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Nie M, Sun Z, Li N, Zhou L, Wang S, Yuan M, Chen R, Zhao L, Li J, Bai C. Genomic and T cell repertoire biomarkers associated with malignant mesothelioma survival. Thorac Cancer 2024; 15:1502-1512. [PMID: 38798202 PMCID: PMC11219294 DOI: 10.1111/1759-7714.15326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Malignant mesothelioma (MM) is an exceedingly rare tumor with poor prognosis due to the limited availability of effective treatment. Immunotherapy has emerged as a novel treatment approach for MM, but less than 40% of the patients benefit from it. Thus, it is necessary to identify accurate and effective biomarkers that can predict the overall survival (OS) and immunotherapy efficacy for MM. METHODS DNA sequencing was used to identify the genomic landscape based on the data from 86 Chinese patients. T cell receptor (TCR) sequencing was used to characterize MM TCR repertoires of 28 patients between October 2016 and April 2023. RESULTS Patients with TP53, NF2, or CDKN2A variants at the genomic level, as well as those exhibiting lower Shannon index (<6.637), lower evenness (<0.028), or higher clonality (≥0.194) according to baseline tumor tissue TCR indexes, demonstrated poorer OS. Furthermore, patients with TP53, CDKN2A, or CDKN2B variants and those with a lower evenness (<0.030) in baseline tumor tissue showed worse immunotherapy efficacy. The present study is the first to identify five special TCR Vβ-Jβ rearrangements associated with MM immunotherapy efficacy. CONCLUSIONS The present study reported the largest-scale genomic landscape and TCR repertoire of MM in Chinese patients and identified genomic and TCR biomarkers for the prognosis and immunotherapy efficacy in MM. The study results might provide new insights for prospective MM trials using specific genes, TCR indexes, and TCR clones as biomarkers and offer a reference for future antitumor drugs based on TCR-specific clones.
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Affiliation(s)
- Muwen Nie
- Department of Medical Oncology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Zhao Sun
- Department of Medical Oncology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Ningning Li
- Department of Medical Oncology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Liangrui Zhou
- Department of Pathology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | | | | | | | - Lin Zhao
- Department of Medical Oncology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Ji Li
- Department of Pathology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Chunmei Bai
- Department of Medical Oncology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
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2
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Parra ER, Zhang J, Duose DY, Gonzalez-Kozlova E, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli ML, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang HH, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst RS, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J, Haymaker C. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial. Clin Cancer Res 2024; 30:1655-1668. [PMID: 38277235 PMCID: PMC11016892 DOI: 10.1158/1078-0432.ccr-23-0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/06/2023] [Accepted: 01/24/2024] [Indexed: 01/28/2024]
Abstract
PURPOSE Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. EXPERIMENTAL DESIGN Tissue and longitudinal blood specimens from phase III trial S1400I in patients with metastatic squamous non-small cell carcinoma (SqNSCLC) treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink. RESULTS Higher immune scores from immune gene expression profiling or immune cell infiltration by mIF were associated with response to ICIs and improved survival, except regulatory T cells, which were associated with worse overall survival (OS) for patients receiving nivo+ipi. Immune cell density and closer proximity of CD8+GZB+ T cells to malignant cells were associated with superior progression-free survival and OS. The cold immune landscape of NSCLC was associated with a higher level of chromosomal copy-number variation (CNV) burden. Patients with LRP1B-mutant tumors had a shorter survival than patients with LRP1B-wild-type tumors. Olink assays revealed soluble proteins such as LAMP3 increased in responders while IL6 and CXCL13 increased in nonresponders. Upregulation of serum CXCL13, MMP12, CSF-1, and IL8 were associated with worse survival before radiologic progression. CONCLUSIONS The frequency, distribution, and clustering of immune cells relative to malignant ones can impact ICI efficacy in patients with SqNSCLC. High CNV burden may contribute to the cold immune microenvironment. Soluble inflammation/immune-related proteins in the blood have the potential to monitor therapeutic benefit from ICI treatment in patients with SqNSCLC.
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Affiliation(s)
- Edwin Roger Parra
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Yawa Duose
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mary W. Redman
- SWOG Statistical Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Hong Chen
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gayatri Kumar
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mario L. Marques-Piubelli
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caddie Laberiano-Fernandez
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frank Rojas
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Baili Zhang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Len Taing
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aashna Jhaveri
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacob Geisberg
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Altreuter
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Michor
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James Provencher
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce Yu
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ethan Cerami
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Radim Moravec
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Kasthuri Kannan
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Alatrash
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer, Houston, Texas
| | - Hsin-Hui Huang
- Precision Immunology Institute, Mount Sinai, New York, New York
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hui Xie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - Kai Nie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | - Jocelyn Harris
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Roshni Biswas
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen Van Nostrand
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Seunghee Kim-Schulze
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Roy S. Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Ignacio I. Wistuba
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Karen Kelly
- International Association for the Study of Lung Cancer, Denver, Colorado
| | - Lyudmila Bazhenova
- University of California San Diego Moores Cancer Center, La Jolla, California
| | - Sacha Gnjatic
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Chen P, Rojas FR, Hu X, Serrano A, Zhu B, Chen H, Hong L, Bandyoyadhyay R, Aminu M, Kalhor N, Lee JJ, El Hussein S, Khoury JD, Pass HI, Moreira AL, Velcheti V, Sterman DH, Fukuoka J, Tabata K, Su D, Ying L, Gibbons DL, Heymach JV, Wistuba II, Fujimoto J, Solis Soto LM, Zhang J, Wu J. Pathomic Features Reveal Immune and Molecular Evolution From Lung Preneoplasia to Invasive Adenocarcinoma. Mod Pathol 2023; 36:100326. [PMID: 37678674 PMCID: PMC10841057 DOI: 10.1016/j.modpat.2023.100326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Recent statistics on lung cancer, including the steady decline of advanced diseases and the dramatically increasing detection of early-stage diseases and indeterminate pulmonary nodules, mark the significance of a comprehensive understanding of early lung carcinogenesis. Lung adenocarcinoma (ADC) is the most common histologic subtype of lung cancer, and atypical adenomatous hyperplasia is the only recognized preneoplasia to ADC, which may progress to adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) and eventually to invasive ADC. Although molecular evolution during early lung carcinogenesis has been explored in recent years, the progress has been significantly hindered, largely due to insufficient materials from ADC precursors. Here, we employed state-of-the-art deep learning and artificial intelligence techniques to robustly segment and recognize cells on routinely used hematoxylin and eosin histopathology images and extracted 9 biology-relevant pathomic features to decode lung preneoplasia evolution. We analyzed 3 distinct cohorts (Japan, China, and United States) covering 98 patients, 162 slides, and 669 regions of interest, including 143 normal, 129 atypical adenomatous hyperplasia, 94 AIS, 98 MIA, and 205 ADC. Extracted pathomic features revealed progressive increase of atypical epithelial cells and progressive decrease of lymphocytic cells from normal to AAH, AIS, MIA, and ADC, consistent with the results from tissue-consuming and expensive molecular/immune profiling. Furthermore, pathomics analysis manifested progressively increasing cellular intratumor heterogeneity along with the evolution from normal lung to invasive ADC. These findings demonstrated the feasibility and substantial potential of pathomics in studying lung cancer carcinogenesis directly from the low-cost routine hematoxylin and eosin staining.
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Affiliation(s)
- Pingjun Chen
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Frank R Rojas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alejandra Serrano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bo Zhu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hong Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rukhmini Bandyoyadhyay
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siba El Hussein
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Joseph D Khoury
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Harvey I Pass
- Department of Surgery, NYU Langone Health, New York, New York
| | - Andre L Moreira
- Department of Pathology, NYU Langone Health, New York, New York
| | - Vamsidhar Velcheti
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Daniel H Sterman
- Department of Medicine, NYU Grossman School of Medicine, New York, New York; Department of Cardiothoracic Surgery, NYU Grossman School of Medicine, New York, New York
| | - Junya Fukuoka
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Dan Su
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Lisha Ying
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Kim T, Lim H, Jun S, Park J, Lee D, Lee JH, Lee JY, Bang D. Globally shared TCR repertoires within the tumor-infiltrating lymphocytes of patients with metastatic gynecologic cancer. Sci Rep 2023; 13:20485. [PMID: 37993659 PMCID: PMC10665396 DOI: 10.1038/s41598-023-47740-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023] Open
Abstract
Gynecologic cancer, including ovarian cancer and endometrial cancer, is characterized by morphological and molecular heterogeneity. Germline and somatic testing are available for patients to screen for pathogenic variants in genes such as BRCA1/2. Tissue expression levels of immunogenomic markers such as PD-L1 are also being used in clinical research. The basic therapeutic approach to gynecologic cancer combines surgery with chemotherapy. Immunotherapy, while not yet a mainstream treatment for gynecologic cancers, is advancing, with Dostarlimab recently receiving approval as a treatment for endometrial cancer. The goal remains to harness stimulated immune cells in the bloodstream to eradicate multiple metastases, a feat currently deemed challenging in a typical clinical setting. For the discovery of novel immunotherapy-based tumor targets, tumor-infiltrating lymphocytes (TILs) give a key insight on tumor-related immune activities by providing T cell receptor (TCR) sequences. Understanding the TCR repertoires of TILs in metastatic tissues and the circulation is important from an immunotherapy standpoint, as a subset of T cells in the blood have the potential to help kill tumor cells. To explore the relationship between distant tissue biopsy regions and blood circulation, we investigated the TCR beta chain (TCRβ) in bulk tumor and matched blood samples from 39 patients with gynecologic cancer. We found that the TCR clones of TILs at different tumor sites were globally shared within patients and had high overlap with the TCR clones in peripheral blood.
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Affiliation(s)
- Taehoon Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Soyeong Jun
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Junsik Park
- Department of Obstetrics and Gynecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Dongin Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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Chagani S, De Macedo MP, Carapeto F, Wang F, Marzese DM, Wani K, Haydu LE, Peng W, Ong GT, Warren SE, Beechem JM, Hoon DSB, Mills GB, Tetzlaff MT, Lazar AJ, Kwong LN, Davies MA. Multiplatform Analysis of Intratumoral PTEN Heterogeneity in Melanoma. J Invest Dermatol 2023; 143:1779-1787.e1. [PMID: 36871660 PMCID: PMC10475489 DOI: 10.1016/j.jid.2023.01.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/11/2023] [Accepted: 01/26/2023] [Indexed: 03/06/2023]
Abstract
Loss of protein expression of the tumor suppressor PTEN is associated with increased cancer aggressiveness, decreased tumor immune infiltration, and resistance to immune and targeted therapies in melanoma. We assessed a unique cohort of eight melanoma samples with focal loss of PTEN protein expression to understand the features and mechanisms of PTEN loss in this disease. We compared the PTEN-negative (PTEN[-]) areas to their adjacent PTEN-positive (PTEN[+]) areas using DNA sequencing, DNA methylation, RNA expression, digital spatial profiling, and immunohistochemical platforms. Variations or homozygous deletions of PTEN were identified in PTEN(-) areas that were not detected in the adjacent PTEN(+) areas in three cases (37.5%), but no clear genomic or DNA methylation basis for loss was identified in the remaining PTEN(-) samples. RNA expression data from two independent platforms identified a consistent increase in chromosome segregation gene expression in PTEN(-) versus adjacent PTEN(+) areas. Proteomic analysis showed a relative paucity of tumor-infiltrating lymphocytes in PTEN(-) versus adjacent PTEN(+) areas. The findings add to our understanding of potential molecular intratumoral heterogeneity in melanoma and the features associated with the loss of PTEN protein in this disease.
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Affiliation(s)
- Sharmeen Chagani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mariana P De Macedo
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fernando Carapeto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory, Health Research Institute of the Balearic Islands, Palma, Balearic Islands, Spain; Saint John's Cancer Institute at Saint John's Health Center, PHS, Santa Monica, California, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lauren E Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, The University of Houston, Houston, Texas, USA
| | - Giang T Ong
- NanoString Technologies, Inc, Seattle, Washington, USA
| | | | | | - Dave S B Hoon
- Saint John's Cancer Institute at Saint John's Health Center, PHS, Santa Monica, California, USA
| | - Gordon B Mills
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Michael T Tetzlaff
- Department of Pathology, The University of California at San Francisco, San Francisco, California, USA
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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MTDH antisense oligonucleotides reshape the immunosuppressive tumor microenvironment to sensitize Hepatocellular Carcinoma to immune checkpoint blockade therapy. Cancer Lett 2022; 541:215750. [DOI: 10.1016/j.canlet.2022.215750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 12/16/2022]
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Yang H, Berezowska S, Dorn P, Zens P, Chen P, Peng RW, Marti TM, Kocher GJ, Schmid RA, Hall SR. Tumor-infiltrating lymphocytes are functionally inactivated by CD90+ stromal cells and reactivated by combined Ibrutinib and Rapamycin in human pleural mesothelioma. Am J Cancer Res 2022; 12:167-185. [PMID: 34987640 PMCID: PMC8690914 DOI: 10.7150/thno.61209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
Rationale: Despite evidence suggesting that the tumor microenvironment (TME) in malignant pleural mesothelioma (MPM) is linked with poor prognosis, there is a lack of studies that functionally characterize stromal cells and tumor-infiltrating lymphocytes (TILs). Here, we aim to characterize the stromal subsets within MPM, investigate their relationship to TILs, and explore the potential therapeutic targets. Methods: We curated a core set of genes defining stromal/immune signatures expressed by mesenchymal cells within the TME using molecular analysis of The Cancer Genome Atlas (TCGA) MPM cohort. Stromal and immune profiles were molecularly characterized using flow cytometry, immunohistochemistry, microarray, and functionally evaluated using T cell-activation/expansion, coculture assays and drug compounds treatment, based on samples from an independent MPM cohort. Results: We found that a high extracellular matrix (ECM)/stromal gene signature, a high ECM score, or the ratio of ECM to an immune activation gene signature are significantly associated with poor survival in the MPM cohort in TCGA. Analysis of an independent MPM cohort (n = 12) revealed that CD8+ and CD4+ TILs were characterized by PD1 overexpression and concomitant downregulation in degranulation and CD127. This coincided with an increase in CD90+ cells that overexpressed PD-L1 and were enriched for ECM/stromal genes, activated PI3K-mTOR signaling and suppressed T cells. Protein array data demonstrated that MPM samples with high PD-L1 expression were most associated with activation of the mTOR pathway. Further, to reactivate functionally indolent TILs, we reprogrammed ex vivo TILs with Ibrutinib plus Rapamycin to block interleukin-2-inducible kinase (ITK) and mTOR pathways, respectively. The combination treatment shifted effector memory (TEM) CD8+ and CD4+ TILs towards T cells that re-expressed CD45RA (TEMRA) while concomitantly downregulating exhaustion markers. Gene expression analysis confirmed that Ibrutinib plus Rapamycin downregulated coinhibitory and T cell signature pathways while upregulating pathways involved in DNA damage and repair and immune cell adhesion and migration. Conclusions: Our results suggest that targeting the TME may represent a novel strategy to redirect the fate of endogenous TILs with the goal of restoring anti-tumor immunity and control of tumor growth in MPM.
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Jin Y, Chen Y, Tang H, Hu X, Hubert SM, Li Q, Su D, Xu H, Fan Y, Yu X, Chen Q, Liu J, Hong W, Xu Y, Deng H, Zhu D, Li P, Gong Y, Xia X, Gay CM, Zhang J, Chen M. Activation of PI3K/AKT pathway is a potential mechanism of treatment resistance in small cell lung cancer. Clin Cancer Res 2021; 28:526-539. [PMID: 34921019 DOI: 10.1158/1078-0432.ccr-21-1943] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/30/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Ying Jin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Yamei Chen
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Huarong Tang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Xiao Hu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Shawna M Hubert
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qian Li
- Geneplus-Beijing Institute, Beijing, China
| | - Dan Su
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Haimiao Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yun Fan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xinmin Yu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qixun Chen
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jinshi Liu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Wei Hong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yujin Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Huan Deng
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
| | - Dapeng Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Pansong Li
- Geneplus-Beijing Institute, Beijing, China
| | - Yuhua Gong
- Geneplus-Beijing Institute, Beijing, China
| | | | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ming Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, China
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9
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Wang E, Li Y, Ming R, Wei J, Du P, Zhou P, Zong S, Xiao H. The Prognostic Value and Immune Landscapes of a m 6A/m 5C/m 1A-Related LncRNAs Signature in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:718974. [PMID: 34917609 PMCID: PMC8670092 DOI: 10.3389/fcell.2021.718974] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Background: N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A) are the main RNA methylation modifications involved in the progression of cancer. However, it is still unclear whether m6A/m5C/m1A-related long non-coding RNAs (lncRNAs) affect the prognosis of head and neck squamous cell carcinoma (HNSCC). Methods: We summarized 52 m6A/m5C/m1A-related genes, downloaded 44 normal samples and 501 HNSCC tumor samples with RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) database, and then searched for m6A/m5C/m1A-related genes co-expressed lncRNAs. We adopt the least absolute shrinkage and selection operator (LASSO) Cox regression to obtain m6A/m5C/m1A-related lncRNAs to construct a prognostic signature of HNSCC. Results: This prognostic signature is based on six m6A/m5C/m1A-related lncRNAs (AL035587.1, AC009121.3, AF131215.5, FMR1-IT1, AC106820.5, PTOV1-AS2). It was found that the high-risk subgroup has worse overall survival (OS) than the low-risk subgroup. Moreover, the results showed that most immune checkpoint genes were significantly different between the two risk groups (p < 0.05). Immunity microenvironment analysis showed that the contents of NK cell resting, macrophages M2, and neutrophils in samples of low-risk group were significantly lower than those of high-risk group (p < 0.05), while the contents of B cells navie, plasma cells, and T cells regulatory (Tregs) were on the contrary (p < 0.05). In addition, patients with high tumor mutational burden (TMB) had the worse overall survival than those with low tumor mutational burden. Conclusion: Our study elucidated how m6A/m5C/m1A-related lncRNAs are related to the prognosis, immune microenvironment, and TMB of HNSCC. In the future, these m6A/m5C/m1A-related lncRNAs may become a new choice for immunotherapy of HNSCC.
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Affiliation(s)
- Enhao Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ruijie Ming
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Wei
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyu Du
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shimin Zong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjun Xiao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Wu W, Liu Y, Zeng S, Han Y, Shen H. Intratumor heterogeneity: the hidden barrier to immunotherapy against MSI tumors from the perspective of IFN-γ signaling and tumor-infiltrating lymphocytes. J Hematol Oncol 2021; 14:160. [PMID: 34620200 PMCID: PMC8499512 DOI: 10.1186/s13045-021-01166-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
In this era of precision medicine, with the help of biomarkers, immunotherapy has significantly improved prognosis of many patients with malignant tumor. Deficient mismatch repair (dMMR)/microsatellite instability (MSI) status is used as a biomarker in clinical practice to predict favorable response to immunotherapy and prognosis. MSI is an important characteristic which facilitates mutation and improves the likelihood of a favorable response to immunotherapy. However, many patients with dMMR/MSI still respond poorly to immunotherapies, which partly results from intratumor heterogeneity propelled by dMMR/MSI. In this review, we discuss how dMMR/MSI facilitates mutations in tumor cells and generates intratumor heterogeneity, especially through type II interferon (IFN-γ) signaling and tumor-infiltrating lymphocytes (TILs). We discuss the mechanism of immunotherapy from the perspective of dMMR/MSI, molecular pathways and TILs, and we discuss how intratumor heterogeneity hinders the therapeutic effect of immunotherapy. Finally, we summarize present techniques and strategies to look at the tumor as a whole to design personalized regimes and achieve favorable prognosis.
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Affiliation(s)
- Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China, 410008.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
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11
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Meiller C, Montagne F, Hirsch TZ, Caruso S, de Wolf J, Bayard Q, Assié JB, Meunier L, Blum Y, Quetel L, Gibault L, Pintilie E, Badoual C, Humez S, Galateau-Sallé F, Copin MC, Letouzé E, Scherpereel A, Zucman-Rossi J, Le Pimpec-Barthes F, Jaurand MC, Jean D. Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma. Genome Med 2021; 13:113. [PMID: 34261524 PMCID: PMC8281651 DOI: 10.1186/s13073-021-00931-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 06/30/2021] [Indexed: 12/23/2022] Open
Abstract
Background Malignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. This study focuses on molecular intra-tumor heterogeneity using the largest series to date in MPM and is the first to report on the multi-omics profiling of a substantial series of multi-site tumor samples. Methods Intra-tumor heterogeneity was investigated in 16 patients from whom biopsies were taken at distinct anatomical sites. The paired biopsies collected from apex, side wall, costo-diaphragmatic, or highest metabolic sites as well as 5 derived cell lines were screened using targeted sequencing. Whole exome sequencing, RNA sequencing, and DNA methylation were performed on a subset of the cohort for deep characterization. Molecular classification, recently defined histo-molecular gradients, and cell populations of the tumor microenvironment were assessed. Results Sequencing analysis identified heterogeneous variants notably in NF2, a key tumor suppressor gene of mesothelial carcinogenesis. Subclonal tumor populations were shared among paired biopsies, suggesting a polyclonal dissemination of the tumor. Transcriptome analysis highlighted dysregulation of cell adhesion and extracellular matrix pathways, linked to changes in histo-molecular gradient proportions between anatomic sites. Methylome analysis revealed the contribution of epigenetic mechanisms in two patients. Finally, significant changes in the expression of immune mediators and genes related to immunological synapse, as well as differential infiltration of immune populations in the tumor environment, were observed and led to a switch from a hot to a cold immune profile in three patients. Conclusions This comprehensive analysis reveals patient-dependent spatial intra-tumor heterogeneity at the genetic, transcriptomic, and epigenetic levels and in the immune landscape of the tumor microenvironment. Results support the need for multi-sampling for the implementation of molecular-based precision medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00931-w.
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Affiliation(s)
- Clément Meiller
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - François Montagne
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France.,Present address: Service de Chirurgie Thoracique, Hôpital Calmette, CHRU de Lille, Lille, France
| | - Theo Z Hirsch
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Julien de Wolf
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France.,Present address: Service de Chirurgie Thoracique et Transplantation Pulmonaire, Hôpital Foch, Suresnes, France
| | - Quentin Bayard
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Jean-Baptiste Assié
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France.,University Paris-Est Créteil (UPEC), CEpiA (Clinical Epidemiology and Ageing), EA 7376- IMRB, UPEC, Créteil, France.,GRC OncoThoParisEst, Service de Pneumologie, CHI Créteil, UPEC, Créteil, France
| | - Léa Meunier
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France.,Present address: IGDR UMR 6290, CNRS, Université de Rennes 1, Rennes, France
| | - Lisa Quetel
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Laure Gibault
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France.,Service d'Anatomopathologie et Cytologie, Université de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Ecaterina Pintilie
- Univ. Lille, CHU Lille, Service de Chirurgie Thoracique, Hôpital Calmette, Lille, France
| | - Cécile Badoual
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France.,Service d'Anatomopathologie et Cytologie, Université de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Sarah Humez
- Univ. Lille, CHU Lille, Institut de Pathologie, Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | | | - Marie-Christine Copin
- Univ. Lille, CHU Lille, Institut de Pathologie, Lille, France.,Present address: Département de Pathologie Cellulaire et Tissulaire, CHU d'Angers, Angers, France
| | - Eric Letouzé
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Arnaud Scherpereel
- Univ. Lille, CHU Lille, Service de Pneumologie et d'Oncologie Thoracique, unité INSERM 1189 OncoThAI, Lille, France.,Réseau National Expert pour le Mésothéliome Pleural Malin (NETMESO), Lille, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France.,Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Françoise Le Pimpec-Barthes
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France.,Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France.,Service de Chirurgie Thoracique, Hôpital Européen Georges Pompidou, Paris, France
| | - Marie-Claude Jaurand
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Didier Jean
- Centre de Recherche des Cordeliers, Inserm UMRS-1138, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France.
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12
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Yang H, Sun B, Xu K, He Y, Zhang T, Hall SRR, Tan ST, Schmid RA, Peng RW, Hu G, Yao F. Pharmaco-transcriptomic correlation analysis reveals novel responsive signatures to HDAC inhibitors and identifies Dasatinib as a synergistic interactor in small-cell lung cancer. EBioMedicine 2021; 69:103457. [PMID: 34224975 PMCID: PMC8264109 DOI: 10.1016/j.ebiom.2021.103457] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Histone acetylation/deacetylase process is one of the most studied epigenetic modifications. Histone deacetylase inhibitors (HDACis) have shown clinical benefits in haematological malignancies but failed in solid tumours due to the lack of biomarker-driven stratification. METHODS We perform integrative pharmaco-transcriptomic analysis by correlating drug response profiles of five pan-HDACis with transcriptomes of solid cancer cell lines (n=659) to systematically identify generalizable gene signatures associated with HDACis sensitivity and resistance. The established signatures are then applied to identify cancer subtypes that are potentially sensitive or resistant to HDACis, and drugs that enhance the efficacy of HDACis. Finally, the reproductivity of the established HDACis signatures is evaluated by multiple independent drug response datasets and experimental assays. FINDINGS We successfully delineate generalizable gene signatures predicting sensitivity (containing 46 genes) and resistance (containing 53 genes) to all five HDACis, with their reproductivity confirmed by multiple external sources and independent internal assays. Using the gene signatures, we identify low-grade glioma harbouring isocitrate dehydrogenase 1/2 (IDH1/2) mutation and non-YAP1-driven subsets of small-cell lung cancer (SCLC) that particularly benefit from HDACis monotherapy. Further, based on the resistance gene signature, we identify clinically-approved Dasatinib as a synthetic lethal drug with HDACi, synergizing in inducing apoptosis and reactive oxygen species on a panel of SCLC. Finally, Dasatinib significantly enhances the therapeutic efficacy of Vorinostat in SCLC xenografts. INTERPRETATION Our work establishes robust gene signatures predicting HDACis sensitivity/resistance in solid cancer and uncovers combined Dasatinib/HDACi as a synthetic lethal combination therapy for SCLC. FUNDING This work was supported by the National Natural Science Foundation of China (82072570 to F. Yao; 82002941 to B. Sun).
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Affiliation(s)
- Haitang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
| | - Beibei Sun
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Ke Xu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Yunfei He
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China, Shanghai, 200030, People's Republic of China
| | - Tuo Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Sean R R Hall
- Gillies McIndoe Research Institute, Wellington, 6242, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Wellington, 6242, New Zealand
| | - Ralph A Schmid
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008, Switzerland
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008, Switzerland
| | - Guohong Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China, Shanghai, 200030, People's Republic of China
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
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13
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Wadowski B, Bueno R, De Rienzo A. Immune Microenvironment and Genetics in Malignant Pleural Mesothelioma. Front Oncol 2021; 11:684025. [PMID: 34178677 PMCID: PMC8226027 DOI: 10.3389/fonc.2021.684025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/28/2021] [Indexed: 01/29/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive malignancy with limited therapeutic options beyond surgery and cytotoxic chemotherapy. The success of immune checkpoint inhibition has been found to correlate with expression of immune-related genes such as CD274 (PD-L1) in lung and other solid cancers. However, only a small subset of MPM patients respond to checkpoint inhibition, and this response has been varied and unpredictable across several clinical trials. Recent advances in next-generation sequencing (NGS) technology have improved our understanding of the molecular features of MPM, also with respect to its genetic signature and how this impacts the immune microenvironment. This article will review current evidence surrounding the interplay between MPM genetics, including epigenetics and transcriptomics, and the immune response.
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Affiliation(s)
- Benjamin Wadowski
- Thoracic Surgery Oncology Laboratory and the International Mesothelioma Program, Division of Thoracic and Cardiovascular Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Raphael Bueno
- Thoracic Surgery Oncology Laboratory and the International Mesothelioma Program, Division of Thoracic and Cardiovascular Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Assunta De Rienzo
- Thoracic Surgery Oncology Laboratory and the International Mesothelioma Program, Division of Thoracic and Cardiovascular Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
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14
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NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma. Cancers (Basel) 2021; 13:cancers13071561. [PMID: 33805359 PMCID: PMC8036327 DOI: 10.3390/cancers13071561] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/12/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary It is a long-held notion that loss-of-function mutations in negative regulators of the Hippo-YAP pathway, such as NF2, LATS1/2, have a similar potential to promote nuclear YAP activity, which is thought to play an essential role in the pathogenesis of MPM. Whether loss-of-function in these individual regulators uniformly affects the Hippo-YAP activity and contributes to a similar disease phenotype has not yet been revealed in MPM. Surprisingly and interestingly, we found in this study that loss-of-function in the upstream regulator NF2 of the Hippo pathway is linked to the aberrant activation of Hippo-YAP-independent signaling. More importantly, our work showed NF2 loss-of-function and dysregulated Hippo-YAP pathway define distinct MPM subsets that differ in molecular features, therapeutic implications, patients’ prognosis, and in particular, infiltrative immune signatures. Our findings in this study may be instrumental for the precise management of immunotherapy and/or targeted therapy for MPM patients. Abstract (1) Inactivation of the tumor suppressor NF2 is believed to play a major role in the pathogenesis of malignant pleural mesothelioma (MPM) by deregulating the Hippo-YAP signaling pathway. However, NF2 has functions beyond regulation of the Hippo pathway, raising the possibility that NF2 contributes to MPM via Hippo-independent mechanisms. (2) We performed weighted gene co-expression analysis (WGCNA) in transcriptomic and proteomic datasets obtained from The Cancer Gene Atlas (TCGA) MPM cohort to identify clusters of co-expressed genes highly correlated with NF2 and phospho (p)-YAP protein, surrogate markers of active Hippo signaling and YAP inactivation. The potential targets are experimentally validated using a cell viability assay. (3) MPM tumors with NF2 loss-of-function are not associated with changes in p-YAP level nor YAP/TAZ activity score, but are characterized by a deficient B-cell receptor (BCR) signaling pathway. Conversely, MPM tumors with YAP activation display exhausted CD8 T-cell-mediated immunity together with significantly upregulated PD-L1, which is validated in an independent MPM cohort, suggesting a potential benefit of immune-checkpoint inhibitors (ICI) in this patient subset. In support of this, mutations in core Hippo signaling components including LATS2, but not NF2, are independently associated with better overall survival in response to ICI in patients. Additionally, based on cancer cell line models, we show that MPM cells with a high Hippo-YAP activity are particularly sensitive to inhibitors of BCR-ABL/SRC, stratifying a unique MPM patient subset that may benefit from BCR-ABL/SRC therapies. Furthermore, we observe that NF2 physically interacts with a considerable number of proteins that are not involved in the canonical Hippo-YAP pathway, providing a possible explanation for its Hippo-independent role in MPM. Finally, survival analyses show that YAP/TAZ scores together with p-YAP protein level, but not NF2, predict the prognosis of MPM patients. (4) NF2 loss-of-function and dysregulated Hippo-YAP pathway define distinct MPM subsets that differ in their molecular features and prognosis, which has important clinical implications for precision oncology in MPM patients.
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Comment on "Heterogeneity in PD-L1 expression in malignant peritoneal mesothelioma with systemic or intraperitoneal chemotherapy". Br J Cancer 2021; 124:1177-1178. [PMID: 33339893 PMCID: PMC7961042 DOI: 10.1038/s41416-020-01214-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 01/29/2023] Open
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Yang H, Yao F, Davis PF, Tan ST, Hall SRR. CD73, Tumor Plasticity and Immune Evasion in Solid Cancers. Cancers (Basel) 2021; 13:cancers13020177. [PMID: 33430239 PMCID: PMC7825701 DOI: 10.3390/cancers13020177] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tumors are ecosystems composed of cancer cells and non-tumor stroma together in a hypoxic environment often described as wounds that do not heal. Accumulating data suggest that solid tumors hijack cellular plasticity possibly to evade detection by the immune system. CD73-mediated generation of the purine nucleoside adenosine, is an important biochemical constituent of the immunosuppressive tumor microenvironment. In this review, the association between CD73 expression and features associated with cellular plasticity involving stemness, epithelial-to-mesenchymal transition and metastasis together with immune infiltration is summarized for a wide range of solid tumor types. Our analyses demonstrate that CD73 correlates with signatures associated with cellular plasticity in solid tumors. In addition, there are strong associations between CD73 expression and type of infiltrating lymphocytes. Collectively, the observations suggest a biomarker-based stratification to identify CD73-adenosinergic rich tumors may help identify patients with solid cancers who will respond to a combinatorial strategy that includes targeting CD73. Abstract Regulatory networks controlling cellular plasticity, important during early development, can re-emerge after tissue injury and premalignant transformation. One such regulatory molecule is the cell surface ectoenzyme ecto-5′-nucleotidase that hydrolyzes the conversion of extracellular adenosine monophosphate to adenosine (eADO). Ecto-5′-nucleotidase (NT5E) or cluster of differentiation 73 (CD73), is an enzyme that is encoded by NT5E in humans. In normal tissue, CD73-mediated generation of eADO has important pleiotropic functions ranging from the promotion of cell growth and survival, to potent immunosuppression mediated through purinergic G protein-coupled adenosine receptors. Importantly, tumors also utilize several mechanisms mediated by CD73 to resist therapeutics and in particular, evade the host immune system, leading to undesired resistance to targeted therapy and immunotherapy. Tumor cell CD73 upregulation is associated with worse clinical outcomes in a variety of cancers. Emerging evidence indicates a link between tumor cell stemness with a limited host anti-tumor immune response. In this review, we provide an overview of a growing body of evidence supporting the pro-tumorigenic role of CD73 and adenosine signaling. We also discuss data that support a link between CD73 expression and tumor plasticity, contributing to dissemination as well as treatment resistance. Collectively, targeting CD73 may represent a novel treatment approach for solid cancers.
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Affiliation(s)
- Haitang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China;
- Correspondence: or (H.Y.); (S.R.R.H.); Tel.: +86-(0)-22200000 (H.Y.); +64-(0)-42820366 (S.R.R.H.)
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Paul F. Davis
- Gillies McIndoe Research Institute, Wellington 6242, New Zealand; (P.F.D.); (S.T.T.)
| | - Swee T. Tan
- Gillies McIndoe Research Institute, Wellington 6242, New Zealand; (P.F.D.); (S.T.T.)
- Wellington Regional Plastic, Maxillofacial and Burns Unit, Hutt Hospital, Lower Hutt 5010, New Zealand
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Sean R. R. Hall
- Gillies McIndoe Research Institute, Wellington 6242, New Zealand; (P.F.D.); (S.T.T.)
- Correspondence: or (H.Y.); (S.R.R.H.); Tel.: +86-(0)-22200000 (H.Y.); +64-(0)-42820366 (S.R.R.H.)
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Fernandez-Cuesta L, Mangiante L, Alcala N, Foll M. Challenges in lung and thoracic pathology: molecular advances in the classification of pleural mesotheliomas. Virchows Arch 2021; 478:73-80. [PMID: 33411030 DOI: 10.1007/s00428-020-02980-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022]
Abstract
The diagnosis and classification of malignant pleural mesothelioma (MPM) is extremely challenging; obtaining an accurate histopathological diagnosis of the different types and subtypes requires expert assessment and suitable biopsies that are not always available, which can leave doctors uncertain about the patient's diagnosis, sometimes resulting in a delay in the start of treatment. In this review, we discuss recent major advances in the molecular characterisation of MPM and their implications for histological classification. We detail what is known of the molecular landscape of MPM at the genomic, transcriptomic, and epigenomic levels, describe the similarities and dissimilarities of the multiple molecular classifications that have been proposed, and provide an overview of the current state of knowledge regarding inter- and intra-tumour heterogeneity. We also highlight the current gaps in knowledge and how addressing them would benefit classification, as well as the patients in general.
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Affiliation(s)
| | - Lise Mangiante
- Section of Genetics, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Nicolas Alcala
- Section of Genetics, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Matthieu Foll
- Section of Genetics, International Agency for Research on Cancer (IARC/WHO), Lyon, France.
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