J, Feiner E, Punekar SR, Gupta S, Leal T, Kwiatkowski DJ, Mak RH, Adib E, Naqash AR, Goldberg SB. Consolidation Osimertinib Versus Durvalumab Versus Observation After Concurrent Chemoradiation in Unresectable EGFR-Mutant NSCLC: A Multicenter Retrospective Cohort Study. J Thorac Oncol 2024:S1556-0864(24)00032-7. [PMID: 38278303 DOI: 10.1016/j.jtho.2024.01.012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/31/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
INTRODUCTION Durvalumab improves survival when used as consolidation therapy after chemoradiation (CRT) in patients with stage III NSCLC. The optimal consolidation therapy for patients with EGFR-mutant (EGFRmut) stage III NSCLC remains unknown. METHODS In this multi-institutional, international retrospective analysis across 24 institutions, we evaluated outcomes in patients with stage III EGFRmut NSCLC treated with concurrent CRT followed by consolidation therapy with osimertinib, durvalumab, or observation between 2015 and 2022. Kaplan-Meier method was used to estimate real-world progression-free survival (rwPFS, primary end point) and overall survival (secondary end point). Treatment-related adverse events (trAEs) during consolidation treatment were defined using Common Terminology Criteria for Adverse Events version 5.0. Multivariable Cox regression analysis was used. RESULTS Of 136 patients with stage III EGFRmut NSCLC treated with definitive concurrent CRT, 56 received consolidation durvalumab, 33 received consolidation osimertinib, and 47 was on observation alone. Baseline characteristics were similar across the three cohorts. With a median follow-up of 46 months for the entire cohort, the median duration of treatment was not reached (NR) for osimertinib (interquartile range: NR-NR) and was 5.5 (interquartile range: 2.4-10.8) months with durvalumab. After adjusting for nodal status, stage III A/B/C, and age, patients treated with consolidation osimertinib had significantly longer 24-month rwPFS compared to those treated with durvalumab or in the observation cohorts (osimertinib: 86%, durvalumab: 30%, observation: 27%, p < 0.001 for both comparisons). There was no difference in rwPFS between the durvalumab and the observation cohorts. No significant difference in overall survival across the three cohorts was detected, likely due to the limited follow-up. Any-grade trAE occurred in 52% (2 [6.1%] grade ≥3) and 48% (10 [18%] grade ≥3) of patients treated with osimertinib and durvalumab, respectively. Of 45 patients who progressed on consolidation durvalumab, 37 (82%) subsequently received EGFR tyrosine kinase inhibitors. Of these, 14 (38%) patients developed trAEs including five patients with pneumonitis (14%; 2 [5.4%] grade ≥3) and five patients with diarrhea (14%; 1 [2.7%] grade ≥3). CONCLUSIONS This study suggests that among patients with stage III unresectable NSCLC with a sensitizing EGFR mutation, consolidation osimertinib was associated with a significantly longer rwPFS compared to durvalumab or observation. No unanticipated safety signals were observed with consolidation osimertinib.
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Affiliation(s)
- Amin H Nassar
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - So Yeon Kim
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - Jacqueline V Aredo
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jamie Feng
- Department of Medical Oncology and Hematology, University Health Network, Princess Margaret Cancer Centre, Toronto, Canada
| | - Frances Shepherd
- Department of Medical Oncology and Hematology, University Health Network, Princess Margaret Cancer Centre, Toronto, Canada
| | - Chao Xu
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - David Kaldas
- Department of Internal Medicine, University of South Florida, Tampa, Florida; Department of Clinical Oncology, Cairo University, Cairo, Egypt
| | - Jhanelle E Gray
- Thoracic Oncology Program, Moffitt Cancer Center, Tampa, Florida
| | - Thomas J Dilling
- Thoracic Oncology Program, Moffitt Cancer Center, Tampa, Florida
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Yufei Liu
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tariq Abuali
- Department of Radiation Oncology, City of Hope National Cancer Center, Duarte, California
| | - Arya Amini
- Department of Radiation Oncology, City of Hope National Cancer Center, Duarte, California
| | - Yunan Nie
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - Tejas Patil
- Department of Medicine, University of Colorado Cancer Center, Aurora, Colorado
| | - Anastasiya Lobachov
- Institute of Oncology, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jair Bar
- Institute of Oncology, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bailey Fitzgerald
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yu Fujiwara
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Thomas U Marron
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rohit Thummalapalli
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helena Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Dwight H Owen
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - John Sharp
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Saira Farid
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Pedro Rocha
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Angelica D'Aiello
- Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Haiying Cheng
- Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Ryan Whitaker
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Luxi Chen
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kamya Sankar
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jeremy P Harris
- Department of Radiation Oncology, University of California Irvine Medical Center, Orange, California
| | - Misako Nagasaka
- Division of Hematology and Oncology, Department of Medicine, University of California Irvine Medical Center, Orange, California
| | | | - Ana I Velazquez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Meera Ragavan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Jessica J Lin
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Zofia Piotrowska
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Molly Wilgucki
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Joshua Reuss
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Heike Luders
- Klinik für Pneumologie-Evangelische Lungenklinik Berlin Buch, Berlin, Germany
| | - Christian Grohe
- Klinik für Pneumologie-Evangelische Lungenklinik Berlin Buch, Berlin, Germany
| | | | - Ella Feiner
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Salman R Punekar
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Shruti Gupta
- Department of Hematology and Medical Oncology, Thoracic Medical Oncology Program, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Ticiana Leal
- Department of Hematology and Medical Oncology, Thoracic Medical Oncology Program, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | | | - Raymond H Mak
- Department of Radiation Oncology, Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elio Adib
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Sarah B Goldberg
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut.
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Bou Farhat E, Adib E, Daou M, Naqash AR, Matulonis U, Ng K, Kwiatkowski DJ, Sholl LM, Nassar AH. Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy. Cancer Cell 2024; 42:6-7. [PMID: 38157866 DOI: 10.1016/j.ccell.2023.12.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
Immunohistochemistry (IHC) is currently the first-line test for mismatch repair deficiency (MMR-D). Bou Farhat et al. show that mismatch repair (MMR) mutation signature by next-generation sequencing is a highly sensitive assay capable of detecting MMR-D cases that are missed in 1% and 5% of patients with MMR-D colorectal cancer (CRC) and endometrial cancer (EC), respectively. Patients with MMR-D tumors missed by IHC have similar clinical outcomes to patients with MMR-D by both IHC and mutation signature.
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Affiliation(s)
| | - Elio Adib
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Abdul Rafeh Naqash
- University of Oklahoma, Stephenson Cancer Center, Oklahoma City, OK, USA
| | | | - Kimmie Ng
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Amin H Nassar
- Brigham and Women's Hospital, Boston, MA, USA; Yale Cancer Center, New Haven, CT, USA.
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8
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Chaft JE, Oezkan F, Kris MG, Bunn PA, Wistuba II, Kwiatkowski DJ, Owen DH, Tang Y, Johnson BE, Lee JM, Lozanski G, Pietrzak M, Seweryn M, Byun WY, Schulze K, Nicholas A, Johnson A, Grindheim J, Hilz S, Shames DS, Rivard C, Toloza E, Haura EB, McNamee CJ, Patterson GA, Waqar SN, Rusch VW, Carbone DP. Author Correction: Neoadjuvant atezolizumab for resectable non-small cell lung cancer: an open-label, single-arm phase II trial. Nat Med 2024; 30:303. [PMID: 37816821 PMCID: PMC10803254 DOI: 10.1038/s41591-023-02627-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Affiliation(s)
- Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Filiz Oezkan
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- University Medicine Essen, Ruhrlandklinik, Department of Interventional Pulmonology, University Duisburg-Essen, Essen, Germany
- German Cancer Research Center (DKFZ), A420, Heidelberg, Germany
- Fifth Medical Department, Section of Pulmonology, Faculty of the University of Heidelberg, University Medicine Mannheim, Mannheim, Germany
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Paul A Bunn
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | - David J Kwiatkowski
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Dwight H Owen
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Yan Tang
- Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce E Johnson
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Jay M Lee
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Gerard Lozanski
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Maciej Pietrzak
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Michal Seweryn
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
- Centre for Data Analysis, Modeling and Computational Sciences, University of Lodz, Lodz, Poland
| | - Woo Yul Byun
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | | | - Ann Johnson
- Genentech, Inc., South San Francisco, CA, USA
| | | | | | | | - Chris Rivard
- University of Colorado School of Medicine, Aurora, CO, USA
| | - Eric Toloza
- Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric B Haura
- Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ciaran J McNamee
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Saiama N Waqar
- Washington University School of Medicine, St. Louis, MO, USA
| | | | - David P Carbone
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, Columbus, OH, USA.
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9
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Dacic S, Travis WD, Giltnane JM, Kos F, Abel J, Hilz S, Fujimoto J, Sholl L, Ritter J, Khalil F, Liu Y, Taylor-Weiner A, Resnick M, Yu H, Hirsch FR, Bunn PA, Carbone DP, Rusch V, Kwiatkowski DJ, Johnson BE, Lee JM, Hennek SR, Wapinski I, Nicholas A, Johnson A, Schulze K, Kris MG, Wistuba II. Artificial Intelligence-Powered Assessment of Pathologic Response to Neoadjuvant Atezolizumab in Patients With NSCLC: Results From the LCMC3 Study. J Thorac Oncol 2023:S1556-0864(23)02415-2. [PMID: 38070597 DOI: 10.1016/j.jtho.2023.12.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/31/2023]
Abstract
INTRODUCTION Pathologic response (PathR) by histopathologic assessment of resected specimens may be an early clinical end point associated with long-term outcomes with neoadjuvant therapy. Digital pathology may improve the efficiency and precision of PathR assessment. LCMC3 (NCT02927301) evaluated neoadjuvant atezolizumab in patients with resectable NSCLC and reported a 20% major PathR rate. METHODS We determined PathR in primary tumor resection specimens using guidelines-based visual techniques and developed a convolutional neural network model using the same criteria to digitally measure the percent viable tumor on whole-slide images. Concordance was evaluated between visual determination of percent viable tumor (n = 151) performed by one of the 47 local pathologists and three central pathologists. RESULTS For concordance among visual determination of percent viable tumor, the interclass correlation coefficient was 0.87 (95% confidence interval [CI]: 0.84-0.90). Agreement for visually assessed 10% or less viable tumor (major PathR [MPR]) in the primary tumor was 92.1% (Fleiss kappa = 0.83). Digitally assessed percent viable tumor (n = 136) correlated with visual assessment (Pearson r = 0.73; digital/visual slope = 0.28). Digitally assessed MPR predicted visually assessed MPR with outstanding discrimination (area under receiver operating characteristic curve, 0.98) and was associated with longer disease-free survival (hazard ratio [HR] = 0.30; 95% CI: 0.09-0.97, p = 0.033) and overall survival (HR = 0.14, 95% CI: 0.02-1.06, p = 0.027) versus no MPR. Digitally assessed PathR strongly correlated with visual measurements. CONCLUSIONS Artificial intelligence-powered digital pathology exhibits promise in assisting pathologic assessments in neoadjuvant NSCLC clinical trials. The development of artificial intelligence-powered approaches in clinical settings may aid pathologists in clinical operations, including routine PathR assessments, and subsequently support improved patient care and long-term outcomes.
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Affiliation(s)
- Sanja Dacic
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut.
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Filip Kos
- Department of Machine Learning, PathAI, Inc., Boston, Massachusetts
| | - John Abel
- Department of Machine Learning, PathAI, Inc., Boston, Massachusetts
| | - Stephanie Hilz
- Research Pathology, Genentech, Inc., South San Francisco, California
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lynette Sholl
- Department of Anatomic Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jon Ritter
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Farah Khalil
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida
| | - Yi Liu
- Department of Machine Learning, PathAI, Inc., Boston, Massachusetts
| | | | - Murray Resnick
- Department of Pathology, PathAI, Inc., Boston, Massachusetts
| | - Hui Yu
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Fred R Hirsch
- Department of Hematology and Medical Oncology, University of Colorado/Icahn School of Medicine, Mount Sinai, New York
| | - Paul A Bunn
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - David P Carbone
- Division of Medical Oncology, The Ohio State University Medical Center and Pelotonia Institute for Immuno-Oncology, Columbus, Ohio
| | - Valerie Rusch
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David J Kwiatkowski
- Department of Anatomic Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bruce E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jay M Lee
- Division of Thoracic Surgery, University of California, Los Angeles, Los Angeles, California
| | - Stephanie R Hennek
- Department of Translational Research, PathAI, Inc., Boston, Massachusetts
| | - Ilan Wapinski
- Department of Translational Research, PathAI, Inc., Boston, Massachusetts
| | - Alan Nicholas
- U.S. Medical Affairs, Genentech, Inc., South San Francisco, California
| | - Ann Johnson
- U.S. Medical Affairs, Genentech, Inc., South San Francisco, California
| | - Katja Schulze
- Research Pathology, Genentech, Inc., South San Francisco, California
| | - Mark G Kris
- Department of Thoracic Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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10
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Gupta S, Wells SL, Jose AM, Seitter RH, Feghali L, Devaraj N, Hartigan PM, Yacoubian S, Kwiatkowski DJ, Burke DM, Barlow J, Bueno R, Leaf DE. High-dose IV magnesium in mesothelioma patients receiving surgery with hyperthermic intraoperative cisplatin: Pilot studies and design of a phase II randomized clinical trial. J Surg Oncol 2023; 128:1141-1149. [PMID: 37702402 PMCID: PMC10592264 DOI: 10.1002/jso.27412] [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: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 09/14/2023]
Abstract
INTRODUCTION Hyperthermic intraoperative cisplatin (HIOC) is associated with acute kidney injury (AKI). Administration of high-dose magnesium attenuates cisplatin-induced AKI (CP-AKI) in animal models but has not been rigorously examined in humans. METHODS We tested the feasibility and safety of different doses of magnesium in mesothelioma patients receiving HIOC. In Pilot Study 1, we administered a 36-h continuous infusion of magnesium at 0.5 g/h, targeting serum magnesium levels between 3 and 4.8 mg/dL. In Pilot Study 2A, we administered a 6 g bolus followed by an infusion starting at 2 g/h, titrated to achieve levels between 4 and 6 mg/dL. We eliminated the bolus in Pilot Study 2B. RESULTS In Pilot Study 1, all five patients enrolled completed the study; however, median postoperative Mg levels were only 2.4 mg/dL. In Pilot Study 2A, two of four patients (50%) were withdrawn due to bradycardia during the bolus. In Pilot Study 2B, two patients completed the study whereas two developed postoperative bradycardia attributed to the magnesium. CONCLUSIONS A 0.5 g/h infusion for 36 h did not achieve therapeutic magnesium levels, while an infusion at 2 g/h was associated with bradycardia. These studies informed the design of a randomized clinical trial testing whether intravenously Mg attenuates HIOC-associated AKI.
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Affiliation(s)
- Shruti Gupta
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
- Adult Survivorship Program, Dana-Farber Cancer Institute, Boston, MA
| | - Sophia L. Wells
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Arunima M. Jose
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Robert H. Seitter
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Lea Feghali
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Nishant Devaraj
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Philip M. Hartigan
- Departments of Anesthesiology, Perioperative, and Pain Medicine, Harvard Medical School, Boston, MA
| | - Stephanie Yacoubian
- Departments of Anesthesiology, Perioperative, and Pain Medicine, Harvard Medical School, Boston, MA
| | | | - Donna M. Burke
- Department of Surgery, Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Julianne Barlow
- Department of Surgery, Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Raphael Bueno
- Department of Surgery, Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - David E. Leaf
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA
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11
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Huschner F, Głowacka-Walas J, Mills JD, Klonowska K, Lasseter K, Asara JM, Moavero R, Hertzberg C, Weschke B, Riney K, Feucht M, Scholl T, Krsek P, Nabbout R, Jansen AC, Petrák B, van Scheppingen J, Zamecnik J, Iyer A, Anink JJ, Mühlebner A, Mijnsbergen C, Lagae L, Curatolo P, Borkowska J, Sadowski K, Domańska-Pakieła D, Blazejczyk M, Jansen FE, Janson S, Urbanska M, Tempes A, Janssen B, Sijko K, Wojdan K, Jozwiak S, Kotulska K, Lehmann K, Aronica E, Jaworski J, Kwiatkowski DJ. Molecular EPISTOP, a comprehensive multi-omic analysis of blood from Tuberous Sclerosis Complex infants age birth to two years. Nat Commun 2023; 14:7664. [PMID: 37996417 PMCID: PMC10667269 DOI: 10.1038/s41467-023-42855-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023] Open
Abstract
We present a comprehensive multi-omic analysis of the EPISTOP prospective clinical trial of early intervention with vigabatrin for pre-symptomatic epilepsy treatment in Tuberous Sclerosis Complex (TSC), in which 93 infants with TSC were followed from birth to age 2 years, seeking biomarkers of epilepsy development. Vigabatrin had profound effects on many metabolites, increasing serum deoxycytidine monophosphate (dCMP) levels 52-fold. Most serum proteins and metabolites, and blood RNA species showed significant change with age. Thirty-nine proteins, metabolites, and genes showed significant differences between age-matched control and TSC infants. Six also showed a progressive difference in expression between control, TSC without epilepsy, and TSC with epilepsy groups. A multivariate approach using enrollment samples identified multiple 3-variable predictors of epilepsy, with the best having a positive predictive value of 0.987. This rich dataset will enable further discovery and analysis of developmental effects, and associations with seizure development in TSC.
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Affiliation(s)
| | - Jagoda Głowacka-Walas
- Transition Technologies Science, Warsaw, Poland
- Warsaw University of Technology, The Institute of Computer Science, Warsaw, Poland
| | - James D Mills
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | | | - Kathryn Lasseter
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John M Asara
- Department of Medicine, Harvard Medical School and Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Romina Moavero
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
- Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Christoph Hertzberg
- Diagnose- und Behandlungszentrum für Kinder, Vivantes-Klinikum Neukölln, Berlin, Germany
| | - Bernhard Weschke
- Department of Child Neurology, Charité University Medicine Berlin, Berlin, Germany
| | - Kate Riney
- Neurosciences Unit, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Martha Feucht
- Epilepsy Service, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Member of ERN EpiCARE, Vienna, Austria
| | - Theresa Scholl
- Epilepsy Service, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Member of ERN EpiCARE, Vienna, Austria
| | - Pavel Krsek
- Department of Paediatric Neurology, Motol University Hospital, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - Rima Nabbout
- Department of Pediatric Neurology, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Université Paris cité, Imagine Institute, Paris, France
| | - Anna C Jansen
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bořivoj Petrák
- Department of Paediatric Neurology, Motol University Hospital, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - Jackelien van Scheppingen
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Josef Zamecnik
- Department. of Pathology and Molecular Medicine, Motol University Hospital, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - Anand Iyer
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Jasper J Anink
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Angelika Mühlebner
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Mijnsbergen
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Lieven Lagae
- Department of Development and Regeneration Section Pediatric Neurology, University Hospitals KU Leuven, Leuven, Belgium
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
| | - Julita Borkowska
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Krzysztof Sadowski
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Dorota Domańska-Pakieła
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Magdalena Blazejczyk
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Floor E Jansen
- Department of Child Neurology, Brain Center University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Malgorzata Urbanska
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Aleksandra Tempes
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Kamil Sijko
- Transition Technologies Science, Warsaw, Poland
| | - Konrad Wojdan
- Transition Technologies Science, Warsaw, Poland
- Warsaw University of Technology, Institute of Heat Engineering, Warsaw, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede the Netherlands, Utrecht, The Netherlands
| | - Jacek Jaworski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
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12
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Engstrom LD, Aranda R, Waters L, Moya K, Bowcut V, Vegar L, Trinh D, Hebbert A, Smith CR, Kulyk S, Lawson JD, He L, Hover LD, Fernandez-Banet J, Hallin J, Vanderpool D, Briere DM, Blaj A, Marx MA, Rodon J, Offin M, Arbour KC, Johnson ML, Kwiatkowski DJ, Jänne PA, Haddox CL, Papadopoulos KP, Henry JT, Leventakos K, Christensen JG, Shazer R, Olson P. MRTX1719 Is an MTA-Cooperative PRMT5 Inhibitor That Exhibits Synthetic Lethality in Preclinical Models and Patients with MTAP-Deleted Cancer. Cancer Discov 2023; 13:2412-2431. [PMID: 37552839 PMCID: PMC10618744 DOI: 10.1158/2159-8290.cd-23-0669] [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] [Received: 06/14/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023]
Abstract
Previous studies implicated protein arginine methyltransferase 5 (PRMT5) as a synthetic lethal target for MTAP-deleted (MTAP del) cancers; however, the pharmacologic characterization of small-molecule inhibitors that recapitulate the synthetic lethal phenotype has not been described. MRTX1719 selectively inhibited PRMT5 in the presence of MTA, which is elevated in MTAP del cancers, and inhibited PRMT5-dependent activity and cell viability with >70-fold selecti-vity in HCT116 MTAP del compared with HCT116 MTAP wild-type (WT) cells. MRTX1719 demonstrated dose-dependent antitumor activity and inhibition of PRMT5-dependent SDMA modification in MTAP del tumors. In contrast, MRTX1719 demonstrated minimal effects on SDMA and viability in MTAP WT tumor xenografts or hematopoietic cells. MRTX1719 demonstrated marked antitumor activity across a panel of xenograft models at well-tolerated doses. Early signs of clinical activity were observed including objective responses in patients with MTAP del melanoma, gallbladder adenocarcinoma, mesothelioma, non-small cell lung cancer, and malignant peripheral nerve sheath tumors from the phase I/II study. SIGNIFICANCE PRMT5 was identified as a synthetic lethal target for MTAP del cancers; however, previous PRMT5 inhibitors do not selectively target this genotype. The differentiated binding mode of MRTX1719 leverages the elevated MTA in MTAP del cancers and represents a promising therapy for the ∼10% of patients with cancer with this biomarker. See related commentary by Mulvaney, p. 2310. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
| | - Ruth Aranda
- Mirati Therapeutics, Inc., San Diego, California
| | - Laura Waters
- Mirati Therapeutics, Inc., San Diego, California
| | - Krystal Moya
- Mirati Therapeutics, Inc., San Diego, California
| | | | - Laura Vegar
- Mirati Therapeutics, Inc., San Diego, California
| | - David Trinh
- Mirati Therapeutics, Inc., San Diego, California
| | | | | | | | | | - Leo He
- Monoceros Biosciences LLC, San Diego, California
| | | | | | - Jill Hallin
- Mirati Therapeutics, Inc., San Diego, California
| | | | | | - Alice Blaj
- Mirati Therapeutics, Inc., San Diego, California
| | | | - Jordi Rodon
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael Offin
- Department of Medicine, Division of Clinical Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathryn C. Arbour
- Department of Medicine, Division of Clinical Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa L. Johnson
- Sarah Cannon Research Institute Tennessee Oncology, Nashville, Tennessee
| | - David J. Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Pasi A. Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Candace L. Haddox
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Jason T. Henry
- Sarah Cannon Research Institute at HealthOne, Denver, Colorado
| | | | | | | | - Peter Olson
- Mirati Therapeutics, Inc., San Diego, California
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13
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Du H, Yang YC, Liu HJ, Yuan M, Asara JM, Wong KK, Henske EP, Singh M, Kwiatkowski DJ. Bi-steric mTORC1 inhibitors induce apoptotic cell death in tumor models with hyperactivated mTORC1. J Clin Invest 2023; 133:e167861. [PMID: 37909334 PMCID: PMC10617776 DOI: 10.1172/jci167861] [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: 12/08/2022] [Accepted: 09/06/2023] [Indexed: 11/03/2023] Open
Abstract
The PI3K/AKT/mTOR pathway is commonly dysregulated in cancer. Rapalogs exhibit modest clinical benefit, likely owing to their lack of effects on 4EBP1. We hypothesized that bi-steric mTORC1-selective inhibitors would have greater potential for clinical benefit than rapalogs in tumors with mTORC1 dysfunction. We assessed this hypothesis in tumor models with high mTORC1 activity both in vitro and in vivo. Bi-steric inhibitors had strong growth inhibition, eliminated phosphorylated 4EBP1, and induced more apoptosis than rapamycin or MLN0128. Multiomics analysis showed extensive effects of the bi-steric inhibitors in comparison with rapamycin. De novo purine synthesis was selectively inhibited by bi-sterics through reduction in JUN and its downstream target PRPS1 and appeared to be the cause of apoptosis. Hence, bi-steric mTORC1-selective inhibitors are a therapeutic strategy to treat tumors driven by mTORC1 hyperactivation.
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Affiliation(s)
- Heng Du
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Yu Chi Yang
- Department of Biology, Revolution Medicines Inc., Redwood City, California, USA
| | - Heng-Jia Liu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Elizabeth P. Henske
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mallika Singh
- Department of Biology, Revolution Medicines Inc., Redwood City, California, USA
| | - David J. Kwiatkowski
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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14
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Gjuka D, Adib E, Garrison K, Chen J, Zhang Y, Li W, Boutz D, Lamb C, Tanno Y, Nassar A, El Zarif T, Kale N, Rakaee M, Mouhieddine TH, Alaiwi SA, Gusev A, Rogers T, Gao J, Georgiou G, Kwiatkowski DJ, Stone E. Enzyme-mediated depletion of methylthioadenosine restores T cell function in MTAP-deficient tumors and reverses immunotherapy resistance. Cancer Cell 2023; 41:1774-1787.e9. [PMID: 37774699 PMCID: PMC10591910 DOI: 10.1016/j.ccell.2023.09.005] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Chromosomal region 9p21 containing tumor suppressors CDKN2A/B and methylthioadenosine phosphorylase (MTAP) is one of the most frequent genetic deletions in cancer. 9p21 loss is correlated with reduced tumor-infiltrating lymphocytes (TILs) and resistance to immune checkpoint inhibitor (ICI) therapy. Previously thought to be caused by CDKN2A/B loss, we now show that it is loss of MTAP that leads to poor outcomes on ICI therapy and reduced TIL density. MTAP loss causes accumulation of methylthioadenosine (MTA) both intracellularly and extracellularly and profoundly impairs T cell function via the inhibition of protein arginine methyltransferase 5 (PRMT5) and by adenosine receptor agonism. Administration of MTA-depleting enzymes reverses this immunosuppressive effect, increasing TILs and drastically impairing tumor growth and importantly, synergizes well with ICI therapy. As several studies have shown ICI resistance in 9p21/MTAP null/low patients, we propose that MTA degrading therapeutics may have substantial therapeutic benefit in these patients by enhancing ICI effectiveness.
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Affiliation(s)
- Donjeta Gjuka
- Department of Chemical Engineering, University of Texas, Austin, TX, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Lank Genitourinary Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kendra Garrison
- Department of Chemical Engineering, University of Texas, Austin, TX, USA
| | - Jianfeng Chen
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuxue Zhang
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenjiao Li
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel Boutz
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Candice Lamb
- Department of Chemical Engineering, University of Texas, Austin, TX, USA; Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas, Austin, TX, USA
| | - Amin Nassar
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Talal El Zarif
- Lank Genitourinary Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Neil Kale
- Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mehrdad Rakaee
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tarek H Mouhieddine
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Lank Genitourinary Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Gusev
- Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas Rogers
- Children's Medical Center Research Institute, University of Texas Southwestern, Dallas, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, TX, USA; Department of Molecular Biosciences, University of Texas, Austin, TX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA; Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, TX, USA
| | | | - Everett Stone
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA; Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, TX, USA.
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15
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Giannikou K, Klonowska K, Tsuji J, Wu S, Zhu Z, Probst CK, Kao KZ, Wu CL, Rodig S, Marino-Enriquez A, Zen Y, Schaefer IM, Kwiatkowski DJ. TSC2 inactivation, low mutation burden and high macrophage infiltration characterise hepatic angiomyolipomas. Histopathology 2023; 83:569-581. [PMID: 37679051 DOI: 10.1111/his.15005] [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: 02/20/2023] [Revised: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 09/09/2023]
Abstract
AIMS Although TSC1 or TSC2 inactivating mutations that lead to mTORC1 hyperactivation have been reported in hepatic angiomyolipomas (hAML), the role of other somatic genetic events that may contribute to hAML development is unknown. There are also limited data regarding the tumour microenvironment (TME) of hAML. The aim of the present study was to identify other somatic events in genomic level and changes in TME that contribute to tumorigenesis in hAML. METHODS AND RESULTS In this study, we performed exome sequencing in nine sporadic hAML tumours and deep-coverage targeted sequencing for TSC2 in three additional hAML. Immunohistochemistry and multiplex immunofluorescence were carried out for 15 proteins to characterise the tumour microenvironment and assess immune cell infiltration. Inactivating somatic variants in TSC2 were identified in 10 of 12 (83%) cases, with a median allele frequency of 13.6%. Five to 18 somatic variants (median number: nine, median allele frequency 21%) not in TSC1 or TSC2 were also identified, mostly of uncertain clinical significance. Copy number changes were rare, but detection was impaired by low tumour purity. Immunohistochemistry demonstrated numerous CD68+ macrophages of distinct appearance from Küpffer cells. Multiplex immunofluorescence revealed low numbers of exhausted PD-1+/PD-L1+, FOXP3+ and CD8+ T cells. CONCLUSION hAML tumours have consistent inactivating mutations in TSC2 and have a low somatic mutation rate, similar to other TSC-associated tumours. Careful histological review, standard IHC and multiplex immunofluorescence demonstrated marked infiltration by non-neoplastic inflammatory cells, mostly macrophages.
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Affiliation(s)
- Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Genome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Genome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Junko Tsuji
- Genomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Zachary Zhu
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clemens K Probst
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlighton, VT, USA
| | - Katrina Z Kao
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yoh Zen
- Department of Diagnostic Pathology, Kobe University Hospital, Kobe, Japan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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16
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Rakaee M, Andersen S, Giannikou K, Paulsen EE, Kilvaer TK, Busund LTR, Berg T, Richardsen E, Lombardi AP, Adib E, Pedersen MI, Tafavvoghi M, Wahl SGF, Petersen RH, Bondgaard AL, Yde CW, Baudet C, Licht P, Lund-Iversen M, Grønberg BH, Fjellbirkeland L, Helland Å, Pøhl M, Kwiatkowski DJ, Donnem T. Machine learning-based immune phenotypes correlate with STK11/KEAP1 co-mutations and prognosis in resectable NSCLC: a sub-study of the TNM-I trial. Ann Oncol 2023; 34:578-588. [PMID: 37100205 DOI: 10.1016/j.annonc.2023.04.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND We aim to implement an immune cell score model in routine clinical practice for resected non-small-cell lung cancer (NSCLC) patients (NCT03299478). Molecular and genomic features associated with immune phenotypes in NSCLC have not been explored in detail. PATIENTS AND METHODS We developed a machine learning (ML)-based model to classify tumors into one of three categories: inflamed, altered, and desert, based on the spatial distribution of CD8+ T cells in two prospective (n = 453; TNM-I trial) and retrospective (n = 481) stage I-IIIA NSCLC surgical cohorts. NanoString assays and targeted gene panel sequencing were used to evaluate the association of gene expression and mutations with immune phenotypes. RESULTS Among the total of 934 patients, 24.4% of tumors were classified as inflamed, 51.3% as altered, and 24.3% as desert. There were significant associations between ML-derived immune phenotypes and adaptive immunity gene expression signatures. We identified a strong association of the nuclear factor-κB pathway and CD8+ T-cell exclusion through a positive enrichment in the desert phenotype. KEAP1 [odds ratio (OR) 0.27, Q = 0.02] and STK11 (OR 0.39, Q = 0.04) were significantly co-mutated in non-inflamed lung adenocarcinoma (LUAD) compared to the inflamed phenotype. In the retrospective cohort, the inflamed phenotype was an independent prognostic factor for prolonged disease-specific survival and time to recurrence (hazard ratio 0.61, P = 0.01 and 0.65, P = 0.02, respectively). CONCLUSIONS ML-based immune phenotyping by spatial distribution of T cells in resected NSCLC is able to identify patients at greater risk of disease recurrence after surgical resection. LUADs with concurrent KEAP1 and STK11 mutations are enriched for altered and desert immune phenotypes.
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Affiliation(s)
- M Rakaee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Clinical Pathology, University Hospital of North Norway, Tromso; Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso.
| | - S Andersen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso; Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - K Giannikou
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, USA
| | - E-E Paulsen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso; Department of Pulmonology, University Hospital of North Norway, Tromso
| | - T K Kilvaer
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso; Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - L-T R Busund
- Department of Clinical Pathology, University Hospital of North Norway, Tromso; Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - T Berg
- Department of Clinical Pathology, University Hospital of North Norway, Tromso; Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - E Richardsen
- Department of Clinical Pathology, University Hospital of North Norway, Tromso; Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - A P Lombardi
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - E Adib
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - M I Pedersen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso
| | - M Tafavvoghi
- Department of Community Medicine, UiT The Arctic University of Norway, Tromso
| | - S G F Wahl
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - R H Petersen
- Department of Cardiothoracic Surgery, Copenhagen University Hospital, Rigshospitalet, Copenhagen; Department of Clinical Medicine, University of Copenhagen, Copenhagen
| | - A L Bondgaard
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen
| | - C W Yde
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen
| | - C Baudet
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen
| | - P Licht
- Department of Cardiothoracic Surgery, Odense University Hospital, Odense, Denmark
| | - M Lund-Iversen
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo
| | - B H Grønberg
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - L Fjellbirkeland
- Department of Respiratory Medicine, Oslo University Hospital, University of Oslo, Oslo
| | - Å Helland
- Department of Cancer Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo; Department of Oncology, Oslo University Hospital, Oslo; Department of Clinical Medicine, University of Oslo, Oslo, Norway
| | - M Pøhl
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - D J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - T Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso; Department of Oncology, University Hospital of North Norway, Tromso, Norway
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17
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Klonowska K, Giannikou K, Grevelink JM, Boeszoermenyi B, Thorner AR, Herbert ZT, Afrin A, Treichel AM, Hamieh L, Kotulska K, Jozwiak S, Moss J, Darling TN, Kwiatkowski DJ. Comprehensive genetic and phenotype analysis of 95 individuals with mosaic tuberous sclerosis complex. Am J Hum Genet 2023; 110:979-988. [PMID: 37141891 PMCID: PMC10257004 DOI: 10.1016/j.ajhg.2023.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is a neurogenetic disorder due to loss-of-function TSC1 or TSC2 variants, characterized by tumors affecting multiple organs, including skin, brain, heart, lung, and kidney. Mosaicism for TSC1 or TSC2 variants occurs in 10%-15% of individuals diagnosed with TSC. Here, we report comprehensive characterization of TSC mosaicism by using massively parallel sequencing (MPS) of 330 TSC samples from a variety of tissues and fluids from a cohort of 95 individuals with mosaic TSC. TSC1 variants in individuals with mosaic TSC are much less common (9%) than in germline TSC overall (26%) (p < 0.0001). The mosaic variant allele frequency (VAF) is significantly higher in TSC1 than in TSC2, in both blood and saliva (median VAF: TSC1, 4.91%; TSC2, 1.93%; p = 0.036) and facial angiofibromas (median VAF: TSC1, 7.7%; TSC2 3.7%; p = 0.004), while the number of TSC clinical features in individuals with TSC1 and TSC2 mosaicism was similar. The distribution of mosaic variants across TSC1 and TSC2 is similar to that for pathogenic germline variants in general TSC. The systemic mosaic variant was not present in blood in 14 of 76 (18%) individuals with TSC, highlighting the value of analysis of multiple samples from each individual. A detailed comparison revealed that nearly all TSC clinical features are less common in individuals with mosaic versus germline TSC. A large number of previously unreported TSC1 and TSC2 variants, including intronic and large rearrangements (n = 11), were also identified.
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Affiliation(s)
- Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Joannes M Grevelink
- Boston Dermatology and Laser Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Barbara Boeszoermenyi
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron R Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Antara Afrin
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA; Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alison M Treichel
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA; Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University Cleveland, Cleveland, OH 44106, USA
| | - Lana Hamieh
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hospital Medicine, Barnes Jewish Hospital, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw 04-736, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw 04-736, Poland; Research Department, Children's Memorial Health Institute, Warsaw 04-736, Poland
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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18
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Liu HJ, Du H, Khabibullin D, Zarei M, Wei K, Freeman GJ, Kwiatkowski DJ, Henske EP. mTORC1 upregulates B7-H3/CD276 to inhibit antitumor T cells and drive tumor immune evasion. Nat Commun 2023; 14:1214. [PMID: 36869048 PMCID: PMC9984496 DOI: 10.1038/s41467-023-36881-7] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Identifying the mechanisms underlying the regulation of immune checkpoint molecules and the therapeutic impact of targeting them in cancer is critical. Here we show that high expression of the immune checkpoint B7-H3 (CD276) and high mTORC1 activity correlate with immunosuppressive phenotypes and worse clinical outcomes in 11,060 TCGA human tumors. We find that mTORC1 upregulates B7-H3 expression via direct phosphorylation of the transcription factor YY2 by p70 S6 kinase. Inhibition of B7-H3 suppresses mTORC1-hyperactive tumor growth via an immune-mediated mechanism involving increased T-cell activity and IFN-γ responses coupled with increased tumor cell expression of MHC-II. CITE-seq reveals strikingly increased cytotoxic CD38+CD39+CD4+ T cells in B7-H3-deficient tumors. In pan-human cancers, a high cytotoxic CD38+CD39+CD4+ T-cell gene signature correlates with better clinical prognosis. These results show that mTORC1-hyperactivity, present in many human tumors including tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM), drives B7-H3 expression leading to suppression of cytotoxic CD4+ T cells.
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Affiliation(s)
- Heng-Jia Liu
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA.
| | - Heng Du
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Damir Khabibullin
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Mahsa Zarei
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA.,Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77843, TX, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, MA, USA
| | - David J Kwiatkowski
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Elizabeth P Henske
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA.
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19
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Treichel AM, Boeszoermenyi B, Lee CCR, Moss J, Kwiatkowski DJ, Darling TN. Diagnosis of Mosaic Tuberous Sclerosis Complex Using Next-Generation Sequencing of Subtle or Unusual Cutaneous Findings. JID Innov 2023; 3:100180. [PMID: 36960317 PMCID: PMC10030254 DOI: 10.1016/j.xjidi.2023.100180] [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: 10/05/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 01/11/2023] Open
Abstract
Skin findings can be critical to determining whether a patient with lymphangioleiomyomatosis (LAM), a progressive pulmonary disease that predominantly affects adult women, has sporadic LAM or LAM in association with tuberous sclerosis complex (TSC). Three individuals with LAM underwent evaluation for TSC-associated mucocutaneous and internal findings. We used our previously published algorithm to confirm the clinical suspicion for mosaicism and guide the selection of tissue specimens and genetic workup. Next-generation sequencing of cutaneous findings was used to confirm clinical suspicion for mosaic TSC in individuals with LAM. Two individuals previously thought to have sporadic LAM were diagnosed with mosaic TSC-associated LAM upon next-generation sequencing of unilateral angiofibromas in one and an unusual cutaneous hamartoma in the other. A third individual, diagnosed with TSC in childhood, was found to have a mosaic pathogenic variant in TSC2 in cutaneous tissue from a digit with macrodactyly. Accurate diagnosis of mosaic TSC-associated LAM may require enhanced genetic testing and is important because of the implications regarding surveillance, prognosis, and risk of transmission to offspring.
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Affiliation(s)
- Alison M. Treichel
- Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Barbara Boeszoermenyi
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Chyi-Chia Richard Lee
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas N. Darling
- Department of Dermatology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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20
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Rusch VW, Nicholas A, Patterson GA, Waqar SN, Toloza EM, Haura EB, Raz DJ, Reckamp KL, Merritt RE, Owen DH, Finley DJ, McNamee CJ, Blasberg JD, Garon EB, Mitchell JD, Doebele RC, Baciewicz F, Nagasaka M, Pass HI, Schulze K, Johnson A, Bunn PA, Johnson BE, Kris MG, Kwiatkowski DJ, Wistuba II, Chaft JE, Carbone DP, Lee JM. Surgical results of the Lung Cancer Mutation Consortium 3 trial: A phase II multicenter single-arm study to investigate the efficacy and safety of atezolizumab as neoadjuvant therapy in patients with stages IB-select IIIB resectable non-small cell lung cancer. J Thorac Cardiovasc Surg 2023; 165:828-839.e5. [PMID: 36369159 PMCID: PMC10288861 DOI: 10.1016/j.jtcvs.2022.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/07/2022] [Accepted: 10/01/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Multimodality treatment for resectable non-small cell lung cancer has long remained at a therapeutic plateau. Immune checkpoint inhibitors are highly effective in advanced non-small cell lung cancer and promising preoperatively in small clinical trials for resectable non-small cell lung cancer. This large multicenter trial tested the safety and efficacy of neoadjuvant atezolizumab and surgery. METHODS Patients with stage IB to select IIIB resectable non-small cell lung cancer and Eastern Cooperative Oncology Group performance status 0/1 were eligible. Patients received atezolizumab 1200 mg intravenously every 3 weeks for 2 cycles or less followed by resection. The primary end point was major pathological response in patients without EGFR/ALK+ alterations. Pre- and post-treatment computed tomography, positron emission tomography, pulmonary function tests, and biospecimens were obtained. Adverse events were recorded by Common Terminology Criteria for Adverse Events v.4.0. RESULTS From April 2017 to February 2020, 181 patients were entered in the study. Baseline characteristics were mean age, 65.1 years; female, 93 of 181 (51%); nonsquamous histology, 112 of 181 (62%); and clinical stages IIB to IIIB, 147 of 181 (81%). In patients without EGFR/ALK alterations who underwent surgery, the major pathological response rate was 20% (29/143; 95% confidence interval, 14-28) and the pathological complete response rate was 6% (8/143; 95% confidence interval, 2-11). There were no grade 4/5 treatment-related adverse events preoperatively. Of 159 patients (87.8%) undergoing surgery, 145 (91%) had pathologic complete resection. There were 5 (3%) intraoperative complications, no intraoperative deaths, and 2 postoperative deaths within 90 days, 1 treatment related. Median disease-free and overall survival have not been reached. CONCLUSIONS Neoadjuvant atezolizumab in resectable stage IB to IIIB non-small cell lung cancer was well tolerated, yielded a 20% major pathological response rate, and allowed safe, complete surgical resection. These results strongly support the further development of immune checkpoint inhibitors as preoperative therapy in locally advanced non-small cell lung cancer.
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Affiliation(s)
- Valerie W Rusch
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY.
| | | | | | | | | | | | - Dan J Raz
- Cedars Sinai (previously City of Hope Comprehensive Cancer Center), Los Angeles, Calif
| | - Karen L Reckamp
- Cedars Sinai (previously City of Hope Comprehensive Cancer Center), Los Angeles, Calif
| | - Robert E Merritt
- The Ohio State Medical Center and the Pelotonia Institute for Immune Oncology, Columbus, Ohio
| | - Dwight H Owen
- The Ohio State Medical Center and the Pelotonia Institute for Immune Oncology, Columbus, Ohio
| | | | | | | | - Edward B Garon
- David Geffen School of Medicine at UCLA, Los Angeles, Calif
| | | | | | | | | | | | | | | | - Paul A Bunn
- University of Colorado Cancer Center, Aurora, Colo
| | | | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY
| | | | | | - Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY
| | - David P Carbone
- The Ohio State Medical Center and the Pelotonia Institute for Immune Oncology, Columbus, Ohio
| | - Jay M Lee
- David Geffen School of Medicine at UCLA, Los Angeles, Calif
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21
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Iyer G, Demeure MJ, Deming DA, Federman N, McKean M, Lee EK, Spira AI, Kwiatkowski DJ, Hussein MA, Gordon EM, Crockett DG, Ganjoo KN, Schulte B, Cranmer LD, Schmid AN, Navarro WH, Itri LM. Phase 2, multicenter, open-label basket trial of nab-sirolimus for patients with malignant solid tumors harboring pathogenic inactivating alterations in TSC1 or TSC2 genes (PRECISION I). J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.6_suppl.tps597] [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: 03/16/2023] Open
Abstract
TPS597 Background: Albumin-bound ( nab)-sirolimus, a novel mTOR inhibitor (mTORi) that utilizes nanoparticle technology to preferentially target tumors, is approved in the US for the treatment of adults with malignant PEComa. In an exploratory analysis of the AMPECT registrational trial of nab-sirolimus in advanced malignant PEComa (NCT02494570), 8/9 (89%) and 1/5 (20%) patients with TSC1 and TSC2 inactivating alterations, respectively, had confirmed response (Wagner, J Clin Oncol. 2021). Importantly, both TSC1 and TSC2 alterations have been observed in patients with various gastrointestinal cancers (Table). Overall, most treatment-related adverse events (TRAEs) in AMPECT were grade 1/2 and manageable for long-term treatment; no grade ≥4 TRAEs occurred. Methods: PRECISION I (NCT05103358) is a phase 2, open-label, multi-institutional basket trial evaluating efficacy and safety of nab-sirolimus in patients with alterations in TSC1 (Arm A) and TSC2 (Arm B). Patients ≥12 years old with malignant solid tumors harboring pathogenic inactivating alterations in TSC1 or TSC2 (confirmed by central review of next-generation sequencing reports) who have progressed on standard therapies and are mTORi-naïve are eligible. nab-Sirolimus 100 mg/m2 will be administered weekly as an intravenous infusion over 30 minutes on Days 1 and 8 of each 21-day cycle. The primary endpoint is overall response rate determined by independent review using RECIST v1.1; other endpoints include duration of response, disease control rate, time to response progression-free survival by independent radiographic review, overall survival, patient-reported quality of life, and safety. Enrollment is ongoing. The most frequent tumor types expected in this tissue-agnostic trial are bladder, hepatobiliary, endometrial, soft tissue sarcoma, ovarian, and esophagogastric based on the prevalence of TSC1 or TSC2 alterations (Table). Clinical trial information: NCT05103358 . [Table: see text]
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Affiliation(s)
- Gopa Iyer
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | - Brian Schulte
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Lee D. Cranmer
- University of Washington/Fred Hutchinson Cancer Consortium, Seattle, WA
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22
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Deming DA, Rodon Ahnert J, Demeure MJ, Federman N, McKean M, Lee EK, Spira AI, Kwiatkowski DJ, Hussein MA, Gordon EM, Crockett DG, Ganjoo KN, Schulte B, Cranmer LD, Schmid AN, Navarro WH, Itri LM, Iyer G. Phase 2, multicenter, open-label basket trial of nab-sirolimus for patients with malignant solid tumors harboring pathogenic inactivating alterations in TSC1 or TSC2 genes (PRECISION I). J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.tps818] [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: 01/25/2023] Open
Abstract
TPS818 Background: Albumin-bound ( nab)-sirolimus, a novel mTOR inhibitor (mTORi) that utilizes nanoparticle technology to preferentially target tumors, is approved in the US for the treatment of adults with malignant PEComa. In an exploratory analysis of the AMPECT registrational trial of nab-sirolimus in advanced malignant PEComa (NCT02494570), 8/9 (89%) and 1/5 (20%) patients with TSC1 and TSC2 inactivating alterations, respectively, had confirmed response (Wagner, J Clin Oncol. 2021). Importantly, both TSC1 and TSC2 alterations have been observed in patients with various gastrointestinal cancers (Table). Overall, most treatment-related adverse events (TRAEs) in AMPECT were grade 1/2 and manageable for long-term treatment; no grade ≥4 TRAEs occurred. Methods: PRECISION I (NCT05103358) is a phase 2, open-label, multi-institutional basket trial evaluating efficacy and safety of nab-sirolimus in patients with alterations in TSC1 (Arm A) and TSC2 (Arm B). Patients ≥12 years old with malignant solid tumors harboring pathogenic inactivating alterations in TSC1 or TSC2 (confirmed by central review of next generation sequencing reports) who have progressed on standard therapies and are mTORi-naïve are eligible. nab-Sirolimus 100 mg/m2 will be administered weekly as an intravenous infusion over 30 minutes on Days 1 and 8 of each 21-day cycle. The primary endpoint is overall response rate determined by independent review using RECIST v1.1; other endpoints include duration of response, disease control rate, time to response, progression-free survival by independent radiographic review, overall survival, patient-reported quality of life, and safety. Enrollment is ongoing. The most frequent tumor types expected in this tissue-agnostic trial are bladder, hepatobiliary, endometrial, soft tissue sarcoma, ovarian, and esophagogastric based on the prevalence of TSC1 or TSC2 alterations (Table). Clinical trial information: NCT05103358 . [Table: see text]
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Affiliation(s)
| | | | - Michael J. Demeure
- Hoag Family Cancer Institute, Hoag Memorial Hospital Presbyterian, Newport Beach, CA
| | | | | | | | | | | | - Maen A. Hussein
- Florida Cancer Specialists North Division, St Petersburg, FL
| | | | | | | | - Brian Schulte
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Lee D. Cranmer
- University of Washington/Fred Hutchinson Cancer Consortium, Seattle, WA
| | | | | | | | - Gopa Iyer
- Memorial Sloan Kettering Cancer Center, New York, NY
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23
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Giannikou K, Martin KR, Abdel-Azim AG, Pamir KJ, Hougard TR, Bagwe S, Tang Y, MacKeigan JP, Kwiatkowski DJ, Henske EP, Lam HC. Spectrum of germline and somatic mitochondrial DNA variants in Tuberous Sclerosis Complex. Front Genet 2023; 13:917993. [PMID: 36793390 PMCID: PMC9923026 DOI: 10.3389/fgene.2022.917993] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/23/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by loss of function variants in either TSC1 or TSC2 and is characterized by broad phenotypic heterogeneity. Currently, there is limited knowledge regarding the role of the mitochondrial genome (mtDNA) in TSC pathogenesis. In this study, we aimed to determine the prevalence and spectrum of germline and somatic mtDNA variants in TSC and identify potential disease modifiers. Analysis of mtDNA amplicon massively parallel sequencing (aMPS) data, off-target mtDNA from whole-exome sequencing (WES), and/or qPCR, revealed mtDNA alterations in 270 diverse tissues (139 TSC-associated tumors and 131 normal tissue samples) from 199 patients and six healthy individuals. Correlation of clinical features to mtDNA variants and haplogroup analysis was done in 102 buccal swabs (age: 20-71 years). No correlation was found between clinical features and either mtDNA variants or haplogroups. No pathogenic variants were identified in the buccal swab samples. Using in silico analysis, we identified three predicted pathogenic variants in tumor samples: MT-ND4 (m.11742G>A, p. Cys328Tyr, VAF: 43%, kidney angiomyolipoma), MT-CYB (m.14775T>C, p. Leu10Pro, VAF: 43%, LAM abdominal tumor) and MT-CYB (m.15555C>T, p. Pro270Leu, VAF: 7%, renal cell carcinoma). Large deletions of the mitochondrial genome were not detected. Analysis of tumors from 23 patients with corresponding normal tissue did not reveal any recurrent tumor-associated somatic variants. The mtDNA/gDNA ratio between tumors and corresponding normal tissue was also unchanged. Overall, our findings demonstrate that the mitochondrial genome is highly stable across tissues and within TSC-associated tumors.
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Affiliation(s)
- Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
- Division of Hematology/Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Katie R. Martin
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Ahmad G. Abdel-Azim
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Kaila J. Pamir
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Thomas R. Hougard
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Shefali Bagwe
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Yan Tang
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Jeffrey P. MacKeigan
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Elizabeth P. Henske
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Hilaire C. Lam
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
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24
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Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. [PMID: 36681680 PMCID: PMC9867739 DOI: 10.1038/s41467-023-35833-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Talal El Zarif
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - David A Braun
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Heng Du
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michel Alchoueiry
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sayed G Matar
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Andres Acosta
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacob E Berchuck
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth Henske
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toni K Choueiri
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
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25
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Wang S, Rong R, Yang DM, Fujimoto J, Bishop JA, Yan S, Cai L, Behrens C, Berry LD, Wilhelm C, Aisner D, Sholl L, Johnson BE, Kwiatkowski DJ, Wistuba II, Bunn PA, Minna J, Xiao G, Kris MG, Xie Y. Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer. J Clin Invest 2023; 133:e160330. [PMID: 36647832 PMCID: PMC9843059 DOI: 10.1172/jci160330] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/08/2022] [Indexed: 01/18/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effective for many patients with lung cancer with EGFR mutations. However, not all patients are responsive to EGFR TKIs, including even those harboring EGFR-sensitizing mutations. In this study, we quantified the cells and cellular interaction features of the tumor microenvironment (TME) using routine H&E-stained biopsy sections. These TME features were used to develop a prediction model for survival benefit from EGFR TKI therapy in patients with lung adenocarcinoma and EGFR-sensitizing mutations in the Lung Cancer Mutation Consortium 1 (LCMC1) and validated in an independent LCMC2 cohort. In the validation data set, EGFR TKI treatment prolonged survival in the predicted-to-benefit group but not in the predicted-not-to-benefit group. Among patients treated with EGFR TKIs, the predicted-to-benefit group had prolonged survival outcomes compared with the predicted not-to-benefit group. The EGFR TKI survival benefit positively correlated with tumor-tumor interaction image features and negatively correlated with tumor-stroma interaction. Moreover, the tumor-stroma interaction was associated with higher activation of the hepatocyte growth factor/MET-mediated PI3K/AKT signaling pathway and epithelial-mesenchymal transition process, supporting the hypothesis of fibroblast-involved resistance to EGFR TKI treatment.
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Affiliation(s)
- Shidan Wang
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ruichen Rong
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Donghan M. Yang
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Justin A. Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shirley Yan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ling Cai
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Carmen Behrens
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lynne D. Berry
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Clare Wilhelm
- Department of Thoracic Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara Aisner
- Department of Pathology, University of Colorado, Denver, Colorado, USA
| | - Lynette Sholl
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, Massachusetts, USA
| | - Bruce E. Johnson
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David J. Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard University, Boston, Massachusetts, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul A. Bunn
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - John Minna
- Hamon Center for Therapeutic Oncology Research
- Departments of Internal Medicine and Pharmacology
- Simmons Comprehensive Cancer Center, and
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, and
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Mark G. Kris
- Department of Thoracic Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, and
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
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26
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Rakaee M, Adib E, Ricciuti B, Sholl LM, Shi W, Alessi JV, Cortellini A, Fulgenzi CAM, Viola P, Pinato DJ, Hashemi S, Bahce I, Houda I, Ulas EB, Radonic T, Väyrynen JP, Richardsen E, Jamaly S, Andersen S, Donnem T, Awad MM, Kwiatkowski DJ. Association of Machine Learning-Based Assessment of Tumor-Infiltrating Lymphocytes on Standard Histologic Images With Outcomes of Immunotherapy in Patients With NSCLC. JAMA Oncol 2023; 9:51-60. [PMID: 36394839 PMCID: PMC9673028 DOI: 10.1001/jamaoncol.2022.4933] [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: 05/22/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022]
Abstract
Importance Currently, predictive biomarkers for response to immune checkpoint inhibitor (ICI) therapy in lung cancer are limited. Identifying such biomarkers would be useful to refine patient selection and guide precision therapy. Objective To develop a machine-learning (ML)-based tumor-infiltrating lymphocytes (TILs) scoring approach, and to evaluate TIL association with clinical outcomes in patients with advanced non-small cell lung cancer (NSCLC). Design, Setting, and Participants This multicenter retrospective discovery-validation cohort study included 685 ICI-treated patients with NSCLC with median follow-up of 38.1 and 43.3 months for the discovery (n = 446) and validation (n = 239) cohorts, respectively. Patients were treated between February 2014 and September 2021. We developed an ML automated method to count tumor, stroma, and TIL cells in whole-slide hematoxylin-eosin-stained images of NSCLC tumors. Tumor mutational burden (TMB) and programmed death ligand-1 (PD-L1) expression were assessed separately, and clinical response to ICI therapy was determined by medical record review. Data analysis was performed from June 2021 to April 2022. Exposures All patients received anti-PD-(L)1 monotherapy. Main Outcomes and Measures Objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) were determined by blinded medical record review. The area under curve (AUC) of TIL levels, TMB, and PD-L1 in predicting ICI response were calculated using ORR. Results Overall, there were 248 (56%) women in the discovery cohort and 97 (41%) in the validation cohort. In a multivariable analysis, high TIL level (≥250 cells/mm2) was independently associated with ICI response in both the discovery (PFS: HR, 0.71; P = .006; OS: HR, 0.74; P = .03) and validation (PFS: HR = 0.80; P = .01; OS: HR = 0.75; P = .001) cohorts. Survival benefit was seen in both first- and subsequent-line ICI treatments in patients with NSCLC. In the discovery cohort, the combined models of TILs/PD-L1 or TMB/PD-L1 had additional specificity in differentiating ICI responders compared with PD-L1 alone. In the PD-L1 negative (<1%) subgroup, TIL levels had superior classification accuracy for ICI response (AUC = 0.77) compared with TMB (AUC = 0.65). Conclusions and Relevance In these cohorts, TIL levels were robustly and independently associated with response to ICI treatment. Patient TIL assessment is relatively easily incorporated into the workflow of pathology laboratories at minimal additional cost, and may enhance precision therapy.
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Affiliation(s)
- Mehrdad Rakaee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Elio Adib
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weiwei Shi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joao V. Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alessio Cortellini
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Claudia A. M. Fulgenzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Medical Oncology, University Campus Bio-Medico, Rome, Italy
| | - Patrizia Viola
- Department of Cellular Pathology, Imperial College London NHS Trust, London, United Kingdom
| | - David J. Pinato
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Sayed Hashemi
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Idris Bahce
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Ilias Houda
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Ezgi B. Ulas
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Teodora Radonic
- Department of Pathology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Juha P. Väyrynen
- Cancer and Translational Medicine Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Elin Richardsen
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Simin Jamaly
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Sigve Andersen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Tom Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David J. Kwiatkowski
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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27
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Mossanen M, Nassar AH, Stokes SM, Martinez-Chanza N, Kumar V, Nuzzo PV, Kwiatkowski DJ, Garber JE, Curran C, Freeman D, Preston M, Mouw KW, Kibel A, Choueiri TK, Sonpavde G, Rana HQ. Incidence of Germline Variants in Familial Bladder Cancer and Among Patients With Cancer Predisposition Syndromes. Clin Genitourin Cancer 2022; 20:568-574. [PMID: 36127252 DOI: 10.1016/j.clgc.2022.08.009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND The familial aggregation of bladder cancers has been observed, but the incidence and association of familial bladder cancer with germline pathogenic and likely pathogenic (P/LP) variants is unknown. PATIENTS AND METHODS A retrospective analysis was conducted of patients with bladder cancer treated at the Dana-Farber Cancer Institute to identify those with a first-degree relative with bladder cancer. A second cohort of patients referred to DFCI for suspicion of a cancer predisposition syndrome was analyzed for candidate P/LP germline variants. Descriptive statistics were generated. RESULTS Among 885 patients with bladder cancer, 38 patients (4.3%) had a family history of bladder cancer in a first-degree relative. No significant association of age of diagnosis was observed between patients with and without a first-degree family history of bladder cancer (P = .3). In the second cohort, 27 of 80 (34%) patients with bladder cancer evaluated for cancer predisposition syndromes harbored a P/LP germline variant. P/LP variants were identified most commonly in the following genes: BRCA1 (n = 5), MSH2 (n = 5), MLH1 (n = 4), ATM (n = 3), and CHEK2 (n = 2). Of the 27 patients with identified germline P/LP variants, 20 (74%) had a family history of a tumor component syndrome in a first- or second-degree relative and 3 were subsequently diagnosed with another genetically-linked associated cancer. CONCLUSION Familial bladder cancer defined as bladder cancer in the proband and a first-degree relative, was present in 4.3% of patients with bladder cancer and was not associated with age of diagnosis. Additionally, among patients suspected to have a familial cancer syndrome, one-third harbored a germline P/LP variant. Further study of germline variants in patients with familial bladder cancer including somatic testing for loss of heterozygosity may provide insights regarding disease pathogenesis and inform therapy.
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Affiliation(s)
- Matthew Mossanen
- Department of Urology, Brigham and Women's Hospital, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Amin H Nassar
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Samantha M Stokes
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Nieves Martinez-Chanza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Vivek Kumar
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - David J Kwiatkowski
- Department of Medicine, Section of Medical Oncology, Brigham and Women's Hospital, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Catherine Curran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Mark Preston
- Department of Urology, Brigham and Women's Hospital, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Kent W Mouw
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Adam Kibel
- Department of Urology, Brigham and Women's Hospital, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA
| | - Guru Sonpavde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA.
| | - Huma Q Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA.
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28
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McNamara MC, Hosios AM, Torrence ME, Zhao T, Fraser C, Wilkinson M, Kwiatkowski DJ, Henske EP, Wu CL, Sarosiek KA, Valvezan AJ, Manning BD. Reciprocal effects of mTOR inhibitors on pro-survival proteins dictate therapeutic responses in tuberous sclerosis complex. iScience 2022; 25:105458. [PMID: 36388985 PMCID: PMC9663903 DOI: 10.1016/j.isci.2022.105458] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/30/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
mTORC1 is aberrantly activated in cancer and in the genetic tumor syndrome tuberous sclerosis complex (TSC), which is caused by loss-of-function mutations in the TSC complex, a negative regulator of mTORC1. Clinically approved mTORC1 inhibitors, such as rapamycin, elicit a cytostatic effect that fails to eliminate tumors and is rapidly reversible. We sought to determine the effects of mTORC1 on the core regulators of intrinsic apoptosis. In TSC2-deficient cells and tumors, we find that mTORC1 inhibitors shift cellular dependence from MCL-1 to BCL-2 and BCL-XL for survival, thereby altering susceptibility to BH3 mimetics that target specific pro-survival BCL-2 proteins. The BCL-2/BCL-XL inhibitor ABT-263 synergizes with rapamycin to induce apoptosis in TSC-deficient cells and in a mouse tumor model of TSC, resulting in a more complete and durable response. These data expose a therapeutic vulnerability in regulation of the apoptotic machinery downstream of mTORC1 that promotes a cytotoxic response to rapamycin.
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Affiliation(s)
- Molly C. McNamara
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Aaron M. Hosios
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Margaret E. Torrence
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Ting Zhao
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Cameron Fraser
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Meghan Wilkinson
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - David J. Kwiatkowski
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth P. Henske
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Kristopher A. Sarosiek
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Alexander J. Valvezan
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Brendan D. Manning
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA,Department of Cell Biology, Harvard Medical School, Boston, MA, USA,Corresponding author
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29
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Nassar AH, Adib E, Abou Alaiwi S, El Zarif T, Groha S, Akl EW, Nuzzo PV, Mouhieddine TH, Perea-Chamblee T, Taraszka K, El-Khoury H, Labban M, Fong C, Arora KS, Labaki C, Xu W, Sonpavde G, Haddad RI, Mouw KW, Giannakis M, Hodi FS, Zaitlen N, Schoenfeld AJ, Schultz N, Berger MF, MacConaill LE, Ananda G, Kwiatkowski DJ, Choueiri TK, Schrag D, Carrot-Zhang J, Gusev A. Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors. Cancer Cell 2022; 40:1161-1172.e5. [PMID: 36179682 PMCID: PMC9559771 DOI: 10.1016/j.ccell.2022.08.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 01/28/2023]
Abstract
The immune checkpoint inhibitor (ICI) pembrolizumab is US FDA approved for treatment of solid tumors with high tumor mutational burden (TMB-high; ≥10 variants/Mb). However, the extent to which TMB-high generalizes as an accurate biomarker in diverse patient populations is largely unknown. Using two clinical cohorts, we investigated the interplay between genetic ancestry, TMB, and tumor-only versus tumor-normal paired sequencing in solid tumors. TMB estimates from tumor-only panels substantially overclassified individuals into the clinically important TMB-high group due to germline contamination, and this bias was particularly pronounced in patients with Asian/African ancestry. Among patients with non-small cell lung cancer treated with ICIs, those misclassified as TMB-high from tumor-only panels did not associate with improved outcomes. TMB-high was significantly associated with improved outcomes only in European ancestries and merits validation in non-European ancestry populations. Ancestry-aware tumor-only TMB calibration and ancestry-diverse biomarker studies are critical to ensure that existing disparities are not exacerbated in precision medicine.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT 06510, USA; Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elio Adib
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Talal El Zarif
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan Groha
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Elie W Akl
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pier Vitale Nuzzo
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tarek H Mouhieddine
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Tomin Perea-Chamblee
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kodi Taraszka
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Habib El-Khoury
- Center for Prevention of Progression of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhieddine Labban
- Department of Urologic Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christopher Fong
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kanika S Arora
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chris Labaki
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wenxin Xu
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guru Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert I Haddad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - F Stephen Hodi
- Melanoma Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Noah Zaitlen
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, 1275 York Avenue, New York, NY 10065, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael F Berger
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guruprasad Ananda
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Toni K Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deborah Schrag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jian Carrot-Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Gusev
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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30
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Chaft JE, Oezkan F, Kris MG, Bunn PA, Wistuba II, Kwiatkowski DJ, Owen DH, Tang Y, Johnson BE, Lee JM, Lozanski G, Pietrzak M, Seweryn M, Byun WY, Schulze K, Nicholas A, Johnson A, Grindheim J, Hilz S, Shames DS, Rivard C, Toloza E, Haura EB, McNamee CJ, Patterson GA, Waqar SN, Rusch VW, Carbone DP. Neoadjuvant atezolizumab for resectable non-small cell lung cancer: an open-label, single-arm phase II trial. Nat Med 2022; 28:2155-2161. [PMID: 36097216 PMCID: PMC9556329 DOI: 10.1038/s41591-022-01962-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [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: 03/08/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
In an ongoing, open-label, single-arm phase II study ( NCT02927301 ), 181 patients with untreated, resectable, stage IB-IIIB non-small cell lung cancer received two doses of neoadjuvant atezolizumab monotherapy. The primary end point was major pathological response (MPR; ≤10% viable malignant cells) in resected tumors without EGFR or ALK alterations. Of the 143 patients in the primary end point analysis, the MPR was 20% (95% confidence interval, 14-28%). With a minimum duration of follow-up of 3 years, the 3-year survival rate of 80% was encouraging. The most common adverse events during the neoadjuvant phase were fatigue (39%, 71 of 181) and procedural pain (29%, 53 of 181), along with expected immune-related toxicities; there were no unexpected safety signals. In exploratory analyses, MPR was predicted using the pre-treatment peripheral blood immunophenotype based on 14 immune cell subsets. Immune cell subsets predictive of MPR in the peripheral blood were also identified in the tumor microenvironment and were associated with MPR. This study of neoadjuvant atezolizumab in a large cohort of patients with resectable non-small cell lung cancer was safe and met its primary end point of MPR ≥ 15%. Data from this single-arm, non-randomized trial suggest that profiles of innate immune cells in pre-treatment peripheral blood may predict pathological response after neoadjuvant atezolizumab, but additional studies are needed to determine whether these profiles can inform patient selection and new therapeutic approaches.
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Affiliation(s)
- Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Filiz Oezkan
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- University Medicine Essen, Ruhrlandklinik, Department of Interventional Pulmonology, University Duisburg-Essen, Essen, Germany
- German Cancer Research Center (DKFZ), A420, Heidelberg, Germany
- Fifth Medical Department, Section of Pulmonology, Faculty of the University of Heidelberg, University Medicine Mannheim, Mannheim, Germany
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Paul A Bunn
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | - David J Kwiatkowski
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Dwight H Owen
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Yan Tang
- Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce E Johnson
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Jay M Lee
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Gerard Lozanski
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Maciej Pietrzak
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Michal Seweryn
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
- Centre for Data Analysis, Modeling and Computational Sciences, University of Lodz, Lodz, Poland
| | - Woo Yul Byun
- The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | | | - Ann Johnson
- Genentech, Inc., South San Francisco, CA, USA
| | | | | | | | - Chris Rivard
- University of Colorado School of Medicine, Aurora, CO, USA
| | - Eric Toloza
- Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric B Haura
- Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ciaran J McNamee
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Saiama N Waqar
- Washington University School of Medicine, St. Louis, MO, USA
| | | | - David P Carbone
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, Columbus, OH, USA.
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31
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Mills JD, Iyer AM, van Scheppingen J, Bongaarts A, Anink JJ, Janssen B, Zimmer TS, Spliet WG, van Rijen PC, Jansen FE, Feucht M, Hainfellner JA, Krsek P, Zamecnik J, Kotulska K, Jozwiak S, Jansen A, Lagae L, Curatolo P, Kwiatkowski DJ, Pasterkamp RJ, Senthilkumar K, von Oerthel L, Hoekman MF, Gorter JA, Crino PB, Mühlebner A, Scicluna BP, Aronica E. Author Correction: Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment. Sci Rep 2022; 12:15457. [PMID: 36104396 PMCID: PMC9474802 DOI: 10.1038/s41598-022-20109-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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32
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Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [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] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
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Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
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33
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Tang Y, Kwiatkowski DJ, Henske EP. Midkine expression by stem-like tumor cells drives persistence to mTOR inhibition and an immune-suppressive microenvironment. Nat Commun 2022; 13:5018. [PMID: 36028490 PMCID: PMC9418323 DOI: 10.1038/s41467-022-32673-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 04/19/2021] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
mTORC1 is hyperactive in multiple cancer types1,2. Here, we performed integrative analysis of single cell transcriptomic profiling, paired T cell receptor (TCR) sequencing, and spatial transcriptomic profiling on Tuberous Sclerosis Complex (TSC) associated tumors with mTORC1 hyperactivity, and identified a stem-like tumor cell state (SLS) linked to T cell dysfunction via tumor-modulated immunosuppressive macrophages. Rapamycin and its derivatives (rapalogs) are the primary treatments for TSC tumors, and the stem-like tumor cells showed rapamycin resistance in vitro, reminiscent of the cytostatic effects of these drugs in patients. The pro-angiogenic factor midkine (MDK) was highly expressed by the SLS population, and associated with enrichment of endothelial cells in SLS-dominant samples. Inhibition of MDK showed synergistic benefit with rapamycin in reducing the growth of TSC cell lines in vitro and in vivo. In aggregate, this study suggests an autocrine rapamycin resistance mechanism and a paracrine tumor survival mechanism via immune suppression adopted by the stem-like state tumor cells with mTORC1 hyperactivity.
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Affiliation(s)
- Yan Tang
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David J Kwiatkowski
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Elizabeth P Henske
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Scheper M, Romagnolo A, Besharat ZM, Iyer AM, Moavero R, Hertzberg C, Weschke B, Riney K, Feucht M, Scholl T, Petrak B, Maulisova A, Nabbout R, Jansen AC, Jansen FE, Lagae L, Urbanska M, Ferretti E, Tempes A, Blazejczyk M, Jaworski J, Kwiatkowski DJ, Jozwiak S, Kotulska K, Sadowski K, Borkowska J, Curatolo P, Mills JD, Aronica E. miRNAs and isomiRs: Serum-Based Biomarkers for the Development of Intellectual Disability and Autism Spectrum Disorder in Tuberous Sclerosis Complex. Biomedicines 2022; 10:biomedicines10081838. [PMID: 36009385 PMCID: PMC9405248 DOI: 10.3390/biomedicines10081838] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a rare multi-system genetic disorder characterized by a high incidence of epilepsy and neuropsychiatric manifestations known as tuberous-sclerosis-associated neuropsychiatric disorders (TANDs), including autism spectrum disorder (ASD) and intellectual disability (ID). MicroRNAs (miRNAs) are small regulatory non-coding RNAs that regulate the expression of more than 60% of all protein-coding genes in humans and have been reported to be dysregulated in several diseases, including TSC. In the current study, RNA sequencing analysis was performed to define the miRNA and isoform (isomiR) expression patterns in serum. A Receiver Operating Characteristic (ROC) curve analysis was used to identify circulating molecular biomarkers, miRNAs, and isomiRs, able to discriminate the development of neuropsychiatric comorbidity, either ASD, ID, or ASD + ID, in patients with TSC. Part of our bioinformatics predictions was verified with RT-qPCR performed on RNA isolated from patients’ serum. Our results support the notion that circulating miRNAs and isomiRs have the potential to aid standard clinical testing in the early risk assessment of ASD and ID development in TSC patients.
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Affiliation(s)
- Mirte Scheper
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
| | - Alessia Romagnolo
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (Z.M.B.); (E.F.)
| | - Anand M. Iyer
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Internal Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Romina Moavero
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, 00133 Rome, Italy; (R.M.); (P.C.)
- Child Neurology Unit, Neuroscience Department, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Christoph Hertzberg
- Diagnose-und Behandlungszentrum für Kinder, Vivantes-Klinikum Neukölln, 12351 Berlin, Germany;
| | - Bernhard Weschke
- Department of Neuropediatrics, Charité University Medicine Berlin, 13353 Berlin, Germany;
| | - Kate Riney
- Faculty of Medicine, The University of Queensland, Herston, QLD 4029, Australia;
- Neurosciences Unit, Queensland Children’s Hospital, South Brisbane, QLD 4101, Australia
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, “Member of ERN EpiCARE”, 1090 Vienna, Austria; (M.F.); (T.S.)
| | - Theresa Scholl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, “Member of ERN EpiCARE”, 1090 Vienna, Austria; (M.F.); (T.S.)
| | - Borivoj Petrak
- Motol University Hospital, Charles University, 15000 Prague, Czech Republic; (B.P.); (A.M.)
| | - Alice Maulisova
- Motol University Hospital, Charles University, 15000 Prague, Czech Republic; (B.P.); (A.M.)
| | - Rima Nabbout
- Reference Centre for Rare Epilepsies, Department of Pediatric Neurology, Necker Enfants Malades University Hospital, APHP, Member of ERN EpiCARE, Université de Paris, 149 Rue de Sèvres, 75015 Paris, France;
| | - Anna C. Jansen
- Department of Translational Neurosciences, University of Antwerp, 2000 Antwerp, Belgium;
| | - Floor E. Jansen
- Department of Child Neurology, Brain Center University Medical Center, Member of ERN EpiCare, 3584 BA Utrecht, The Netherlands;
| | - Lieven Lagae
- Department of Development and Regeneration Section Pediatric Neurology, University Hospitals KU Leuven, 3000 Leuven, Belgium;
| | - Malgorzata Urbanska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (Z.M.B.); (E.F.)
| | - Aleksandra Tempes
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | - Magdalena Blazejczyk
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | - Jacek Jaworski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | | | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
- Department of Child Neurology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Krzysztof Sadowski
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Julita Borkowska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, 00133 Rome, Italy; (R.M.); (P.C.)
| | - James D. Mills
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London WC1E 6BT, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
- Correspondence: (J.D.M.); (E.A.)
| | - Eleonora Aronica
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Correspondence: (J.D.M.); (E.A.)
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Dickson MA, Ravi V, Riedel RF, Ganjoo KN, Van Tine BA, Chugh R, Cranmer LD, Gordon EM, Chen JL, Murphy MC, Schmid AN, Desai N, Alonzo Palma N, Kwiatkowski DJ, Wagner AJ. nab-Sirolimus for patients with advanced malignant PEComa with or without prior mTOR inhibitors: Biomarker results from AMPECT and an expanded access program. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.11574] [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
11574 Background: Malignant perivascular epithelioid cell tumor (PEComa) is a rare and aggressive sarcoma. nab-Sirolimus is an albumin-bound intravenous (IV) mTOR inhibitor (mTORi) approved for the treatment of adult patients with locally advanced unresectable or metastatic malignant PEComa. The AMPECT trial (NCT02494570) was the first prospective study in advanced malignant PEComa. In exploratory biomarker analyses, TSC1 or TSC2 alterations were associated with response. We report data from the final analysis of AMPECT patients, who were naïve to mTORi, and in patients with malignant PEComa with prior mTORi exposure treated with nab-sirolimus in an expanded access program (EAP) (NCT03817515). Methods: In AMPECT, patients with malignant PEComa naïve to mTORi received nab-sirolimus (100 mg/m2 IV days 1 and 8 of every 21-day cycle) until progression or unacceptable toxicity. The primary endpoint was ORR by independent radiology review. Other endpoints included duration of response (DOR) and disease control rate (DCR), defined as complete response (CR), partial response (PR), or stable disease (SD) at ≥12 weeks. In the EAP, patients with malignant PEComa and prior mTORi exposure received the same dose of nab-sirolimus as in AMPECT. Responses and DCR were evaluated post hoc via electronic medical record review. Genetic profiling, including TSC1 or TSC2 status, was assessed in both protocols, but no specific mutation criteria were required for enrollment. Results: Data include 47 total efficacy-evaluable patients, 31 in AMPECT and 16 with malignant PEComa and prior mTORi exposure treated in the EAP from July 2019–July 2021. Prior mTORi on the EAP included sirolimus, everolimus, temsirolimus, or sapanisertib; 12 patients had exposure to 1 prior mTORi and 4 to ≥2 prior mTORi, and 50% had had progressive disease as best response on mTORi. In AMPECT, ORR was 39% (12/31 patients), and DCR was 71%. Median DOR was not reached after 3 years of follow-up. On the EAP, 4/16 patients (25%) achieved PR (DOR range: 1.3+–25.2+ months, 3 ongoing), and 8/16 (50%) had SD as best response; the DCR was 63% (10/16). Of patients with known TSC1 or TSC2 inactivating alterations in the combined datasets (n = 23), 57% had a response (AMPECT, 64%; EAP, 44%). There were no Grade 4 or 5 treatment-related adverse events on either protocol Conclusions: nab-Sirolimus provided durable responses in mTORi-naïve patients with malignant PEComa and clinical benefit in an expanded access protocol for patients with malignant PEComa with prior mTORi therapy. Although AMPECT and the EAP cannot be directly compared, response rates showed similar trends regardless of prior mTORi exposure and in patients with TSC1 or TSC2 alterations. Based on the emerging biomarker results, a tissue-agnostic study in patients with TSC1 and TSC2 alterations has been initiated (NCT05103358). Clinical trial information: NCT02494570, NCT03817515.
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Affiliation(s)
| | - Vinod Ravi
- University of Texas MD Anderson Cancer Center, Department of Sarcoma Medical Oncology, Houston, TX
| | | | | | | | | | - Lee D. Cranmer
- University of Washington/Fred Hutchinson Cancer Research Center, Seattle, WA
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Sepesi B, Jones DR, Meyers BF, Chaft JE, Sholl LM, Shyr Y, Kelly K, Lin J, Bunn PA, Minna JD, Rusch VW, Wistuba II, Kwiatkowski DJ, Carbone DP, Berry LD, Lee JM, Tolba K, Kris MG. LCMC LEADER neoadjuvant screening trial: LCMC4 evaluation of actionable drivers in early-stage lung cancers. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.tps8596] [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
TPS8596 Background: Comprehensive genomic profiling (CGP) has transformed the care of patients with advanced non-small cell lung cancer (NSCLC), giving many patients access to precision targeted treatment and immunotherapy with remarkable improvements in outcomes. Studies show that patients with lung cancers with oncogenic drivers are the least likely group to benefit from checkpoint inhibitors and are better served by enrollment in studies of targeted therapies. Early-stage NSCLC is now poised to benefit from these precision approaches with the regulatory approval of the first tyrosine kinase inhibitors and checkpoint inhibitors for the adjuvant treatment of resected NSCLC, each requiring testing for precision biomarkers. Neoadjuvant precision therapy for NSCLC has the potential to further improve treatment outcomes. Methods: The LCMC4 Evaluation of Actionable Drivers in EaRly Stage Lung Cancer (LEADER) Neoadjuvant Screening Trial (NCT04712877) is a collaborative diagnostic study developed by the Lung Cancer Mutation Consortium (LCMC), supported by the Thoracic Surgery Oncology Group and the Lung Cancer Research Foundation. The primary objective is to determine the proportion of patients with stage IA2-III lung cancers who possess actionable oncogenic drivers, defined as 1 of 11 actionable genomic alterations: mutations in EGFR, BRAFV600E, MET exon 14, KRAS G12C, and HER2, rearrangements in ALK, RET, NTRK, and ROS1, and amplification of MET and HER2. The study will also assess the feasibility of CGP to detect actionable oncogenic drivers in patients with suspected early-stage lung cancers scheduled to undergo biopsies to establish the diagnosis of lung cancer. The protocol will enroll 1000 patients with operable stage IA2-III (TNM 8th edition) lung cancer who will undergo CGP utilizing the Foundation Medicine 324 gene assay as well as paired liquid biopsy analysis. Results will enable selection of neoadjuvant therapy and enrollment onto independent therapeutic trials with genomically matched neoadjuvant treatment, standard therapies, or other trials if no driver is detected. The approach will be considered feasible if >35% of non-squamous NSCLCs have 1 of the 11 actionable alterations. Tumor mutational burden and PD-L1 IHC will be assessed. Plasma specimens collected pre- and post neoadjuvant treatment and post-surgery will be used for research to study the ability of circulating tumor DNA to assess neoadjuvant treatment response and minimal residual disease. 26 academic sites in the US plan to enroll patients. Clinical trial information: NCT04712877.
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Affiliation(s)
- Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Lynette M. Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Yu Shyr
- Vanderbilt University Medical Center, Nashville, TN
| | - Karen Kelly
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
| | - Jules Lin
- University of Michigan, Ann Arbor, MI
| | | | - John D. Minna
- The University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Ignacio Ivan Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | | | - Jay M. Lee
- David Geffen School of Medicine at UCLA, Los Angeles, CA
| | | | - Mark G. Kris
- Memorial Sloan Kettering Cancer Center, New York, NY
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Nassar A, Adib E, El Zarif T, Mouhieddine TH, El-Am E, Alaiwi SA, Heald B, Palovcak E, Esplin ED, Choueiri TK, Kwiatkowski DJ, Sonpavde GP. Germline variants across self-reported racial populations with urothelial carcinoma (UC). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.4569] [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
4569 Background: Prior studies of the UC germline landscape centered around White patients with minimal representation of other racial populations. Herein, we examine the frequency of germline pathogenic and likely pathogenic (P/LP) variants in 2,582 patients with UC from various racial populations. Methods: 2,582 patients with UC underwent germline testing of 1 to 126 genes using massively parallel sequencing with customized capture bait-sets to analyze exonic regions, flanking intronic regions, and copy number alterations (CNAs). P/LP variants including single nucleotide variants, indels and CNAs were reported. Fisher’s Exact test and multivariable logistic regression were used after accounting for the number of genes tested, age at diagnosis, site of disease (upper versus lower tract), gender, family history of UC, and personal history of any cancer. Results: Among the 2,582 patients with UC, median age at diagnosis was 63 years (range, 4-90) and 1158 (44.8%) were female. There were 58 Asians (2.2%), 110 Blacks (4.3%), and 2,414 Whites (93.5%). Overall, 1,639/2,582 (63.5%) patients had a personal history of another cancer and 284/2,393 (11.9%) had history of UC in a family member. 465 P/LP variants were identified in 18% of patients, among whom 286 (11.1%) harbored ≥1 clinically actionable variants. P/LP in cancer-associated genes were most frequently reported in MSH2 (72/2,512, 2.9%), monoallelic MUTYH (45/2,136, 2.1%), BRCA2 (44/2,299, 1.9%) and MSH6 (47/2,511, 1.9%). Patients with upper tract UC had significantly more P/LP (72/247, 29.1%) compared to lower tract UC (332/2,076, 16%, p= 1.3x10-5). Age at diagnosis, gender, personal history of other primary cancers, or family history of UC were not significantly associated with the prevalence of P/LP variants. There were no significant differences ( p= 0.33) in P/LP variants across Asians (11/58, 19.0%), Blacks (14/110, 12.7%), and Whites (440/2,414, 18.2%) although a trend towards lower P/LP in Blacks is notable. Compared to Whites, Blacks and Asians harbored significantly more variants of unknown significance (VUS, Whites vs Blacks: 241/2414 vs 25/110, p= 0.0015; Whites vs Asians: 241/2414 vs 17/58, p= 4e-7). Asians with UC harbored significantly more P/LP variants in ATM (2/50, 4%) compared to Whites (30/2122, 1.4%, OR = 1.1 [95% CI, 1.0-1.2]) and Asian controls from the gnomAD Database. There were no significant differences across racial populations for other highly altered genes ( BRCA1/2, CHEK2, FH, MSH2/6, MUTYH) or for actionable variants. Conclusions: Germline P/LP variants were identified in 18% of patients with UC and were enriched in upper tract tumors. Although no significant differences in P/LP prevalence were noted among patients of different racial populations, a trend towards lower P/LP in Blacks and a higher rate of VUS in Asians and Blacks suggest that ongoing analysis by genetic ancestry may provide richer admixture data and insights.
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Affiliation(s)
| | - Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | | | | | | | | | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Adib E, Nassar A, El Zarif T, Kale N, Rakaee M, Mouhieddine TH, Abou Alaiwi S, Freeman D, Labban M, Akl E, Haddad RI, Hodi FS, Sonpavde GP, Giannakis M, Braun DA, Gusev A, Choueiri TK, Overstreet E, Stone E, Kwiatkowski DJ. Dual CDKN2A/MTAP loss compared to CDKN2A loss alone and response to immune-checkpoint inhibitors (ICI) in advanced solid tumors. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2622] [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
2622 Background: We previously showed that CDKN2A genomic alterations (GAs) are associated with resistance to ICI (Adib E, Clinical Cancer Research, 2021). The majority of such GAs are homozygous deletions, which commonly (̃50-80%) include MTAP, located 100kb telomeric of CDKN2A. MTAP loss leads to 5′-deoxy-5′-methylthioadenosine (MTA) accumulation and immunosuppressive effects in tumors. We examined combined CDKN2A/MTAP deletion vs. CDKN2A deletion/mutation alone as predictors of poor ICI response. Methods: We curated clinical data for cancer patients (pts) treated with ICI at Dana-Farber Cancer Institute through 6/2021, who had targeted panel sequencing. Inclusion criteria were: ICI in metastatic setting, ≥2 cycles, no concurrent systemic therapy, cancer type with > 50 pts treated. CDKN2A/ MTAP GAs were defined as a deep deletion affecting both genes; CDKN2A only GAs included both homozygous deletions and truncating mutations. Hazard ratios (HR) for overall survival (OS) and time-to-treatment failure (TTF) were derived using multivariable Cox regression, adjusted for prior lines of therapy, treatment type (single vs. combination ICI), tumor mutational burden and ECOG PS. We also used a machine learning approach to quantify the density of tumor-infiltrating lymphocytes (TILs) in digital whole-slide H&E images of 144 melanoma pts with available genomic data. Results: 921 pts with 6 cancer types were studied: non-small cell lung cancer (NSCLC, n = 366), melanoma (mel, n = 228), urothelial carcinoma (UC, n = 120), esophagogastric carcinoma (EGC,n = 90), head and neck squamous cell carcinoma (HNSCC, n = 58), and renal cell carcinoma (RCC, n = 59). UC pts with MTAP/ CDKN2A GAs had shorter OS and TTF than pts without GA in either gene (OS HR = 1.9[1.1-3.4], p = 0.005; TTF HR = 1.8[1.0-3.1], p = 0.0016) after adjusting for covariates. Similar results were seen for melanoma (OS HR = 2.5[1.4-2.6],p = 0.00065; TTF HR = 1.9[1.1-3.2],p = 0.018). There was no significant difference between pts with CDKN2A GA only and those without GA in either gene for OS or TTF in either UC or melanoma. CDKN2A/MTAP status was not associated with significantly shorter survival for NSCLC and EGC; while the analysis was confounded by HPV events for HNSCC, and underpowered for RCC. ML-based analysis of digital slides for melanoma, showed that tumors with CDKN2A GAs only (n = 42) had similar median density of TILs compared to tumors without GAs in either gene (n = 84; 920 vs. 943 TILs/mm2; p = 0.42). In contrast, tumors with co-occurring CDKN2A/ MTAP GAs had lower TIL density (529 TIL/mm2, n = 17 vs. 925 TIL/mm2, n = 126 (pooled); p = 0.018, Wilcoxon rank sum). Conclusions: In this study, we showed that co-occurrence of MTAP/CDKN2A GAs, but not CDKN2A GA only, was associated with worse outcomes in pts with UC and melanoma treated with ICI. Lower TIL density was also seen in melanoma tissue samples with combined MTAP/CDKN2A GA.
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Affiliation(s)
- Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | | | | | - Neil Kale
- Worcester Polytechnic Institute, Worcester, MA
| | | | | | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Muhieddine Labban
- Division of Urological Surgery and Center for Surgery and Public Health, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Eli Akl
- Johns Hopkins Medical Institute, Baltimore, MD
| | - Robert I. Haddad
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | | | - David A. Braun
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | | | | | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Giannikou K, Azim AA, Adib E, Schaefer IM, Kesten N, Taing L, Zhu Z, Hornick J, Hirsch MS, Long H, Wagner AJ, Hemming ML, Kwiatkowski DJ. Distinct oncogenic signatures in malignant PEComa and leiomyosarcoma identified by integrative RNA-seq and H3K27ac ChIP-seq analysis. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.11552] [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
11552 Background: Malignant perivascular epithelioid cell tumor (PEComa) and leiomyosarcoma (LMS) are two sarcomas with overlapping morphologic and immunophenotypic features which can make their diagnostic distinction challenging. We aimed to characterize the transcriptional and epigenetic landscape of PEComa and LMS to identify distinguishing features. Methods: We performed whole transcriptome RNA-sequencing on 19 PEComas and compared their gene expression profile to 259 sarcomas from The Cancer Genome Atlas (TCGA) including 104 LMS. ChIP-sequencing for H3K27ac, a histone modification associated with activation of nearby genes/open chromatin, was conducted on 9 malignant PEComas and 12 LMS and were compared with publicly available data from 4 other sarcoma subtypes (chordoma; osteosarcoma; undifferentiated pleomorphic sarcoma; rhabdomyosarcoma; n = 29 tumors). Results: Genome-wide epigenetic and transcriptional analyses revealed overlapping patterns between PEComa and LMS, which were distinct from other sarcomas. However, we also identified a set of highly expressed and epigenetically distinct transcripts which may represent diagnostic?biomarkers: e.g., DAPL1, MLANA, SULT1C2, GPR143, and CHI3L1 for PEComa; and MYOCD, WDFC2, DES, MYH11, and CNN1 for LMS; each of which showed >17x fold higher expression for each tumor entity by DESeq2 (FDR<0.0001). Gene Set Enrichment Analyses (GSEA) demonstrated enrichment in the KEGG Lysosome pathway for PEComa (FDR=0.11), whereas myogenesis and smooth muscle contraction pathways were enriched in LMS (FDR=0.09). Integrative transcriptomic and epigenetic analyses revealed a unique set of master core transcription factors for each tumor type including among others MYOCD for LMS; MITF for PEComa, which require further functional investigation. Twelve selected genes including new as well as known and standard diagnostic markers (e.g., DAPL1, MLANA, GPR143, PNL2, CHI3L1, DES, MYH11, ER, CD68, PU.1, pS6 and CNN1) were validated by immunohistochemistry (IHC) in multiple sections from PEComa and LMS (n = 26). The combination of three melanocytic markers (HMB45, MLANA, PNL2) and pS6 can distinguish LMS from PEComas (**** p<0.0001). IHC for CD68 and PU.1 macrophage markers did not show any difference regarding the degree of immune infiltration in PEComa vs. LMS. Conclusions: Our studies revealed novel epigenetic signatures translating into lysosomal and melanocytic proteins for PEComa and myogenic proteins for LMS, which may serve as useful diagnostic biomarkers in the distinction of these two sarcoma subtypes.
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Affiliation(s)
- Krinio Giannikou
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ahmad-Abdel Azim
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | | | - Nikolas Kesten
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Len Taing
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Zachary Zhu
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jason Hornick
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Michelle S. Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Andrew J. Wagner
- Center for Sarcoma and Bone Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew Louis Hemming
- Center for Sarcoma and Bone Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Probst CK, Adib E, Losko M, Du H, Hirsch MS, Giannikou K, Kwiatkowski DJ. TSC1-mutant bladder cancer expression signature in relation to nuclear localization of TFE3 and potential for targetable dependency. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e16532] [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
e16532 Background: Mutation and inactivation of the tumor suppressor gene TSC1 is a recurrent (6-10%) event in bladder cancer, but whether it functions as a driver event for tumor development has been uncertain. Methods: We performed differential gene expression and pathway analyses using RNA-seq data from the curated TCGA TSC1 mutant BLCA (n = 26) and TSC1 wild-type BLCA (n = 382) cohort and compared to an internal cohort of putative TSC1/TSC2-driven tumors (n = 63). Mechanistic studies, as well as RNA-seq and H3K27ac ChIP-seq analyses, were conducted in 2 TSC1 mutant/WT BLCA cell lines. Results: Comparison of The Cancer Genome Atlas (TCGA) TSC1-mutant bladder cancers ( TSC1mBLCA) with TCGA TSC1 wildtype tumors ( TSC1WTBLCA) identified a conserved TSC-associated expression signature, similar to ones seen in syndromic TSC tumors. GSEA and DESeq2 analyses implicated both mTORC1 hyperactivation, as well as activation of lysosomal pathways in TSC1mBLCA. We validated our findings by IHC analysis of a separate cohort of TSC1mBLCA (n = 5), compared to TSC1WTBLCA (n = 5). In addition, we found that TFE3, a transcriptional regulator of lysosomal gene expression, was relatively highly expressed in BLCA (compared to other MiT-TFE genes) and was localized to the nucleus in TSC1mBLCA but not in TSC1WTBLCA. Mechanistic studies of two TSC1mBLCA cell lines and their respective TSC1 addback derivatives, recapitulated the phenotype found in human tumors and demonstrated that TFE3 was both post-translationally modified and predominantly nuclear in TSC1-null cell lines compared to TSC1 addbacks. RNA-seq and H3K27ac ChIP-Seq analyses showed that TSC1mBLCA cell lines retained elements of the TSC-associated expression signature that was seen in TSC1mBLCA tumors, confirming differential activation of TFE3 in response to TSC1 loss. Nuclear localization of TFE3 in TSC1mBLCA cell lines was only partially reversed by rapamycin treatment and was unaffected by treatment of Torin1. SiRNA mediated knockdown of TFE3 significantly decreased cell growth and viability in TSC1mBLCA cell lines and did not result in compensatory upregulation of TFEB and MITF. Conclusions: Our findings indicate that TSC1 mutant bladder tumors retain elements of a conserved transcriptional signature that is characterized by nuclear localization and activation of TFE3. Aberrant TFE3 activation likely contributes to TSC1mBLCA development and may therefore be amenable to targeted therapy.
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Affiliation(s)
| | - Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | | | - Heng Du
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Michelle S. Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Rakaee M, Adib E, Ricciuti B, Sholl LM, Shi W, Alessi JVM, Cortellini A, Fulgenzi CA, Pinato DJJ, Hashemi SMS, Bahce I, Houda I, Jamaly S, Andersen S, Donnem T, Awad MM, Kwiatkowski DJ. Artificial intelligence in digital pathology approach identifies the predictive impact of tertiary lymphoid structures with immune-checkpoints therapy in NSCLC. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.9065] [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
9065 Background: The presence of Tertiary Lymphoid Structures (TLS) in multiple cancer types has been recognized as a potential predictive biomarker for response to immune-checkpoint blockade. However, there is no standardized method to quantify their presence. In this context, Artificial Intelligence (AI)-based assessment of histology images may well contribute to improve reproducibility, accuracy and speed of TLS quantification. Methods: We developed an automated workflow for quantification of TLS on digitized H&E slides through A) pixel-level classification of tissue using supervised artificial neural networks model, B) object-level cell classification of candidate TLS regions, C) merging the two approaches for curation and validation of TLS versus non-TLS regions. 433 advanced stage non-small cell lung cancer (NSCLC) patients treated with first or subsequent line of anti-PD-(L)1 single agent at DFCI were included in this study. Results: TLS were detected in 37% (n = 161) of the patients H&E slides, with the highest score of 4.7 TLS per mm2 (interquartile range: Q1 = 0, Q2 = 0, Q3 = 0.03 TLS/mm2). TLS density (per mm2) was significantly higher in surgically resected (n = 246; TLSPOS= 49%) compared to bioptic samples (n = 187; TLSPOS= 21%). No association was observed between TLS and tumor mutational burden (TMB) or PD-L1 protein expression as continuous variables. Among clinically actionable mutations, EGFR (all subtypes) mutated patients (n = 38) had a significantly lower number of TLS compared to patients without EGFR mutations. Patients with ≥ 0.01 TLS/mm2 had a significantly higher objective response rate (32% vs 22%, p = 0.03), a significantly longer median progression-free survival (PFS, 4.8 vs 2.7 months, HR: 0.73, 95% CI: 0.59-0.90, p = 0.004), and a significantly improved median overall survival (OS, 16.5 vs 12.5 months, HR: 0.72, 95% CI: 0.57-0.92, p = 0.008). In multivariable analysis, after adjusting for PD-L1 (≥ vs < 50%), TMB (≥ vs < 10 mu/Mb), sex, age, ECOG score, smoking and line of treatment, TLS/mm2 (≥ vs < 0.01) levels were found to be an independent positive predictive factor for both PFS (HR:0.69, 95% CI: 0.54-0.88, p = 0.003) and OS (HR: 0.70, 95% CI: 0.52-0.93, p = 0.01). Conclusions: These findings suggest that TLS status is an independent predictor of immunotherapy effectiveness in NSCLC, with predictive value similar to that of PD-L1 expression and TMB. This novel AI system has potential for automated identification and quantification of the TLS on digital histopathological slides, and could be utilized in a standard pathology workflow with relative ease. These findings are currently being validated in other solid tumors and cohorts.
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Affiliation(s)
| | - Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Weiwei Shi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | - Alessio Cortellini
- Department of Surgery and Cancer, Imperial College London, Faculty of Medicine, Hammersmith Hospital, London, United Kingdom; Department of Biotechnology and Applied Clinical Sciences, University of L'Aquila, London, United Kingdom
| | - Claudia A.M. Fulgenzi
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | | | | | - Idris Bahce
- VU medisch centrum School of Medical Sciences, Amsterdam, Netherlands
| | | | - Simin Jamaly
- UiT The Arctic University of Norway, Tromso, Norway
| | - Sigve Andersen
- Institute of Clinical Medicine, University of Tromsø/Department of Oncology, University Hospital of Tromsø, Tromsø, Norway
| | - Tom Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Rakaee M, Adib E, Ricciuti B, Sholl LM, Alessi JVM, Cortellini A, Fulgenzi CA, Pinato DJJ, Hashemi SMS, Bahce I, Houda I, Väyrynen JP, Richardsen E, Busund LTR, Andersen S, Donnem T, Awad MM, Kwiatkowski DJ. Digital quantification of lymphocytic infiltration on routine H&E images and immunotherapy response in non–small cell lung cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.9066] [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
9066 Background: Current biomarker(s) for immuno-oncology (IO) therapy response prediction in lung cancer are limited. Additional predictive biomarkers are useful to help refine patient selection and guide precision therapy. Methods: Biopsy and surgical specimens stained with hematoxylin-eosin (H&E) were subjected to whole-slide scanning for 446 advanced stage non-small cell lung cancer (NSCLC) treated with single agent immune check point inhibitors (ICI). A machine learning model was trained on H&E images for classification of tumor infiltrating lymphocytes (TILs), tumor cells, and stromal cells in specific tissue types. Results: TIL levels were found to be highly variable, with a range of 12 to 4270 cells/mm2, and median of 319 (Q1 = 159, Q3 = 681). TIL levels were assessed on tissue samples from multiple organs which had shown primary or metastatic NSCLC, and were similar across all specimen sites except the liver, for which median TIL levels were significantly lower, at 90 cells/mm2. There was no correlation between tumor mutational burden (TMB) and TIL levels, while high TIL levels were correlated with high PD-L1 (≥ 50%) expression. Patients who experienced a partial/complete response to ICI therapy had a trend to higher median TILs compared to those who had progressive/stable disease (350 versus 310 cells/mm2, P = 0.09). In a multivariable analysis after controlling for covariates (incl. sex, age, cigarette smoking, ECOG, PD-L1, TMB & treatment line), a higher TIL level (≥ 250 cells/mm2) was an independent predictor of IO response for both progression-free survival (PFS; HRadj 0.70; 95% CI, 0.55 - 0.89; P = 0.003) and overall survival (HRadj 0.73; 95% CI, 0.56 - 0.95; P = 0.02). In a ROC analysis considering single biomarkers, PD-L1 had the highest AUC (0.68, P < 0.001), while TIL (AUC = 0.53, P = 0.08) and TMB (AUC = 0.55, P = 0.05) had similar AUC values for classifying responders from non-responders based on objective response rate. Using weighted linear regression approach to combine the biomarkers, paired PD-L1/TMB had the greatest AUC (0.70, P < 0.001) compared to PD-L1 single assay. In the PD-L1 negative (< 1%, N = 50) subgroup, TIL levels had superior predictive performance for classification of IO responders (AUC = 0.77, P = 0.02) compared to TMB (AUC = 0.57, P = 0.3), such that patients with a high TIL level (≥ 250 cells/mm2) had an improved PFS (median PFS: 2.7 vs 2.2 months; HR = 0.48; 95% CI, 0.26 - 0.87; P = 0.02). Conclusions: Digital TIL quantification with use of machine learning is feasible. TIL levels appear to be a robust and independent biomarker of likelihood of response to IO treatment in NSCLC, especially in the PD-L1 negative subgroup. The findings of this study are under validation in additional lung cancer cohorts.
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Affiliation(s)
- Mehrdad Rakaee
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | | | - Alessio Cortellini
- Department of Surgery and Cancer, Imperial College London, Faculty of Medicine, Hammersmith Hospital, London, United Kingdom; Department of Biotechnology and Applied Clinical Sciences, University of L'Aquila, London, United Kingdom
| | - Claudia A.M. Fulgenzi
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | | | | | - Idris Bahce
- VU medisch centrum School of Medical Sciences, Amsterdam, Netherlands
| | | | | | - Elin Richardsen
- Department of Medical Biology, UiT The Arctic University of Tromsø, Tromsø, Norway
| | | | - Sigve Andersen
- Institute of Clinical Medicine, University of Tromsø/Department of Oncology, University Hospital of Tromsø, Tromsø, Norway
| | - Tom Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Adib E, Nassar AH, Abou Alaiwi S, Groha S, Akl EW, Sholl LM, Michael KS, Awad MM, Jӓnne PA, Gusev A, Kwiatkowski DJ. Variation in targetable genomic alterations in non-small cell lung cancer by genetic ancestry, sex, smoking history, and histology. Genome Med 2022; 14:39. [PMID: 35428358 PMCID: PMC9013075 DOI: 10.1186/s13073-022-01041-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/22/2022] [Indexed: 11/21/2022] Open
Abstract
Background Genomic alterations in 8 genes are now the targets of FDA-approved therapeutics in non-small cell lung cancer (NSCLC), but their distribution according to genetic ancestry, sex, histology, and smoking is not well established. Methods Using multi-institutional genetic testing data from GENIE, we characterize the distribution of targetable genomic alterations in 8 genes among 8675 patients with NSCLC (discovery cohort: DFCI, N = 3115; validation cohort: Duke, Memorial Sloan Kettering Cancer Center, Vanderbilt, N = 5560). For the discovery cohort, we impute genetic ancestry from tumor-only sequencing and identify differences in the frequency of targetable alterations across ancestral groups, smoking pack-years, and histologic subtypes. Results We identified variation in the prevalence of KRASG12C, sensitizing EGFR mutations, MET alterations, ALK, and ROS1 fusions according to the number of smoking pack-years. A novel method for computing continental (African, Asian, European) and Ashkenazi Jewish ancestries from panel sequencing enables quantitative analysis of the correlation between ancestry and mutation rates. This analysis identifies a correlation between Asian ancestry and EGFR mutations and an anti-correlation between Asian ancestry and KRASG12C mutation. It uncovers 2.7-fold enrichment for MET exon 14 skipping mutations and amplifications in patients of Ashkenazi Jewish ancestry. Among never/light smokers, targetable alterations in LUAD are significantly enriched in those with Asian (80%) versus African (49%) and European (55%) ancestry. Finally, we show that 5% of patients with squamous cell carcinoma (LUSC) and 17% of patients with large cell carcinoma (LCLC) harbor targetable alterations. Conclusions Among patients with NSCLC, there was significant variability in the prevalence of targetable genomic alterations according to genetic ancestry, histology, and smoking. Patients with LUSC and LCLC have 5% rates of targetable alterations supporting consideration for sequencing in those subtypes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01041-x.
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De Ridder J, Kotulska K, Curatolo P, Jansen AC, Aronica E, Kwiatkowski DJ, Jansen FE, Jóźwiak S, Lagae L. Evolution of electroencephalogram in infants with tuberous sclerosis complex and neurodevelopmental outcome: a prospective cohort study. Dev Med Child Neurol 2022; 64:495-501. [PMID: 34601720 DOI: 10.1111/dmcn.15073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 01/20/2023]
Abstract
AIM To describe the evolution of electroencephalogram (EEG) characteristics in infants with tuberous sclerosis complex (TSC) and the relationship with neurodevelopmental outcome at 24 months. METHOD Eighty-three infants were enrolled in the EPISTOP trial and underwent serial EEG follow-up until the age of 24 months (males n=45, females n=37, median age at enrolment 28d, interquartile range 14-54d). Maturation of the EEG background and epileptiform discharges were compared between the TSC1 and TSC2 variants and between preventive and conventional groups respectively. RESULTS Children with TSC2 more frequently had a slower posterior dominant rhythm (PDR) at 24 months (51% vs 11%, p=0.002), a higher number of epileptiform foci (median=8 vs 4, p=0.003), and a lower fraction of EEGs without epileptiform discharges (18% vs 61%, p=0.001) at follow-up. A slower PDR at 24 months was significantly associated with lower cognitive (median=70 vs 80, p=0.028) and motor developmental quotients (median=70 vs 79, p=0.008). A higher fraction of EEGs without epileptiform discharges was associated with a lower probability of autism spectrum disorder symptoms (odds ratio=0.092, 95% confidence interval=0.009-0.912, p=0.042) and higher cognitive (p=0.004), language (p=0.002), and motor (p=0.001) developmental quotients at 24 months. INTERPRETATION TSC2 is associated with more abnormal EEG characteristics compared to TSC1, which are predictive for neurodevelopmental outcome.
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Affiliation(s)
- Jessie De Ridder
- Department of Development and Regeneration, Section Pediatric Neurology, Catholic University of Leuven (KU Leuven), Leuven, Belgium
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
| | - Anna C Jansen
- Pediatric Neurology Unit, University Hospital Brussel, Brussels, Belgium
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands.,Stichting Epilepsie Instellingen Nederland, Heemstede, the Netherlands
| | | | - Floor E Jansen
- Department of Child Neurology, Brain Centre, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Sergiusz Jóźwiak
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland.,Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Lieven Lagae
- Department of Development and Regeneration, Section Pediatric Neurology, Catholic University of Leuven (KU Leuven), Leuven, Belgium
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Klonowska K, Grevelink JM, Giannikou K, Ogorek BA, Herbert ZT, Thorner AR, Darling TN, Moss J, Kwiatkowski DJ. Ultrasensitive profiling of UV mutations identifies thousands of subclinical facial tumors in tuberous sclerosis complex. J Clin Invest 2022; 132:155858. [PMID: 35358092 PMCID: PMC9106361 DOI: 10.1172/jci155858] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tuberous Sclerosis Complex (TSC) is a neurogenetic syndrome due to loss-of-function mutations in TSC2 or TSC1, characterized by tumors at multiple body sites, including facial angiofibroma (FAF). Here, an ultrasensitive assessment of the extent and range of UV-induced mutations in TSC facial skin was performed. METHODS A Multiplex High-sensitivity PCR Assay (MHPA) was developed, enabling mutation detection at extremely low (<0.1%) variant allele frequencies (VAF). RESULTS MHPA assays were developed for both TSC2 and TP53, and applied to 81 samples, including 66 skin biopsies. UV-induced second hit mutation causing inactivation of TSC2 was pervasive in TSC facial skin with an average of 4.8 mutations per 2 mm biopsy at median VAF 0.08%, generating >150,000 incipient facial tumors (subclinical 'micro-FAFs') in the average TSC subject. The MHPA analysis also led to the identification of a refined UV-related indel signature and a recurrent complex mutation pattern, consisting of both a single or dinucleotide variant, and a 1-9 nt deletion, in cis. CONCLUSION TSC facial skin can be viewed as harboring a patchwork of clonal fibroblast proliferations (micro-FAF) with indolent growth, a small proportion of which develop into clinically observable FAF. Our observations also expand the spectrum of UV-related mutation signatures. FUNDING This work was supported by the TSC Alliance, Engles Family Fund for Research in TSC and LAM, and National Institutes of Health, National Heart, Lung, and Blood Institute [U01HL131022-04; Intramural Research Program].
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Affiliation(s)
- Katarzyna Klonowska
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Joannes M Grevelink
- Boston Dermatology and Laser Center, Massachusetts General Hospital, Boston, United States of America
| | - Krinio Giannikou
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Barbara A Ogorek
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, United States of America
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, United States of America
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University, Bethesda, United States of America
| | - Joel Moss
- Pulmonary Branch, National Heart Lung and Blood Institute, NIH, Bethesda, United States of America
| | - David J Kwiatkowski
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
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Adib E, El Zarif T, Freeman D, Labban M, Curran C, Sharma B, Song J, Felt K, Nassar A, Davidsohn M, Rodig SJ, Choueiri TK, Kwiatkowski DJ, Ravi P, Sonpavde GP. FOXP3+ T-cell infiltration is associated with improved outcomes in metastatic urothelial carcinoma (mUC) treated with immune-checkpoint inhibitors (ICI). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.549] [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
549 Background: Given that ICIs benefit a minority of mUC patients and are associated with significant costs, biomarkers are necessary to optimally utilize them in the clinic. Although FOXP3+ T-cells have been associated with an immune-cold environment in many cancers, studies in urothelial carcinoma have shown an opposite trend. Methods: Formalin-fixed paraffin-embedded slides from tumor specimens were collected for patients with mUC treated with ICI at Dana-Farber Cancer Institute. A novel multiplex immunofluorescence (mIF) panel, ImmunoProfile, was performed for PD-L1, PD-1, FOXP3, CD8 and DAPI, then scanned by a Vectra Polaris platform. Regions of interest were defined and used for quantitative analysis using PerkinElmer/Akoya. Intratumoral (IT) and tumor-stroma interface (TSI) density (cells/mm2) of each cell type was calculated. Clinical data was collected through chart review, and associations between cell density and response were assessed. Wilcoxon Rank-Sum test between responders (CR/PR) and non-responders (SD/PD) was used to generate p-values, followed by Benjamini-Hochberg correction. Receiver-operating curve (ROC) and area-under-curve (AUC) calculations were performed to determine the optimal cutoff (OC) differentiating responders from non-responders. Cox proportional hazards models were used to estimate OS and PFS, accounting for type of therapy (single vs. combination ICI), baseline neutrophil-to-lymphocyte ratio (NLR), PD-L1 CPS, prior therapy, non-urothelial component, ECOG-PS and liver metastases (mets). Results: Of 35 patients assessed by ImmunoProfile, 32 were evaluable for response. Most patients (88%) were male and the median age at ICI start was 73 years. Median number of prior lines of therapy was 1 (range 0 – 3), and the majority (72%) was treated with single-agent ICI. Eight patients (25%) had CR/PR, eight had SD and 16 had PD as best response. Of all IF stains assessed, IT-TSI FOXP3 was the strongest predictor of objective response (q-value = 0.006), followed by IT-CD8 (q = 0.014). ROC analysis yielded an AUC of 0.812 (0.656 – 0.969) and the optimal cutpoint was set at 75 IT-TSI-FOXP3 cells/mm2. ORR was 46% in FOXP3-high ( > 75/mm2) vs 14% in FOXP3-low mUCs. A combined model using IT-TSI-FOXP3 and clinical covariates (NLR, ECOG-PS, line of therapy, histology, and liver mets) had an AUC of 0.929. PFS was significantly longer in the FOXP3-high group (7.9 [5.7 – NR] months) compared to the FOXP3-low group (2.3 [2.1 – 6.1] months) on multivariable analysis (p = 0.007). OS also showed the same trend (p = 0.1). Conclusions: In this pilot study of ImmunoProfile, a novel mIF panel, higher FOXP3+ infiltration in tumors was associated with better outcomes and a composite clinico-IHC panel exhibited robust prognostic impact in mUC pts treated with ICI. Further study of this mIF panel is warranted to implement it in routine practice.
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Affiliation(s)
- Elio Adib
- The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | | | - Jane Song
- Dana-Farber Cancer Institute, Boston, MA
| | - Kristen Felt
- ImmunoProfile, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Scott J. Rodig
- Department of Pathology and Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Toni K. Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA
| | | | | | - Guru P. Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
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McGregor BA, Xie W, Adib E, Stadler WM, Zakharia Y, Alva A, Michaelson MD, Gupta S, Lam ET, Farah S, Nassar AH, Wei XX, Kilbridge KL, Harshman L, Signoretti S, Sholl L, Kwiatkowski DJ, McKay RR, Choueiri TK. Biomarker-Based Phase II Study of Sapanisertib (TAK-228): An mTORC1/2 Inhibitor in Patients With Refractory Metastatic Renal Cell Carcinoma. JCO Precis Oncol 2022; 6:e2100448. [PMID: 35171658 PMCID: PMC8865529 DOI: 10.1200/po.21.00448] [Citation(s) in RCA: 4] [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] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Sapanisertib is a kinase inhibitor that inhibits both mammalian target of rapamycin complex 1 (mTORC1) and mTORC2. In this multicenter, single-arm phase II trial, we evaluated the efficacy of sapanisertib in patients with treatment-refractory metastatic renal cell carcinoma (mRCC; NCT03097328). METHODS Patients with mRCC of any histology progressing through standard therapy (including prior mTOR inhibitors) had baseline biopsy and received sapanisertib 30 mg by mouth once weekly until unacceptable toxicity or disease progression. The primary end point was objective response rate by RECIST 1.1. Tissue biomarkers of mTOR pathway activation were explored. RESULTS We enrolled 38 patients with mRCC (clear cell = 28; variant histology = 10) between August 2017 and November 2019. Twenty-four (63%) had received ≥ 3 prior lines of therapy; 17 (45%) had received prior rapalog therapy. The median follow-up was 10.4 (range 1-27.4) months. Objective response rate was two of 38 (5.3%; 90% CI, 1 to 15.6); the median progression-free survival (PFS) was 2.5 months (95% CI, 1.8 to 3.7). Twelve patients (32%) developed treatment-related grade 3 adverse events, with no grade 4 or 5 toxicities. Alterations in the mTOR pathway genes were seen in 5 of 29 evaluable patients (MTOR n = 1, PTEN n = 3, and TSC1 n = 1) with no association with response or PFS. Diminished or loss of PTEN expression by immunohistochemistry was seen in 8 of 21 patients and trended toward shorter PFS compared with intact PTEN (median 1.9 v 3.7 months; hazard ratio 2.5; 95% CI, 0.9 to 6.7; P = .055). CONCLUSION Sapanisertib had minimal activity in treatment-refractory mRCC independent of mTOR pathway alterations. Additional therapeutic strategies are needed for patients with refractory mRCC.
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Affiliation(s)
| | | | - Elio Adib
- Dana-Farber Cancer Institute, Boston, MA
- Brigham and Women's Hospital, Boston, MA
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Hulshof HM, Kuijf HJ, Kotulska K, Curatolo P, Weschke B, Riney K, Krsek P, Feucht M, Nabbout R, Lagae L, Jansen A, Otte WM, Lequin MH, Sijko K, Benvenuto A, Hertzberg C, Benova B, Scholl T, De Ridder J, Aronica EA, Kwiatkowski DJ, Jozwiak S, Jurkiewicz E, Braun K, Jansen FE. Association of Early MRI Characteristics With Subsequent Epilepsy and Neurodevelopmental Outcomes in Children With Tuberous Sclerosis Complex. Neurology 2022; 98:e1216-e1225. [PMID: 35101906 DOI: 10.1212/wnl.0000000000200027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Multiple factors have been found to contribute to the high risk of epilepsy in infants with Tuberous Sclerosis Complex (TSC), including evolution of EEG abnormalities, TSC gene mutation and MRI characteristics. The aim of the present prospective multi-center study was to: 1) identify early MRI biomarkers of epilepsy in infants with TSC aged < 6 months and before seizure onset, and 2) associate these MRI biomarkers with neurodevelopmental outcomes at 2 years of age. The study was part of the EPISTOP project. METHODS We evaluated brain MRIs performed in infants with TSC younger than 6 months of age. We used harmonized MRI-protocols across centers and children were monitored closely with neuropsychological evaluation, and serial video EEG. MRI characteristics defined as tubers, radial migration lines, white matter abnormalities, cysts, calcifications, subependymal nodules (SEN) and subependymal giant cell astrocytoma (SEGA) were visually evaluated and lesions were detected semi-automatically. Lesion to brain volume ratios were calculated and associated with epilepsy and neurodevelopmental outcomes at two years. RESULTS Lesions were assessed on MRIs from 77 TSC infants, 62 MRIs were sufficient for volume analysis. The presence of tubers and higher tuber-brain ratios were associated with the development of clinical seizures, independently of TSC gene mutation and preventive treatment. Furthermore, higher tuber-brain ratios were associated with lower cognitive and motor development quotients at two years, independently of TSC gene mutation and presence of epilepsy. DISCUSSION In infants with TSC, there is a significant association between characteristic TSC lesions detected on early brain MRI and development of clinical seizures, as well as neurodevelopmental outcomes in the first two years of life. According to our results, early brain MRI findings may guide clinical care for young children with TSC. CLASSIFICATION OF EVIDENCE This study provides Class I evidence that in infants with TSC, there is a significant association between characteristic TSC lesions on early brain MRI and the development of clinical seizures and neurodevelopmental outcomes in the first two years of life.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Wim M Otte
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Maarten H Lequin
- Department of Radiology, University Medical Center, Utrecht, the Netherlands
| | - Kamil Sijko
- Instytut Pomnik-Centrum Zdrowia Dziecka, The Children's Memorial Health Institute, Warsaw, Poland, Member of the European Reference Network EpiCARE
| | | | | | | | | | | | - EleonoraM A Aronica
- Stichting Epilepsie Instellingen Nederland (SEIN), Hoofddorp, the Netherlands
| | | | - Sergiusz Jozwiak
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Elzbieta Jurkiewicz
- Instytut Pomnik-Centrum Zdrowia Dziecka, The Children's Memorial Health Institute, Warsaw, Poland, Member of the European Reference Network EpiCARE
| | - Kees Braun
- Department of Pediatric Neurology, Brain Center UMC Utrecht, The Netherlands, Member of the European Reference Network EpiCARE
| | - Floor E Jansen
- Department of Pediatric Neurology, Brain Center UMC Utrecht, The Netherlands, Member of the European Reference Network EpiCARE
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Korotkov A, Luinenburg MJ, Romagnolo A, Zimmer TS, van Scheppingen J, Bongaarts A, Broekaart DWM, Anink JJ, Mijnsbergen C, Jansen FE, van Hecke W, Spliet WG, van Rijen PC, Feucht M, Hainfellner JA, Krsek P, Zamecnik J, Crino PB, Kotulska K, Lagae L, Jansen AC, Kwiatkowski DJ, Jozwiak S, Curatolo P, Mühlebner A, van Vliet EA, Mills JD, Aronica E. Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period. J Neurodev Disord 2022; 14:8. [PMID: 35030990 PMCID: PMC8903535 DOI: 10.1186/s11689-022-09416-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/03/2022] [Indexed: 12/13/2022] Open
Abstract
Background The genetic disorder tuberous sclerosis complex (TSC) is frequently accompanied by the development of neuropsychiatric disorders, including autism spectrum disorder and intellectual disability, with varying degrees of impairment. These co-morbidities in TSC have been linked to the structural brain abnormalities, such as cortical tubers, and recurrent epileptic seizures (in 70–80% cases). Previous transcriptomic analysis of cortical tubers revealed dysregulation of genes involved in cell adhesion in the brain, which may be associated with the neurodevelopmental deficits in TSC. In this study we aimed to investigate the expression of one of these genes – cell-adhesion molecule contactin-3. Methods Reverse transcription quantitative polymerase chain reaction for the contactin-3 gene (CNTN3) was performed in resected cortical tubers from TSC patients with drug-resistant epilepsy (n = 35, age range: 1–48 years) and compared to autopsy-derived cortical control tissue (n = 27, age range: 0–44 years), as well as by western blot analysis of contactin-3 (n = 7 vs n = 7, age range: 0–3 years for both TSC and controls) and immunohistochemistry (n = 5 TSC vs n = 4 controls). The expression of contactin-3 was further analyzed in fetal and postnatal control tissue by western blotting and in-situ hybridization, as well as in the SH-SY5Y neuroblastoma cell line differentiation model in vitro. Results CNTN3 gene expression was lower in cortical tubers from patients across a wide range of ages (fold change = − 0.5, p < 0.001) as compared to controls. Contactin-3 protein expression was lower in the age range of 0–3 years old (fold change = − 3.8, p < 0.001) as compared to the age-matched controls. In control brain tissue, contactin-3 gene and protein expression could be detected during fetal development, peaked around birth and during infancy and declined in the adult brain. CNTN3 expression was induced in the differentiated SH-SY5Y neuroblastoma cells in vitro (fold change = 6.2, p < 0.01). Conclusions Our data show a lower expression of contactin-3 in cortical tubers of TSC patients during early postnatal period as compared to controls, which may affect normal brain development and might contribute to neuropsychiatric co-morbidities observed in patients with TSC. Supplementary Information The online version contains supplementary material available at 10.1186/s11689-022-09416-2.
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Affiliation(s)
- Anatoly Korotkov
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Mark J Luinenburg
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Alessia Romagnolo
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Till S Zimmer
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Jackelien van Scheppingen
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands.,Department of Neuroimmunology, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
| | - Anika Bongaarts
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Diede W M Broekaart
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Jasper J Anink
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Caroline Mijnsbergen
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Floor E Jansen
- Department of Paediatric Neurology, University Medical Center, Brain Center, Utrecht, the Netherlands
| | - Wim van Hecke
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wim G Spliet
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter C van Rijen
- Rudolf Magnus Institute for Neuroscience, University Medical Center, Brain Center, Utrecht, the Netherlands
| | - Martha Feucht
- Department of Pediatrics, Medical University Vienna, Vienna, Austria
| | | | - Pavel Krsek
- Department of Pediatric Neurology, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Lieven Lagae
- Department of Development and Regeneration-Section Pediatric Neurology, University Hospitals KU Leuven, Leuven, Belgium
| | - Anna C Jansen
- Pediatric Neurology Unit, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Sergiusz Jozwiak
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Paolo Curatolo
- Department of Clinical and Experimental Epilepsy, University College London, London, UK
| | - Angelika Mühlebner
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Erwin A van Vliet
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands.,Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - James D Mills
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands. .,Stichting Epilepsie Instellingen Nederland, Heemstede, the Netherlands.
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Hou S, Du H, Schmid AN, Kwiatkowski DJ, Desai NP. Abstract P138: nab-Sirolimus improves mTOR pathway suppression and antitumor activity versus oral mTOR inhibitors in PTEN null bladder cancer (UMUC3) and TSC2 null liver cancer (SNU398) xenografts. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-p138] [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
Background: TSC1, TSC2, and PTEN genes are tumor suppressors in the mTOR pathway and can be inactivated or deleted across many cancers (Kwiatkowski, Clin Cancer Res 2016). The mTORC1 pathway is frequently activated in cancer and causes phosphorylation of downstream targets S6K (activation) and 4EBP1 (inactivation). Nanomolar concentrations of mTOR inhibitors (mTORi) sirolimus and everolimus can effectively inhibit S6K but not 4EBP1 and may lead to therapeutic resistance (Kang, Science 2013). In a registrational phase 2 trial (AMPECT) with malignant PEComa, nab-sirolimus (ABI-009) had a response rate of 64% (9/14) in patients with TSC1 or TSC2 mutations. In an expanded access program (NCT03817515), of 8 patients with TSC1 or TSC2 mutations (2 had prior mTORi) treated with nab-sirolimus, 5 had partial responses (all mTORi naïve). This study investigated mTOR pathway inhibition, tumor drug levels, and antitumor activity of nab-sirolimus vs equal doses of oral mTORi in PTEN-null and TSC2-null xenograft models. Methods: Athymic mice bearing subcutaneous PTEN-null UMUC3 bladder cancer xenografts were treated with either saline or equal weekly doses (15 mg/kg) of nab-sirolimus (IV, 7.5 mg/kg, 2x/wk), and sirolimus or everolimus (PO, 3 mg/kg/day, 5 days/wk). Tumors were harvested and analyzed for tumor drug levels (LC-MS/MS) and pS6 inhibition by immunohistochemistry (IHC). The same treatment conditions were repeated in a subsequent experiment with TSC2-null SNU-398 hepatocellular carcinoma xenografts, which further analyzed pS6K, pS6, and p4EBP1 via western blot (WB). Results: In UMUC3 xenografts, compared with oral mTORi, IV nab-sirolimus resulted in significantly higher drug exposure (AUC 7d) in the tumor (P<0.0001) and greater pS6 inhibition as measured by IHC (P=0.0001 vs sirolimus, P=0.0034 vs everolimus). Correspondingly, nab-sirolimus resulted in significantly greater tumor growth inhibition (TGI) than sirolimus (69.6% vs 24.3%, P<0.0001) and everolimus (36.2%, P=0.0023), and prolonged animal survival vs both oral mTORi (P<0.05 log-rank). Based on WB in SNU-398 xenografts, IV nab-sirolimus consistently inhibited mTOR targets pS6K, pS6, and p4EBP1, whereas oral sirolimus only partially decreased pS6K and pS6 and did not appear to reduce p4EBP1 levels. Correspondingly, nab-sirolimus resulted in significantly greater TGI than sirolimus (67.8% vs 36.2%, P<0.05) and prolonged animal survival (P<0.05 log-rank). Conclusions: The relatively low tumor concentrations achieved with oral mTORi may limit their effectiveness as anticancer therapies. IV nab-sirolimus at equal dose showed significantly higher tumor accumulation and inhibition of pS6 in a PTEN-null bladder cancer xenograft and increased inhibition of mTOR targets pS6K, pS6, and p4EBP1 in a TSC2-null hepatocellular carcinoma xenograft. This was accompanied with significantly greater antitumor activity, suggesting that nab-sirolimus may have a more optimal pharmacologic profile than the oral mTORi. Clinical studies in cancers harboring these alterations are planned.
Citation Format: Shihe Hou, Heng Du, Anita N. Schmid, David J. Kwiatkowski, Neil P. Desai. nab-Sirolimus improves mTOR pathway suppression and antitumor activity versus oral mTOR inhibitors in PTEN null bladder cancer (UMUC3) and TSC2 null liver cancer (SNU398) xenografts [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P138.
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Affiliation(s)
- Shihe Hou
- 1Aadi Bioscience, Pacific Palisades, CA,
| | - Heng Du
- 2Brigham and Women’s Hospital, Boston, MA
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