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Kerepesi C, Abushukair HM, Ricciuti B, Nassar AH, Adib E, Alessi JV, Pecci F, Rakaee M, Fadlullah MZH, Tőkés AM, Rodig SJ, Awad MM, Tan AC, Bakacs T, Naqash AR. Association of Baseline Tumor-Specific Neoantigens and CD8 + T-Cell Infiltration With Immune-Related Adverse Events Secondary to Immune Checkpoint Inhibitors. JCO Precis Oncol 2024; 8:e2300439. [PMID: 38330262 DOI: 10.1200/po.23.00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/12/2023] [Accepted: 11/01/2023] [Indexed: 02/10/2024] Open
Abstract
PURPOSE Recent evidence has shown that higher tumor mutational burden strongly correlates with an increased risk of immune-related adverse events (irAEs). By using an integrated multiomics approach, we further studied the association between relevant tumor immune microenvironment (TIME) features and irAEs. METHODS Leveraging the US Food and Drug Administration Adverse Event Reporting System, we extracted cases of suspected irAEs to calculate the reporting odds ratios (RORs) of irAEs for cancers treated with immune checkpoint inhibitors (ICIs). TIME features for 32 cancer types were calculated on the basis of the cancer genomic atlas cohorts and indirectly correlated with each cancer's ROR for irAEs. A separate ICI-treated cohort of non-small-cell lung cancer (NSCLC) was used to evaluate the correlation between tissue-based immune markers (CD8+, PD-1/L1+, FOXP3+, tumor-infiltrating lymphocytes [TILs]) and irAE occurrence. RESULTS The analysis of 32 cancers and 33 TIME features demonstrated a significant association between irAE RORs and the median number of base insertions and deletions (INDEL), neoantigens (r = 0.72), single-nucleotide variant neoantigens (r = 0.67), and CD8+ T-cell fraction (r = 0.51). A bivariate model using the median number of INDEL neoantigens and CD8 T-cell fraction had the highest accuracy in predicting RORs (adjusted r2 = 0.52, P = .002). Immunoprofile assessment of 156 patients with NSCLC revealed a strong trend for higher baseline median CD8+ T cells within patients' tumors who experienced any grade irAEs. Using machine learning, an expanded ICI-treated NSCLC cohort (n = 378) further showed a treatment duration-independent association of an increased proportion of high TIL (>median) in patients with irAEs (59.7% v 44%, P = .005). This was confirmed by using the Fine-Gray competing risk approach, demonstrating higher baseline TIL density (>median) associated with a higher cumulative incidence of irAEs (P = .028). CONCLUSION Our findings highlight a potential role for TIME features, specifically INDEL neoantigens and baseline-immune infiltration, in enabling optimal irAE risk stratification of patients.
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Affiliation(s)
- Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, Hungary
| | | | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Elio Adib
- Brigham and Women's Hospital, Boston, MA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mehrdad Rakaee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | - Anna-Mária Tőkés
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Scott J Rodig
- ImmunoProfile, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Aik Choon Tan
- Departments of Oncological Sciences and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Tibor Bakacs
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, Hungary
| | - Abdul Rafeh Naqash
- Department of Probability, Alfred Renyi Institute of Mathematics, The Eötvös Loránd Research Network, Budapest, Hungary
- Medical Oncology/TSET Phase 1 Program, Stephenson Cancer Center @The University of Oklahoma, Oklahoma City, OK
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Nibid L, Greco C, Cordelli E, Sabarese G, Fiore M, Liu CZ, Ippolito E, Sicilia R, Miele M, Tortora M, Taffon C, Rakaee M, Soda P, Ramella S, Perrone G. Deep pathomics: A new image-based tool for predicting response to treatment in stage III non-small cell lung cancer. PLoS One 2023; 18:e0294259. [PMID: 38015944 PMCID: PMC10684067 DOI: 10.1371/journal.pone.0294259] [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: 07/03/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023] Open
Abstract
Despite the advantages offered by personalized treatments, there is presently no way to predict response to chemoradiotherapy in patients with non-small cell lung cancer (NSCLC). In this exploratory study, we investigated the application of deep learning techniques to histological tissue slides (deep pathomics), with the aim of predicting the response to therapy in stage III NSCLC. We evaluated 35 digitalized tissue slides (biopsies or surgical specimens) obtained from patients with stage IIIA or IIIB NSCLC. Patients were classified as responders (12/35, 34.7%) or non-responders (23/35, 65.7%) based on the target volume reduction shown on weekly CT scans performed during chemoradiation treatment. Digital tissue slides were tested by five pre-trained convolutional neural networks (CNNs)-AlexNet, VGG, MobileNet, GoogLeNet, and ResNet-using a leave-two patient-out cross validation approach, and we evaluated the networks' performances. GoogLeNet was globally found to be the best CNN, correctly classifying 8/12 responders and 10/11 non-responders. Moreover, Deep-Pathomics was found to be highly specific (TNr: 90.1) and quite sensitive (TPr: 0.75). Our data showed that AI could surpass the capabilities of all presently available diagnostic systems, supplying additional information beyond that currently obtainable in clinical practice. The ability to predict a patient's response to treatment could guide the development of new and more effective therapeutic AI-based approaches and could therefore be considered an effective and innovative step forward in personalised medicine.
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Affiliation(s)
- Lorenzo Nibid
- Research Unit of Anatomical Pathology, Department of of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Carlo Greco
- Radiation Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Radiation Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Ermanno Cordelli
- Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Giovanna Sabarese
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Michele Fiore
- Radiation Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Radiation Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Charles Z. Liu
- Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Edy Ippolito
- Radiation Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Radiation Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Rosa Sicilia
- Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Marianna Miele
- Radiation Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Radiation Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Matteo Tortora
- Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Chiara Taffon
- Research Unit of Anatomical Pathology, Department of of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Mehrdad Rakaee
- Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paolo Soda
- Unit of Computer Systems and Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
- Department of Radiation Sciences, Radiation Physics, Biomedical Engineering, Umeå University, Umeå, Sweden
| | - Sara Ramella
- Radiation Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Radiation Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Giuseppe Perrone
- Research Unit of Anatomical Pathology, Department of of Medicine and Surgery, Università Campus Bio-Medico di Roma, Rome, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
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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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4
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Ricciuti B, Elkrief A, Alessi J, Wang X, Li Y, Gupta H, Muldoon DM, Bertram AA, Pecci F, Lamberti G, Di Federico A, Barrichello A, Vaz VR, Gandhi M, Lee E, Shapiro GI, Park H, Nishino M, Lindsay J, Felt KD, Sharma B, Cherniack AD, Rodig S, Gomez DR, Shaverdian N, Rakaee M, Bandlamudi C, Ladanyi M, Janne PA, Schoenfeld AJ, Sholl LM, Awad MM, Cheng ML. Clinicopathologic, Genomic, and Immunophenotypic Landscape of ATM Mutations in Non-Small Cell Lung Cancer. Clin Cancer Res 2023; 29:2540-2550. [PMID: 37097610 DOI: 10.1158/1078-0432.ccr-22-3413] [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: 11/04/2022] [Revised: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
PURPOSE ATM is the most commonly mutated DNA damage and repair gene in non-small cell lung cancer (NSCLC); however, limited characterization has been pursued. EXPERIMENTAL DESIGN Clinicopathologic, genomic, and treatment data were collected for 5,172 patients with NSCLC tumors which underwent genomic profiling. ATM IHC was performed on 182 NSCLCs with ATM mutations. Multiplexed immunofluorescence was performed on a subset of 535 samples to examine tumor-infiltrating immune cell subsets. RESULTS A total of 562 deleterious ATM mutations were identified in 9.7% of NSCLC samples. ATM-mutant (ATMMUT) NSCLC was significantly associated with female sex (P = 0.02), ever smoking status (P < 0.001), non-squamous histology (P = 0.004), and higher tumor mutational burden (DFCI, P < 0.0001; MSK, P < 0.0001) compared with ATM-wild-type (ATMWT) cases. Among 3,687 NSCLCs with comprehensive genomic profiling, co-occurring KRAS, STK11, and ARID2 oncogenic mutations were significantly enriched among ATMMUT NSCLCs (Q < 0.05), while TP53 and EGFR mutations were enriched in ATMWT NSCLCs. Among 182 ATMMUT samples with ATM IHC, tumors with nonsense, insertions/deletions, or splice site mutations were significantly more likely to display ATM loss by IHC (71.4% vs. 28.6%; P < 0.0001) compared with tumors with only predicted pathogenic missense mutations. Clinical outcomes to PD-(L)1 monotherapy (N = 1,522) and chemo-immunotherapy (N = 951) were similar between ATMMUT and ATMWT NSCLCs. Patients with concurrent ATM/TP53 mutations had significantly improved response rate and progression-free survival with PD-(L)1 monotherapy. CONCLUSIONS Deleterious ATM mutations defined a subset of NSCLC with unique clinicopathologic, genomic, and immunophenotypic features. Our data may serve as resource to guide interpretation of specific ATM mutations in NSCLC.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Arielle Elkrief
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joao Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Xinan Wang
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Yvonne Li
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Hersh Gupta
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Daniel M Muldoon
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arrien A Bertram
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alessandro Di Federico
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adriana Barrichello
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Malini Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hyesun Park
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - James Lindsay
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen D Felt
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bijaya Sharma
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew D Cherniack
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Daniel R Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Narek Shaverdian
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mehrdad Rakaee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chaitanya Bandlamudi
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pasi A Janne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael L Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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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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6
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Paulsen EE, Andersen S, Rakaee M, Pedersen MI, Lombardi AP, Pøhl M, Kilvaer T, Busund LT, Pezzella F, Donnem T. Impact of microvessel patterns and immune status in NSCLC: a non-angiogenic vasculature is an independent negative prognostic factor in lung adenocarcinoma. Front Oncol 2023; 13:1157461. [PMID: 37182191 PMCID: PMC10169734 DOI: 10.3389/fonc.2023.1157461] [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: 02/02/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Non-small cell lung carcinomas (NSCLC) exhibit different microvessel patterns (MVPs). Basal (BA), diffuse (DA) and papillary (PA) patterns show signs of angiogenesis (new blood vessels), while an alveolar pattern indicates that tumors are co-opting existing normal vessels (non-angiogenic alveolar, NAA). NAA tumor growth is known to exist in NSCLC, but little is known about its prognostic impact in different histological subgroups, and about associations between MVPs and immune cell infiltration. Methods Detailed patterns of angiogenic and non-angiogenic tumor growth were evaluated by CD34 immunohistochemistry in whole tissue slides from 553 surgically treated patients with NSCLC stage I-IIIB disease. Associations with clinicopathological variables and markers related to tumor immunology-, angiogenesis- and hypoxia/metabolism were explored, and disease-specific survival (DSS) was analyzed according to histological subtypes. Results The predominant MVP was angiogenic in 82% of tumors: BA 40%, DA 34%, PA 8%, while a NAA pattern dominated in 18%. A contribution of the NAA pattern >5% (NAA+), i.e., either dominant or minority, was observed in 40.1% of tumors and was associated with poor disease-specific survival (DSS) (p=0.015). When stratified by histology, a significantly decreased DSS for NAA+ was found for adenocarcinomas (LUAD) only (p< 0.003). In multivariate analyses, LUAD NAA+ pattern was a significant independent prognostic factor; HR 2.37 (CI 95%, 1.50-3.73, p< 0.001). The immune cell density (CD3, CD4, CD8, CD45RO, CD204, PD1) added prognostic value in squamous cell carcinoma (LUSC) and LUAD with 0-5% NAA (NAA-), but not in LUAD NAA+. In correlation analyses, there were several significant associations between markers related to tumor metabolism (MCT1, MCT4, GLUT1) and different MVPs. Conclusion The NAA+ pattern is an independent poor prognostic factor in LUAD. In NAA+ tumors, several immunological markers add prognostic impact in LUSC but not in LUAD.
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Affiliation(s)
- Erna-Elise Paulsen
- Department of Pulmonology, University Hospital of North Norway, Tromso, Norway
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Sigve Andersen
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Mehrdad Rakaee
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Molecular Pathology, University Hospital of North Norway, Tromso, Norway
| | - Mona Irene Pedersen
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Ana Paola Lombardi
- Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Mette Pøhl
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Thomas Kilvaer
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Lill-Tove Busund
- Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Francesco Pezzella
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tom Donnem
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
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7
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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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8
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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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9
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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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10
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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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Jamaly S, Rakaee M, Abdi R, Tsokos GC, Fenton KA. Interplay of immune and kidney resident cells in the formation of tertiary lymphoid structures in lupus nephritis. Autoimmun Rev 2021; 20:102980. [PMID: 34718163 DOI: 10.1016/j.autrev.2021.102980] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023]
Abstract
Kidney involvement confers significant morbidity and mortality in patients with systemic lupus erythematosus (SLE). The pathogenesis of lupus nephritis (LN) involves diverse mechanisms instigated by elements of the autoimmune response which alter the biology of kidney resident cells. Processes in the glomeruli and in the interstitium may proceed independently albeit crosstalk between the two is inevitable. Podocytes, mesangial cells, tubular epithelial cells, kidney resident macrophages and stromal cells with input from cytokines and autoantibodies present in the circulation alter the expression of enzymes, produce cytokines and chemokines which lead to their injury and damage of the kidney. Several of these molecules can be targeted independently to prevent and reverse kidney failure. Tertiary lymphoid structures with true germinal centers are present in the kidneys of patients with lupus nephritis and have been increasingly recognized to associate with poorer renal outcomes. Stromal cells, tubular epithelial cells, high endothelial vessel and lymphatic venule cells produce chemokines which enable the formation of structures composed of a T-cell-rich zone with mature dendritic cells next to a B-cell follicle with the characteristics of a germinal center surrounded by plasma cells. Following an overview on the interaction of the immune cells with kidney resident cells, we discuss the cellular and molecular events which lead to the formation of tertiary lymphoid structures in the interstitium of the kidneys of mice and patients with lupus nephritis. In parallel, molecules and processes that can be targeted therapeutically are presented.
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Affiliation(s)
- Simin Jamaly
- Department of Medical Biology, Faculty of Health Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Mehrdad Rakaee
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Reza Abdi
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - George C Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kristin Andreassen Fenton
- Department of Medical Biology, Faculty of Health Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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12
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Stoen MJ, Andersen S, Rakaee M, Pedersen MI, Ingebriktsen LM, Donnem T, Lombardi APG, Kilvaer TK, Busund LTR, Richardsen E. Overexpression of miR-20a-5p in Tumor Epithelium Is an Independent Negative Prognostic Indicator in Prostate Cancer-A Multi-Institutional Study. Cancers (Basel) 2021; 13:cancers13164096. [PMID: 34439249 PMCID: PMC8394585 DOI: 10.3390/cancers13164096] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary MicroRNAs (miRs) have critical regulatory roles in cell functions, and are involved in prostate cancer tumorigenesis. miR-20a-5p is a member of the oncogenic miR-17-92 cluster. Overexpressed miR-20a-5p has been shown to increase both cell proliferation and cell migration in cancers. The aim of our cohort study was to evaluate the prognostic role of miR-20a-5p in prostate cancer. We found miR-20a-5p associated with biochemical failure in tumor epithelium and tumor stroma. In the multivariable analysis miR-20a-5p in tumor epithelium was found to be an independent prognostic predictor for biochemical failure. In the functional studies, migration and invasion were significantly increased in miR-20a-5p transfected prostate cancer cell lines. In conclusion, high miR-20a-5p expression in tumor epithelium is a negative independent prognostic factor for biochemical failure in prostate cancer. Abstract Objective: assessing the prognostic role of miR-20a-5p, in terms of clinical outcome, in a large multi-institutional cohort study. Methods: Tissue microarrays from 535 patients’ prostatectomy specimens were constructed. In situ hybridization was performed to assess the expression level of miR-20a-5p in different tissue subregions: tumor stroma (TS) and tumor epithelium (TE). In vitro analysis was performed on prostate cancer cell lines. Results: A high miR-20a-5p expression was found negatively in association with biochemical failure in TE, TS and TE + TS (p = 0.001, p = 0.003 and p = 0.001, respectively). Multivariable analysis confirmed that high miR-20a-5p expression in TE independently predicts dismal prognosis for biochemical failure (HR = 1.56, 95% CI: 1.10–2.21, p = 0.014). Both DU145 and PC3 cells exhibited increased migration ability after transient overexpression of miR-20a-5p, as well as significant elevation of invasion in DU145 cells. Conclusion: A high miR-20a-5p expression in tumor epithelium is an independent negative predictor for biochemical prostate cancer recurrence.
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Affiliation(s)
- Maria J. Stoen
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (L.M.I.); (A.P.G.L.); (T.K.K.); (L.-T.R.B.); (E.R.)
- Correspondence: ; Tel.: +47-97419736
| | - Sigve Andersen
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (S.A.); (M.R.); (M.I.P.); (T.D.)
- Department of Oncology, University Hospital of North Norway, N-9038 Tromso, Norway
| | - Mehrdad Rakaee
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (S.A.); (M.R.); (M.I.P.); (T.D.)
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mona I. Pedersen
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (S.A.); (M.R.); (M.I.P.); (T.D.)
| | - Lise M. Ingebriktsen
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (L.M.I.); (A.P.G.L.); (T.K.K.); (L.-T.R.B.); (E.R.)
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, N-5021 Bergen, Norway
| | - Tom Donnem
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (S.A.); (M.R.); (M.I.P.); (T.D.)
- Department of Oncology, University Hospital of North Norway, N-9038 Tromso, Norway
| | - Ana P. G. Lombardi
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (L.M.I.); (A.P.G.L.); (T.K.K.); (L.-T.R.B.); (E.R.)
| | - Thomas K. Kilvaer
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (L.M.I.); (A.P.G.L.); (T.K.K.); (L.-T.R.B.); (E.R.)
- Department of Oncology, University Hospital of North Norway, N-9038 Tromso, Norway
| | - Lill-Tove R. Busund
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (L.M.I.); (A.P.G.L.); (T.K.K.); (L.-T.R.B.); (E.R.)
- Department of Clinical Pathology, University Hospital of North Norway, N-9038 Tromso, Norway
| | - Elin Richardsen
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, N-9037 Tromso, Norway; (L.M.I.); (A.P.G.L.); (T.K.K.); (L.-T.R.B.); (E.R.)
- Department of Clinical Pathology, University Hospital of North Norway, N-9038 Tromso, Norway
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13
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Stoen MJ, Andersen S, Rakaee M, Pedersen MI, Ingebriktsen LM, Bremnes RM, Donnem T, Lombardi APG, Kilvaer TK, Busund LT, Richardsen E. High expression of miR-17-5p in tumor epithelium is a predictor for poor prognosis for prostate cancer patients. Sci Rep 2021; 11:13864. [PMID: 34226620 PMCID: PMC8257715 DOI: 10.1038/s41598-021-93208-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 07/25/2020] [Accepted: 06/15/2021] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRs) are small non-coding RNA molecules, which are involved in the development of various malignancies, including prostate cancer (PCa). miR-17-5p is considered the most prominent member of the miR-17-92 cluster, with an essential regulatory function of fundamental cellular processes. In many malignancies, up-regulation of miR-17-5p is associated with worse outcome. In PCa, miR-17-5p has been reported to increase cell proliferation and the risk of metastasis. In this study, prostatectomy specimens from 535 patients were collected. Tissue microarrays were constructed and in situ hybridization was performed, followed by scoring of miR-17-5p expression on different tumor compartments. High expression of miR-17-5p in tumor epithelium was associated with biochemical failure (BF, p < 0.001) and clinical failure (CF, p = 0.019). In multivariate analyses, high miR-17-5p expression in tumor epithelial cells was an independent negative prognostic factor for BF (HR 1.87, 95% CI 1.32-2.67, p < 0.001). In vitro analyses confirmed association between overexpression of miR-17-5p and proliferation, migration and invasion in prostate cancer cell lines (PC3 and DU145). In conclusion, our study suggests that a high cancer cell expression of miR-17-5p was an independent negative prognostic factor in PCa.
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Affiliation(s)
- Maria Jenvin Stoen
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway.
| | - S Andersen
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT the Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - M Rakaee
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway.,Translational Cancer Research Group, Institute of Clinical Medicine, UiT the Arctic University of Norway, Tromso, Norway
| | - M I Pedersen
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT the Arctic University of Norway, Tromso, Norway
| | - L M Ingebriktsen
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway.,Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Section for Pathology, University of Bergen, 5021, Bergen, Norway
| | - R M Bremnes
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT the Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - T Donnem
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT the Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - A P G Lombardi
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway
| | - T K Kilvaer
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - L T Busund
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - E Richardsen
- Translational Cancer Research Group, Institute of Medical Biology, UiT the Arctic University of Norway, 9037, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
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14
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Kilvaer TK, Paulsen EE, Andersen S, Rakaee M, Bremnes RM, Busund LTR, Donnem T. Digitally quantified CD8+ cells: the best candidate marker for an immune cell score in non-small cell lung cancer? Carcinogenesis 2021; 41:1671-1681. [PMID: 33035322 PMCID: PMC7791621 DOI: 10.1093/carcin/bgaa105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 07/18/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
The TNM classification is well established as a state-of-the-art prognostic and treatment-decision-making tool for non-small cell lung cancer (NSCLC) patients. However, incorporation of biological data may hone the TNM system. This article focuses on choosing and incorporating subsets of tissue-infiltrating lymphocyte (TIL), detected by specific immunohistochemistry and automatically quantified by open source software, into a TNM-Immune cell score (TNM-I) for NSCLC. We use common markers (CD3, CD4, CD8, CD20 and CD45RO) of TILs to identify TIL subsets in tissue micro-arrays comprising tumor tissue from 553 patients resected for primary NSCLC. The number of TILs is automatically quantified using open source software (QuPath). Their prognostic efficacy, alone and within a TNM-I model, is evaluated in all patients and histological subgroups. Compared with previous manual semi-quantitative scoring of TILs in the same cohort, the present digital quantification proved superior. As a proof-of-concept, we construct a TNM-I, using TNM categories and the CD8+ TIL density. The TNM-I is an independent prognosticator of favorable diagnosis in both the overall cohort and in the main histological subgroups. In conclusion, CD8+ TIL density is the most promising candidate marker for a TNM-I in NSCLC. The prognostic efficacy of the CD8+ TIL density is strongest in lung squamous cell carcinomas, whereas both CD8+ TILs and CD20+ TILs, or a combination of these, may be candidates for a TNM-I in lung adenocarcinoma. Furthermore, based on the presented results, digital quantification is the preferred method for scoring TILs in the future.
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Affiliation(s)
- Thomas K Kilvaer
- Department of Oncology, University Hospital of North Norway, Tromso, Norway.,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Erna-Elise Paulsen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Pulmonary Medicine, University Hospital of North Norway, Tromso, Norway
| | - Sigve Andersen
- Department of Oncology, University Hospital of North Norway, Tromso, Norway.,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Mehrdad Rakaee
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Roy M Bremnes
- Department of Oncology, University Hospital of North Norway, Tromso, Norway.,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Lill-Tove Rasmussen Busund
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Tom Donnem
- Department of Oncology, University Hospital of North Norway, Tromso, Norway.,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
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15
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Rakaee M, Kilvaer TK, Jamaly S, Berg T, Paulsen EE, Berglund M, Richardsen E, Andersen S, Al-Saad S, Poehl M, Pezzella F, Kwiatkowski DJ, Bremnes RM, Busund LTR, Donnem T. Tertiary lymphoid structure score: a promising approach to refine the TNM staging in resected non-small cell lung cancer. Br J Cancer 2021; 124:1680-1689. [PMID: 33723388 PMCID: PMC8110789 DOI: 10.1038/s41416-021-01307-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 08/18/2020] [Revised: 01/19/2021] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND We previously proposed an immune cell score (tumour node metastasis (TNM)-Immune cell score) classifier as an add-on to the existing TNM staging system for non-small cell lung cancer (NSCLC). Herein, we examined how to reliably assess a tertiary lymphoid structure (TLS) score to refine the TNM staging system. METHODS Using immunohistochemistry (CD8/cytokeratin), we quantified TLS in resected NSCLC whole-tumour tissue sections with three different scoring models on two independent collections (total of 553 patients). In a pilot setting, NanoString gene expression signatures were analysed for associations with TLS. RESULTS The number of TLSs significantly decreased in stage III patients as compared to stage II. The TLS score was an independent positive prognostic factor, regardless of the type of (semi)-quantification strategy used (four-scale semi-quantitative; absolute count of total TLS; subpopulation of mature TLS) or the endpoint (disease-specific survival; overall survival; time to recurrence). Subgroup analyses revealed a significant prognostic impact of TLS score within each pathological stage, patient cohort and main histological subtype. Targeted gene expression analysis showed that high TLS levels were associated with the expression of B cell and adaptive immunity genes/metagenes including tumour inflammation signature. CONCLUSIONS The TLS score increases the prognostic power in each pathological stage and hence has the potential to refine TNM staging in resected NSCLC.
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Affiliation(s)
- Mehrdad Rakaee
- grid.10919.300000000122595234Department of Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway ,grid.10919.300000000122595234Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway
| | - Thomas K. Kilvaer
- grid.10919.300000000122595234Department of Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Simin Jamaly
- grid.10919.300000000122595234Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway
| | - Thomas Berg
- grid.412244.50000 0004 4689 5540Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Erna-Elise Paulsen
- grid.10919.300000000122595234Department of Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Marte Berglund
- grid.412244.50000 0004 4689 5540Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Elin Richardsen
- grid.10919.300000000122595234Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Sigve Andersen
- grid.10919.300000000122595234Department of Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Samer Al-Saad
- grid.412244.50000 0004 4689 5540Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Mette Poehl
- grid.475435.4Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Francesco Pezzella
- grid.4991.50000 0004 1936 8948Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
| | - David J. Kwiatkowski
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.62560.370000 0004 0378 8294Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Roy M. Bremnes
- grid.10919.300000000122595234Department of Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Lill-Tove Rasmussen Busund
- grid.10919.300000000122595234Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Tom Donnem
- grid.10919.300000000122595234Department of Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway ,grid.412244.50000 0004 4689 5540Department of Oncology, University Hospital of North Norway, Tromso, Norway
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16
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Ramberg H, Richardsen E, de Souza GA, Rakaee M, Stensland ME, Braadland PR, Nygård S, Ögren O, Guldvik IJ, Berge V, Svindland A, Taskén KA, Andersen S. Proteomic analyses identify major vault protein as a prognostic biomarker for fatal prostate cancer. Carcinogenesis 2021; 42:685-693. [PMID: 33609362 PMCID: PMC8163044 DOI: 10.1093/carcin/bgab015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/09/2020] [Revised: 01/25/2021] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
The demographic shift toward an older population will increase the number of prostate cancer cases. A challenge in the treatment of prostate cancer is to avoid undertreatment of patients at high risk of progression following curative treatment. These men can benefit from early salvage treatment. An explorative cohort consisting of tissue from 16 patients who underwent radical prostatectomy, and were either alive or had died from prostate cancer within 10 years postsurgery, was analyzed by mass spectrometry analysis. Following proteomic and bioinformatic analyses, major vault protein (MVP) was identified as a putative prognostic biomarker. A publicly available tissue proteomics dataset and a retrospective cohort of 368 prostate cancer patients were used for validation. The prognostic value of the MVP was verified by scoring immunohistochemical staining of a tissue microarray. High level of MVP was associated with more than 4-fold higher risk for death from prostate cancer (hazard ratio = 4.41, 95% confidence interval: 1.45–13.38; P = 0.009) in a Cox proportional hazard models, adjusted for Cancer of the Prostate Risk Assessments Post-surgical (CAPRA-S) score and perineural invasion. Decision curve analyses suggested an improved standardized net benefit, ranging from 0.06 to 0.18, of adding MVP onto CAPRA-S score. This observation was confirmed by receiver operator characteristics curve analyses for the CAPRA-S score versus CAPRA-S and MVP score (area under the curve: 0.58 versus 0.73). From these analyses, one can infer that MVP levels in combination with CAPRA-S score might add onto established risk parameters to identify patients with lethal prostate cancer.
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Affiliation(s)
- Håkon Ramberg
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Elin Richardsen
- Department of Medical Biology, The Arctic University of Norway, Tromsø, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Gustavo A de Souza
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.,Department of Immunology, Proteomics Core Facility, Oslo University Hospital, Oslo, Norway
| | - Mehrdad Rakaee
- Department of Medical Biology, The Arctic University of Norway, Tromsø, Norway.,Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
| | - Maria Ekman Stensland
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.,Department of Immunology, Proteomics Core Facility, Oslo University Hospital, Oslo, Norway
| | - Peder Rustøen Braadland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ståle Nygård
- Department of Tumorbiology, Bioinformatic Core Facility, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olov Ögren
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ingrid J Guldvik
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Viktor Berge
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | - Aud Svindland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kristin A Taskén
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sigve Andersen
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway.,Department of Oncology, University Hospital of North Norway, Tromsø, Norway
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17
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Richardsen E, Andersen S, Al-Saad S, Rakaee M, Nordby Y, Pedersen MI, Ness N, Ingebriktsen LM, Fassina A, Taskén KA, Mills IG, Donnem T, Bremnes RM, Busund LT. Low Expression of miR-424-3p is Highly Correlated with Clinical Failure in Prostate Cancer. Sci Rep 2019; 9:10662. [PMID: 31337863 PMCID: PMC6650397 DOI: 10.1038/s41598-019-47234-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 01/04/2019] [Accepted: 07/15/2019] [Indexed: 01/16/2023] Open
Abstract
Prostate cancer (PC) is a highly heterogenous disease and one of the leading causes of mortality in developed countries. Recently, studies have shown that expression of immune checkpoint proteins are directly or indirectly repressed by microRNAs (miRs) in many types of cancers. The great advantages of using miRs based therapy is the capacity of these short transcripts to target multiple molecules for the same- or different pathways with synergistic immune inhibition effects. miR-424 has previously been described as a biomarker of poor prognosis in different types of cancers. miR-424 is also found to target both the CTLA-4/CD80- and PD-1/PD-L1 axis. In the present study, the clinical significance of miR-424-3p expression in PC tissue was evaluated. Naïve radical prostatectomy specimens from 535 patients was used for tissue microarray construction. In situ hybridization was used to evaluate the expression of miR-424-3p and immunohistochemistry was used for CTLA-4 protein detection. In univariate- and multivariate analyses, low expression of miR-424-3p was significant associated with clinical failure-free survival, (p = 0.004) and p = 0.018 (HR:0.44, CI95% 0.22-0.87). Low expression of miR-424-3p also associated strongly with aggressive phenotype of PC. This highlight the importance of miR-424-3p as potential target for therapeutic treatment in prostate cancer.
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Affiliation(s)
- E Richardsen
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway. .,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway.
| | - S Andersen
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - S Al-Saad
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - M Rakaee
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Y Nordby
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Urology, University Hospital of North Norway, Tromso, Norway
| | - M I Pedersen
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - N Ness
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - L M Ingebriktsen
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - A Fassina
- Department of Medicine, University of Padua, 35121, Padova, Italy
| | - K A Taskén
- Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - I G Mills
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - T Donnem
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - R M Bremnes
- Translational Cancer Research Group, Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - L T Busund
- Translational Cancer Research Group, Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
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18
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Kilvaer TK, Rakaee M, Hellevik T, Vik J, Petris LD, Donnem T, Strell C, Ostman A, Busund LTR, Martinez-Zubiaurre I. Differential prognostic impact of platelet-derived growth factor receptor expression in NSCLC. Sci Rep 2019; 9:10163. [PMID: 31308421 PMCID: PMC6629689 DOI: 10.1038/s41598-019-46510-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 02/03/2019] [Accepted: 06/28/2019] [Indexed: 12/25/2022] Open
Abstract
Preclinical evidence suggests that stromal expression of platelet-derived growth factor receptors (PDGFRs) stimulates tumor development and diminishes intratumoral drug uptake. In non-small cell lung cancer (NSCLC), the clinical relevance of stromal PDGFR expression remains uncertain. Tumor specimens from 553 patients with primary operable stage I-IIIB NSCLC was obtained and tissue micro-arrays (TMA) were constructed (Norwegian cohort). Immunohistochemistry (IHC) was used to evaluate the expression of PDGFRα and -β in stromal cells and to explore their impact on patient survival. Results were validated in a non-related cohort consisting of TMAs of 367 stage I (A and B) NSCLC patients (Swedish cohort). High stromal PDGFRα expression was an independent predictor of increased survival in the overall populations and SCC (squamous cell carcinoma) subgroups of both investigated cohorts. PDGFRβ was an independent predictor of poor survival in the overall Norwegian cohort and an independent predictor of increased survival in the ADC (adenocarcinoma) subgroup of the Swedish cohort. Tumors displaying the combination PDGFRα-low/PDGFRβ-high exhibited inferior survival according to increasing stage in the Norwegian cohort. This study confirms that high stromal expression of PDGFRα is a predictor of increased survival in NSCLC. Further exploration of the prognostic impact of PDGFRβ and the relationship between PDGFRα and -β is warranted.
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Affiliation(s)
- Thomas Karsten Kilvaer
- Department of Oncology, University Hospital of North Norway, Tromso, Norway. .,Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.
| | - Mehrdad Rakaee
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Turid Hellevik
- Department of Oncology, University Hospital of North Norway, Tromso, Norway.,Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Jørg Vik
- Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Luigi De Petris
- Department of Oncology-Pathology Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden
| | - Tom Donnem
- Department of Oncology, University Hospital of North Norway, Tromso, Norway.,Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Carina Strell
- Department of Oncology-Pathology Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden
| | - Arne Ostman
- Department of Oncology-Pathology Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden
| | - Lill-Tove Rasmussen Busund
- Institute of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
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Rakaee M, Busund LTR, Jamaly S, Paulsen EE, Richardsen E, Andersen S, Al-Saad S, Bremnes RM, Donnem T, Kilvaer TK. Prognostic Value of Macrophage Phenotypes in Resectable Non-Small Cell Lung Cancer Assessed by Multiplex Immunohistochemistry. Neoplasia 2019; 21:282-293. [PMID: 30743162 PMCID: PMC6369140 DOI: 10.1016/j.neo.2019.01.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [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: 12/11/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Macrophages are important inflammatory cells that regulate innate and adaptive immunity in cancer. Tumor-associated macrophages (TAMs) are thought to differentiate into two main phenotypes: proinflammatory M1 and protumorigenic M2. Currently, the prognostic impact of TAMs and their M1 and M2 phenotypes is unclear in non–small cell cancer (NSCLC). The present study was set up to evaluate an approach for identifying common M1 and M2 macrophage markers and explore their clinical significance in NSCLC. Using multiplex chromogenic immunohistochemistry, tissue microarrays of 553 primary tumors and 143 paired metastatic lymph nodes of NSCLC specimens were stained to detect various putative macrophage phenotypes: M1 (HLA-DR/CD68), M2 (CD163/CD68), M2 (CD204/CD68), and pan-macrophage (CD68/CK). Correlation analyses were performed to examine the relationship between TAMs and adaptive/innate immune infiltrates. HLA-DR+/CD68+M1 TAM level significantly decreased from pathological stage I to III. In a compartment-specific correlation analysis, moderate to strong correlations were observed between both TAM subsets (M1 and M2) with CD3-, CD8-, CD4-, and CD45RO-positive immune cells. Survival analyses, in both stromal and intratumoral compartments, revealed that high levels of HLA-DR+/CD68+M1 (stroma, hazard ratio [HR] = 0.73, P = .03; intratumor, HR = 0.7, P = .04), CD204+M2 (stroma, HR = 0.7, P = .02; intratumor, HR = 0.6, P = .004), and CD68 (stroma, HR = 0.69, P = .02; intratumor, HR = 0.73, P = .04) infiltration were independently associated with improved NSCLC-specific survival. In lymph nodes, the intratumoral level of HLA-DR+/CD68+M1 was an independent positive prognostic indicator (Cox model, HR = 0.38, P = .001). In conclusion, high levels of M1, CD204+M2, and CD68 macrophages are independent prognosticators of prolonged survival in NSCLC.
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Affiliation(s)
- Mehrdad Rakaee
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway, 9019.
| | - Lill-Tove Rasmussen Busund
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Simin Jamaly
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway, 9019.
| | - Erna-Elise Paulsen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Oncology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Elin Richardsen
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Sigve Andersen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Oncology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Samer Al-Saad
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Roy M Bremnes
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Oncology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Tom Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Oncology, University Hospital of North Norway, Tromsø, Norway, 9019.
| | - Thomas K Kilvaer
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway, 9019; Department of Oncology, University Hospital of North Norway, Tromsø, Norway, 9019.
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20
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Rakaee M, Kilvaer TK, Dalen SM, Richardsen E, Paulsen EE, Hald SM, Al-Saad S, Andersen S, Donnem T, Bremnes RM, Busund LT. Evaluation of tumor-infiltrating lymphocytes using routine H&E slides predicts patient survival in resected non–small cell lung cancer. Hum Pathol 2018; 79:188-198. [DOI: 10.1016/j.humpath.2018.05.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/14/2018] [Accepted: 05/16/2018] [Indexed: 12/25/2022]
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21
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Kilvaer TK, Rakaee M, Hellevik T, Østman A, Strell C, Bremnes RM, Busund LT, Dønnem T, Martinez-Zubiaurre I. Tissue analyses reveal a potential immune-adjuvant function of FAP-1 positive fibroblasts in non-small cell lung cancer. PLoS One 2018; 13:e0192157. [PMID: 29415055 PMCID: PMC5802915 DOI: 10.1371/journal.pone.0192157] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/17/2018] [Indexed: 01/08/2023] Open
Abstract
Objectives Selective targeting of cancer-associated fibroblasts (CAFs) has been proposed to synergize with immune-checkpoint inhibitors. While the roles of CAFs in cancer development are well described, their immune-regulatory properties remain incompletely understood. This study investigates correlations between CAF and immune-markers in tumor stroma from non-small cell lung cancer (NSCLC) patients, and examines whether a combination of CAF and immune cell scores impact patient prognosis. Methods Tumor specimens from 536 primary operable stage I-III NSCLC patients were organized in tissue microarrays. Expression of protein-markers was evaluated by immunohistochemistry. Results Fibroblast and stromal markers PDGFRα, PDGFRβ, FAP-1 and vimentin showed weak correlations while αSMA, and Masson’s trichrome did not correlate with any of the investigated markers. Hierarchical clustering indicated the existence of different CAF-subsets. No relevant correlations were found between any CAF-marker and the immune-markers CD3, CD4, CD8, CD20, CD68, CD1a, CD56, FoxP3 and CD45RO. High density of fibroblast-activation protein positive mesenchymal cells (CAFFAP) was associated with better prognosis in tumors with high infiltration of CD8 and CD3 T-lymphocytes. Conclusions The presented data suggest that CAFs, irrespective of identity, have low influence on the degree of tumor infiltration by inflammatory- and/or immune-cells. However, CAFFAP may exert immuno-adjuvant roles in NSCLC, and targeting CAFs should be cautiously considered.
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Affiliation(s)
- Thomas Karsten Kilvaer
- Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway
- Department of Clinical Medicine, UiT The Artic University of Norway, Tromsø, Norway
| | - Mehrdad Rakaee
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Turid Hellevik
- Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway
| | - Arne Østman
- Department of Oncology-Pathology Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden
| | - Carina Strell
- Department of Oncology-Pathology Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden
| | - Roy M. Bremnes
- Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway
- Department of Clinical Medicine, UiT The Artic University of Norway, Tromsø, Norway
| | - Lill-Tove Busund
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Pathology, University Hospital of Northern Norway, Tromsø, Norway
| | - Tom Dønnem
- Department of Oncology, University Hospital of Northern Norway, Tromsø, Norway
- Department of Clinical Medicine, UiT The Artic University of Norway, Tromsø, Norway
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22
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Hald SM, Rakaee M, Martinez I, Richardsen E, Al-Saad S, Paulsen EE, Blix ES, Kilvaer T, Andersen S, Busund LT, Bremnes RM, Donnem T. LAG-3 in Non-Small-cell Lung Cancer: Expression in Primary Tumors and Metastatic Lymph Nodes Is Associated With Improved Survival. Clin Lung Cancer 2017; 19:249-259.e2. [PMID: 29396238 DOI: 10.1016/j.cllc.2017.12.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 09/03/2017] [Revised: 11/22/2017] [Accepted: 12/01/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Lymphocyte activation gene-3 (LAG-3) is an immune checkpoint receptor and a putative therapeutic target in non-small-cell lung cancer (NSCLC). We explored the prognostic effect of LAG-3+ tumor-infiltrating lymphocytes (TILs) in primary tumors and metastatic lymph nodes in NSCLC and its potential for inclusion in an immunoscore, supplementing the TNM classification. MATERIALS AND METHODS Primary tumor tissue from 553 stage I-IIIB NSCLC patients and 143 corresponding metastatic lymph nodes were collected. The expression of LAG-3 was evaluated by immunohistochemistry on tissue microarrays. RESULTS On univariate analysis, LAG-3+ TILs in the intraepithelial and stromal compartments of primary tumors and in the intraepithelial and extraepithelial compartments of metastatic lymph nodes were associated with improved disease-specific survival (DSS). On multivariate analysis, stromal LAG-3+ TILs were a significant independent predictor of improved DSS (hazard ratio [HR], 0.59; 95% confidence interval [CI], 0.43-0.82; P = .002). Stromal LAG-3+ TILs did not have prognostic impact across all pathologic stages. In the metastatic lymph nodes, intraepithelial (HR, 0.61; 95% CI, 0.38-0.99; P = .049) and extraepithelial (HR, 0.54; 95% CI, 0.29-0.70; P < .001) LAG-3+ TILs were independently associated with favorable DSS. CONCLUSION LAG-3+ TILs are an independent positive prognostic factor in stage I-IIIB NSCLC. LAG-3 in metastatic lymph nodes is a candidate marker for an immunoscore in NSCLC.
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Affiliation(s)
- Sigurd M Hald
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.
| | - Mehrdad Rakaee
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Inigo Martinez
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Elin Richardsen
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway; Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Samer Al-Saad
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway; Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Erna-Elise Paulsen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway; Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Egil Støre Blix
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway; Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Thomas Kilvaer
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway; Department of Oncology, University Hospital of North 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
| | - Lill-Tove Busund
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway; Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Roy M Bremnes
- 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
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23
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Andersen S, Richardsen E, Rakaee M, Bertilsson H, Bremnes R, Børset M, Busund LT, Slørdahl T. Expression of phosphatase of regenerating liver (PRL)-3, is independently associated with biochemical failure, clinical failure and death in prostate cancer. PLoS One 2017; 12:e0189000. [PMID: 29190795 PMCID: PMC5708709 DOI: 10.1371/journal.pone.0189000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022] Open
Abstract
Background Prostate cancer (PC) stratification needs new prognostic tools to reduce overtreatment. Phosphatase of regenerating liver (PRL-3) is a phosphatase found at high levels in several cancer types, where its expression is associated with survival. A recent PC cell line study has shown it to be involved in PC growth and migration. Methods We used a monoclonal antibody to evaluate the expression of PRL-3 in PC tissue of patients in an unselected cohort of 535 prostatectomy patients. We analyzed associations between PRL-3 expression and biochemical failure-free survival (BFFS), clinical failure-free survival (CFFS) and PC death-free survival (PCDFS). Results Cytoplasmic PRL-3 staining in tumor cells was significantly correlated to expression of molecules in the VEGFR-axis, but not to the clinicopathological variables. High PRL-3 was not significantly associated with survival in the univariate analysis for BFFS (p = 0.131), but significantly associated with CFFS (p = 0.044) and PCDFS (p = 0.041). In multivariate analysis for the various end points, PRL-3 came out as an independent and significant indicator of poor survival for BFFS (HR = 1.53, CI95% 1.10–2.13, p = 0.012), CFFS (HR = 2.41, CI95% 1.17–4.98, p = 0.017) and PCDFS (HR = 3.99, CI95% 1.21–13.1, p = 0.023). Conclusions PRL-3 is independently associated with all PC endpoints in this study. Since high PRL-3 expression also correlates with poor prognosis in other cancers and functional studies in PC support these findings, PRL-3 emerges as a potential treatment target in PC.
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Affiliation(s)
- Sigve Andersen
- Translational Cancer Research Group, Department Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway
- Department Oncology, University Hospital of North Norway, Tromso, Norway
- * E-mail:
| | - Elin Richardsen
- Translational Cancer Research Group, Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway
- Department Pathology, University Hospital of North Norway, Tromso, Norway
| | - Mehrdad Rakaee
- Translational Cancer Research Group, Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway
| | - Helena Bertilsson
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Urology, St. Olavs Hospital - Trondheim University Hospital, Trondheim, Norway
| | - Roy Bremnes
- Translational Cancer Research Group, Department Clinical Medicine, UiT, The Arctic University of Norway, Tromso, Norway
- Department Oncology, University Hospital of North Norway, Tromso, Norway
| | - Magne Børset
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Immunology and Transfusion Medicine, St. Olavs Hospital - Trondheim University Hospital, Trondheim, Norway
| | - Lill-Tove Busund
- Translational Cancer Research Group, Department of Medical Biology, UiT, The Arctic University of Norway, Tromso, Norway
- Department Pathology, University Hospital of North Norway, Tromso, Norway
| | - Tobias Slørdahl
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Hematology, St. Olavs Hospital - Trondheim University Hospital, Trondheim, Norway
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Paulsen EE, Kilvaer TK, Rakaee M, Richardsen E, Hald SM, Andersen S, Busund LT, Bremnes RM, Donnem T. CTLA-4 expression in the non-small cell lung cancer patient tumor microenvironment: diverging prognostic impact in primary tumors and lymph node metastases. Cancer Immunol Immunother 2017; 66:1449-1461. [PMID: 28707078 PMCID: PMC5645427 DOI: 10.1007/s00262-017-2039-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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: 10/30/2016] [Accepted: 07/07/2017] [Indexed: 12/11/2022]
Abstract
The immune checkpoint receptor CTLA-4 plays a crucial part in negatively regulating T cell activation and maintaining self-tolerance. It is frequently overexpressed in a variety of malignancies, yet its prognostic impact in non-small cell lung cancer (NSCLC) remains unclear. We constructed tissue microarrays from tumor tissue samples and evaluated the immunohistochemical expression of CTLA-4 in 536 patients with primary resected stage I-IIIA NSCLC. Expression of CTLA-4 was analyzed in tumor and stromal primary tumor tissue and in locoregional metastatic lymph nodes. CTLA-4 expression in neither tumor epithelial cells (T-CTLA-4) nor stromal cells (S-CTLA-4) of primary tumors was significantly associated with disease-specific survival (DSS) in all patients. However, high S-CTLA-4 expression independently predicted significantly improved DSS in the squamous cell carcinoma subgroup (HR 0.62, 95% CI 0.41-0.93, P = 0.021). In contrast, there was an independent negative prognostic impact of T-CTLA-4 expression in metastatic lymph nodes (HR 1.65, 95% CI 1.03-2.65, P = 0.039). Our results indicate that the expression of CTLA-4 has diverging prognostic impacts in metastatic NSCLC lymph nodes versus primary tumors. The presented results highlight important differences in the tumor microenvironments of primary and metastatic NSCLC tissues, and have potential to guide treatment and clinical sampling strategies.
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Affiliation(s)
- Erna-Elise Paulsen
- Department of Oncology, University Hospital of North Norway, Mailbox 13, 9038, Tromso, Norway.
- Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway.
- Translational Cancer Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9038, Tromso, Norway.
| | - Thomas K Kilvaer
- Department of Oncology, University Hospital of North Norway, Mailbox 13, 9038, Tromso, Norway
- Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Mehrdad Rakaee
- Department of Medical Biology, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Elin Richardsen
- Department of Clinical Pathology, University Hospital of North Norway, Mailbox 46, 9038, Tromso, Norway
- Department of Medical Biology, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Sigurd M Hald
- Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Sigve Andersen
- Department of Oncology, University Hospital of North Norway, Mailbox 13, 9038, Tromso, Norway
- Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Lill-Tove Busund
- Department of Clinical Pathology, University Hospital of North Norway, Mailbox 46, 9038, Tromso, Norway
- Department of Medical Biology, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Roy M Bremnes
- Department of Oncology, University Hospital of North Norway, Mailbox 13, 9038, Tromso, Norway
- Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
| | - Tom Donnem
- Department of Oncology, University Hospital of North Norway, Mailbox 13, 9038, Tromso, Norway
- Department of Clinical Medicine, UiT The Arctic University of Norway, Mailbox 6050, Langnes, 9037, Tromso, Norway
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25
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Ramberg H, Braadland PR, Stensland ME, Rakaee M, Nygård S, Øgren O, Berge V, Svindland A, Richardsson E, Souza GAD, Andersen S, Taskén KA. Abstract 2210: Scavenging for lethal prostate cancer biomarkers in FFPE tissue. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2210] [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
The aim of this study was to identify protein biomarkers that can be used to stratify indolent and aggressive prostate cancer using formalin-fixed paraffin-embedded tissue (FFPE) from radical prostatectomy specimens. The protein expression profiles of benign and malign samples from 23 patients, who had either died of prostate cancer or were alive 10 years after diagnosis, were determined using an Easy nLC1000 Nano-LC system connected to a quadrupole-Orbitrap (Q Exactive) mass spectrometer equipped with a nanoelectrospray ion source. The generated MS raw files were submitted to MaxQuant software for protein identification. Differential expression of LFQ-normalized intensities was tested by Cox proportional hazards modeling and LASSO (least absolute shrinkage and selection operator) regression analysis within the R software environment. The label free Orbitrap analysis identified 3523 unique proteins from the FFPE tissue samples. LASSO of protein expression profiles of indolent and aggressive prostate cancer tissue samples identified ten proteins which could stratify the groups. Seven of the proteins were significantly correlated with time to prostate cancer specific mortality in Cox proportional hazards modeling (p-value < 0.05). The selected proteins were found to be linked to NFkappaB signaling, cell structure, translation and metabolic pathways. Finally, proteins capable of distinguishing benign from malignant prostate tissue were identified by LASSO, and 22 of these were significantly different between the groups (Bonferroni-adjusted p-value < 0.05). Selected candidate biomarkers are currently being validated by immunohistochemical analyses of 535 radical prostatectomy specimens from two independent Norwegian cohorts with long follow-up time.
Citation Format: Håkon Ramberg, Peder R. Braadland, Maria E. Stensland, Mehrdad Rakaee, Ståle Nygård, Olov Øgren, Viktor Berge, Aud Svindland, Elin Richardsson, Gustavo A. de Souza, Sigve Andersen, Kristin A. Taskén. Scavenging for lethal prostate cancer biomarkers in FFPE tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2210. doi:10.1158/1538-7445.AM2017-2210
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Affiliation(s)
| | | | | | | | | | | | | | - Aud Svindland
- 2Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Elin Richardsson
- 5University Hospital of North Norway and University of Tromsø, Tromsø, Norway
| | | | - Sigve Andersen
- 5University Hospital of North Norway and University of Tromsø, Tromsø, Norway
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