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Traynor S, Jakobsen MK, Green TM, Komic H, Palarasah Y, Pedersen CB, Ditzel HJ, Thoren FB, Guldberg P, Gjerstorff MF. Single-cell sequencing unveils extensive intratumoral heterogeneity of cancer/testis antigen expression in melanoma and lung cancer. J Immunother Cancer 2024; 12:e008759. [PMID: 38886115 PMCID: PMC11184195 DOI: 10.1136/jitc-2023-008759] [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] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
Cancer/testis antigens (CTAs) are widely expressed in melanoma and lung cancer, emerging as promising targets for vaccination strategies and T-cell-based therapies in these malignancies. Despite recognizing the essential impact of intratumoral heterogeneity on clinical responses to immunotherapy, our understanding of intratumoral heterogeneity in CTA expression has remained limited. We employed single-cell mRNA sequencing to delineate the CTA expression profiles of cancer cells in clinically derived melanoma and lung cancer samples. Our findings reveal a high degree of intratumoral transcriptional heterogeneity in CTA expression. In melanoma, every cell expressed at least one CTA. However, most individual CTAs, including the widely used therapeutic targets NY-ESO-1 and MAGE, were confined to subpopulations of cells and were uncoordinated in their expression, resulting in mosaics of cancer cells with diverse CTA profiles. Coordinated expression was observed, however, mainly among highly structurally and evolutionarily related CTA genes. Importantly, a minor subset of CTAs, including PRAME and several members of the GAGE and MAGE-A families, were homogenously expressed in melanomas, highlighting their potential as therapeutic targets. Extensive heterogeneity in CTA expression was also observed in lung cancer. However, the frequency of CTA-positive cancer cells was notably lower and homogenously expressed CTAs were only identified in one of five tumors in this cancer type. Our findings underscore the need for careful CTA target selection in immunotherapy development and clinical testing and offer a rational framework for identifying the most promising candidates.
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Affiliation(s)
- Sofie Traynor
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mie K Jakobsen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Tina M Green
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Hana Komic
- TIMM Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Goteborg, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Goteborg, Sweden
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Christina B Pedersen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Fredrik B Thoren
- TIMM Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Goteborg, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Goteborg, Sweden
| | - Per Guldberg
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Danish Cancer Institute, Kobenhavn, Denmark
| | - Morten F Gjerstorff
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Oncology, Odense University Hospital, Odense, Denmark
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2
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Shireman JM, White Q, Ni Z, Mohanty C, Cai Y, Zhao L, Agrawal N, Gonugunta N, Wang X, Mccarthy L, Kasulabada V, Pattnaik A, Ahmed AU, Miller J, Kulwin C, Cohen-Gadol A, Payner T, Lin CT, Savage JJ, Lane B, Shiue K, Kamer A, Shah M, Iyer G, Watson G, Kendziorski C, Dey M. Genomic analysis of human brain metastases treated with stereotactic radiosurgery reveals unique signature based on treatment failure. iScience 2024; 27:109601. [PMID: 38623341 PMCID: PMC11016778 DOI: 10.1016/j.isci.2024.109601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Stereotactic radiosurgery (SRS) has been shown to be efficacious for the treatment of limited brain metastasis (BM); however, the effects of SRS on human brain metastases have yet to be studied. We performed genomic analysis on resected brain metastases from patients whose resected lesion was previously treated with SRS. Our analyses demonstrated for the first time that patients possess a distinct genomic signature based on type of treatment failure including local failure, leptomeningeal spread, and radio-necrosis. Examination of the center and peripheral edge of the tumors treated with SRS indicated differential DNA damage distribution and an enrichment for tumor suppressor mutations and DNA damage repair pathways along the peripheral edge. Furthermore, the two clinical modalities used to deliver SRS, LINAC and GK, demonstrated differential effects on the tumor landscape even between controlled primary sites. Our study provides, in human, biological evidence of differential effects of SRS across BM's.
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Affiliation(s)
- Jack M. Shireman
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Quinn White
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Zijian Ni
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Yujia Cai
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Lei Zhao
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Namita Agrawal
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nikita Gonugunta
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Xiaohu Wang
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Liam Mccarthy
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Varshitha Kasulabada
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Akshita Pattnaik
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Atique U. Ahmed
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - James Miller
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Charles Kulwin
- Goodman Campbell Brain and Spine Neurological Surgery, Indianapolis, IN, USA
| | - Aaron Cohen-Gadol
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Troy Payner
- Goodman Campbell Brain and Spine Neurological Surgery, Indianapolis, IN, USA
| | - Chih-Ta Lin
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jesse J. Savage
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Brandon Lane
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kevin Shiue
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aaron Kamer
- Department of Clinical Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mitesh Shah
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Gordon Watson
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Mahua Dey
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
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3
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Passaro A, Al Bakir M, Hamilton EG, Diehn M, André F, Roy-Chowdhuri S, Mountzios G, Wistuba II, Swanton C, Peters S. Cancer biomarkers: Emerging trends and clinical implications for personalized treatment. Cell 2024; 187:1617-1635. [PMID: 38552610 PMCID: PMC7616034 DOI: 10.1016/j.cell.2024.02.041] [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: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
The integration of cancer biomarkers into oncology has revolutionized cancer treatment, yielding remarkable advancements in cancer therapeutics and the prognosis of cancer patients. The development of personalized medicine represents a turning point and a new paradigm in cancer management, as biomarkers enable oncologists to tailor treatments based on the unique molecular profile of each patient's tumor. In this review, we discuss the scientific milestones of cancer biomarkers and explore future possibilities to improve the management of patients with solid tumors. This progress is primarily attributed to the biological characterization of cancers, advancements in testing methodologies, elucidation of the immune microenvironment, and the ability to profile circulating tumor fractions. Integrating these insights promises to continually advance the precision oncology field, fostering better patient outcomes.
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Affiliation(s)
- Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emily G Hamilton
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabrice André
- Gustave-Roussy Cancer Center, Paris Saclay University, Villejuif, France
| | - Sinchita Roy-Chowdhuri
- Department of Anatomic Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, Athens, Greece
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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4
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Enokido T, Horie M, Yoshino S, Suzuki HI, Matsuki R, Brunnström H, Micke P, Nagase T, Saito A, Miyashita N. Distinct microRNA Signature and Suppression of ZFP36L1 Define ASCL1-Positive Lung Adenocarcinoma. Mol Cancer Res 2024; 22:29-40. [PMID: 37801008 DOI: 10.1158/1541-7786.mcr-23-0229] [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: 04/03/2023] [Revised: 08/23/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
Achaete-scute family bHLH transcription factor 1 (ASCL1) is a master transcription factor involved in neuroendocrine differentiation. ASCL1 is expressed in approximately 10% of lung adenocarcinomas (LUAD) and exerts tumor-promoting effects. Here, we explored miRNA profiles in ASCL1-positive LUADs and identified several miRNAs closely associated with ASCL1 expression, including miR-375, miR-95-3p/miR-95-5p, miR-124-3p, and members of the miR-17∼92 family. Similar to small cell lung cancer, Yes1 associated transcriptional regulator (YAP1), a representative miR-375 target gene, was suppressed in ASCL1-positive LUADs. ASCL1 knockdown followed by miRNA profiling in a cell culture model further revealed that ASCL1 positively regulates miR-124-3p and members of the miR-17∼92 family. Integrative transcriptomic analyses identified ZFP36 ring finger protein like 1 (ZFP36L1) as a target gene of miR-124-3p, and IHC studies demonstrated that ASCL1-positive LUADs are associated with low ZFP36L1 protein levels. Cell culture studies showed that ectopic ZFP36L1 expression inhibits cell proliferation, survival, and cell-cycle progression. Moreover, ZFP36L1 negatively regulated several genes including E2F transcription factor 1 (E2F1) and snail family transcriptional repressor 1 (SNAI1). In conclusion, our study revealed that suppression of ZFP36L1 via ASCL1-regulated miR-124-3p could modulate gene expression, providing evidence that ASCL1-mediated regulation of miRNAs shapes molecular features of ASCL1-positive LUADs. IMPLICATIONS Our study revealed unique miRNA profiles of ASCL1-positive LUADs and identified ASCL1-regulated miRNAs with functional relevance.
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Affiliation(s)
- Takayoshi Enokido
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Horie
- Department of Molecular and Cellular Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Seiko Yoshino
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi I Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan
| | - Rei Matsuki
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hans Brunnström
- Lund University, Laboratory Medicine Region Skåne, Department of Clinical Sciences Lund, Pathology, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Naoya Miyashita
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina
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5
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Elfving H, Thurfjell V, Mattsson JSM, Backman M, Strell C, Micke P. Tumor Heterogeneity Confounds Lymphocyte Metrics in Diagnostic Lung Cancer Biopsies. Arch Pathol Lab Med 2024; 148:e18-e24. [PMID: 37382890 DOI: 10.5858/arpa.2022-0327-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 06/30/2023]
Abstract
CONTEXT.— The immune microenvironment is involved in fundamental aspects of tumorigenesis, and immune scores are now being developed for clinical diagnostics. OBJECTIVE.— To evaluate how well small diagnostic biopsies and tissue microarrays (TMAs) reflect immune cell infiltration compared to the whole tumor slide, in tissue from patients with non-small cell lung cancer. DESIGN.— A TMA was constructed comprising tissue from surgical resection specimens of 58 patients with non-small cell lung cancer, with available preoperative biopsy material. Whole sections, biopsies, and TMA were stained for the pan-T lymphocyte marker CD3 to determine densities of tumor-infiltrating lymphocytes. Immune cell infiltration was assessed semiquantitatively as well as objectively with a microscopic grid count. For 19 of the cases, RNA sequencing data were available. RESULTS.— The semiquantitative comparison of immune cell infiltration between the whole section and the biopsy displayed fair agreement (intraclass correlation coefficient [ICC], 0.29; P = .01; CI, 0.03-0.51). In contrast, the TMA showed substantial agreement compared with the whole slide (ICC, 0.64; P < .001; CI, 0.39-0.79). The grid-based method did not enhance the agreement between the different tissue materials. The comparison of CD3 RNA sequencing data with CD3 cell annotations confirmed the poor representativity of biopsies as well as the stronger correlation for the TMA cores. CONCLUSIONS.— Although overall lymphocyte infiltration is relatively well represented on TMAs, the representativity in diagnostic lung cancer biopsies is poor. This finding challenges the concept of using biopsies to establish immune scores as prognostic or predictive biomarkers for diagnostic applications.
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Affiliation(s)
- Hedvig Elfving
- From the Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Viktoria Thurfjell
- From the Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Max Backman
- From the Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Carina Strell
- From the Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- From the Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
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6
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Hikmet F, Rassy M, Backman M, Méar L, Mattsson JSM, Djureinovic D, Botling J, Brunnström H, Micke P, Lindskog C. Expression of cancer-testis antigens in the immune microenvironment of non-small cell lung cancer. Mol Oncol 2023; 17:2603-2617. [PMID: 37341056 DOI: 10.1002/1878-0261.13474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 06/22/2023] Open
Abstract
The antigenic repertoire of tumors is critical for successful anti-cancer immune response and the efficacy of immunotherapy. Cancer-testis antigens (CTAs) are targets of humoral and cellular immune reactions. We aimed to characterize CTA expression in non-small cell lung cancer (NSCLC) in the context of the immune microenvironment. Of 90 CTAs validated by RNA sequencing, eight CTAs (DPEP3, EZHIP, MAGEA4, MAGEB2, MAGEC2, PAGE1, PRAME, and TKTL1) were selected for immunohistochemical profiling in cancer tissues from 328 NSCLC patients. CTA expression was compared with immune cell densities in the tumor environment and with genomic, transcriptomic, and clinical data. Most NSCLC cases (79%) expressed at least one of the analyzed CTAs, and CTA protein expression correlated generally with RNA expression. CTA profiles were associated with immune profiles: high MAGEA4 expression was related to M2 macrophages (CD163) and regulatory T cells (FOXP3), low MAGEA4 was associated with T cells (CD3), and high EZHIP was associated with plasma cell infiltration (adj. P-value < 0.05). None of the CTAs correlated with clinical outcomes. The current study provides a comprehensive evaluation of CTAs and suggests that their association with immune cells may indicate in situ immunogenic effects. The findings support the rationale to harness CTAs as targets for immunotherapy.
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Affiliation(s)
- Feria Hikmet
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Marc Rassy
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Loren Méar
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | | | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
- Department of Medicine (Medical Oncology), Yale University School of Medicine, New Haven, CT, USA
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Hans Brunnström
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
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7
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Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS OPEN 2023; 16:9-16. [PMID: 38204702 PMCID: PMC10775106 DOI: 10.1016/j.xjon.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Cameron N. Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G. Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tetsuhiko Asao
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
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8
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Bakhshi P, Nourizadeh M, Sharifi L, Farajollahi MM, Mohsenzadegan M. Development of dendritic cell loaded MAGE-A2 long peptide; a potential target for tumor-specific T cell-mediated prostate cancer immunotherapy. Cancer Cell Int 2023; 23:270. [PMID: 37951911 PMCID: PMC10638778 DOI: 10.1186/s12935-023-03108-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the second leading cause of cancer-related deaths among men worldwide. Immunotherapy is an emerging treatment modality for cancers that harnesses the immune system's ability to eliminate tumor cells. In particular, dendritic cell (DC) vaccines, have demonstrated promise in eliciting a tumor-specific immune response. In this study, we investigated the potential of using DCs loaded with the MAGE-A2 long peptide to activate T cell cytotoxicity toward PCa cell lines. METHODS Here, we generated DCs from monocytes and thoroughly characterized their phenotypic and functional properties. Then, DCs were pulsed with MAGE-A2 long peptide (LP) as an antigen source, and monitored for their transition from immature to mature DCs by assessing the expression levels of several costimulatory and maturation molecules like CD14, HLA-DR, CD40, CD11c, CD80, CD83, CD86, and CCR7. Furthermore, the ability of MAGE-A2 -LP pulsed DCs to stimulate T cell proliferation in a mixed lymphocyte reaction (MLR) setting and induction of cytotoxic T cells (CTLs) in coculture with autologous T cells were examined. Finally, CTLs were evaluated for their capacity to produce interferon-gamma (IFN-γ) and kill PCa cell lines (PC3 and LNCaP). RESULTS The results demonstrated that the antigen-pulsed DCs exhibited a strong ability to stimulate the expansion of T cells. Moreover, the induced CTLs displayed substantial cytotoxicity against the target cells and exhibited increased IFN-γ production during activation compared to the controls. CONCLUSIONS Overall, this innovative approach proved efficacious in targeting PCa cell lines, showcasing its potential as a foundation for the development and improved PCa cancer immunotherapy.
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Affiliation(s)
- Parisa Bakhshi
- Department of Medical Biotechnology, School of Allied Medical Sciences, Iran University of Medical Sciences (IUMS), Hemmat Highway, Tehran, Iran
| | - Maryam Nourizadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Laleh Sharifi
- Uro-Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, School of Allied Medical Sciences, Iran University of Medical Sciences (IUMS), Hemmat Highway, Tehran, Iran.
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Iran University of Medical Sciences (IUMS), Hemmat Highway, Tehran, Iran.
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9
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Abelin JG, Bergstrom EJ, Rivera KD, Taylor HB, Klaeger S, Xu C, Verzani EK, Jackson White C, Woldemichael HB, Virshup M, Olive ME, Maynard M, Vartany SA, Allen JD, Phulphagar K, Harry Kane M, Rachimi S, Mani DR, Gillette MA, Satpathy S, Clauser KR, Udeshi ND, Carr SA. Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. Nat Commun 2023; 14:1851. [PMID: 37012232 PMCID: PMC10070353 DOI: 10.1038/s41467-023-37547-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.
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Affiliation(s)
- Jennifer G Abelin
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Keith D Rivera
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Hannah B Taylor
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Susan Klaeger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Charles Xu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Eva K Verzani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - C Jackson White
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Hilina B Woldemichael
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Maya Virshup
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Meagan E Olive
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Myranda Maynard
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Stephanie A Vartany
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Joseph D Allen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Kshiti Phulphagar
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Suzanna Rachimi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
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10
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Backman M, Strell C, Lindberg A, Mattsson JSM, Elfving H, Brunnström H, O'Reilly A, Bosic M, Gulyas M, Isaksson J, Botling J, Kärre K, Jirström K, Lamberg K, Pontén F, Leandersson K, Mezheyeuski A, Micke P. Spatial immunophenotyping of the tumour microenvironment in non-small cell lung cancer. Eur J Cancer 2023; 185:40-52. [PMID: 36963351 DOI: 10.1016/j.ejca.2023.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/19/2022] [Accepted: 02/12/2023] [Indexed: 03/12/2023]
Abstract
INTRODUCTION Immune cells in the tumour microenvironment are associated with prognosis and response to therapy. We aimed to comprehensively characterise the spatial immune phenotypes in the mutational and clinicopathological background of non-small cell lung cancer (NSCLC). METHODS We established a multiplexed fluorescence imaging pipeline to spatially quantify 13 immune cell subsets in 359 NSCLC cases: CD4 effector cells (CD4-Eff), CD4 regulatory cells (CD4-Treg), CD8 effector cells (CD8-Eff), CD8 regulatory cells (CD8-Treg), B-cells, natural killer cells, natural killer T-cells, M1 macrophages (M1), CD163+ myeloid cells (CD163), M2 macrophages (M2), immature dendritic cells (iDCs), mature dendritic cells (mDCs) and plasmacytoid dendritic cells (pDCs). RESULTS CD4-Eff cells, CD8-Eff cells and M1 macrophages were the most abundant immune cells invading the tumour cell compartment and indicated a patient group with a favourable prognosis in the cluster analysis. Likewise, single densities of lymphocytic subsets (CD4-Eff, CD4-Treg, CD8-Treg, B-cells and pDCs) were independently associated with longer survival. However, when these immune cells were located close to CD8-Treg cells, the favourable impact was attenuated. In the multivariable Cox regression model, including cell densities and distances, the densities of M1 and CD163 cells and distances between cells (CD8-Treg-B-cells, CD8-Eff-cancer cells and B-cells-CD4-Treg) demonstrated positive prognostic impact, whereas short M2-M1 distances were prognostically unfavourable. CONCLUSION We present a unique spatial profile of the in situ immune cell landscape in NSCLC as a publicly available data set. Cell densities and cell distances contribute independently to prognostic information on clinical outcomes, suggesting that spatial information is crucial for diagnostic use.
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Affiliation(s)
- Max Backman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Carina Strell
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Amanda Lindberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hedvig Elfving
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hans Brunnström
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Aine O'Reilly
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Martina Bosic
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Miklos Gulyas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johan Isaksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Klas Kärre
- Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Kristina Lamberg
- Department of Respiratory Medicine, Akademiska Sjukhuset, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Karin Leandersson
- Department of Translational Medicine, Lund University, Skånes University Hospital, Malmö, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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11
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Sandström Gerdtsson A, Knulst M, Botling J, Mezheyeuski A, Micke P, Ek S. Phenotypic characterization of spatial immune infiltration niches in non-small cell lung cancer. Oncoimmunology 2023; 12:2206725. [PMID: 37139184 PMCID: PMC10150622 DOI: 10.1080/2162402x.2023.2206725] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The immune microenvironment of non-small cell lung cancer (NSCLC) is heterogeneous, which impedes the prediction of response to immune checkpoint inhibitors. We have mapped the expression of 49 proteins to spatial immune niches in 33 NSCLC tumors and report key differences in phenotype and function associated with the spatial context of immune infiltration. Tumor-infiltrating leukocytes (TIL), identified in 42% of tumors, had a similar proportion of lymphocyte antigens compared to stromal leukocytes (SL) but displayed significantly higher levels of functional, mainly immune suppressive, markers including PD-L1, PD-L2, CTLA-4, B7-H3, OX40L, and IDO1. In contrast, SL expressed higher levels of the targetable T-cell activation marker CD27, which increased with a longer distance to the tumor. Correlation analysis confirmed that metabolic-driven immune regulatory mechanisms, including ARG1 and IDO1, are present in the TIL. Tertiary lymphoid structures (TLS) were identified in 30% of patients. They displayed less variation in the expression profile and with significantly higher levels of pan lymphocyte and activation markers, dendritic cells, and antigen presentation compared to other immune niches. TLS also had higher CTLA-4 expression than non-structured SL, which may indicate immune dysfunction. Neither the presence of TIL nor TLS was associated with improved clinical outcomes. The apparent discrimination in functional profiles of distinct immune niches, independent of the overall level of leukocytes, illustrates the importance of spatial profiling to deconvolute how the immune microenvironment can dictate a therapeutic response and to identify biomarkers in the context of immunomodulatory treatment.
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Affiliation(s)
- Anna Sandström Gerdtsson
- Department of Immunotechnology, CREATE Health, Lund University, Lund, Sweden
- CONTACT Anna Sandström Gerdtsson Department of Immunotechnology, CREATE Health, Lund University, Medicon Village 406, Scheelevägen 8, Lund223 87, Sweden
| | - Mattis Knulst
- Department of Immunotechnology, CREATE Health, Lund University, Lund, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sara Ek
- Department of Immunotechnology, CREATE Health, Lund University, Lund, Sweden
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12
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Thurfjell V, Micke P, Yu H, Krupar R, Svensson MA, Brunnström H, Lamberg K, Moens LNJ, Strell C, Gulyas M, Helenius G, Yoshida A, Goldmann T, Mattsson JSM. Comparison of ROS1-rearrangement detection methods in a cohort of surgically resected non-small cell lung carcinomas. Transl Lung Cancer Res 2022; 11:2477-2494. [PMID: 36636421 PMCID: PMC9830269 DOI: 10.21037/tlcr-22-504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/06/2022] [Indexed: 12/14/2022]
Abstract
Background Patients with non-small cell lung cancer (NSCLC) harboring a ROS proto-oncogene 1 (ROS1)-rearrangement respond to treatment with ROS1 inhibitors. To distinguish these rare cases, screening with immunohistochemistry (IHC) for ROS1 protein expression has been suggested. However, the reliability of such an assay and the comparability of the antibody clones has been debated. Therefore we evaluated the diagnostic performance of current detection strategies for ROS1-rearrangement in two NSCLC-patient cohorts. Methods Resected tissue samples, retrospectively collected from consecutive NSCLC-patients surgically treated at Uppsala University Hospital were incorporated into tissue microarrays [all n=676, adenocarcinomas (AC) n=401, squamous cell carcinomas (SCC) n=213, other NSCLC n=62]. ROS1-rearrangements were detected using fluorescence in situ hybridization (FISH) (Abbott Molecular; ZytoVision). In parallel, ROS1 protein expression was detected using IHC with three antibody clones (D4D6, SP384, EPMGHR2) and accuracy, sensitivity, and specificity were determined. Gene expression microarray data (Affymetrix) and RNA-sequencing data were available for a subset of patients. NanoString analyses were performed for samples with positive or ambiguous results (n=21). Results Using FISH, 2/630 (0.3% all NSCLC; 0.5% non-squamous NSCLC) cases were positive for ROS1 fusion. Additionally, nine cases demonstrated ambiguous FISH results. Using IHC, ROS1 protein expression was detected in 24/665 (3.6% all NSCLC; 5.1% non-squamous NSCLC) cases with clone D4D6, in 18/639 (2.8% all NSCLC; 3.9% non-squamous NSCLC) cases with clone SP384, and in 1/593 (0.2% all NSCLC; 0.3% non-squamous NSCLC) case with clone EPMGHR2. Elevated RNA-levels were seen in 19/369 (5.1%) cases (Affymetrix and RNA-sequencing combined). The overlap of positive results between the assays was poor. Only one of the FISH-positive cases was positive with all antibodies and demonstrated high RNA-expression. This rearrangement was confirmed in the NanoString-assay and also in the RNA-sequencing data. Other cases with high protein/RNA-expression or ambiguous FISH were negative in the NanoString-assay. Conclusions The occurrence of ROS1 fusions is low in our cohorts. The IHC assays detected the fusions, but the accuracy varied depending on the clone. The presumably false-positive and uncertain FISH results questions this method for detection of ROS1-rearrangements. Thus, when IHC is used for screening, transcript-based assays are preferable for validation in clinical diagnostics.
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Affiliation(s)
- Viktoria Thurfjell
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hui Yu
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rosemarie Krupar
- Division of Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany;,Institute of Pathology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Maria A. Svensson
- Clinical Research Center, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Hans Brunnström
- Division of Pathology, Lund University and Laboratory Medicine Region Skåne, Lund, Sweden
| | - Kristina Lamberg
- Department of Pulmonary and Allergic Diseases, Uppsala University Hospital, Uppsala, Sweden
| | - Lotte N. J. Moens
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden;,Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala, Sweden
| | - Carina Strell
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Miklos Gulyas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gisela Helenius
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Torsten Goldmann
- Division of Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany;,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany
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13
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Kurose K, Sakaeda K, Fukuda M, Sakai Y, Yamaguchi H, Takemoto S, Shimizu K, Masuda T, Nakatomi K, Kawase S, Tanaka R, Suetsugu T, Mizuno K, Hasegawa T, Atarashi Y, Irino Y, Sato T, Inoue H, Hattori N, Kanda E, Nakata M, Mukae H, Oga T, Oka M. Immune checkpoint therapy and response biomarkers in non-small-cell lung cancer: Serum NY-ESO-1 and XAGE1 antibody as predictive and monitoring markers. Adv Clin Chem 2022; 112:155-204. [PMID: 36642483 DOI: 10.1016/bs.acc.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Immune checkpoint inhibitors (ICI) are key drugs in systemic therapy for advanced non-small-cell lung cancer (NSCLC) and have recently been incorporated into neoadjuvant and adjuvant settings for surgical resection. Currently, ICI combinations with cytotoxic agents are frequently used in clinical practice, although several ICI clinical trials have failed to produce long-term clinical benefits. Unfortunately, clinical benefit is moderate and limited considering physical and financial burden. Therefore, selecting appropriate patients and regimens for ICI therapy is important, and biomarkers are necessary for their selection. Tumor PD-L1 expression is universally used as a biomarker; however, PD-L1 assays show low analytical validity and reproducibility due to the visual-scoring system by pathologists. Recent tumor immunology studies explore that neoantigens derived from somatic mutations and the collaboration between T and B cells efficiently elicit antitumor responses. This suggests that high tumor mutational burden and T-cell infiltration are predictive biomarkers. However, B cells producing antibody (Ab) remain poorly understood and analyzed as biomarkers. We found that NY-ESO-1 and XAGE1 of cancer-testis antigen frequently elicit spontaneous humoral and cellular immune responses in NSCLC. Serum Ab against these antigens were detected in approximately 25% of NSCLC patients and predicted ICI monotherapy responses. In addition, the Ab levels were decreased with tumor shrinkage after ICI therapy. Thus, NY-ESO-1 and XAGE1 Ab are potentially biomarkers predicting and monitoring response to ICI therapy. For clinical applications, a fully-automated assay system measuring the Ab was developed. Here, we review current ICI therapy, tumor immunology, and biomarkers in NSCLC, and discuss the applicability of the serum biomarkers NY-ESO-1 and XAGE1 Ab.
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Affiliation(s)
- Koji Kurose
- Department of Respiratory Medicine, Kawasaki Medical School, Okayama, Japan
| | - Kanako Sakaeda
- Central Research Laboratories, Sysmex Corporation, Hyogo, Japan
| | - Minoru Fukuda
- Cancer Treatment Center, Nagasaki Prefecture Shimabara Hospital, Nagasaki, Japan
| | - Yumiko Sakai
- Central Research Laboratories, Sysmex Corporation, Hyogo, Japan
| | - Hiroyuki Yamaguchi
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinnosuke Takemoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | - Takeshi Masuda
- Department of Respiratory Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Katsumi Nakatomi
- Department of Respiratory Medicine, NHO Ureshino Medical Center, Saga, Japan
| | - Shigeo Kawase
- Department of Respiratory Medicine, Kure Kyosai Hospital, Hiroshima, Japan
| | - Ryo Tanaka
- Department of Dermatology, Kawasaki Medical School, Okayama, Japan
| | - Takayuki Suetsugu
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Keiko Mizuno
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | | | - Yusuke Atarashi
- Central Research Laboratories, Sysmex Corporation, Hyogo, Japan
| | - Yasuhiro Irino
- Central Research Laboratories, Sysmex Corporation, Hyogo, Japan
| | - Toshiyuki Sato
- Central Research Laboratories, Sysmex Corporation, Hyogo, Japan
| | - Hiromasa Inoue
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Noboru Hattori
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, Japan
| | - Eiichiro Kanda
- Department of Medical Science, Kawasaki Medical School, Okayama, Japan
| | - Masao Nakata
- General Thoracic Surgery, Kawasaki Medical School, Okayama, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toru Oga
- Department of Respiratory Medicine, Kawasaki Medical School, Okayama, Japan
| | - Mikio Oka
- Department of Immuno-Oncology, Kawasaki Medical School, Okayama, Japan.
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14
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Yang P, Qiao Y, Meng M, Zhou Q. Cancer/Testis Antigens as Biomarker and Target for the Diagnosis, Prognosis, and Therapy of Lung Cancer. Front Oncol 2022; 12:864159. [PMID: 35574342 PMCID: PMC9092596 DOI: 10.3389/fonc.2022.864159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/17/2022] [Indexed: 11/15/2022] Open
Abstract
Lung cancer is the leading type of malignant tumour among cancer-caused death worldwide, and the 5-year survival rate of lung cancer patients is only 18%. Various oncogenes are abnormally overexpressed in lung cancer, including cancer/testis antigens (CTAs), which are restrictively expressed in the male testis but are hardly expressed in other normal tissues, if at all. CTAs are aberrantly overexpressed in various types of cancer, with more than 60 CTAs abnormally overexpressed in lung cancer. Overexpression of oncogenic CTAs drives the initiation, metastasis and progression of lung cancer, and is closely associated with poor prognosis in cancer patients. Several CTAs, such as XAGE, SPAG9 and AKAP4, have been considered as biomarkers for the diagnosis and prognostic prediction of lung cancer. More interestingly, due to the high immunogenicity and specificity of CTAs in cancer, several CTAs, including CT45, BCAP31 and ACTL8, have been targeted for developing novel therapeutics against cancer. CTA-based vaccines, chimeric antigen receptor-modified T cells (CAR-T) and small molecules have been used in lung cancer treatment in pre-clinical and early clinical trials, with encouraging results being obtained. However, there are still many hurdles to be overcome before these therapeutics can be routinely used in clinical lung cancer therapy. This review summarises the recent rapid progress in oncogenic CTAs, focusing on CTAs as biomarkers for lung cancer diagnosis and prognostic prediction, and as targets for novel anti-cancer drug discovery and lung cancer therapy. We also identify challenges and opportunities in CTA-based cancer diagnosis and treatment. Finally, we provide perspectives on the mechanisms of oncogenic CTAs in lung cancer development, and we also suggest CTAs as a new platform for lung cancer diagnosis, prognostic prediction, and novel anti-cancer drug discovery.
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Affiliation(s)
- Ping Yang
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, China
| | - Yingnan Qiao
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, China
| | - Mei Meng
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, China
| | - Quansheng Zhou
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, China.,State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,2011 Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.,National Clinical Research Center for Hematologic Diseases, The Affiliated Hospital of Soochow University, Suzhou, China
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15
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Khazan-Kost S, Cafri G, Melamed Kadosh D, Mooshayef N, Chatterji S, Dominissini D, Manor S, Zisser B, Broday L, Talalai E, Shemer A, Zadok O, Ofek E, Onn A, Admon A, Peled M. Soluble HLA peptidome of pleural effusions is a valuable source for tumor antigens. J Immunother Cancer 2022; 10:jitc-2021-003733. [PMID: 35580925 PMCID: PMC9114951 DOI: 10.1136/jitc-2021-003733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
Background Soluble human leucocyte antigen (sHLA) molecules, released into the plasma, carry their original peptide cargo and provide insight into the protein synthesis and degradation schemes of their source cells and tissues. Other body fluids, such as pleural effusions, may also contain sHLA-peptide complexes, and can potentially serve as a source of tumor antigens since these fluids are drained from the tumor microenvironment. We explored this possibility by developing a methodology for purifying and analyzing large pleural effusion sHLA class I peptidomes of patients with malignancies or benign diseases. Methods Cleared pleural fluids, cell pellets present in the pleural effusions, and the primary tumor cells cultured from cancer patients’ effusions, were used for immunoaffinity purification of the HLA molecules. The recovered HLA peptides were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and the resulting LC-MS/MS data were analyzed with the MaxQuant software tool. Selected tumor antigen peptides were tested for their immunogenicity potential with donor peripheral blood mononuclear cells (PBMCs) in an in vitro assay. Results Mass spectrometry analysis of the pleural effusions revealed 39,669 peptides attributable to 11,305 source proteins. The majority of peptides identified from the pleural effusions were defined as HLA ligands that fit the patients’ HLA consensus sequence motifs. The membranal and soluble HLA peptidomes of each individual patient correlated to each other. Additionally, soluble HLA peptidomes from the same patient, obtained at different visits to the clinic, were highly similar. Compared with benign effusions, the soluble HLA peptidomes of malignant pleural effusions were larger and included HLA peptides derived from known tumor-associated antigens, including cancer/testis antigens, lung-related proteins, and vascular endothelial growth factor pathway proteins. Selected tumor-associated antigens that were identified by the immunopeptidomics were able to successfully prime CD8+ T cells. Conclusions Pleural effusions contain sHLA-peptide complexes, and the pleural effusion HLA peptidome of patients with malignant tumors can serve as a rich source of biomarkers for tumor diagnosis and potential candidates for personalized immunotherapy.
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Affiliation(s)
- Sofia Khazan-Kost
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Gal Cafri
- Chaim Sheba Medical Center, Ramat Gan, Israel
| | | | - Navit Mooshayef
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Sumit Chatterji
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dan Dominissini
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Manor
- Ezer Mizion Bone Marrow Donor Registry, Petah Tikva, Israel
| | - Bracha Zisser
- Ezer Mizion Bone Marrow Donor Registry, Petah Tikva, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Efrosiniia Talalai
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anat Shemer
- Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oranit Zadok
- Institute of Oncology, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Ofek
- Pathology Department, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Amir Onn
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arie Admon
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Michael Peled
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel .,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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16
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Graph Based Feature Selection for Reduction of Dimensionality in Next-Generation RNA Sequencing Datasets. ALGORITHMS 2022. [DOI: 10.3390/a15010021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Analysis of high-dimensional data, with more features (p) than observations (N) (p>N), places significant demand in cost and memory computational usage attributes. Feature selection can be used to reduce the dimensionality of the data. We used a graph-based approach, principal component analysis (PCA) and recursive feature elimination to select features for classification from RNAseq datasets from two lung cancer datasets. The selected features were discretized for association rule mining where support and lift were used to generate informative rules. Our results show that the graph-based feature selection improved the performance of sequential minimal optimization (SMO) and multilayer perceptron classifiers (MLP) in both datasets. In association rule mining, features selected using the graph-based approach outperformed the other two feature-selection techniques at a support of 0.5 and lift of 2. The non-redundant rules reflect the inherent relationships between features. Biological features are usually related to functions in living systems, a relationship that cannot be deduced by feature selection and classification alone. Therefore, the graph-based feature-selection approach combined with rule mining is a suitable way of selecting and finding associations between features in high-dimensional RNAseq data.
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17
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Jenseit A, Camgöz A, Pfister SM, Kool M. EZHIP: a new piece of the puzzle towards understanding pediatric posterior fossa ependymoma. Acta Neuropathol 2022; 143:1-13. [PMID: 34762160 PMCID: PMC8732814 DOI: 10.1007/s00401-021-02382-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/14/2022]
Abstract
Ependymomas (EPN) are tumors of the central nervous system (CNS) that can arise in the supratentorial brain (ST-EPN), hindbrain or posterior fossa (PF-EPN) or anywhere in the spinal cord (SP-EPN), both in children and adults. Molecular profiling studies have identified distinct groups and subtypes in each of these anatomical compartments. In this review, we give an overview on recent findings and new insights what is driving PFA ependymomas, which is the most common group. PFA ependymomas are characterized by a young median age at diagnosis, an overall balanced genome and a bad clinical outcome (56% 10-year overall survival). Sequencing studies revealed no fusion genes or other highly recurrently mutated genes, suggesting that the disease is epigenetically driven. Indeed, recent findings have shown that the characteristic global loss of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark in PFA ependymoma is caused by aberrant expression of the enhancer of zeste homolog inhibitory protein (EZHIP) or in rare cases by H3K27M mutations, which both inhibit EZH2 thereby preventing the polycomb repressive complex 2 (PRC2) from spreading H3K27me3. We present the current status of the ongoing work on EZHIP and its essential role in the epigenetic disturbance of PFA biology. Comparisons to the oncohistone H3K27M and its role in diffuse midline glioma (DMG) are drawn, highlighting similarities but also differences between the tumor entities and underlying mechanisms. A strong focus is to point out missing information and to present directions of further research that may result in new and improved therapies for PFA ependymoma patients.
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Affiliation(s)
- Anne Jenseit
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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18
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Berner F, Niederer R, Luimstra JJ, Pop OT, Jochum AK, Purde MT, Hasan Ali O, Bomze D, Bauer J, Freudenmann LK, Marcu A, Wolfschmitt EM, Haen S, Gross T, Dubbelaar ML, Abdou MT, Baumgaertner P, Appenzeller C, Cicin-Sain C, Lenz T, Speiser DE, Ludewig B, Driessen C, Jörger M, Früh M, Jochum W, Cozzio A, Rammensee HG, Walz J, Neefjes J, Flatz L. Keratinocyte differentiation antigen-specific T cells in immune checkpoint inhibitor-treated NSCLC patients are associated with improved survival. Oncoimmunology 2021; 10:2006893. [PMID: 34858733 PMCID: PMC8632109 DOI: 10.1080/2162402x.2021.2006893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) have improved the survival of patients with non-small cell lung cancer (NSCLC) by reinvigorating tumor-specific T cell responses. However, the specificity of such T cells and the human leukocyte antigen (HLA)-associated epitopes recognized, remain elusive. In this study, we identified NSCLC T cell epitopes of recently described NSCLC-associated antigens, termed keratinocyte differentiation antigens. Epitopes of these antigens were presented by HLA-A 03:01 and HLA-C 04:01 and were associated with responses to ICI therapy. Patients with CD8+ T cell responses to these epitopes had improved overall and progression-free survival. T cells specific for such epitopes could eliminate HLA class I-matched NSCLC cells ex vivo and were enriched in patient lung tumors. The identification of novel lung cancer HLA-associated epitopes that correlate with improved ICI-dependent treatment outcomes suggests that keratinocyte-specific proteins are important tumor-associated antigens in NSCLC. These findings improve our understanding of the mechanisms of ICI therapy and may help support the development of vaccination strategies to improve ICI-based treatment of these tumors.
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Affiliation(s)
- Fiamma Berner
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Rebekka Niederer
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Jolien J Luimstra
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Oltin Tiberiu Pop
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Ann-Kristin Jochum
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Mette-Triin Purde
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Omar Hasan Ali
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David Bomze
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Eva-Maria Wolfschmitt
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sebastian Haen
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Thorben Gross
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marissa Lisa Dubbelaar
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Marie-Therese Abdou
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Petra Baumgaertner
- Department of Oncology, Ludwig Cancer Research, University of Lausanne, Switzerland
| | - Christina Appenzeller
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Caroline Cicin-Sain
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Tobias Lenz
- Research Unit Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Daniel E Speiser
- Department of Oncology, Ludwig Cancer Research, University of Lausanne, Switzerland
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christoph Driessen
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Markus Jörger
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Martin Früh
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Oncology, University of Bern, Bern, Switzerland
| | - Wolfram Jochum
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Antonio Cozzio
- Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Hans-Georg Rammensee
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Juliane Walz
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
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19
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Miyashita N, Enokido T, Horie M, Fukuda K, Urushiyama H, Strell C, Brunnström H, Micke P, Saito A, Nagase T. TGF-β-mediated epithelial-mesenchymal transition and tumor-promoting effects in CMT64 cells are reflected in the transcriptomic signature of human lung adenocarcinoma. Sci Rep 2021; 11:22380. [PMID: 34789779 PMCID: PMC8599691 DOI: 10.1038/s41598-021-01799-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/02/2021] [Indexed: 12/31/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a cellular process during which epithelial cells acquire mesenchymal phenotypes. Cancer cells undergo EMT to acquire malignant features and TGF-β is a key regulator of EMT. Here, we demonstrate for the first time that TGF-β could elicit EMT in a mouse lung adenocarcinoma cell line. TGF-β signaling activation led to cell morphological changes corresponding to EMT and enhanced the expression of mesenchymal markers and EMT-associated transcription factors in CMT64 lung cancer cells. RNA-sequencing analyses revealed that TGF-β increases expression of Tead transcription factors and an array of Tead2 target genes. TGF-β stimulation also resulted in alternative splicing of several genes including Cd44, tight junction protein 1 (Tjp1), and Cortactin (Cttn). In parallel with EMT, TGF-β enhanced cell growth of CMT64 cells and promoted tumor formation in a syngeneic transplantation model. Of clinical importance, the expression of TGF-β-induced genes identified in CMT64 cells correlated with EMT gene signatures in human lung adenocarcinoma tissue samples. Furthermore, TGF-β-induced gene enrichment was related to poor prognosis, underscoring the tumor-promoting role of TGF-β signaling in lung adenocarcinoma. Our cellular and syngeneic transplantation model would provide a simple and useful experimental tool to study the significance of TGF-β signaling and EMT.
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Affiliation(s)
- Naoya Miyashita
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Takayoshi Enokido
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masafumi Horie
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kensuke Fukuda
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hirokazu Urushiyama
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Carina Strell
- Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Hans Brunnström
- Laboratory Medicine Region Skåne, Department of Clinical Sciences Lund, Pathology, Lund University, 22185, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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20
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Benamozig O, Baudrier L, Billon P. A detection method for the capture of genomic signatures: From disease diagnosis to genome editing. Methods Enzymol 2021; 661:251-282. [PMID: 34776215 DOI: 10.1016/bs.mie.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Variations in the genetic information originate from errors during DNA replication, error-prone repair of DNA damages, or genome editing. The most common approach to detect changes in DNA sequences employs sequencing technologies. However, they remain expensive and time-consuming, limiting their utility for routine laboratory experiments. We recently developed DinucleoTidE Signature CapTure (DTECT). DTECT is a marker-free and versatile detection method that captures targeted dinucleotide signatures resulting from the digestion of genomic amplicons by the type IIS restriction enzyme AcuI. Here, we describe the DTECT protocol to identify mutations introduced by CRISPR-based precision genome editing technologies or resulting from genetic variation. DTECT enables accurate detection of mutations using basic laboratory equipment and off-the-shelf reagents with qualitative or quantitative capture of signatures.
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Affiliation(s)
- Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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21
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Single-Cell Transcriptomics Reveals the Expression of Aging- and Senescence-Associated Genes in Distinct Cancer Cell Populations. Cells 2021; 10:cells10113126. [PMID: 34831349 PMCID: PMC8623328 DOI: 10.3390/cells10113126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/31/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
The human aging process is associated with molecular changes and cellular degeneration, resulting in a significant increase in cancer incidence with age. Despite their potential correlation, the relationship between cancer- and ageing-related transcriptional changes is largely unknown. In this study, we aimed to analyze aging-associated transcriptional patterns in publicly available bulk mRNA-seq and single-cell RNA-seq (scRNA-seq) datasets for chronic myelogenous leukemia (CML), colorectal cancer (CRC), hepatocellular carcinoma (HCC), lung cancer (LC), and pancreatic ductal adenocarcinoma (PDAC). Indeed, we detected that various aging/senescence-induced genes (ASIGs) were upregulated in malignant diseases compared to healthy control samples. To elucidate the importance of ASIGs during cell development, pseudotime analyses were performed, which revealed a late enrichment of distinct cancer-specific ASIG signatures. Notably, we were able to demonstrate that all cancer entities analyzed in this study comprised cell populations expressing ASIGs. While only minor correlations were detected between ASIGs and transcriptome-wide changes in PDAC, a high proportion of ASIGs was induced in CML, CRC, HCC, and LC samples. These unique cellular subpopulations could serve as a basis for future studies on the role of aging and senescence in human malignancies.
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22
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Ouidir M, Chatterjee S, Mendola P, Zhang C, Grantz KL, Tekola-Ayele F. Placental Gene Co-expression Network for Maternal Plasma Lipids Revealed Enrichment of Inflammatory Response Pathways. Front Genet 2021; 12:681095. [PMID: 34745199 PMCID: PMC8567461 DOI: 10.3389/fgene.2021.681095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Maternal dyslipidemia during pregnancy has been associated with suboptimal fetal growth and increased cardiometabolic diseasse risk in offspring. Altered placental function driven by placental gene expression is a hypothesized mechanism underlying these associations. We tested the relationship between maternal plasma lipid concentrations and placental gene expression. Among 64 pregnant women from the NICHD Fetal Growth Studies–Singleton cohort with maternal first trimester plasma lipids we extracted RNA-Seq on placental samples obtained at birth. Placental gene co-expression networks were validated by regulatory network analysis that integrated transcription factors and gene expression, and genome-wide transcriptome analysis. Network analysis detected 24 gene co-expression modules in placenta, of which one module was correlated with total cholesterol (r = 0.27, P-value = 0.03) and LDL-C (r = 0.31, P-value = 0.01). Genes in the module (n = 39 genes) were enriched in inflammatory response pathways. Out of the 39 genes in the module, three known lipid-related genes (MPO, PGLYRP1 and LTF) and MAGEC2 were validated by the regulatory network analysis, and one known lipid-related gene (ALX4) and two germ-cell development-related genes (MAGEC2 and LUZP4) were validated by genome-wide transcriptome analysis. Placental gene expression signatures associated with unfavorable maternal lipid concentrations may be potential pathways underlying later life offspring cardiometabolic traits. Clinical Trial Registration:ClinicalTrials.gov, identifier NCT00912132.
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Affiliation(s)
- Marion Ouidir
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Suvo Chatterjee
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Pauline Mendola
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States.,Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Katherine L Grantz
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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23
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Kim J, Xu Z, Marignani PA. Single-cell RNA sequencing for the identification of early-stage lung cancer biomarkers from circulating blood. NPJ Genom Med 2021; 6:87. [PMID: 34654834 PMCID: PMC8519939 DOI: 10.1038/s41525-021-00248-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/23/2021] [Indexed: 02/07/2023] Open
Abstract
Lung cancer accounts for more than half of the new cancers diagnosed world-wide with poor survival rates. Despite the development of chemical, radiological, and immunotherapies, many patients do not benefit from these therapies, as recurrence is common. We performed single-cell RNA-sequencing (scRNA-seq) analysis using Fluidigm C1 systems to characterize human lung cancer transcriptomes at single-cell resolution. Validation of scRNA-seq differentially expressed genes (DEGs) through quantitative real time-polymerase chain reaction (qRT-PCR) found a positive correlation in fold-change values between C-X-C motif chemokine ligand 1 (CXCL1) and 2 (CXCL2) compared with bulk-cell level in 34 primary lung adenocarcinomas (LUADs) from Stage I patients. Furthermore, we discovered an inverse correlation between chemokine mRNAs, miR-532-5p, and miR-1266-3p in early-stage primary LUADs. Specially, miR-532-5p was quantifiable in plasma from the corresponding LUADs. Collectively, we identified markers of early-stage lung cancer that were validated in primary lung tumors and circulating blood.
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Affiliation(s)
- Jinhong Kim
- grid.55602.340000 0004 1936 8200Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Room 9F1, 5850 College Street, Halifax, Nova Scotia B3H1X5 Canada
| | - Zhaolin Xu
- grid.55602.340000 0004 1936 8200Department of Pathology, Faculty of Medicine, Dalhousie University, Room 734C, 5788 University Avenue, Halifax, Nova Scotia B3H1V8 Canada
| | - Paola A. Marignani
- grid.55602.340000 0004 1936 8200Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Room 9F1, 5850 College Street, Halifax, Nova Scotia B3H1X5 Canada ,grid.55602.340000 0004 1936 8200Department of Pathology, Faculty of Medicine, Dalhousie University, Room 734C, 5788 University Avenue, Halifax, Nova Scotia B3H1V8 Canada
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24
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Belousov PV. Analysis of the Repertoires of Circulating Autoantibodies' Specificities as a Tool for Identification of the Tumor-Associated Antigens: Current Problems and Solutions. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1225-1242. [PMID: 34903148 DOI: 10.1134/s0006297921100060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 06/14/2023]
Abstract
Circulating autoantibodies against tumor-associated autoantigens (TAA) may serve as valuable biomarkers for a wide range of diagnostic purposes. Modern immunology offers a large variety of methods for in-depth comparative analysis of the repertoires of circulating antibodies' antigenic specificities in health and disease. Nevertheless, this research field so far has met somewhat limited clinical success, while numerous data on the repertoires of circulating autoantibodies' specificities in cancer patients are poorly integrated into the contemporary picture of the immunological and molecular landscapes of human tumors. This review is an attempt to identify and systematize the key and essentially universal conceptual and methodological limitations of analyses of the repertoires of circulating antibodies' antigenic specificities in cancer (expression bias, redundancy of TAA repertoires, identification of natural IgG, the absence of the pathogenetically relevant context in the experimental systems used to detect TAA), as well as to discuss potential and already known methodological improvements that may significantly increase the detectability of the pathogenetically relevant and diagnostically significant bona fide TAA.
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Affiliation(s)
- Pavel V Belousov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
- National Center for Personalized Medicine of Endocrine Diseases, National Medical Research Center of Endocrinology, Ministry of Health of the Russian Federation, Moscow, 117036, Russia
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25
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Xiao MZX, Hennessey D, Iyer A, O'Keefe S, Zhang F, Sivanand A, Gniadecki R. Transcriptomic Changes During Stage Progression of Mycosis Fungoides. Br J Dermatol 2021; 186:520-531. [PMID: 34528236 DOI: 10.1111/bjd.20760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Mycosis fungoides (MF) is the most common cutaneous T cell lymphoma, which in the early patch/plaque stages runs an indolent course. However, ~25% of MF patients develop skin tumors, a hallmark of progression to the advanced stage and is associated with high mortality. The mechanisms involved in stage progression are poorly elucidated. METHODS We performed whole-transcriptome and whole-exome sequencing of malignant MF cells from skin biopsies obtained by laser-capture microdissection. We compared three types of MF lesions: early-stage plaques (ESP, n=12) as well as plaques and tumors from patients in late-stage disease (late-stage plaques [LSP], n=10, and tumors [TMR], n=15). Gene Ontology (GO) and KEGG analysis were used to determine pathway changes specific for different lesions which were linked to the recurrent somatic mutations overrepresented in MF tumors. RESULTS The key upregulated pathways during stage progression were those related to cell proliferation and survival (MEK/ERK, Akt-mTOR), Th2/Th9 signaling (IL4, STAT3, STAT5, STAT6), meiomitosis (CT45A1, CT45A3, STAG3, GTSF1, REC8) and DNA repair (PARP1, MYCN, OGG1). Principal coordinate clustering of the transcriptome revealed extensive gene expression differences between early (ESP) and advanced-stage lesions (LSP and TMR). LSP and TMR showed remarkable similarities at the level of the transcriptome, which we interpreted as evidence of cell percolation between lesions via hematogenous self-seeding. CONCLUSION Stage progression in MF is associated with Th2/Th9 polarization of malignant cells, activation of proliferation, survival, as well as increased genomic instability. Global transcriptomic changes in multiple lesions may be caused by hematogenous cell percolation between discrete skin lesions.
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Affiliation(s)
- M Z X Xiao
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
| | - D Hennessey
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
| | - A Iyer
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
| | - S O'Keefe
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
| | - F Zhang
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - A Sivanand
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
| | - R Gniadecki
- Division of Dermatology, University of Alberta, Edmonton, AB, Canada
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26
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Zhang Y, Yu X, Liu Q, Gong H, Chen AA, Zheng H, Zhong S, Li Y. SAGE1: a Potential Target Antigen for Lung Cancer T-Cell Immunotherapy. Mol Cancer Ther 2021; 20:2302-2313. [PMID: 34465596 DOI: 10.1158/1535-7163.mct-21-0203] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/17/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022]
Abstract
A fundamental understanding of cancer-specific antigens is crucial for successful T-cell immunotherapy. Sarcoma antigen 1 (SAGE1) is a cancer/testis antigen that has not yet been verified for T-cell immunotherapy applications. Here, we examined SAGE1 RNA expression and carried out IHC analyses, revealing that SAGE1 is expressed in 50% of non-small cell lung-cancer samples (n = 40). To verify the immunogenicity of SAGE1, we discovered a novel HLA-A*24:02 (HLA-A24)-restricted SAGE1 epitope (SAGE1597-606, VFSTAPPAFI) using mass spectrometry and identified SAGE1597-606-specific T-cell clones and T-cell receptors (TCR) from peripheral bloods of HLA-A24+ donors. The highest affinity TCR VF3 (KD = 4.3 μM) demonstrated the highest antitumor potency. Moreover, VF3-transduced T cells mediated the efficient killing of HLA-A24+/SAGE1+ tumor cells in vitro and effectively inhibited the growth of lung cancer xenografts in mice. Together, our data suggest that SAGE1 could be a target for T-cell immunotherapies against lung cancer, while its specific TCRs could be candidates for developing reagents to treat SAGE1+ tumors.
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Affiliation(s)
- Yajing Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Yu
- Xiangxue Pharmaceutical Co., Ltd., Guangzhou, Guangdong, China
| | - Qiuping Liu
- Xiangxue Pharmaceutical Co., Ltd., Guangzhou, Guangdong, China
| | - Haiping Gong
- Xiangxue Pharmaceutical Co., Ltd., Guangzhou, Guangdong, China
| | - An-An Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Hongjun Zheng
- Xiangxue Pharmaceutical Co., Ltd., Guangzhou, Guangdong, China
| | - Shi Zhong
- Xiangxue Pharmaceutical Co., Ltd., Guangzhou, Guangdong, China.
| | - Yi Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- University of Chinese Academy of Sciences, Beijing, China
- Xiangxue Pharmaceutical Co., Ltd., Guangzhou, Guangdong, China
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27
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Cirenajwis H, Lauss M, Planck M, Vallon-Christersson J, Staaf J. Performance of gene expression-based single sample predictors for assessment of clinicopathological subgroups and molecular subtypes in cancers: a case comparison study in non-small cell lung cancer. Brief Bioinform 2021; 21:729-740. [PMID: 30721923 PMCID: PMC7299291 DOI: 10.1093/bib/bbz008] [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: 10/09/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
The development of multigene classifiers for cancer prognosis, treatment prediction, molecular subtypes or clinicopathological groups has been a cornerstone in transcriptomic analyses of human malignancies for nearly two decades. However, many reported classifiers are critically limited by different preprocessing needs like normalization and data centering. In response, a new breed of classifiers, single sample predictors (SSPs), has emerged. SSPs classify samples in an N-of-1 fashion, relying on, e.g. gene rules comparing expression values within a sample. To date, several methods have been reported, but there is a lack of head-to-head performance comparison for typical cancer classification problems, representing an unmet methodological need in cancer bioinformatics. To resolve this need, we performed an evaluation of two SSPs [k-top-scoring pair classifier (kTSP) and absolute intrinsic molecular subtyping (AIMS)] for two case examples of different magnitude of difficulty in non-small cell lung cancer: gene expression–based classification of (i) tumor histology and (ii) molecular subtype. Through the analysis of ~2000 lung cancer samples for each case example (n = 1918 and n = 2106, respectively), we compared the performance of the methods for different sample compositions, training data set sizes, gene expression platforms and gene rule selections. Three main conclusions are drawn from the comparisons: both methods are platform independent, they select largely overlapping gene rules associated with actual underlying tumor biology and, for large training data sets, they behave interchangeably performance-wise. While SSPs like AIMS and kTSP offer new possibilities to move gene expression signatures/predictors closer to a clinical context, they are still importantly limited by the difficultness of the classification problem at hand.
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Affiliation(s)
- Helena Cirenajwis
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
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28
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Backman M, La Fleur L, Kurppa P, Djureinovic D, Elfving H, Brunnström H, Mattsson JSM, Lindberg A, Pontén V, Eltahir M, Mangsbo S, Gulyas M, Isaksson J, Jirström K, Kärre K, Leandersson K, Mezheyeuski A, Pontén F, Strell C, Lindskog C, Botling J, Micke P. Infiltration of NK and plasma cells is associated with a distinct immune subset in non-small cell lung cancer. J Pathol 2021; 255:243-256. [PMID: 34339045 DOI: 10.1002/path.5772] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/13/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022]
Abstract
Immune cells of the tumor microenvironment are central but erratic targets for immunotherapy. The aim of this study was to characterize novel patterns of immune cell infiltration in non-small cell lung cancer (NSCLC) in relation to its molecular and clinicopathologic characteristics. Lymphocytes (CD3+, CD4+, CD8+, CD20+, FOXP3+, CD45RO+), macrophages (CD163+), plasma cells (CD138+), NK cells (NKp46+), PD1+, and PD-L1+ were annotated on a tissue microarray including 357 NSCLC cases. Somatic mutations were analyzed by targeted sequencing for 82 genes and a tumor mutational load score was estimated. Transcriptomic immune patterns were established in 197 patients based on RNA sequencing data. The immune cell infiltration was variable and showed only poor association with specific mutations. The previously defined immune phenotypic patterns, desert, inflamed, and immune excluded, comprised 30, 13, and 57% of cases, respectively. Notably, mRNA immune activation and high estimated tumor mutational load were unique only for the inflamed pattern. However, in the unsupervised cluster analysis, including all immune cell markers, these conceptual patterns were only weakly reproduced. Instead, four immune classes were identified: (1) high immune cell infiltration, (2) high immune cell infiltration with abundance of CD20+ B cells, (3) low immune cell infiltration, and (4) a phenotype with an imprint of plasma cells and NK cells. This latter class was linked to better survival despite exhibiting low expression of immune response-related genes (e.g. CXCL9, GZMB, INFG, CTLA4). This compartment-specific immune cell analysis in the context of the molecular and clinical background of NSCLC reveals two previously unrecognized immune classes. A refined immune classification, including traits of the humoral and innate immune response, is important to define the immunogenic potency of NSCLC in the era of immunotherapy. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Max Backman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linnéa La Fleur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pinja Kurppa
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hedvig Elfving
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hans Brunnström
- Division of Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | | | - Amanda Lindberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Victor Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mohamed Eltahir
- Department of Pharmaceutical Bioscience, Uppsala University, Uppsala, Sweden
| | - Sara Mangsbo
- Department of Pharmaceutical Bioscience, Uppsala University, Uppsala, Sweden
| | - Miklos Gulyas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johan Isaksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund, Sweden
| | - Klas Kärre
- Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Skånes University Hospital, Malmö, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Carina Strell
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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29
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Bogatyrova O, Mattsson JSM, Ross EM, Sanderson MP, Backman M, Botling J, Brunnström H, Kurppa P, La Fleur L, Strell C, Wilm C, Zimmermann A, Esdar C, Micke P. FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response. Eur J Cancer 2021; 151:136-149. [PMID: 33984662 DOI: 10.1016/j.ejca.2021.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/11/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023]
Abstract
Amplification of fibroblast growth factor receptor 1 (FGFR1) in non-small cell lung cancer (NSCLC) has been considered as an actionable drug target. However, pan-FGFR tyrosine kinase inhibitors did not demonstrate convincing clinical efficacy in FGFR1-amplified NSCLC patients. This study aimed to characterise the molecular context of FGFR1 expression and to define biomarkers predictive of FGFR1 inhibitor response. In this study, 635 NSCLC samples were characterised for FGFR1 protein expression by immunohistochemistry and copy number gain (CNG) by in situ hybridisation (n = 298) or DNA microarray (n = 189). FGFR1 gene expression (n = 369) and immune cell profiles (n = 309) were also examined. Furthermore, gene expression, methylation and microRNA data from The Cancer Genome Atlas (TCGA) were compared. A panel of FGFR1-amplified NSCLC patient-derived xenograft (PDX) models were tested for response to the selective FGFR1 antagonist M6123. A minority of patients demonstrated FGFR1 CNG (10.5%) or increased FGFR1 mRNA (8.7%) and protein expression (4.4%). FGFR1 CNG correlated weakly with FGFR1 gene and protein expression. Tumours overexpressing FGFR1 protein were typically devoid of driver alterations (e.g. EGFR, KRAS) and showed reduced infiltration of T-lymphocytes and lower PD-L1 expression. Promoter methylation and microRNA were identified as regulators of FGFR1 expression in NSCLC and other cancers. Finally, NSCLC PDX models demonstrating FGFR1 amplification and FGFR1 protein overexpression were sensitive to M6123. The unique molecular and immune features of tumours with high FGFR1 expression provide a rationale to stratify patients in future clinical trials of FGFR1 pathway-targeting agents.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- B7-H1 Antigen/metabolism
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Female
- Gene Amplification
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mice, Inbred NOD
- Mice, SCID
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Targeted Therapy
- Receptor, Fibroblast Growth Factor, Type 1/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Tumor Microenvironment
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Olga Bogatyrova
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Johanna S M Mattsson
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Edith M Ross
- Translational Medicine, Merck KGaA, Darmstadt, Germany
| | - Michael P Sanderson
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Max Backman
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hans Brunnström
- Division of Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Pinja Kurppa
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linnéa La Fleur
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Carina Strell
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Claudia Wilm
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Astrid Zimmermann
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Christina Esdar
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Patrick Micke
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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30
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Bailey C, Black JRM, Reading JL, Litchfield K, Turajlic S, McGranahan N, Jamal-Hanjani M, Swanton C. Tracking Cancer Evolution through the Disease Course. Cancer Discov 2021; 11:916-932. [PMID: 33811124 PMCID: PMC7611362 DOI: 10.1158/2159-8290.cd-20-1559] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023]
Abstract
During cancer evolution, constituent tumor cells compete under dynamic selection pressures. Phenotypic variation can be observed as intratumor heterogeneity, which is propagated by genome instability leading to mutations, somatic copy-number alterations, and epigenomic changes. TRACERx was set up in 2014 to observe the relationship between intratumor heterogeneity and patient outcome. By integrating multiregion sequencing of primary tumors with longitudinal sampling of a prospectively recruited patient cohort, cancer evolution can be tracked from early- to late-stage disease and through therapy. Here we review some of the key features of the studies and look to the future of the field. SIGNIFICANCE: Cancers evolve and adapt to environmental challenges such as immune surveillance and treatment pressures. The TRACERx studies track cancer evolution in a clinical setting, through primary disease to recurrence. Through multiregion and longitudinal sampling, evolutionary processes have been detailed in the tumor and the immune microenvironment in non-small cell lung cancer and clear-cell renal cell carcinoma. TRACERx has revealed the potential therapeutic utility of targeting clonal neoantigens and ctDNA detection in the adjuvant setting as a minimal residual disease detection tool primed for translation into clinical trials.
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Affiliation(s)
- Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - James R M Black
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
| | - James L Reading
- Research Department of Haematology, University College London Cancer Institute, University College London, London, UK
| | - Kevin Litchfield
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, University College London Cancer Institute, University College London, London, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
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31
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Tomassen T, Kester LA, Tops BB, Driehuis E, van Noesel MM, van Ewijk R, van Gorp JM, Hulsker CC, Terwisscha-van Scheltinga SEJ, Merks HHM, Flucke U, Hiemcke-Jiwa LS. Loss of H3K27me3 occurs in a large subset of embryonal rhabdomyosarcomas: Immunohistochemical and molecular analysis of 25 cases. Ann Diagn Pathol 2021; 52:151735. [PMID: 33770660 DOI: 10.1016/j.anndiagpath.2021.151735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Loss of histone 3 lysine 27 trimethylation (H3K27me3) has been described as a diagnostic marker for malignant peripheral nerve sheath tumor (MPNST), also discriminating MPNST with rhabdomyoblastic differentiation (malignant Triton tumor) from rhabdomyosarcoma (RMS). We studied the immunohistochemical expression of H3K27me3 in embryonal RMSs (ERMSs), performed methylation profiling in order to support the diagnosis and RNA-sequencing for comparison of the transcriptome of H3K27me3-positive and -negative cases. Of the 25 ERMS patients, 17 were males and 8 were females with an age range from 1 to 67 years (median, 6 years). None were known with neurofibromatosis type 1. One patient had Li-Fraumeni syndrome. Tumor localization included paratesticular (n = 9), genitourinary (n = 6), head/neck (n = 5), retroperitoneal (n = 4) and lower arm (n = 1). Five MPNSTs served as reference group. All ERMS had classical features including a variable spindle cell component. Immunohistochemical loss (partial or complete) of H3K27me3 was detected in 18/25 cases (72%). Based on methylation profiling, 22/22 cases were classified as ERMS. Using RNA sequencing, the ERMS group (n = 14) had a distinct gene expression profile in contrast to MPNSTs, confirming that the H3K27me3 negative ERMS cases do not represent malignant Triton tumors. When comparing H3K27me3-negative and -positive ERMSs, gene set enrichment analysis revealed differential expression of genes related to histone acetylation and normal muscle function with H3K27me3 negative ERMSs being associated with acetylation. Conclusion: Loss of H3K27me3 frequently occurs in ERMSs and correlates with H3K27 acetylation. H3K27me3 is not a suitable marker to differentiate ERMS (with spindle cell features) from malignant Triton tumor.
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Affiliation(s)
- Tess Tomassen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lennart A Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Bastiaan B Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Else Driehuis
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Roelof van Ewijk
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Joost M van Gorp
- Department of Pathology, St Antonius Hospital, Nieuwegein, the Netherlands
| | | | | | - Hans H M Merks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Uta Flucke
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Laura S Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
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32
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de Jonge H, Iamele L, Maggi M, Pessino G, Scotti C. Anti-Cancer Auto-Antibodies: Roles, Applications and Open Issues. Cancers (Basel) 2021; 13:813. [PMID: 33672007 PMCID: PMC7919283 DOI: 10.3390/cancers13040813] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
Auto-antibodies are classically associated with autoimmune diseases, where they are an integral part of diagnostic panels. However, recent evidence is accumulating on the presence of auto-antibodies against single or selected panels of auto-antigens in many types of cancer. Auto-antibodies might initially represent an epiphenomenon derived from the inflammatory environment induced by the tumor. However, their effect on tumor evolution can be crucial, as is discussed in this paper. It has been demonstrated that some of these auto-antibodies can be used for early detection and cancer staging, as well as for monitoring of cancer regression during treatment and follow up. Interestingly, certain auto-antibodies were found to promote cancer progression and metastasis, while others contribute to the body's defense against it. Moreover, auto-antibodies are of a polyclonal nature, which means that often several antibodies are involved in the response to a single tumor antigen. Dissection of these antibody specificities is now possible, allowing their identification at the genetic, structural, and epitope levels. In this review, we report the evidence available on the presence of auto-antibodies in the main cancer types and discuss some of the open issues that still need to be addressed by the research community.
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Affiliation(s)
| | | | | | | | - Claudia Scotti
- Unit of Immunology and General Pathology, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (H.d.J.); (L.I.); (M.M.); (G.P.)
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33
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PD-L1 amplification is associated with an immune cell rich phenotype in squamous cell cancer of the lung. Cancer Immunol Immunother 2021; 70:2577-2587. [PMID: 33576873 PMCID: PMC8360842 DOI: 10.1007/s00262-020-02825-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022]
Abstract
Gene amplification is considered to be one responsible cause for upregulation of Programmed Death Ligand-1 (PD-L1) in non-small cell lung cancer (NSCLC) and to represent a specific molecular subgroup possibly associated with immunotherapy response. Our aim was to analyze the frequency of PD-L1 amplification, its relation to PD-L1 mRNA and protein expression, and to characterize the immune microenvironment of amplified cases. The study was based on two independent NSCLC cohorts, including 354 and 349 cases, respectively. Tissue microarrays were used to evaluate PD-L1 amplification by FISH and PD-L1 protein by immunohistochemistry. Immune infiltrates were characterized immunohistochemically by a panel of immune markers (CD3, CD4, CD8, PD-1, Foxp3, CD20, CD138, CD168, CD45RO, NKp46). Mutational status was determined by targeted sequencing. RNAseq data was available for 197 patients. PD-L1 amplification was detected in 4.5% of all evaluable cases. PD-L1 amplification correlated only weakly with mRNA and protein expression. About 37% of amplified cases were negative for PD-L1 protein. PD-L1 amplification did not show any association with the mutational status. In squamous cell cancer, PD-L1 amplified cases were enriched among patients with high tumoral immune cell infiltration and showed gene expression profiles related to immune exhaustion. In conclusion, PD-L1 amplification correlates with PD-L1 expression in squamous cell cancer and was associated with an immune cell rich tumor phenotype. The correlative findings help to understand the role of PD-L1 amplification as an important immune escape mechanism in NSCLC and suggest the need to further evaluate PD-L1 amplification as predictive biomarker for checkpoint inhibitor therapy.
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34
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Jakobsen MK, Traynor S, Stæhr M, Duijf PG, Nielsen AY, Terp MG, Pedersen CB, Guldberg P, Ditzel HJ, Gjerstorff MF. The Cancer/Testis Antigen Gene VCX2 Is Rarely Expressed in Malignancies but Can Be Epigenetically Activated Using DNA Methyltransferase and Histone Deacetylase Inhibitors. Front Oncol 2021; 10:584024. [PMID: 33634013 PMCID: PMC7900521 DOI: 10.3389/fonc.2020.584024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/14/2020] [Indexed: 01/25/2023] Open
Abstract
Identification of novel tumor-specific targets is important for the future development of immunotherapeutic strategies using genetically engineered T cells or vaccines. In this study, we characterized the expression of VCX2, a member of the VCX/Y cancer/testis antigen family, in a large panel of normal tissues and tumors from multiple cancer types using immunohistochemical staining and RNA expression data. In normal tissues, VCX2 was detected in the germ cells of the testis at all stages of maturation but not in any somatic tissues. Among malignancies, VCX2 was only found in tumors of a small subset of melanoma patients and thus rarely expressed compared to other cancer/testis antigens such as GAGE and MAGE-A. The expression of VCX2 correlated with that of other VCX/Y genes. Importantly, we found that expression of VCX2 was inversely correlated with promoter methylation and could be activated by treatment with a DNA methyltransferase inhibitor in multiple breast cancer and melanoma cell lines and a breast cancer patient-derived xenograft. The effect could be further potentiated by combining the DNA methyltransferase inhibitor with a histone deacetylase inhibitor. Our results show that the expression of VCX2 can be epigenetically induced in cancer cells and therefore could be an attractive target for immunotherapy of cancer.
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Affiliation(s)
- Mie K Jakobsen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Sofie Traynor
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mette Stæhr
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Pascal G Duijf
- Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Aaraby Y Nielsen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mikkel G Terp
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Christina B Pedersen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Per Guldberg
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Molecular Diagnostics Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
| | - Morten F Gjerstorff
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
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35
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Jamin SP, Hikmet F, Mathieu R, Jégou B, Lindskog C, Chalmel F, Primig M. Combined RNA/tissue profiling identifies novel Cancer/testis genes. Mol Oncol 2021; 15:3003-3023. [PMID: 33426787 PMCID: PMC8564638 DOI: 10.1002/1878-0261.12900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/19/2020] [Accepted: 12/24/2020] [Indexed: 11/14/2022] Open
Abstract
Cancer/Testis (CT) genes are induced in germ cells, repressed in somatic cells, and derepressed in somatic tumors, where these genes can contribute to cancer progression. CT gene identification requires data obtained using standardized protocols and technologies. This is a challenge because data for germ cells, gonads, normal somatic tissues, and a wide range of cancer samples stem from multiple sources and were generated over substantial periods of time. We carried out a GeneChip‐based RNA profiling analysis using our own data for testis and enriched germ cells, data for somatic cancers from the Expression Project for Oncology, and data for normal somatic tissues from the Gene Omnibus Repository. We identified 478 candidate loci that include known CT genes, numerous genes associated with oncogenic processes, and novel candidates that are not referenced in the Cancer/Testis Database (www.cta.lncc.br). We complemented RNA expression data at the protein level for SPESP1, GALNTL5, PDCL2, and C11orf42 using cancer tissue microarrays covering malignant tumors of breast, uterus, thyroid, and kidney, as well as published RNA profiling and immunohistochemical data provided by the Human Protein Atlas (www.proteinatlas.org). We report that combined RNA/tissue profiling identifies novel CT genes that may be of clinical interest as therapeutical targets or biomarkers. Our findings also highlight the challenges of detecting truly germ cell‐specific mRNAs and the proteins they encode in highly heterogenous testicular, somatic, and tumor tissues.
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Affiliation(s)
- Soazik P Jamin
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
| | - Romain Mathieu
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France.,Department of Urology, University Hospital, Rennes, France
| | - Bernard Jégou
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
| | - Frédéric Chalmel
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Michael Primig
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
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Abstract
Lung cancer is one of the serious malignant tumors with high morbidity and mortality due to the poor diagnosis and early metastasis. The developing nanotechnology provides novel concepts and research strategies for the lung cancer diagnosis by employing nanomaterials as diagnostic reagents to enhance diagnostic efficiency. This commentary introduces recent progress using nanoparticles for lung cancer diagnosis from two aspects of in vivo and in vitro detection. The challenges and future research perspectives are proposed at the end of the paper.
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Evaluation of NTRK immunohistochemistry as a screening method for NTRK gene fusion detection in non-small cell lung cancer. Lung Cancer 2020; 151:53-59. [PMID: 33310622 DOI: 10.1016/j.lungcan.2020.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022]
Abstract
PURPOSE The small molecule inhibitors larotrectinib and entrectinib have recently been approved as cancer agnostic drugs in patients with tumours harbouring a rearrangement of the neurotrophic tropomyosin receptor kinase (NTRK). These oncogenic fusions are estimated to occur in 0.1-3 % of non-small cell lung cancers (NSCLC). Although molecular techniques are most reliable for fusion detection, immunohistochemical analysis is considered valuable for screening. Therefore, we evaluated the newly introduced diagnostic immunohistochemical assay (clone EPR17341) on a representative NSCLC cohort. METHODS Cancer tissue from 688 clinically and molecularly extensively annotated NSCLC patients were comprised on tissue microarrays and stained with the pan-TRK antibody clone EPR17341. Positive cases were further analysed with the TruSight Tumor 170 RNA assay (Illumina). Selected cases were also tested with a NanoString NTRK fusion assay. For 199 cases, NTRK RNA expression data were available from previous RNA sequencing analysis. RESULTS Altogether, staining patterns for 617 NSCLC cases were evaluable. Of these, four cases (0.6 %) demonstrated a strong diffuse cytoplasmic and membranous staining, and seven cases a moderate staining (1.1 %). NanoString or TST170-analysis could not confirm an NTRK fusion in any of the IHC positive cases, or any of the cases with high mRNA levels. In the four cases with strong staining intensity in the tissue microarray, whole section staining revealed marked heterogeneity of NTRK protein expression. CONCLUSION The presence of NTRK fusion genes in non-small cell lung cancer is exceedingly rare. The use of the immunohistochemical NTRK assay will result in a small number of false positive cases. This should be considered when the assay is applied as a screening tool in clinical diagnostics.
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Yang L, Zhang J, Song Y, Yang G, Xu H, Li J, Guo L, Li X, Shi X, Mao B, Yang Y, Wu L, Wei J, Zhang H, Ying J, Wang Y. Genomic profile and immune microenvironment in patients with relapsed stage IA lung adenocarcinoma. Transl Oncol 2020; 14:100942. [PMID: 33221686 PMCID: PMC7689326 DOI: 10.1016/j.tranon.2020.100942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
This finding may provide a novelty insight to help elucidate the mechanisms of the relapses. Relapsed tumours from stage IA LUAD patients exhibited a weakened immune phenotype. A targeted 395-gene expression NGS assay helps assess tumour immunity.
Patients with early-stage non-small cell lung cancer (NSCLC), even stage IA, are at substantial risk of relapse and death. We explored the distinct features of molecular alterations and immune-related gene expression in Formalin-fixed paraffin-embedded (FFPE) samples from 25 relapsed patients compared with 25 non-relapsed patients through using whole-exome sequencing and an immune oncology panel RNA sequencing platform. Results showed that the chemokine, cytolytic activity and tumour-associated antigen gene signatures exhibited significantly higher expression in non-relapsed tumours from stage IA lung adenocarcinoma (LUAD) than that in relapsed tumours. Besides, Kaplan–Meier survival analysis revealed that the gene signatures of chemokines and tumour-associated antigens were significantly associated with the patients’ disease-free survival (DFS), indicating their prognostic value in early-stage LUAD. Cytolytic activity displayed a similar trend but failed to reach statistical significance. These findings revealed a weakened immune phenotype in relapsed tumours and provide valuable information for improving the treatment management of these high-risk patients. Due to the overall small patient number in this study, these differences should be further validated in a larger cohort.
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Affiliation(s)
- Lu Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jing Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yane Song
- Genecast Precision Medicine Technology Institute, Beijing 100021, China
| | - Guangjian Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Haiyan Xu
- Department of Comprehensive Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Junling Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xinying Shi
- Genecast Precision Medicine Technology Institute, Beijing 100021, China
| | - Beibei Mao
- Genecast Precision Medicine Technology Institute, Beijing 100021, China
| | - Ying Yang
- Genecast Precision Medicine Technology Institute, Beijing 100021, China
| | - Lijia Wu
- Genecast Precision Medicine Technology Institute, Beijing 100021, China
| | - Jiyu Wei
- Genecast Precision Medicine Technology Institute, Beijing 100021, China
| | - Henghui Zhang
- Genecast Precision Medicine Technology Institute, Beijing 100021, China; Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Yan Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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Staaf J, Tran L, Söderlund L, Nodin B, Jirström K, Vidarsdottir H, Planck M, Mattsson JSM, Botling J, Micke P, Brunnström H. Diagnostic Value of Insulinoma-Associated Protein 1 (INSM1) and Comparison With Established Neuroendocrine Markers in Pulmonary Cancers. Arch Pathol Lab Med 2020; 144:1075-1085. [PMID: 31913660 DOI: 10.5858/arpa.2019-0250-oa] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2019] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The diagnostic distinction of pulmonary neuroendocrine (NE) tumors from non-small cell lung carcinomas (NSCLCs) is clinically relevant for prognostication and treatment. Diagnosis is based on morphology and immunohistochemical staining. OBJECTIVE.— To determine the diagnostic value of insulinoma-associated protein 1 (INSM1), in comparison with established NE markers, in pulmonary tumors. DESIGN.— Fifty-four pulmonary NE tumors and 632 NSCLCs were stained for INSM1, CD56, chromogranin A, and synaptophysin. In a subset, gene expression data were available for analysis. Also, 419 metastases to the lungs were stained for INSM1. A literature search identified 39 additional studies with data on NE markers in lung cancers from the last 15 years. Seven of these included data on INSM1. RESULTS.— A positive INSM1 staining was seen in 39 of 54 NE tumors (72%) and 6 of 623 NSCLCs (1%). The corresponding numbers were 47 of 54 (87%) and 14 of 626 (2%) for CD56, 30 of 54 (56%) and 6 of 629 (1%) for chromogranin A, and 46 of 54 (85%) and 49 of 630 (8%) for synaptophysin, respectively. Analysis of literature data revealed that CD56 and INSM1 were the best markers for identification of high-grade NE pulmonary tumors when considering both sensitivity and specificity, while synaptophysin also showed good sensitivity. INSM1 gene expression was clearly associated with NE histology. CONCLUSIONS.— The solid data of both our and previous studies confirm the diagnostic value of INSM1 as a NE marker in pulmonary pathology. The combination of CD56 with INSM1 and/or synaptophysin should be the first-hand choice to confirm pulmonary high-grade NE tumors. INSM1 gene expression could be used to predict NE tumor histology.
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Affiliation(s)
- Johan Staaf
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (Staaf, Nodin, Jirström, Vidarsdottir, Planck, Brunnström)
| | - Lena Tran
- Department of Genetics and Pathology, Division of Laboratory Medicine, Region Skåne, Lund, Sweden (Tran, Söderlund, Jirström, Brunnström)
| | - Linnea Söderlund
- Department of Genetics and Pathology, Division of Laboratory Medicine, Region Skåne, Lund, Sweden (Tran, Söderlund, Jirström, Brunnström)
| | - Björn Nodin
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (Staaf, Nodin, Jirström, Vidarsdottir, Planck, Brunnström)
| | - Karin Jirström
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (Staaf, Nodin, Jirström, Vidarsdottir, Planck, Brunnström).,Department of Genetics and Pathology, Division of Laboratory Medicine, Region Skåne, Lund, Sweden (Tran, Söderlund, Jirström, Brunnström)
| | - Halla Vidarsdottir
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (Staaf, Nodin, Jirström, Vidarsdottir, Planck, Brunnström).,Department of Surgery, Helsingborg Hospital, Helsingborg, Sweden (Vidarsdottir)
| | - Maria Planck
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden (Planck)
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden (Mattsson, Botling, Micke)
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden (Mattsson, Botling, Micke)
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden (Mattsson, Botling, Micke)
| | - Hans Brunnström
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (Staaf, Nodin, Jirström, Vidarsdottir, Planck, Brunnström).,Department of Genetics and Pathology, Division of Laboratory Medicine, Region Skåne, Lund, Sweden (Tran, Söderlund, Jirström, Brunnström)
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Liljedahl H, Karlsson A, Oskarsdottir GN, Salomonsson A, Brunnström H, Erlingsdottir G, Jönsson M, Isaksson S, Arbajian E, Ortiz-Villalón C, Hussein A, Bergman B, Vikström A, Monsef N, Branden E, Koyi H, de Petris L, Patthey A, Behndig AF, Johansson M, Planck M, Staaf J. A gene expression-based single sample predictor of lung adenocarcinoma molecular subtype and prognosis. Int J Cancer 2020; 148:238-251. [PMID: 32745259 PMCID: PMC7689824 DOI: 10.1002/ijc.33242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Disease recurrence in surgically treated lung adenocarcinoma (AC) remains high. New approaches for risk stratification beyond tumor stage are needed. Gene expression-based AC subtypes such as the Cancer Genome Atlas Network (TCGA) terminal-respiratory unit (TRU), proximal-inflammatory (PI) and proximal-proliferative (PP) subtypes have been associated with prognosis, but show methodological limitations for robust clinical use. We aimed to derive a platform independent single sample predictor (SSP) for molecular subtype assignment and risk stratification that could function in a clinical setting. Two-class (TRU/nonTRU=SSP2) and three-class (TRU/PP/PI=SSP3) SSPs using the AIMS algorithm were trained in 1655 ACs (n = 9659 genes) from public repositories vs TCGA centroid subtypes. Validation and survival analysis were performed in 977 patients using overall survival (OS) and distant metastasis-free survival (DMFS) as endpoints. In the validation cohort, SSP2 and SSP3 showed accuracies of 0.85 and 0.81, respectively. SSPs captured relevant biology previously associated with the TCGA subtypes and were associated with prognosis. In survival analysis, OS and DMFS for cases discordantly classified between TCGA and SSP2 favored the SSP2 classification. In resected Stage I patients, SSP2 identified TRU-cases with better OS (hazard ratio [HR] = 0.30; 95% confidence interval [CI] = 0.18-0.49) and DMFS (TRU HR = 0.52; 95% CI = 0.33-0.83) independent of age, Stage IA/IB and gender. SSP2 was transformed into a NanoString nCounter assay and tested in 44 Stage I patients using RNA from formalin-fixed tissue, providing prognostic stratification (relapse-free interval, HR = 3.2; 95% CI = 1.2-8.8). In conclusion, gene expression-based SSPs can provide molecular subtype and independent prognostic information in early-stage lung ACs. SSPs may overcome critical limitations in the applicability of gene signatures in lung cancer.
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Affiliation(s)
- Helena Liljedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Gudrun N Oskarsdottir
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Annette Salomonsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Hans Brunnström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Gigja Erlingsdottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland.,Department of Laboratory Medicine, Department of Pathology, Skåne University Hospital, Malmö, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Sofi Isaksson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Elsa Arbajian
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | | | - Aziz Hussein
- Department of Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bengt Bergman
- Department of Respiratory Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Vikström
- Department of Pulmonary Medicine, University Hospital Linköping, Linköping, Sweden
| | - Nastaran Monsef
- Department of Pathology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Branden
- Respiratory Medicine Unit, Department of Medicine Solna and CMM, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Hirsh Koyi
- Respiratory Medicine Unit, Department of Medicine Solna and CMM, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Luigi de Petris
- Thoracic Oncology Unit, Karolinska University Hospital and Department Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Annika Patthey
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Annelie F Behndig
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
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Zhong S, Cui Y, Liu Q, Chen S. CAR-T cell therapy for lung cancer: a promising but challenging future. J Thorac Dis 2020; 12:4516-4521. [PMID: 32944366 PMCID: PMC7475572 DOI: 10.21037/jtd.2020.03.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/20/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Shupeng Zhong
- Department of Oncology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Treatment, Guangzhou 510080, China
| | - Yingqiang Cui
- Department of Oncology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Treatment, Guangzhou 510080, China
| | - Qian Liu
- Central Laboratory, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Treatment, Guangzhou 510080, China
| | - Size Chen
- Department of Oncology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Treatment, Guangzhou 510080, China
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42
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Zhang YP, Bao ZW, Wu JB, Chen YH, Chen JR, Xie HY, Zhou L, Wu J, Zheng SS. Cancer-Testis Gene Expression in Hepatocellular Carcinoma: Identification of Prognostic Markers and Potential Targets for Immunotherapy. Technol Cancer Res Treat 2020; 19:1533033820944274. [PMID: 32715976 PMCID: PMC7453447 DOI: 10.1177/1533033820944274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cancer-testis genes can serve as prognostic biomarkers and valuable targets for immunotherapy in multiple tumors because of their restricted expression in testis and cancer. However, their expression pattern in hepatocellular carcinoma is still not well understood. The purpose is to comprehensively characterize the cancer-testis gene expression in hepatocellular carcinoma as well as identify prognostic markers and potential targets for immunotherapy. METHODS Cancer-testis database and publicly available data sets reporting new cancer-testis genes were integrated, and then restricted them in a testis and hepatocellular carcinoma expression pattern. Pathway enrichment analysis and survival analysis were conducted to evaluate the biological function and prognostic effect of cancer-testis genes. Clustering analysis and coexpression analysis were performed to illustrate cancer-testis gene expression patterns in hepatocellular carcinoma. The association of gene expression of each cancer-testis gene to the corresponding methylation status was detected. Finally, we explored the associations between cancer-testis genes and CD8+ T-cell infiltration in hepatocellular carcinoma by TISIDB, and then validated it in an independent hepatocellular carcinoma cohort with 72 patients. RESULTS A total of 59 testis-specific genes were identified highly expressed in hepatocellular carcinoma. Pathway enrichment analysis revealed that cancer-testis genes in hepatocellular carcinoma significantly involves in the process of cell cycle regulation. Most of the cancer-testis genes were coexpressed, and cluster analysis suggested that cancer-testis gene expressed in hepatocellular carcinoma is independent of sex, hepatitis status, and histology type. We also found that demethylation might be a regulatory mechanism of cancer-testis gene expression in hepatocellular carcinoma. Survival analysis indicated that cancer-testis genes could predict the prognosis of patients with hepatocellular carcinoma. Furthermore, BUB1B was identified contributing to the resistance of CD8+ T-cell infiltration in hepatocellular carcinoma and was an independent prognostic factor both for overall survival and disease-free survival. CONCLUSIONS Our analysis enables better understanding of cancer-testis genes in hepatocellular carcinoma and provides potential targets for hepatocellular carcinoma treatment. Experimental and clinical studies are needed for further validations.
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Affiliation(s)
- Yan-Peng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Zhi-Wei Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing-Bang Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Yun-Hao Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Jun-Ru Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Hai-Yang Xie
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Shu-Sen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
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Arbajian E, Aine M, Karlsson A, Vallon-Christersson J, Brunnström H, Davidsson J, Mohlin S, Planck M, Staaf J. Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer. Cancers (Basel) 2020; 12:E2003. [PMID: 32707835 PMCID: PMC7464146 DOI: 10.3390/cancers12082003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the worldwide leading cause of death from cancer. Epigenetic modifications such as methylation and changes in chromatin accessibility are major gene regulatory mechanisms involved in tumorigenesis and cellular lineage commitment. We aimed to characterize these processes in the context of neuroendocrine (NE) lung cancer. Illumina 450K DNA methylation data were collected for 1407 lung cancers including 27 NE tumors. NE differentially methylated regions (NE-DMRs) were identified and correlated with gene expression data for 151 lung cancers and 31 human tissue entities from the Genotype-Tissue Expression (GTEx) consortium. Assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) were performed on eight lung cancer cell lines, including three NE cell lines, to identify neuroendocrine specific gene regulatory elements. We identified DMRs with methylation patterns associated with differential gene expression and an NE tumor phenotype. DMR-associated genes could further be split into six functional modules, including one highly specific gene module for NE lung cancer showing high expression in both normal and malignant brain tissue. The regulatory potential of NE-DMRs was further validated in vitro using paired ATAC- and RNA-seq and revealed both proximal and distal regulatory elements of canonical NE-marker genes such as CHGA, NCAM1, INSM1, as well as a number of novel candidate markers of NE lung cancer. Using multilevel genomic analyses of both tumor bulk tissue and lung cancer cell lines, we identified a large catalogue of gene regulatory elements related to the NE phenotype of lung cancer.
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Affiliation(s)
- Elsa Arbajian
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden; (E.A.); (M.A.); (A.K.); (J.V.-C.); (M.P.)
| | - Mattias Aine
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden; (E.A.); (M.A.); (A.K.); (J.V.-C.); (M.P.)
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, SE 22184 Lund, Sweden;
| | - Anna Karlsson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden; (E.A.); (M.A.); (A.K.); (J.V.-C.); (M.P.)
| | - Johan Vallon-Christersson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden; (E.A.); (M.A.); (A.K.); (J.V.-C.); (M.P.)
| | - Hans Brunnström
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, SE 22100 Lund, Sweden;
- Division of Genetics and Pathology, Department of Laboratory Medicine, Region Skåne, SE 22185 Lund, Sweden
| | - Josef Davidsson
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, SE 22184 Lund, Sweden;
| | - Sofie Mohlin
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, SE 22381 Lund, Sweden;
- Division of Pediatrics, Department of Clinical Sciences Lund, Lund University, SE 22185 Lund, Sweden
| | - Maria Planck
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden; (E.A.); (M.A.); (A.K.); (J.V.-C.); (M.P.)
- Department of Respiratory Medicine and Allergology, Skåne University Hospital, SE 22185 Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden; (E.A.); (M.A.); (A.K.); (J.V.-C.); (M.P.)
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44
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Hikmet F, Méar L, Edvinsson Å, Micke P, Uhlén M, Lindskog C. The protein expression profile of ACE2 in human tissues. Mol Syst Biol 2020; 16:e9610. [PMID: 32715618 PMCID: PMC7383091 DOI: 10.15252/msb.20209610] [Citation(s) in RCA: 642] [Impact Index Per Article: 160.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 01/08/2023] Open
Abstract
The novel SARS-coronavirus 2 (SARS-CoV-2) poses a global challenge on healthcare and society. For understanding the susceptibility for SARS-CoV-2 infection, the cell type-specific expression of the host cell surface receptor is necessary. The key protein suggested to be involved in host cell entry is angiotensin I converting enzyme 2 (ACE2). Here, we report the expression pattern of ACE2 across > 150 different cell types corresponding to all major human tissues and organs based on stringent immunohistochemical analysis. The results were compared with several datasets both on the mRNA and protein level. ACE2 expression was mainly observed in enterocytes, renal tubules, gallbladder, cardiomyocytes, male reproductive cells, placental trophoblasts, ductal cells, eye, and vasculature. In the respiratory system, the expression was limited, with no or only low expression in a subset of cells in a few individuals, observed by one antibody only. Our data constitute an important resource for further studies on SARS-CoV-2 host cell entry, in order to understand the biology of the disease and to aid in the development of effective treatments to the viral infection.
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Affiliation(s)
- Feria Hikmet
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Loren Méar
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Åsa Edvinsson
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Patrick Micke
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Mathias Uhlén
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH ‐ Royal Institute of TechnologyStockholmSweden
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | - Cecilia Lindskog
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
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45
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Hikmet F, Méar L, Edvinsson Å, Micke P, Uhlén M, Lindskog C. The protein expression profile of ACE2 in human tissues. Mol Syst Biol 2020. [PMID: 32715618 DOI: 10.1101/2020.03.31.016048v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
The novel SARS-coronavirus 2 (SARS-CoV-2) poses a global challenge on healthcare and society. For understanding the susceptibility for SARS-CoV-2 infection, the cell type-specific expression of the host cell surface receptor is necessary. The key protein suggested to be involved in host cell entry is angiotensin I converting enzyme 2 (ACE2). Here, we report the expression pattern of ACE2 across > 150 different cell types corresponding to all major human tissues and organs based on stringent immunohistochemical analysis. The results were compared with several datasets both on the mRNA and protein level. ACE2 expression was mainly observed in enterocytes, renal tubules, gallbladder, cardiomyocytes, male reproductive cells, placental trophoblasts, ductal cells, eye, and vasculature. In the respiratory system, the expression was limited, with no or only low expression in a subset of cells in a few individuals, observed by one antibody only. Our data constitute an important resource for further studies on SARS-CoV-2 host cell entry, in order to understand the biology of the disease and to aid in the development of effective treatments to the viral infection.
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Affiliation(s)
- Feria Hikmet
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Loren Méar
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Åsa Edvinsson
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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46
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Miyashita N, Horie M, Mikami Y, Urushiyama H, Fukuda K, Miyakawa K, Matsuzaki H, Makita K, Morishita Y, Harada H, Backman M, Lindskog C, Brunnström H, Micke P, Nagase T, Saito A. ASCL1 promotes tumor progression through cell-autonomous signaling and immune modulation in a subset of lung adenocarcinoma. Cancer Lett 2020; 489:121-132. [PMID: 32534174 DOI: 10.1016/j.canlet.2020.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 01/05/2023]
Abstract
The master regulator of neuroendocrine differentiation, achaete-scute complex homolog 1 (ASCL1) defines a subgroup of lung adenocarcinoma. However, the mechanistic role of ASCL1 in lung tumorigenesis and its relation to the immune microenvironment is principally unknown. Here, the immune landscape of ASCL1-positive lung adenocarcinomas was characterized by immunohistochemistry. Furthermore, ASCL1 was transduced in mouse lung adenocarcinoma cell lines and comparative RNA-sequencing and secretome analyses were performed. The effects of ASCL1 on tumorigenesis were explored in an orthotopic syngeneic transplantation model. ASCL1-positive lung adenocarcinomas revealed lower infiltration of CD8+, CD4+, CD20+, and FOXP3+ lymphocytes and CD163+ macrophages indicating an immune desert phenotype. Ectopic ASCL1 upregulated cyclin transcript levels, stimulated cell proliferation, and enhanced tumor growth in mice. ASCL1 suppressed secretion of chemokines, including CCL20, CXCL2, CXCL10, and CXCL16, indicating effects on immune cell trafficking. In accordance with lower lymphocytes infiltration, ASCL1-positive lung adenocarcinomas demonstrated lower abundance of CXCR3-and CCR6-expressing cells. In conclusion, ASCL1 mediates its tumor-promoting effect not only through cell-autonomous signaling but also by modulating chemokine production and immune responses. These findings suggest that ASCL1-positive tumors represent a clinically relevant lung cancer entity.
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Affiliation(s)
- Naoya Miyashita
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masafumi Horie
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Mikami
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hirokazu Urushiyama
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kensuke Fukuda
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kazuko Miyakawa
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hirotaka Matsuzaki
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kosuke Makita
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Yasuyuki Morishita
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Harada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Hans Brunnström
- Lund University, Laboratory Medicine Region Skåne, Department of Clinical Sciences Lund, Pathology, SE-22185, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Division for Health Service Promotion, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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47
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Salomonsson A, Micke P, Mattsson JSM, La Fleur L, Isaksson J, Jönsson M, Nodin B, Botling J, Uhlén M, Jirström K, Staaf J, Planck M, Brunnström H. Comprehensive analysis of RNA binding motif protein 3 (RBM3) in non-small cell lung cancer. Cancer Med 2020; 9:5609-5619. [PMID: 32491279 PMCID: PMC7402820 DOI: 10.1002/cam4.3149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/11/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023] Open
Abstract
AIMS High expression of the RNA-binding motif protein 3 (RBM3) correlates with improved prognosis in several major types of cancer. The aim of the present study was to examine the prognostic value of RBM3 protein and mRNA expression in non-small cell lung cancer (NSCLC). METHODS AND RESULTS Immunohistochemical expression of RBM3 was evaluated in surgically treated NSCLC from two independent patient populations (n = 213 and n = 306). Staining patterns were correlated with clinicopathological parameters, overall survival (OS), and recurrence-free interval (RFI). Cases with high nuclear RBM3 protein expression had a prolonged 5-year OS in both cohorts when analyzing adenocarcinomas separately (P = .02 and P = .01). RBM3 remained an independent prognostic factor for OS in multivariable analysis of cohort I (HR 0.44, 95% CI 0.21-0.90) and for RFI in cohort II (HR 0.38, 95% CI 0.22-0.74). In squamous cell carcinoma, there was instead an insignificant association to poor prognosis. Also, the expression levels of RBM3 mRNA were investigated in 2087 lung adenocarcinomas and 899 squamous cell carcinomas assembled from 13 and 8 public gene expression microarray datasets, respectively. The RBM3 mRNA levels were not clearly associated with patient outcome in either adenocarcinomas or squamous cell carcinomas. CONCLUSIONS The results from this study support that high protein expression of RBM3 is linked to improved outcome in lung adenocarcinoma.
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Affiliation(s)
- Annette Salomonsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Linnea La Fleur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Johan Isaksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden.,Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden.,Centre for Research and Development, Uppsala university/County Council of Gävleborg, Gävle, Sweden
| | - Mats Jönsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Björn Nodin
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden.,School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Maria Planck
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Respiratory medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Hans Brunnström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
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48
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Zutz A, Schölz C, Schneider S, Pierini V, Münchhoff M, Sutter K, Wittmann G, Dittmer U, Draenert R, Bogner JR, Fackler OT, Keppler OT. SERINC5 Is an Unconventional HIV Restriction Factor That Is Upregulated during Myeloid Cell Differentiation. J Innate Immun 2020; 12:399-409. [PMID: 31935717 DOI: 10.1159/000504888] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
Classical antiviral restriction factors promote cellular immunity by their ability to interfere with virus replication and induction of their expression by proinflammatory cytokines such as interferons. The serine incorporator proteins SERINC3 and SERINC5 potently reduce the infectivity of HIV-1 particles when overexpressed, and RNA interference or knockout approaches in T cells have indicated antiviral activity also of the endogenous proteins. Due to lack of reagents for detection of endogenous SERINC proteins, it is still unclear whether SERINC3/5 are expressed to functionally relevant levels in different primary target cells of HIV infection and how the expression levels of these innate immunity factors are regulated. In the current study, analysis of SERINC3/5 mRNA steady-state levels in primary lymphoid and monocyte-derived cells revealed selective induction of their expression upon differentiation of myeloid cells. Contrary to classical antiviral restriction factors, various antiviral α-interferon subtypes and proinflammatory interleukins had no effect on SERINC levels, which were also not dysregulated in CD4+ T cells and monocytes isolated from patients with chronic HIV-1 infection. Notably, HIV-1 particles produced by terminally differentiated monocyte-derived macrophages with high SERINC5 expression, but not by low-expressing monocytes, showed a Nef-dependent infectivity defect. Overall, these findings suggest endogenous expression of SERINC5 to antivirally active levels in macrophages. Our results classify SERINC5 as an unconventional HIV-1 restriction factor whose expression is specifically induced upon differentiation of cells towards the myeloid lineage.
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Affiliation(s)
- Ariane Zutz
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany,
| | - Stephanie Schneider
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Virginia Pierini
- Center for Infectious Diseases, Integrative Virology, University of Heidelberg, Heidelberg, Germany
| | - Maximilian Münchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Georg Wittmann
- Department of Transfusion Medicine, Cell Therapeutics, and Hemostaseology, Department of Anesthesiology, University Hospital Munich, Munich, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rika Draenert
- Division of Infectious Diseases, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| | - Johannes R Bogner
- Division of Infectious Diseases, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| | - Oliver T Fackler
- Center for Infectious Diseases, Integrative Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Site Heidelberg, Heidelberg, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
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49
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Niemira M, Collin F, Szalkowska A, Bielska A, Chwialkowska K, Reszec J, Niklinski J, Kwasniewski M, Kretowski A. Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA). Cancers (Basel) 2019; 12:E37. [PMID: 31877723 PMCID: PMC7017323 DOI: 10.3390/cancers12010037] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) represents a heterogeneous group of malignancies consisting essentially of adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Although the diagnosis and treatment of ADC and SCC have been greatly improved in recent decades, there is still an urgent need to identify accurate transcriptome profile associated with the histological subtypes of NSCLC. The present study aims to identify the key dysregulated pathways and genes involved in the development of lung ADC and SCC and to relate them with the clinical traits. The transcriptional changes between tumour and normal lung tissues were investigated by RNA-seq. Gene ontology (GO), canonical pathways analysis with the prediction of upstream regulators, and weighted gene co-expression network analysis (WGCNA) to identify co-expressed modules and hub genes were used to explore the biological functions of the identified dysregulated genes. It was indicated that specific gene signatures differed significantly between ADC and SCC related to the distinct pathways. Of identified modules, four and two modules were the most related to clinical features in ADC and SCC, respectively. CTLA4, MZB1, NIP7, and BUB1B in ADC, as well as GNG11 and CCNB2 in SCC, are novel top hub genes in modules associated with tumour size, SUVmax, and recurrence-free survival. Our research provides a more effective understanding of the importance of biological pathways and the relationships between major genes in NSCLC in the perspective of searching for new molecular targets.
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Affiliation(s)
- Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Francois Collin
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Anna Szalkowska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Agnieszka Bielska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
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50
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Kong T, Ahn R, Yang K, Zhu X, Fu Z, Morin G, Bramley R, Cliffe NC, Xue Y, Kuasne H, Li Q, Jung S, Gonzalez AV, Camilleri-Broet S, Guiot MC, Park M, Ursini-Siegel J, Huang S. CD44 Promotes PD-L1 Expression and Its Tumor-Intrinsic Function in Breast and Lung Cancers. Cancer Res 2019; 80:444-457. [PMID: 31722999 DOI: 10.1158/0008-5472.can-19-1108] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/18/2019] [Accepted: 11/08/2019] [Indexed: 11/16/2022]
Abstract
The PD-L1 (CD274) immune-checkpoint ligand is often upregulated in cancers to inhibit T cells and elicit immunosuppression. Independent of this activity, PD-L1 has recently been shown to also exert a cancer cell-intrinsic function promoting tumorigenesis. Here, we establish this tumor-intrinsic role of PD-L1 in triple-negative breast cancer (TNBC) and non-small cell lung cancer (NSCLC). Using FACS-assisted shRNA screens, we identified the cell-surface adhesion receptor CD44 as a key positive regulator of PD-L1 expression in these cancers. Mechanistically, CD44 activated PD-L1 transcription in part through its cleaved intracytoplasmic domain (ICD), which bound to a regulatory region of the PD-L1 locus containing a consensus CD44-ICD binding site. Supporting this genetic interaction, CD44 positively correlated with PD-L1 expression at the mRNA and protein levels in primary tumor samples of TNBC and NSCLC patients. These data provide a novel basis for CD44 as a critical therapeutic target to suppress PD-L1 tumor-intrinsic function. SIGNIFICANCE: CD44 is a potential target to suppress PD-L1 function in TNBC. This finding has the potential to open a new area of therapy for TNBC.
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Affiliation(s)
- Tim Kong
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Ryuhjin Ahn
- Lady Davis Institute for Medical Research, Montréal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montréal, Quebec, Canada
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Rachel Bramley
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Nikki C Cliffe
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Hellen Kuasne
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Qinghao Li
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Sungmi Jung
- Department of Pathology, Glen Site, McGill University Health Centre Montreal, Quebec, Canada
| | - Anne V Gonzalez
- Department of Medicine, Division of Respiratory Medicine, McGill University Health Centre, Montreal Chest Institute, Montreal, Quebec, Canada
| | - Sophie Camilleri-Broet
- Department of Pathology, Glen Site, McGill University Health Centre Montreal, Quebec, Canada
| | - Marie-Christine Guiot
- Departments of Pathology, Montreal Neurological Hospital/Institute, McGill University Health Centre, Montreal, Quebec, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Josie Ursini-Siegel
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada. .,Lady Davis Institute for Medical Research, Montréal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montréal, Quebec, Canada.,Department of Oncology, McGill University, Montréal, Quebec, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada. .,Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
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