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Zhu Z, Jin Y, Zhou J, Chen F, Chen M, Gao Z, Hu L, Xuan J, Li X, Song Z, Guo X. PD1/PD-L1 blockade in clear cell renal cell carcinoma: mechanistic insights, clinical efficacy, and future perspectives. Mol Cancer 2024; 23:146. [PMID: 39014460 PMCID: PMC11251344 DOI: 10.1186/s12943-024-02059-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
The advent of PD1/PD-L1 inhibitors has significantly transformed the therapeutic landscape for clear cell renal cell carcinoma (ccRCC). This review provides an in-depth analysis of the biological functions and regulatory mechanisms of PD1 and PD-L1 in ccRCC, emphasizing their role in tumor immune evasion. We comprehensively evaluate the clinical efficacy and safety profiles of PD1/PD-L1 inhibitors, such as Nivolumab and Pembrolizumab, through a critical examination of recent clinical trial data. Furthermore, we discuss the challenges posed by resistance mechanisms to these therapies and potential strategies to overcome them. We also explores the synergistic potential of combination therapies, integrating PD1/PD-L1 inhibitors with other immunotherapies, targeted therapies, and conventional modalities such as chemotherapy and radiotherapy. In addition, we examine emerging predictive biomarkers for response to PD1/PD-L1 blockade and biomarkers indicative of resistance, providing a foundation for personalized therapeutic approaches. Finally, we outline future research directions, highlighting the need for novel therapeutic strategies, deeper mechanistic insights, and the development of individualized treatment regimens. Our work summarizes the latest knowledge and progress in this field, aiming to provide a valuable reference for improving clinical efficacy and guiding future research on the application of PD1/PD-L1 inhibitors in ccRCC.
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Affiliation(s)
- Zhaoyang Zhu
- Jiaxing University Master Degree Cultivation Base, Zhejiang Chinese Medical University, Hangzhou, 310000, Zhejiang, P.R. China
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Yigang Jin
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Jing Zhou
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Fei Chen
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Minjie Chen
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Zhaofeng Gao
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Lingyu Hu
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Jinyan Xuan
- Department of General Practice, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Xiaoping Li
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China.
| | - Zhengwei Song
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China.
| | - Xiao Guo
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China.
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2
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Camarena ME, Theunissen P, Ruiz M, Ruiz-Orera J, Calvo-Serra B, Castelo R, Castro C, Sarobe P, Fortes P, Perera-Bel J, Albà MM. Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort. SCIENCE ADVANCES 2024; 10:eadn3628. [PMID: 38985879 PMCID: PMC11235171 DOI: 10.1126/sciadv.adn3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Here, we investigate if microproteins encoded by noncanonical open reading frames (ncORFs) are a relevant source of tumor-specific antigens. We analyze RNA sequencing data from 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue together with ribosome profiling and immunopeptidomics data. Combining human leukocyte antigen-epitope binding predictions and experimental validation experiments, we conclude that around 40% of the tumor-specific antigens in HCC are likely to be derived from ncORFs, including two peptides that can trigger an immune response in humanized mice. We identify a subset of 33 tumor-specific long noncoding RNAs expressing novel cancer antigens shared by more than 10% of the HCC samples analyzed, which, when combined, cover a large proportion of the patients. The results of the study open avenues for extending the range of anticancer vaccines.
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Affiliation(s)
| | - Patrick Theunissen
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Marta Ruiz
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Beatriz Calvo-Serra
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Robert Castelo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carla Castro
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Pablo Sarobe
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | | | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
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3
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Feng T, Wang Y, Zhang W, Cai T, Tian X, Su J, Zhang Z, Zheng S, Ye S, Dai B, Wang Z, Zhu Y, Zhang H, Chang K, Ye D. Machine Learning-based Framework Develops a Tumor Thrombus Coagulation Signature in Multicenter Cohorts for Renal Cancer. Int J Biol Sci 2024; 20:3590-3620. [PMID: 38993563 PMCID: PMC11234220 DOI: 10.7150/ijbs.94555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/17/2024] [Indexed: 07/13/2024] Open
Abstract
Background: Renal cell carcinoma (RCC) is frequently accompanied by tumor thrombus in the venous system with an extremely dismal prognosis. The current Tumor Node Metastasis (TNM) stage and Mayo clinical classification do not appropriately identify preference-sensitive treatment. Therefore, there is an urgent need to develop a better ideal model for precision medicine. Methods: In this study, we developed a coagulation tumor thrombus signature for RCC with 10 machine-learning algorithms (101 combinations) based on a novel computational framework using multiple independent cohorts. Results: The established tumor thrombus coagulation-related risk stratification (TTCRRS) signature comprises 10 prognostic coagulation-related genes (CRGs). This signature could predict survival outcomes in public and in-house protein cohorts and showed high performance compared to 129 published signatures. Additionally, the TTCRRS signature was significantly related to some immune landscapes, immunotherapy response, and chemotherapy. Furthermore, we also screened out hub genes, transcription factors, and small compounds based on the TTCRRS signature. Meanwhile, CYP51A1 can regulate the proliferation and migration properties of RCC. Conclusions: The TTCRRS signature can complement the traditional anatomic TNM staging system and Mayo clinical stratification and provide clinicians with more therapeutic options.
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Affiliation(s)
- Tao Feng
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Yue Wang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Wei Zhang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Tingting Cai
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Xi Tian
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Jiaqi Su
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Zihao Zhang
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Shengfeng Zheng
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Shiqi Ye
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Bo Dai
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Ziliang Wang
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 274 Middle Zhijiang Road, Shanghai 200071, China
| | - Yiping Zhu
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Hailiang Zhang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Kun Chang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Dingwei Ye
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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5
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Derosa L, Iebba V, Silva CAC, Piccinno G, Wu G, Lordello L, Routy B, Zhao N, Thelemaque C, Birebent R, Marmorino F, Fidelle M, Messaoudene M, Thomas AM, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Sibilot DM, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Bouchard N, Sow C, Darik I, Zoppi S, Ly P, Reni A, Daillère R, Deutsch E, Lee KA, Bolte LA, Björk JR, Weersma RK, Barlesi F, Padilha L, Finzel A, Isaksen ML, Escudier B, Albiges L, Planchard D, André F, Cremolini C, Martinez S, Besse B, Zhao L, Segata N, Wojcik J, Kroemer G, Zitvogel L. Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome. Cell 2024; 187:3373-3389.e16. [PMID: 38906102 DOI: 10.1016/j.cell.2024.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/16/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The gut microbiota influences the clinical responses of cancer patients to immunecheckpoint inhibitors (ICIs). However, there is no consensus definition of detrimental dysbiosis. Based on metagenomics (MG) sequencing of 245 non-small cell lung cancer (NSCLC) patient feces, we constructed species-level co-abundance networks that were clustered into species-interacting groups (SIGs) correlating with overall survival. Thirty-seven and forty-five MG species (MGSs) were associated with resistance (SIG1) and response (SIG2) to ICIs, respectively. When combined with the quantification of Akkermansia species, this procedure allowed a person-based calculation of a topological score (TOPOSCORE) that was validated in an additional 254 NSCLC patients and in 216 genitourinary cancer patients. Finally, this TOPOSCORE was translated into a 21-bacterial probe set-based qPCR scoring that was validated in a prospective cohort of NSCLC patients as well as in colorectal and melanoma patients. This approach could represent a dynamic diagnosis tool for intestinal dysbiosis to guide personalized microbiota-centered interventions.
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Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France.
| | - Valerio Iebba
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | - Guojun Wu
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Leonardo Lordello
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Bertrand Routy
- Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Department of Medicine, Montréal, QC, Canada; Centre de Recherche du CHUM (CRCHUM), Montréal, QC, Canada
| | - Naisi Zhao
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Cassandra Thelemaque
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Federica Marmorino
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marine Fidelle
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | | | - Gerard Zalcman
- Université Paris Cité, Thoracic Oncology Department-CIC1425/CLIP2 Paris-Nord, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Julien Mazieres
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | | | - Denis Moro- Sibilot
- Department of Thoracic Oncology, Centre Hospitalier Universitaire, Grenoble, France
| | - François Goldwasser
- INSERM U1016-CNRS UMR8104, Paris Cité University, Paris, France; Department of Medical Oncology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | - Arnaud Scherpereel
- Department of Pulmonary and Thoracic Oncology, University of Lille, University Hospital (CHU), Lille, France
| | | | - François Ghiringhelli
- Cancer Biology Transfer Platform, Centre Georges-François Leclerc, Dijon, France; Centre de Recherche INSERM LNC-UMR1231, Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | | | - Cissé Sow
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Ines Darik
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Silvia Zoppi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Pierre Ly
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Anna Reni
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Section of Oncology, Department of Medicine, University of Verona School of Medicine and Verona University Hospital Trust, Verona, Italy
| | | | - Eric Deutsch
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Radiation Oncology, Gustave Roussy, Villejuif, France; INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Lucas Padilha
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | - Ana Finzel
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | | | - Bernard Escudier
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Laurence Albiges
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - David Planchard
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Fabrice André
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Chiara Cremolini
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Stéphanie Martinez
- Service des Maladies Respiratoires, Centre Hospitalier d'Aix-en-Provence, Aix-en-Provence, France
| | - Benjamin Besse
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Liping Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA; State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Guido Kroemer
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Centre de Recherche des Cordeliers, Equipe labellisée-Ligue contre le cancer, Université de Paris Cité, Sorbonne Université, Institut Universitaire de France, Inserm U1138, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France.
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6
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Hu Z, Guo X, Li Z, Meng Z, Huang S. The neoantigens derived from transposable elements - A hidden treasure for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189126. [PMID: 38849060 DOI: 10.1016/j.bbcan.2024.189126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/26/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
Neoantigen-based therapy is a promising approach that selectively activates the immune system of the host to recognize and eradicate cancer cells. Preliminary clinical trials have validated the feasibility, safety, and immunogenicity of personalized neoantigen-directed vaccines, enhancing their effectiveness and broad applicability in immunotherapy. While many ongoing oncological trials concentrate on neoantigens derived from mutations, these targets do not consistently provoke an immune response in all patients harboring the mutations. Additionally, tumors like ovarian cancer, which have a low tumor mutational burden (TMB), may be less amenable to mutation-based neoantigen therapies. Recent advancements in next-generation sequencing and bioinformatics have uncovered a rich source of neoantigens from non-canonical RNAs associated with transposable elements (TEs). Considering the substantial presence of TEs in the human genome and the proven immunogenicity of TE-derived neoantigens in various tumor types, this review investigates the latest findings on TE-derived neoantigens, examining their clinical implications, challenges, and unique advantages in enhancing tumor immunotherapy.
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Affiliation(s)
- Zhixiang Hu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyi Guo
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ziteng Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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7
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Wang-Bishop L, Wehbe M, Pastora LE, Yang J, Kimmel BR, Garland KM, Becker KW, Carson CS, Roth EW, Gibson-Corley KN, Ulkoski D, Krishnamurthy V, Fedorova O, Richmond A, Pyle AM, Wilson JT. Nanoparticle Retinoic Acid-Inducible Gene I Agonist for Cancer Immunotherapy. ACS NANO 2024; 18:11631-11643. [PMID: 38652829 PMCID: PMC11080455 DOI: 10.1021/acsnano.3c06225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
Pharmacological activation of the retinoic acid-inducible gene I (RIG-I) pathway holds promise for increasing tumor immunogenicity and improving the response to immune checkpoint inhibitors (ICIs). However, the potency and clinical efficacy of 5'-triphosphate RNA (3pRNA) agonists of RIG-I are hindered by multiple pharmacological barriers, including poor pharmacokinetics, nuclease degradation, and inefficient delivery to the cytosol where RIG-I is localized. Here, we address these challenges through the design and evaluation of ionizable lipid nanoparticles (LNPs) for the delivery of 3p-modified stem-loop RNAs (SLRs). Packaging of SLRs into LNPs (SLR-LNPs) yielded surface charge-neutral nanoparticles with a size of ∼100 nm that activated RIG-I signaling in vitro and in vivo. SLR-LNPs were safely administered to mice via both intratumoral and intravenous routes, resulting in RIG-I activation in the tumor microenvironment (TME) and the inhibition of tumor growth in mouse models of poorly immunogenic melanoma and breast cancer. Significantly, we found that systemic administration of SLR-LNPs reprogrammed the breast TME to enhance the infiltration of CD8+ and CD4+ T cells with antitumor function, resulting in enhanced response to αPD-1 ICI in an orthotopic EO771 model of triple-negative breast cancer. Therapeutic efficacy was further demonstrated in a metastatic B16.F10 melanoma model, with systemically administered SLR-LNPs significantly reducing lung metastatic burden compared to combined αPD-1 + αCTLA-4 ICI. Collectively, these studies have established SLR-LNPs as a translationally promising immunotherapeutic nanomedicine for potent and selective activation of RIG-I with the potential to enhance response to ICIs and other immunotherapeutic modalities.
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Affiliation(s)
- Lihong Wang-Bishop
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Mohamed Wehbe
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Lucinda E. Pastora
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Jinming Yang
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Department
of Veterans Affairs, Tennessee Valley Healthcare
System, Nashville, Tennessee 37212, United States
| | - Blaise R. Kimmel
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Kyle M. Garland
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Kyle W. Becker
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Carcia S. Carson
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Eric W. Roth
- Northwestern
University Atomic and Nanoscale Characterization Experimental (NUANCE)
Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine N. Gibson-Corley
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Medicine, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
| | - David Ulkoski
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Venkata Krishnamurthy
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Olga Fedorova
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
- Howard
Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Ann Richmond
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Department
of Veterans Affairs, Tennessee Valley Healthcare
System, Nashville, Tennessee 37212, United States
| | - Anna Marie Pyle
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
- Howard
Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - John T. Wilson
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37212, United States
- Vanderbilt
Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
- Vanderbilt
Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee 37212, United States
- Vanderbilt
Center for Immunobiology, Vanderbilt University
Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Ingram Cancer Center, Nashville, Tennessee 37232, United States
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8
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Noronha N, Durette C, Cahuzac M, E Silva B, Courtois J, Humeau J, Sauvat A, Hardy MP, Vincent K, Laverdure JP, Lanoix J, Baron F, Thibault P, Perreault C, Ehx G. Autophagy degrades immunogenic endogenous retroelements induced by 5-azacytidine in acute myeloid leukemia. Leukemia 2024; 38:1019-1031. [PMID: 38627586 DOI: 10.1038/s41375-024-02250-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024]
Abstract
The hypomethylating agent 5-azacytidine (AZA) is the first-line treatment for AML patients unfit for intensive chemotherapy. The effect of AZA results in part from T-cell cytotoxic responses against MHC-I-associated peptides (MAPs) deriving from hypermethylated genomic regions such as cancer-testis antigens (CTAs), or endogenous retroelements (EREs). However, evidence supporting higher ERE MAPs presentation after AZA treatment is lacking. Therefore, using proteogenomics, we examined the impact of AZA on the repertoire of MAPs and their source transcripts. AZA-treated AML upregulated both CTA and ERE transcripts, but only CTA MAPs were presented at greater levels. Upregulated ERE transcripts triggered innate immune responses against double-stranded RNAs but were degraded by autophagy, and not processed into MAPs. Autophagy resulted from the formation of protein aggregates caused by AZA-dependent inhibition of DNMT2. Autophagy inhibition had an additive effect with AZA on AML cell proliferation and survival, increased ERE levels, increased pro-inflammatory responses, and generated immunogenic tumor-specific ERE-derived MAPs. Finally, autophagy was associated with a lower abundance of CD8+ T-cell markers in AML patients expressing high levels of EREs. This work demonstrates that AZA-induced EREs are degraded by autophagy and shows that inhibiting autophagy can improve the immune recognition of AML blasts in treated patients.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Azacitidine/pharmacology
- Autophagy/drug effects
- Antimetabolites, Antineoplastic/pharmacology
- Antimetabolites, Antineoplastic/therapeutic use
- DNA Methylation/drug effects
- Cell Proliferation
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
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Affiliation(s)
| | | | | | - Bianca E Silva
- GIGA Institute, Laboratory of Hematology, University of Liege, Liege, Belgium
| | - Justine Courtois
- GIGA Institute, Laboratory of Hematology, University of Liege, Liege, Belgium
| | | | - Allan Sauvat
- Equipe labellisée par la Ligue contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
| | | | | | | | - Joël Lanoix
- IRIC, Université de Montréal, Montreal, QC, Canada
| | - Frédéric Baron
- GIGA Institute, Laboratory of Hematology, University of Liege, Liege, Belgium
| | | | | | - Gregory Ehx
- IRIC, Université de Montréal, Montreal, QC, Canada.
- GIGA Institute, Laboratory of Hematology, University of Liege, Liege, Belgium.
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9
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Emilius L, Bremm F, Binder AK, Schaft N, Dörrie J. Tumor Antigens beyond the Human Exome. Int J Mol Sci 2024; 25:4673. [PMID: 38731892 PMCID: PMC11083240 DOI: 10.3390/ijms25094673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
With the advent of immunotherapeutics, a new era in the combat against cancer has begun. Particularly promising are neo-epitope-targeted therapies as the expression of neo-antigens is tumor-specific. In turn, this allows the selective targeting and killing of cancer cells whilst healthy cells remain largely unaffected. So far, many advances have been made in the development of treatment options which are tailored to the individual neo-epitope repertoire. The next big step is the achievement of efficacious "off-the-shelf" immunotherapies. For this, shared neo-epitopes propose an optimal target. Given the tremendous potential, a thorough understanding of the underlying mechanisms which lead to the formation of neo-antigens is of fundamental importance. Here, we review the various processes which result in the formation of neo-epitopes. Broadly, the origin of neo-epitopes can be categorized into three groups: canonical, noncanonical, and viral neo-epitopes. For the canonical neo-antigens that arise in direct consequence of somatic mutations, we summarize past and recent findings. Beyond that, our main focus is put on the discussion of noncanonical and viral neo-epitopes as we believe that targeting those provides an encouraging perspective to shape the future of cancer immunotherapeutics.
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Affiliation(s)
- Lisabeth Emilius
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Franziska Bremm
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Amanda Katharina Binder
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
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10
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Guo X, Zhao Y, You F. Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection. Front Immunol 2024; 15:1294020. [PMID: 38646531 PMCID: PMC11026653 DOI: 10.3389/fimmu.2024.1294020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/14/2024] [Indexed: 04/23/2024] Open
Abstract
Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.
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11
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Dopkins N, Nixon DF. Activation of human endogenous retroviruses and its physiological consequences. Nat Rev Mol Cell Biol 2024; 25:212-222. [PMID: 37872387 DOI: 10.1038/s41580-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the human genome as remnants of ancient retroviral infections. These sequences became fixed and accumulate mutations or deletions over time. HERVs have affected human evolution and physiology by providing a unique repertoire of coding and non-coding sequences to the genome. In healthy individuals, HERVs participate in immune responses, formation of syncytiotrophoblasts and cell-fate specification. In this Review, we discuss how endogenized retroviral motifs and regulatory sequences have been co-opted into human physiology and how they are tightly regulated. Infections and mutations can derail this regulation, leading to differential HERV expression, which may contribute to pathologies including neurodegeneration, pathological inflammation and oncogenesis. Emerging evidence demonstrates that HERVs are crucial to human health and represent an understudied facet of many diseases, and we therefore argue that investigating their fundamental properties could improve existing therapies and help develop novel therapeutic strategies.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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12
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Jia L, Cowell LG, Kapur P. Understanding Factors that Influence Prognosis and Response to Therapy in Clear Cell Renal Cell Carcinoma. Adv Anat Pathol 2024; 31:96-104. [PMID: 38179997 DOI: 10.1097/pap.0000000000000428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In this review, we highlight and contextualize emerging morphologic prognostic and predictive factors in renal cell carcinoma. We focus on clear cell renal cell carcinoma (ccRCC), the most common histologic subtype. Our understanding of the molecular characterization of ccRCC has dramatically improved in the last decade. Herein, we highlight how these discoveries have laid the foundation for new approaches to prognosis and therapeutic decision-making for patients with ccRCC. We explore the clinical relevance of common mutations, established gene expression signatures, intratumoral heterogeneity, sarcomatoid/rhabdoid morphology and PD-L1 expression, and discuss their impact on predicting response to therapy.
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Affiliation(s)
| | - Lindsay G Cowell
- Peter O'Donnell School of Public Health
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, TX
| | - Payal Kapur
- Department of Pathology
- Department of Urology, University of Texas Southwestern Medical Center
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, Dallas, TX
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13
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Cherkasova EA, Chen L, Childs RW. Mechanistic regulation of HERV activation in tumors and implications for translational research in oncology. Front Cell Infect Microbiol 2024; 14:1358470. [PMID: 38379771 PMCID: PMC10877039 DOI: 10.3389/fcimb.2024.1358470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Transcription of distinct loci of human endogenous retroviruses (HERVs) and in some cases, translation of these transcripts have been consistently observed in many types of cancer. It is still debated whether HERV activation serves as a trigger for carcinogenesis or rather occurs as a consequence of epigenetic alterations and other molecular sequelae that characterize cellular transformation. Here we review the known molecular and epigenetic mechanisms of HERV activation in cancer cells as well as its potential contribution to carcinogenesis. Further, we describe the use of HERV expression in cancer diagnostic and characterize the potential of HERV-derived antigens to serve as novel targets for cancer immunotherapy. We believe this review, which summarizes both what is known as well as unknown in this rapidly developing field, will boost interest in research on the therapeutic potential of targeting HERV elements in tumors and the impact of HERV activation in oncogenesis.
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Affiliation(s)
| | | | - Richard W. Childs
- Laboratory of Transplantation Immunotherapy, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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14
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Liang Y, Qu X, Shah NM, Wang T. Towards targeting transposable elements for cancer therapy. Nat Rev Cancer 2024; 24:123-140. [PMID: 38228901 DOI: 10.1038/s41568-023-00653-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Transposable elements (TEs) represent almost half of the human genome. Historically deemed 'junk DNA', recent technological advancements have stimulated a wave of research into the functional impact of TEs on gene-regulatory networks in evolution and development, as well as in diseases including cancer. The genetic and epigenetic evolution of cancer involves the exploitation of TEs, whereby TEs contribute directly to cancer-specific gene activities. This Review provides a perspective on the role of TEs in cancer as being a 'double-edged sword', both promoting cancer evolution and representing a vulnerability that could be exploited in cancer therapy. We discuss how TEs affect transcriptome regulation and other cellular processes in cancer. We highlight the potential of TEs as therapeutic targets for cancer. We also summarize technical hurdles in the characterization of TEs with genomic assays. Last, we outline open questions and exciting future research avenues.
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Affiliation(s)
- Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nakul M Shah
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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15
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Su D, Ding C, Qiu J, Yang G, Wang R, Liu Y, Tao J, Luo W, Weng G, Zhang T. Ribosome profiling: a powerful tool in oncological research. Biomark Res 2024; 12:11. [PMID: 38273337 PMCID: PMC10809610 DOI: 10.1186/s40364-024-00562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.
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Affiliation(s)
- Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Chen Ding
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Gang Yang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Guihu Weng
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China.
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16
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Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics 2024; 25:5. [PMID: 38166631 PMCID: PMC10759522 DOI: 10.1186/s12864-023-09909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline "hervQuant" to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1-0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Manvendra Singh
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Nicholas Collins
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
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17
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Saliby RM, Saad E, Kashima S, Schoenfeld DA, Braun DA. Update on Biomarkers in Renal Cell Carcinoma. Am Soc Clin Oncol Educ Book 2024; 44:e430734. [PMID: 38207251 DOI: 10.1200/edbk_430734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Immune checkpoint inhibitors have significantly transformed the treatment paradigm for metastatic renal cell carcinoma (RCC), offering prolonged overall survival and achieving remarkable deep and durable responses. However, given the multiple ICI-containing, standard-of-care regimens approved for RCC, identifying biomarkers that predict therapeutic response and resistance is of critical importance. Although tumor-intrinsic features such as pathological characteristics, genomic alterations, and transcriptional signatures have been extensively investigated, they have yet to provide definitive, robust predictive biomarkers. Current research is exploring host factors through in-depth characterization of the immune system. Additionally, innovative technological approaches are being developed to overcome challenges presented by existing techniques, such as tumor heterogeneity. Promising avenues in biomarker discovery include the study of the microbiome, radiomics, and spatial transcriptomics.
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Affiliation(s)
- Renée M Saliby
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
- Yale Center of Cellular and Molecular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | - Eddy Saad
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Soki Kashima
- Yale Center of Cellular and Molecular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | - David A Schoenfeld
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - David A Braun
- Yale Center of Cellular and Molecular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
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18
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Coley AK, Lu C, Pankaj A, Emmett MJ, Lang ER, Song Y, Xu KH, Xu N, Patel BK, Chougule A, Nieman LT, Aryee MJ, Ferrone CR, Deshpande V, Franses JW, Ting DT. Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.570014. [PMID: 38105940 PMCID: PMC10723373 DOI: 10.1101/2023.12.04.570014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Purpose Dysregulation of viral-like repeat RNAs are a common feature across many malignancies that are linked with immunological response, but the characterization of these in hepatocellular carcinoma (HCC) is understudied. In this study, we performed RNA in situ hybridization (RNA-ISH) of different repeat RNAs, immunohistochemistry (IHC) for immune cell subpopulations, and spatial transcriptomics to understand the relationship of HCC repeat expression, immune response, and clinical outcomes. Experimental Design RNA-ISH for LINE1, HERV-K, HERV-H, and HSATII repeats and IHC for T-cell, Treg, B-cell, macrophage, and immune checkpoint markers were performed on 43 resected HCC specimens. Spatial transcriptomics on tumor and vessel regions of interest was performed on 28 specimens from the same cohort. Results High HERV-K and high LINE1 expression were both associated with worse overall survival. There was a positive correlation between LINE1 expression and FOXP3 T-regulatory cells (r = 0.51 p < 0.001) as well as expression of the TIM3 immune checkpoint (r = 0.34, p = 0.03). Spatial transcriptomic profiling of HERV-K high and LINE-1 high tumors identified elevated expression of multiple genes previously associated with epithelial mesenchymal transition, cellular proliferation, and worse overall prognosis in HCC including SSX1, MAGEC2, and SPINK1. Conclusion Repeat RNAs may serve as useful prognostic biomarkers in HCC and may also serve as novel therapeutic targets. Additional study is needed to understand the mechanisms by which repeat RNAs impact HCC tumorigenesis.
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Affiliation(s)
- Avril K. Coley
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital Harvard Medical School; Boston, MA, USA
| | - Chenyue Lu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
| | - Amaya Pankaj
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Matthew J. Emmett
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Evan R. Lang
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Yuhui Song
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Katherine H. Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Nova Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Bidish K. Patel
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Abhijit Chougule
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Linda T. Nieman
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Martin J. Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA, USA
- Broad Institute of Harvard and MIT; Cambridge, MA, USA
| | | | - Vikram Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA, USA
| | - Joseph W. Franses
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
- Section of Hematology-Oncology, Department of Medicine, University of Chicago; Chicago, IL, USA
| | - David T. Ting
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Health Sciences and Technology Program; Cambridge, MA, USA
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19
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Shin W, Mun S, Han K. Human Endogenous Retrovirus-K (HML-2)-Related Genetic Variation: Human Genome Diversity and Disease. Genes (Basel) 2023; 14:2150. [PMID: 38136972 PMCID: PMC10742618 DOI: 10.3390/genes14122150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs) comprise a significant portion of the human genome, making up roughly 8%, a notable comparison to the 2-3% represented by coding sequences. Numerous studies have underscored the critical role and importance of HERVs, highlighting their diverse and extensive influence on the evolution of the human genome and establishing their complex correlation with various diseases. Among HERVs, the HERV-K (HML-2) subfamily has recently attracted significant attention, integrating into the human genome after the divergence between humans and chimpanzees. Its insertion in the human genome has received considerable attention due to its structural and functional characteristics and the time of insertion. Originating from ancient exogenous retroviruses, these elements succeeded in infecting germ cells, enabling vertical transmission and existing as proviruses within the genome. Remarkably, these sequences have retained the capacity to form complete viral sequences, exhibiting activity in transcription and translation. The HERV-K (HML-2) subfamily is the subject of active debate about its potential positive or negative effects on human genome evolution and various pathologies. This review summarizes the variation, regulation, and diseases in human genome evolution arising from the influence of HERV-K (HML-2).
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Affiliation(s)
- Wonseok Shin
- NGS Clinical Laboratory, Division of Cancer Research, Dankook University Hospital, Cheonan 31116, Republic of Korea;
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
| | - Seyoung Mun
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Kyudong Han
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Republic of Korea
- R&D Center, HuNBiome Co., Ltd., Seoul 08507, Republic of Korea
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20
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Rediti M, Fernandez-Martinez A, Venet D, Rothé F, Hoadley KA, Parker JS, Singh B, Campbell JD, Ballman KV, Hillman DW, Winer EP, El-Abed S, Piccart M, Di Cosimo S, Symmans WF, Krop IE, Salgado R, Loi S, Pusztai L, Perou CM, Carey LA, Sotiriou C. Immunological and clinicopathological features predict HER2-positive breast cancer prognosis in the neoadjuvant NeoALTTO and CALGB 40601 randomized trials. Nat Commun 2023; 14:7053. [PMID: 37923752 PMCID: PMC10624889 DOI: 10.1038/s41467-023-42635-2] [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: 12/01/2022] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
The identification of prognostic markers in patients receiving neoadjuvant therapy is crucial for treatment optimization in HER2-positive breast cancer, with the immune microenvironment being a key factor. Here, we investigate the complexity of B and T cell receptor (BCR and TCR) repertoires in the context of two phase III trials, NeoALTTO and CALGB 40601, evaluating neoadjuvant paclitaxel with trastuzumab and/or lapatinib in women with HER2-positive breast cancer. BCR features, particularly the number of reads and clones, evenness and Gini index, are heterogeneous according to hormone receptor status and PAM50 subtypes. Moreover, BCR measures describing clonal expansion, namely evenness and Gini index, are independent prognostic factors. We present a model developed in NeoALTTO and validated in CALGB 40601 that can predict event-free survival (EFS) by integrating hormone receptor and clinical nodal status, breast pathological complete response (pCR), stromal tumor-infiltrating lymphocyte levels (%) and BCR repertoire evenness. A prognostic score derived from the model and including those variables, HER2-EveNT, allows the identification of patients with 5-year EFS > 90%, and, in those not achieving pCR, of a subgroup of immune-enriched tumors with an excellent outcome despite residual disease.
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Affiliation(s)
- Mattia Rediti
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - David Venet
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jordan D Campbell
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Karla V Ballman
- Alliance Statistics and Data Management Center, Weill Cornell Medicine, New York, NY, USA
| | - David W Hillman
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Eric P Winer
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Martine Piccart
- Medical Oncology Department, Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
| | - Serena Di Cosimo
- Integrated biology platform unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - William Fraser Symmans
- Department of Pathology, University of Texas, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ian E Krop
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Ziekenhuizen, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lajos Pusztai
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Lisa A Carey
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium.
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21
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Lee B, Park J, Voshall A, Maury E, Kang Y, Kim YJ, Lee JY, Shim HR, Kim HJ, Lee JW, Jung MH, Kim SC, Chu HBK, Kim DW, Kim M, Choi EJ, Hwang OK, Lee HW, Ha K, Choi JK, Kim Y, Choi Y, Park WY, Lee EA. Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562422. [PMID: 37905014 PMCID: PMC10614793 DOI: 10.1101/2023.10.16.562422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Transposon-derived transcripts are abundant in RNA sequences, yet their landscape and function, especially for fusion transcripts derived from unannotated or somatically acquired transposons, remains underexplored. Here, we developed a new bioinformatic tool to detect transposon-fusion transcripts in RNA-sequencing data and performed a pan-cancer analysis of 10,257 cancer samples across 34 cancer types as well as 3,088 normal tissue samples. We identified 52,277 cancer-specific fusions with ~30 events per cancer and hotspot loci within transposons vulnerable to fusion formation. Exonization of intronic transposons was the most prevalent genic fusions, while somatic L1 insertions constituted a small fraction of cancer-specific fusions. Source L1s and HERVs, but not Alus showed decreased DNA methylation in cancer upon fusion formation. Overall cancer-specific L1 fusions were enriched in tumor suppressors while Alu fusions were enriched in oncogenes, including recurrent Alu fusions in EZH2 predictive of patient survival. We also demonstrated that transposon-derived peptides triggered CD8+ T-cell activation to the extent comparable to EBV viruses. Our findings reveal distinct epigenetic and tumorigenic mechanisms underlying transposon fusions across different families and highlight transposons as novel therapeutic targets and the source of potent neoantigens.
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Affiliation(s)
- Boram Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Junseok Park
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Adam Voshall
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Bioinformatics and Integrative Genomics Program; Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Yeeok Kang
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Yoen Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jin-Young Lee
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Hye-Ran Shim
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Hyo-Ju Kim
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Jung-Woo Lee
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Min-Hyeok Jung
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Si-Cho Kim
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Hoang Bao Khanh Chu
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Da-Won Kim
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Minjeong Kim
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Eun-Ji Choi
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Ok Kyung Hwang
- New Drug Development Center, KBiohealth, Cheongju-Si, Chungbuk, Republic of Korea
| | - Ho Won Lee
- New Drug Development Center, KBiohealth, Cheongju-Si, Chungbuk, Republic of Korea
| | - Kyungsoo Ha
- New Drug Development Center, KBiohealth, Cheongju-Si, Chungbuk, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Yongjoon Kim
- Cancer Genome Research Center (CGRC), Yonsei University, Seoul, Republic of Korea
| | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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22
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Braun DA, Chakraborty AA. Immunobiology and Metabolic Pathways of Renal Cell Carcinoma. Hematol Oncol Clin North Am 2023; 37:827-840. [PMID: 37246090 DOI: 10.1016/j.hoc.2023.04.012] [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] [Indexed: 05/30/2023]
Abstract
The treatment of advanced renal cell carcinoma (RCC) has changed dramatically with immune checkpoint inhibitors, yet most patients do not have durable responses. There is consequently a tremendous need for novel therapeutic development. RCC, and particularly the most common histology clear cell RCC, is an immunobiologically and metabolically distinct tumor. An improved understanding of RCC-specific biology will be necessary for the successful identification of new treatment targets for this disease. In this review, we discuss the current understanding of RCC immune pathways and metabolic dysregulation, with a focus on topics important for future clinical development.
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Affiliation(s)
- David A Braun
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, 300 George Street (Suite 6400), New Haven, CT 06511, USA.
| | - Abhishek A Chakraborty
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinical, 9500 Euclid Avenue (NB40), Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.
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23
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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24
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Yang K, Halima A, Chan TA. Antigen presentation in cancer - mechanisms and clinical implications for immunotherapy. Nat Rev Clin Oncol 2023; 20:604-623. [PMID: 37328642 DOI: 10.1038/s41571-023-00789-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
Over the past decade, the emergence of effective immunotherapies has revolutionized the clinical management of many types of cancers. However, long-term durable tumour control is only achieved in a fraction of patients who receive these therapies. Understanding the mechanisms underlying clinical response and resistance to treatment is therefore essential to expanding the level of clinical benefit obtained from immunotherapies. In this Review, we describe the molecular mechanisms of antigen processing and presentation in tumours and their clinical consequences. We examine how various aspects of the antigen-presentation machinery (APM) shape tumour immunity. In particular, we discuss genomic variants in HLA alleles and other APM components, highlighting their influence on the immunopeptidomes of both malignant cells and immune cells. Understanding the APM, how it is regulated and how it changes in tumour cells is crucial for determining which patients will respond to immunotherapy and why some patients develop resistance. We focus on recently discovered molecular and genomic alterations that drive the clinical outcomes of patients receiving immune-checkpoint inhibitors. An improved understanding of how these variables mediate tumour-immune interactions is expected to guide the more precise administration of immunotherapies and reveal potentially promising directions for the development of new immunotherapeutic approaches.
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Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA.
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA.
- National Center for Regenerative Medicine, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
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25
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Kobayashi S, Tokita S, Moniwa K, Kitahara K, Iuchi H, Matsuo K, Kakizaki H, Kanaseki T, Torigoe T. Proteogenomic identification of an immunogenic antigen derived from human endogenous retrovirus in renal cell carcinoma. JCI Insight 2023; 8:e167712. [PMID: 37606040 PMCID: PMC10543709 DOI: 10.1172/jci.insight.167712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
CD8+ T cells can recognize tumor antigens displayed by HLA class I molecules and eliminate tumor cells. Despite their low tumor mutation burden, immune checkpoint blockade (ICB) is often beneficial in patients with renal cell carcinoma (RCC). Here, using a proteogenomic approach, we directly and comprehensively explored the HLA class I-presenting peptidome of RCC tissues and demonstrated that the immunopeptidomes contain a small subset of peptides derived from human endogenous retroviruses (hERV). A comparison between tumor and normal kidney tissues revealed tumor-associated hERV antigens, one of which was immunogenic and recognized by host tumor-infiltrating lymphocytes (TIL). Stimulation with the hERV antigen induced reactive CD8+ T cells in healthy donor-derived (HD-derived) peripheral blood mononuclear cells (PBMC). These results highlight the presence of antitumor CD8+ T cell surveillance against hERV3895 antigens, suggesting their clinical applications in patients with RCC.
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Affiliation(s)
- Shin Kobayashi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Department of Renal and Urologic Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Joint Research Center for Immunoproteogenomics and
| | - Keigo Moniwa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | | | | | | | - Hidehiro Kakizaki
- Department of Renal and Urologic Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Joint Research Center for Immunoproteogenomics and
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Joint Research Center for Immunoproteogenomics and
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Pandey K, Wang SS, Mifsud NA, Faridi P, Davenport AJ, Webb AI, Sandow JJ, Ayala R, Monje M, Cross RS, Ramarathinam SH, Jenkins MR, Purcell AW. A combined immunopeptidomics, proteomics, and cell surface proteomics approach to identify immunotherapy targets for diffuse intrinsic pontine glioma. Front Oncol 2023; 13:1192448. [PMID: 37637064 PMCID: PMC10455951 DOI: 10.3389/fonc.2023.1192448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Diffuse intrinsic pontine glioma (DIPG), recently reclassified as a subtype of diffuse midline glioma, is a highly aggressive brainstem tumor affecting children and young adults, with no cure and a median survival of only 9 months. Conventional treatments are ineffective, highlighting the need for alternative therapeutic strategies such as cellular immunotherapy. However, identifying unique and tumor-specific cell surface antigens to target with chimeric antigen receptor (CAR) or T-cell receptor (TCR) therapies is challenging. Methods In this study, a multi-omics approach was used to interrogate patient-derived DIPG cell lines and to identify potential targets for immunotherapy. Results Through immunopeptidomics, a range of targetable peptide antigens from cancer testis and tumor-associated antigens as well as peptides derived from human endogenous retroviral elements were identified. Proteomics analysis also revealed upregulation of potential drug targets and cell surface proteins such as Cluster of differentiation 27 (CD276) B7 homolog 3 protein (B7H3), Interleukin 13 alpha receptor 2 (IL-13Rα2), Human Epidermal Growth Factor Receptor 3 (HER2), Ephrin Type-A Receptor 2 (EphA2), and Ephrin Type-A Receptor 3 (EphA3). Discussion The results of this study provide a valuable resource for the scientific community to accelerate immunotherapeutic approaches for DIPG. Identifying potential targets for CAR and TCR therapies could open up new avenues for treating this devastating disease.
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Affiliation(s)
- Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stacie S. Wang
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Children’s Cancer Centre, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Nicole A. Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Clinical Sciences, Department of Medicine, Monash University, Clayton, VIC, Australia
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Alexander J. Davenport
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I. Webb
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jarrod J. Sandow
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michelle Monje
- Department of Neurology and Neurological Sciences and Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Ryan S. Cross
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- LaTrobe Institute for Molecular Science, LaTrobe University, Bundoora, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Astore S, Baciarello G, Cerbone L, Calabrò F. Primary and acquired resistance to first-line therapy for clear cell renal cell carcinoma. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:517-546. [PMID: 37842234 PMCID: PMC10571064 DOI: 10.20517/cdr.2023.33] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 10/17/2023]
Abstract
The introduction of first-line combinations had improved the outcomes for metastatic renal cell carcinoma (mRCC) compared to sunitinib. However, some patients either have inherent resistance or develop resistance as a result of the treatment. Depending on the kind of therapy employed, many factors underlie resistance to systemic therapy. Angiogenesis and the tumor immune microenvironment (TIME), nevertheless, are inextricably linked. Although angiogenesis and the manipulation of the tumor microenvironment are linked to hypoxia, which emerges as a hallmark of renal cell carcinoma (RCC) pathogenesis, it is only one of the potential elements involved in the distinctive intra- and inter-tumor heterogeneity of RCC that is still dynamic. We may be able to more correctly predict therapy response and comprehend the mechanisms underlying primary or acquired resistance by integrating tumor genetic and immunological markers. In order to provide tools for patient selection and to generate hypotheses for the development of new strategies to overcome resistance, we reviewed the most recent research on the mechanisms of primary and acquired resistance to immune checkpoint inhibitors (ICIs) and tyrosine kinase inhibitors (TKIs) that target the vascular endothelial growth factor receptor (VEGFR).We can choose patients' treatments and cancer preventive strategies using an evolutionary approach thanks to the few evolutionary trajectories that characterize ccRCC.
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Affiliation(s)
- Serena Astore
- Medical Oncology, San Camillo Forlanini Hospital, Rome 00152, Italy
| | | | - Linda Cerbone
- Medical Oncology, San Camillo Forlanini Hospital, Rome 00152, Italy
| | - Fabio Calabrò
- Medical Oncology, San Camillo Forlanini Hospital, Rome 00152, Italy
- Medical Oncology, IRCSS, National Cancer Institute Regina Elena, Rome 00128, Italy
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Chang YS, Hsu MH, Chung CC, Chen HD, Tu SJ, Lee YT, Yen JC, Liu TC, Chang JG. Comprehensive Analysis and Drug Modulation of Human Endogenous Retrovirus in Hepatocellular Carcinomas. Cancers (Basel) 2023; 15:3664. [PMID: 37509325 PMCID: PMC10377948 DOI: 10.3390/cancers15143664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) play an important role in the development of cancer and many diseases. Here, we comprehensively explored the impact of HERVs on hepatocellular carcinomas (HCCs). METHODS We employed Telescope to identify HERVs and quantify their expression in the total RNA sequencing data obtained from 254 HCC samples, comprising 254 tumor tissues and 34 matched normal tissues. RESULTS In total, 3357 locus-specific activations of HERVs were differentially expressed, and 180 were correlated with patient survival. Using these 180 HERVs for classification, we found four subgroups with survival correlation. Higher expression levels of the 180 HERVs were correlated with poorer survival, while age, AFP, some mutations, and copy and structural variants differed among subgroups. The differential expression of host genes in high expression of these 180 HERVs primarily involved the activation of pathways related to immunity and infection, lipid and atherosclerosis, MAPK and NF-kB signaling, and cytokine-cytokine receptor interactions. Conversely, there was a suppression of pathways associated with RNA processing, including nucleocytoplasmic transport, surveillance and ribosome biogenesis, and transcriptional misregulation in cancer pathways. Almost all genes involved in HERV activation restriction, KRAB zinc finger proteins, RNA nucleocytoplasmic transport, stemness, HLA and antigen processing and presentation, and immune checkpoints were overexpressed in cancerous tissues, and many over-expressed HERV-related nearby genes were correlated with high HERV activation and poor survival. Twenty-three immune and stromal cells showed higher expression in non-cancerous than cancerous tissues, and seven were correlated with HERV activation. Small-molecule modulation of alternative splicing (AS) altered the expression of survival-related HERVs and their activation-related genes, as well as nearby genes. CONCLUSION Comprehensive and integrated approaches for evaluating HERV expression and their correlation with specific pathways have the potential to provide new companion diagnostics and therapeutic strategies for HCC.
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Affiliation(s)
- Ya-Sian Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- School of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Ming-Hon Hsu
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chin-Chun Chung
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Hong-Da Chen
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Siang-Jyun Tu
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ya-Ting Lee
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ju-Chen Yen
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ta-Chih Liu
- Department of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua 50544, Taiwan
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 40447, Taiwan
- School of Medicine, China Medical University, Taichung 40402, Taiwan
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Wolf MM, Rathmell WK, de Cubas AA. Immunogenicity in renal cell carcinoma: shifting focus to alternative sources of tumour-specific antigens. Nat Rev Nephrol 2023; 19:440-450. [PMID: 36973495 PMCID: PMC10801831 DOI: 10.1038/s41581-023-00700-5] [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] [Accepted: 02/27/2023] [Indexed: 03/29/2023]
Abstract
Renal cell carcinoma (RCC) comprises a group of malignancies arising from the kidney with unique tumour-specific antigen (TSA) signatures that can trigger cytotoxic immunity. Two classes of TSAs are now considered potential drivers of immunogenicity in RCC: small-scale insertions and deletions (INDELs) that result in coding frameshift mutations, and activation of human endogenous retroviruses. The presence of neoantigen-specific T cells is a hallmark of solid tumours with a high mutagenic burden, which typically have abundant TSAs owing to non-synonymous single nucleotide variations within the genome. However, RCC exhibits high cytotoxic T cell reactivity despite only having an intermediate non-synonymous single nucleotide variation mutational burden. Instead, RCC tumours have a high pan-cancer proportion of INDEL frameshift mutations, and coding frameshift INDELs are associated with high immunogenicity. Moreover, cytotoxic T cells in RCC subtypes seem to recognize tumour-specific endogenous retrovirus epitopes, whose presence is associated with clinical responses to immune checkpoint blockade therapy. Here, we review the distinct molecular landscapes in RCC that promote immunogenic responses, discuss clinical opportunities for discovery of biomarkers that can inform therapeutic immune checkpoint blockade strategies, and identify gaps in knowledge for future investigations.
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Affiliation(s)
- Melissa M Wolf
- Department of Medicine, Program in Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Program in Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Aguirre A de Cubas
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA.
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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30
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Zhang M, Liu YF, Gao Y, Zhao C, Chen M, Pan KH. Immune-pyroptosis-related genes predict the prognosis of kidney renal clear cell carcinoma. Transl Oncol 2023; 34:101693. [PMID: 37315507 DOI: 10.1016/j.tranon.2023.101693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/30/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is a common cancer of the adult urological system. Recent developments in tumor immunology and pyroptosis biology have provided new directions for kidney cancer treatment. Therefore, there is an urgent need to identify potential targets and prognostic biomarkers for the combination of immunotherapy and pyroptosis-targeted therapy. METHODS The expression of immune-pyroptosis-related differentially expressed genes (IPR-DEGs) between KIRC and healthy tissues was examined using the Gene Expression Omnibus datasets. The GSE168845 dataset was selected for subsequent analyses. Data of 1793 human immune-related genes were downloaded from the ImmPort database (https://www.immport.org./home), while those of 33 pyroptosis-related genes were extracted from previous reviews. The independent prognostic value of IPR-DEGs was determined using differential expression, prognostic, and univariate and multivariate Cox regression analyses. The GSE53757 dataset was used to further verify the GSDMB and PYCARD levels. In our cohorts, the association among DEGs and clinicopathological features and overall survival was analyzed. The least absolute shrinkage and selection operator Cox regression model was established to evaluate the correlation of IPR-DEGs with the immune score, immune checkpoint gene expression, and one-class logistic regression (OCLR) score. KIRC cells and clinical tissue samples were subjected to quantitative real-time polymerase chain reaction to examine the GSDMB and PYCARD mRNA levels. The GSDMB and PYCARD levels in a healthy kidney cell line (HK-2 cells) and two KIRC cell lines (786-O and Caki-1 cells) were verified. The tissue levels of GSDMB and PYCARD were evaluated using immunohistochemical analysis. GSDMB and PYCARD were knocked down in 786-O cells using short-interfering RNA. Cell proliferation was examined using the cell counting kit-8 assay. Cell migration was measured by transwell migration assays RESULTS: GSDMB and PYCARD were determined to be IPR-DEGs with independent prognostic values. A risk prognostic model based on GSDMB and PYCARD was successfully established. In the GSE53757 dataset, the GSDMB and PYCARD levels in KIRC tissues were significantly higher than those in healthy tissues. The GSDMB and PYCARD expression was related to T stage and OS in our cohort. The GSDMB and PYCARD levels were significantly correlated with the immune score, immune checkpoint gene expression, and OCLR score. The results of experimental studies were consistent with those of bioinformatics analysis. The GSDMB and PYCARD levels in KIRC cells were significantly upregulated when compared with those in healthy kidney cells. Consistently, GSDMB and PYCARD in KIRC tissues were significantly upregulated when compared with those in adjacent healthy kidney tissues. GSDMB and PYCARD knockdown significantly decreased 786-O cell proliferation (p < 0.05). Transwell migration result reflects that silencing GSDMB and PYCARD inhibited 786-O cell migration (p < 0.05) . CONCLUSIONS GSDMB and PYCARD are potential targets and effective prognostic biomarkers for the combination of immunotherapy and pyroptosis-targeted therapy in KIRC.
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Affiliation(s)
- Minhao Zhang
- Department of Urology, XiShan People's Hospital Of Wuxi City, Wuxi, China
| | - Yi-Fan Liu
- Southeast University, 87 Dingjia Bridge Hunan Road, Nanjing, China
| | - Yue Gao
- Affiliated Zhongda Hospital of Southeast University, Southeast University, 87 Dingjia Bridge Hunan Road, Nanjing, China
| | - Chenggui Zhao
- Affiliated Zhongda Hospital of Southeast University, Southeast University, 87 Dingjia Bridge Hunan Road, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Lishui District People's Hospital, 87 Dingjia Bridge Hunan Road, Nanjing, China
| | - Ke-Hao Pan
- Affiliated Zhongda Hospital of Southeast University, Southeast University, 87 Dingjia Bridge Hunan Road, Nanjing, China.
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Singh B, Dopkins N, Fei T, Marston JL, Michael S, Reyes-Gopar H, Curty G, Heymann JJ, Chadburn A, Martin P, Leal FE, Cesarman E, Nixon DF, Bendall ML. Locus specific human endogenous retroviruses reveal new lymphoma subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544208. [PMID: 37333202 PMCID: PMC10274920 DOI: 10.1101/2023.06.08.544208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification of B-cell lymphomas have been defined by considering these characteristics. However, the expression and contribution of transposable elements (TEs) to B cell lymphoma oncogenesis or classification have been overlooked. We hypothesized that incorporating TE signatures would increase the resolution of B-cell identity during healthy and malignant conditions. Here, we present the first comprehensive, locus-specific characterization of TE expression in benign germinal center (GC) B-cells, diffuse large B-cell lymphoma (DLBCL), Epstein-Barr virus (EBV)-positive and EBV-negative Burkitt lymphoma (BL), and follicular lymphoma (FL). Our findings demonstrate unique human endogenous retrovirus (HERV) signatures in the GC and lymphoma subtypes whose activity can be used in combination with gene expression to define B-cell lineage in lymphoid malignancies, highlighting the potential of retrotranscriptomic analyses as a tool in lymphoma classification, diagnosis, and the identification of novel treatment groups.
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Affiliation(s)
- Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jez L. Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helena Reyes-Gopar
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gislaine Curty
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Jonas J. Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Peter Martin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Fabio E. Leal
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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Kang Q, Guo X, Li T, Yang C, Han J, Jia L, Liu Y, Wang X, Zhang B, Li J, Wen HL, Li H, Li L. Identification of differentially expressed HERV-K(HML-2) loci in colorectal cancer. Front Microbiol 2023; 14:1192900. [PMID: 37342563 PMCID: PMC10277637 DOI: 10.3389/fmicb.2023.1192900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/23/2023] Open
Abstract
Colorectal cancer is one of the malignant tumors with the highest mortality rate in the world. Survival rates vary significantly among patients at various stages of the disease. A biomarker capable of early diagnosis is required to facilitate the early detection and treatment of colorectal cancer. Human endogenous retroviruses (HERVs) are abnormally expressed in various diseases, including cancer, and have been involved in cancer development. Real-time quantitative PCR was used to detect the transcript levels of HERV-K(HML-2) gag, pol, and env in colorectal cancer to systematically investigate the connection between HERV-K(HML-2) and colorectal cancer. The results showed that HERV-K(HML-2) transcript expression was significantly higher than healthy controls and was consistent at the population and cell levels. We also used next-generation sequencing to identify and characterize HERV-K(HML-2) loci that were differentially expressed between colorectal cancer patients and healthy individuals. The analysis revealed that these loci were concentrated in immune response signaling pathways, implying that HERV-K impacts the tumor-associated immune response. Our results indicated that HERV-K might serve as a screening tumor marker and a target for tumor immunotherapy in colorectal cancer.
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Affiliation(s)
- Qian Kang
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Xin Guo
- Key Laboratory for the Prevention and Control of Infectious Diseases, Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tianfu Li
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Caiqin Yang
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Bohan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hong-Ling Wen
- Key Laboratory for the Prevention and Control of Infectious Diseases, Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of Virology, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
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Felley-Bosco E. Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and Immunotherapy. Cancers (Basel) 2023; 15:cancers15112969. [PMID: 37296931 DOI: 10.3390/cancers15112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Recent high-throughput RNA sequencing technologies have confirmed that a large part of the non-coding genome is transcribed. The priority for further investigations is nevertheless generally given in cancer to coding sequences, due to the obvious interest of finding therapeutic targets. In addition, several RNA-sequencing pipelines eliminate repetitive sequences, which are difficult to analyze. In this review, we shall focus on endogenous retroviruses. These sequences are remnants of ancestral germline infections by exogenous retroviruses. These sequences represent 8% of human genome, meaning four-fold the fraction of the genome encoding for proteins. These sequences are generally mostly repressed in normal adult tissues, but pathological conditions lead to their de-repression. Specific mesothelioma-associated endogenous retrovirus expression and their association to clinical outcome is discussed.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, Zürich University Hospital, 8091 Zurich, Switzerland
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34
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Vensko SP, Olsen K, Bortone D, Smith CC, Chai S, Beckabir W, Fini M, Jadi O, Rubinsteyn A, Vincent BG. LENS: Landscape of Effective Neoantigens Software. Bioinformatics 2023; 39:btad322. [PMID: 37184881 PMCID: PMC10246587 DOI: 10.1093/bioinformatics/btad322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/04/2023] [Accepted: 05/12/2023] [Indexed: 05/16/2023] Open
Abstract
MOTIVATION Elimination of cancer cells by T cells is a critical mechanism of anti-tumor immunity and cancer immunotherapy response. T cells recognize cancer cells by engagement of T cell receptors with peptide epitopes presented by major histocompatibility complex molecules on the cancer cell surface. Peptide epitopes can be derived from antigen proteins coded for by multiple genomic sources. Bioinformatics tools used to identify tumor-specific epitopes via analysis of DNA and RNA-sequencing data have largely focused on epitopes derived from somatic variants, though a smaller number have evaluated potential antigens from other genomic sources. RESULTS We report here an open-source workflow utilizing the Nextflow DSL2 workflow manager, Landscape of Effective Neoantigens Software (LENS), which predicts tumor-specific and tumor-associated antigens from single nucleotide variants, insertions and deletions, fusion events, splice variants, cancer-testis antigens, overexpressed self-antigens, viruses, and endogenous retroviruses. The primary advantage of LENS is that it expands the breadth of genomic sources of discoverable tumor antigens using genomics data. Other advantages include modularity, extensibility, ease of use, and harmonization of relative expression level and immunogenicity prediction across multiple genomic sources. We present an analysis of 115 acute myeloid leukemia samples to demonstrate the utility of LENS. We expect LENS will be a valuable platform and resource for T cell epitope discovery bioinformatics, especially in cancers with few somatic variants where tumor-specific epitopes from alternative genomic sources are an elevated priority. AVAILABILITY AND IMPLEMENTATION More information about LENS, including code, workflow documentation, and instructions, can be found at (https://gitlab.com/landscape-of-effective-neoantigens-software).
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Affiliation(s)
- Steven P Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Kelly Olsen
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Dante Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Christof C Smith
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Shengjie Chai
- Uber Technologies, Inc., San Francisco, CA, United States
| | - Wolfgang Beckabir
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Misha Fini
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Othmane Jadi
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Alex Rubinsteyn
- Department of Genetics, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Computational Medicine Program, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Computational Medicine Program, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology, Department of Medicine, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
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35
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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Abstract
Recent advances in cancer immunotherapy - ranging from immune-checkpoint blockade therapy to adoptive cellular therapy and vaccines - have revolutionized cancer treatment paradigms, yet the variability in clinical responses to these agents has motivated intense interest in understanding how the T cell landscape evolves with respect to response to immune intervention. Over the past decade, the advent of multidimensional single-cell technologies has provided the unprecedented ability to dissect the constellation of cell states of lymphocytes within a tumour microenvironment. In particular, the rapidly expanding capacity to definitively link intratumoural phenotypes with the antigen specificity of T cells provided by T cell receptors (TCRs) has now made it possible to focus on investigating the properties of T cells with tumour-specific reactivity. Moreover, the assessment of TCR clonality has enabled a molecular approach to track the trajectories, clonal dynamics and phenotypic changes of antitumour T cells over the course of immunotherapeutic intervention. Here, we review the current knowledge on the cellular states and antigen specificities of antitumour T cells and examine how fine characterization of T cell dynamics in patients has provided meaningful insights into the mechanisms underlying effective cancer immunotherapy. We highlight those T cell subsets associated with productive T cell responses and discuss how diverse immunotherapies might leverage the pre-existing tumour-reactive T cell pool or instruct de novo generation of antitumour specificities. Future studies aimed at elucidating the factors associated with the elicitation of productive antitumour T cell immunity are anticipated to instruct the design of more efficacious treatment strategies.
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Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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37
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Zhong F, Lin Y, Zhao L, Yang C, Ye Y, Shen Z. Reshaping the tumour immune microenvironment in solid tumours via tumour cell and immune cell DNA methylation: from mechanisms to therapeutics. Br J Cancer 2023:10.1038/s41416-023-02292-0. [PMID: 37117649 DOI: 10.1038/s41416-023-02292-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
In recent years, the tumour microenvironment (TME) of solid tumours has attracted more and more attention from researchers, especially those non-tumour components such as immune cells. Infiltration of various immune cells causes tumour immune microenvironment (TIME) heterogeneity, and results in different therapeutic effects. Accumulating evidence showed that DNA methylation plays a crucial role in remodelling TIME and is associated with the response towards immune checkpoint inhibitors (ICIs). During carcinogenesis, DNA methylation profoundly changes, specifically, there is a global loss of DNA methylation and increased DNA methylation at the promoters of suppressor genes. Immune cell differentiation is disturbed, and exclusion of immune cells from the TME occurs at least in part due to DNA methylation reprogramming. Therefore, pharmaceutical interventions targeting DNA methylation are promising. DNA methyltransferase inhibitors (DNMTis) enhance antitumor immunity by inducing transcription of transposable elements and consequent viral mimicry. DNMTis upregulate the expression of tumour antigens, mediate immune cells recruitment and reactivate exhausted immune cells. In preclinical studies, DNMTis have shown synergistic effect when combined with immunotherapies, suggesting new strategies to treat refractory solid tumours.
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Affiliation(s)
- Fengyun Zhong
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 100044, Beijing, P. R. China.
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, 100044, Beijing, P. R. China.
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38
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Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
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Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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39
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Ursino C, Mouric C, Gros L, Bonnefoy N, Faget J. Intrinsic features of the cancer cell as drivers of immune checkpoint blockade response and refractoriness. Front Immunol 2023; 14:1170321. [PMID: 37180110 PMCID: PMC10169604 DOI: 10.3389/fimmu.2023.1170321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Immune checkpoint blockade represents the latest revolution in cancer treatment by substantially increasing patients' lifetime and quality of life in multiple neoplastic pathologies. However, this new avenue of cancer management appeared extremely beneficial in a minority of cancer types and the sub-population of patients that would benefit from such therapies remain difficult to predict. In this review of the literature, we have summarized important knowledge linking cancer cell characteristics with the response to immunotherapy. Mostly focused on lung cancer, our objective was to illustrate how cancer cell diversity inside a well-defined pathology might explain sensitivity and refractoriness to immunotherapies. We first discuss how genomic instability, epigenetics and innate immune signaling could explain differences in the response to immune checkpoint blockers. Then, in a second part we detailed important notions suggesting that altered cancer cell metabolism, specific oncogenic signaling, tumor suppressor loss as well as tight control of the cGAS/STING pathway in the cancer cells can be associated with resistance to immune checkpoint blockade. At the end, we discussed recent evidences that could suggest that immune checkpoint blockade as first line therapy might shape the cancer cell clones diversity and give rise to the appearance of novel resistance mechanisms.
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Affiliation(s)
| | | | | | | | - Julien Faget
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U1194, Univ Montpellier, Institut du Cancer de Montpellier (ICM), Montpellier, France
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40
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Hou L, Liu X. Immunotherapy and Immune Infiltration in Patients with Clear Cell Renal Cell Carcinoma: A Comprehensive Analysis. Genet Res (Camb) 2023; 2023:3898610. [PMID: 37065178 PMCID: PMC10101751 DOI: 10.1155/2023/3898610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 04/08/2023] Open
Abstract
On a global scale, renal cell carcinoma (RCC) is the second most common form of cancer and the 10th leading cause of cancer-related deaths. There are about 70% of cases of RCC that are clear cell renal cell carcinomas (ccRCCs). This study explores possible targets for immune therapy in patients with RCC. In the recent years, immunotherapy has been applied to RCC patients. In order to identify genes that are closely associated with immune cells, a weighted gene coexpression network analysis (WGCNA) was conducted. A close association was found between genes involved in MEred and M0 macrophages, M1 macrophages, and M2 macrophages. A prognostic prediction model is subsequently developed by incorporating the OS and the expression level of key genes from the RCC cohort into a univariate COX regression analysis, a multivariate COX regression analysis, and a combined COX regression analysis. We finally discovered that 6 genes are closely associated with the prognosis of RCC patients, including SLC16A12, SLC2A9, IGF2BP2, EMX2, ANK3, and METTL7A. The survival analysis proved the prognostic prediction value of the model. The 1-year, 3-year, and 5-year AUC of ROC curves are 0.759, 0.723, and 0.733, respectively. For clinical ROC curves, the AUC score for risk score, stage, grade, and T stage is 0.759, 0.824, 0722, and 0.736, respectively. The nomogram was constructed for better prognosis prediction of RCC patients. In addition, GSVA and GO enrichment analysis was performed to explore the potential pathways that are closely associated with genes involved in the prognostic prediction model. Accordingly, our study demonstrates that immune cells play a crucial role in RCC infiltration. The development of a prognostic prediction model is a potential new prognostic biomarker and potential immunotherapy target for tumors.
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Affiliation(s)
- Lin Hou
- Operating Room, West China Hospital, Sichuan University, West China School of Nursing, Chengdu, China
| | - Xinyue Liu
- Operating Room, West China Hospital, Sichuan University, West China School of Nursing, Chengdu, China
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41
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Moeckel C, Bakhl K, Georgakopoulos-Soares I, Zaravinos A. The Efficacy of Tumor Mutation Burden as a Biomarker of Response to Immune Checkpoint Inhibitors. Int J Mol Sci 2023; 24:ijms24076710. [PMID: 37047684 PMCID: PMC10095310 DOI: 10.3390/ijms24076710] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Cancer is one of the leading causes of death in the world; therefore, extensive research has been dedicated to exploring potential therapeutics, including immune checkpoint inhibitors (ICIs). Initially, programmed-death ligand-1 was the biomarker utilized to predict the efficacy of ICIs. However, its heterogeneous expression in the tumor microenvironment, which is critical to cancer progression, promoted the exploration of the tumor mutation burden (TMB). Research in various cancers, such as melanoma and lung cancer, has shown an association between high TMB and response to ICIs, increasing its predictive value. However, the TMB has failed to predict ICI response in numerous other cancers. Therefore, future research is needed to analyze the variations between cancer types and establish TMB cutoffs in order to create a more standardized methodology for using the TMB clinically. In this review, we aim to explore current research on the efficacy of the TMB as a biomarker, discuss current approaches to overcoming immunoresistance to ICIs, and highlight new trends in the field such as liquid biopsies, next generation sequencing, chimeric antigen receptor T-cell therapy, and personalized tumor vaccines.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Katrina Bakhl
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
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42
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Zhou M, Kim WY. Viewing RCC with a DNA Methylation Lens ENHANCES Understanding of ICI Resistance. Clin Cancer Res 2023; 29:1170-1172. [PMID: 36700785 PMCID: PMC10073255 DOI: 10.1158/1078-0432.ccr-22-3574] [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: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/27/2023]
Abstract
Clear-cell renal cell carcinoma tumors with an enhancer demethylator phenotype (TED) harbor a worse prognosis and derive less clinical benefit from immunotherapy. The TED phenotype may help predict immunotherapy resistance. See related article by Lu et al., p. 1279.
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Affiliation(s)
- Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - William Y. Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
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43
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Kapur P, Rajaram S, Brugarolas J. The expanding role of BAP1 in clear cell renal cell carcinoma. Hum Pathol 2023; 133:22-31. [PMID: 35932824 PMCID: PMC9898467 DOI: 10.1016/j.humpath.2022.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023]
Abstract
Mutations drive renal cell carcinoma biology and tumor growth. The BRCA1-associated protein-1 (BAP1) gene is frequently mutated in clear cell renal cell carcinoma (ccRCC) and has emerged as a prognostic and putative predictive biomarker. In this review, we discuss the role of BAP1 as a signature event of a subtype of ccRCC marked by aggressiveness, inflammation, and possibly a heightened response to immunotherapy.
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Affiliation(s)
- Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, Dallas, TX, 75390, USA.
| | - Satwik Rajaram
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, Dallas, TX, 75390, USA; Department of Internal Medicine (Hematology-Oncology), University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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44
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Inozume T, Namikawa K, Kato H, Yoshikawa S, Kiniwa Y, Yoshino K, Mizuhashi S, Ito T, Takenouchi T, Matsushita S, Fujisawa Y, Matsuzawa T, Sugihara S, Asai J, Kitagawa H, Maekawa T, Isei T, Yasuda M, Yamazaki N, Uhara H, Nakamura Y. Analyzing the relationship between the efficacy of first-line immune checkpoint inhibitors and cumulative sun damage in Japanese patients with advanced BRAF wild-type nonacral cutaneous melanoma: A retrospective real-world, multicenter study. J Dermatol Sci 2023; 110:19-26. [PMID: 37045720 DOI: 10.1016/j.jdermsci.2023.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND Efficacy of anti-PD-1 antibody monotherapy (PD1) or anti-PD-1 plus anti-CTLA-4 combination therapy (PD1 +CTLA4) for melanoma is affected by its clinical subtype. The amount of tumor mutation burden (TMB) caused by cumulative sun damage (CSD) is occasionally used to explain this; however, their relationship in Japanese nonacral cutaneous melanoma (NACM) is still unclear. OBJECTIVE To analyze the ICI efficacy and its relationship with CSD of the primary lesion in Japanese patients with NACM. METHODS Japanese patients with advanced BRAF wild-type NACM who received first-line ICIs were recruited. Objective response rate (ORR), progression-free survival (PFS), and overall survival (OS), and the degree of solar elastosis (SE) were evaluated. RESULTS A total of 146 patients (PD1 group 113 and PD1 +CTLA4 group 33) were included. No significant differences in ORR were observed between the PD1 and PD1 +CTLA4 groups (35 % vs. 36 %; P = 0.67) or PFS and OS (median PFS 6.1 months vs. 8.5 months; P = 0.46, median OS 28.1 months vs. not reached; P = 0.59). Multivariate survival analysis revealed that PD1 +CTLA4 did not prolong the PFS and OS. The SE score had no effect on either PFS or OS. CONCLUSIONS ICI efficacy was not as high as those reported in Western countries, and PD1 +CTLA4 did not present better clinical efficacy compared to PD1. Indicators of CSD did not serve as a predictor for clinical advantage. These findings may partially support the theory that ICI efficacy is affected by CSD; however, other unrecognized factors may also exist.
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45
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Elbasir A, Ye Y, Schäffer DE, Hao X, Wickramasinghe J, Tsingas K, Lieberman PM, Long Q, Morris Q, Zhang R, Schäffer AA, Auslander N. A deep learning approach reveals unexplored landscape of viral expression in cancer. Nat Commun 2023; 14:785. [PMID: 36774364 PMCID: PMC9922274 DOI: 10.1038/s41467-023-36336-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/25/2023] [Indexed: 02/13/2023] Open
Abstract
About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
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Affiliation(s)
| | - Ying Ye
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Daniel E Schäffer
- The Wistar Institute, Philadelphia, PA, 19104, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Xue Hao
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | | | - Konstantinos Tsingas
- The Wistar Institute, Philadelphia, PA, 19104, USA.,University of Pennsylvania, Philadelphia, PA, USA
| | | | - Qi Long
- University of Pennsylvania, Philadelphia, PA, USA
| | - Quaid Morris
- Computational and Systems Biology, Sloan Kettering Institute, New York City, NY, 10065, USA
| | - Rugang Zhang
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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46
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Dhillon P, Mulholland KA, Hu H, Park J, Sheng X, Abedini A, Liu H, Vassalotti A, Wu J, Susztak K. Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development. Nat Commun 2023; 14:559. [PMID: 36732547 PMCID: PMC9895454 DOI: 10.1038/s41467-023-36212-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Inflammation is a common feature of all forms of chronic kidney disease; however, the underlying mechanism remains poorly understood. Evolutionarily inherited endogenous retroviruses (ERVs) have the potential to trigger an immune reaction. Comprehensive RNA-sequencing of control and diseased kidneys from human and mouse disease models indicated higher expression of transposable elements (TEs) and ERVs in diseased kidneys. Loss of cytosine methylation causing epigenetic derepression likely contributes to an increase in ERV levels. Genetic deletion/pharmacological inhibition of DNA methyltransferase 1 (DNMT1) induces ERV expression. In cultured kidney tubule cells, ERVs elicit the activation of cytosolic nucleotide sensors such as RIG-I, MDA5, and STING. ERVs expressions in kidney tubules trigger RIG-I/STING, and cytokine expression, and correlate with the presence of immune cells. Genetic deletion of RIG-I or STING or treatment with reverse transcriptase inhibitor ameliorates kidney fibroinflammation. Our data indicate an important role of epigenetic derepression-induced ERV activation triggering renal fibroinflammation.
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Affiliation(s)
- Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Kelly Ann Mulholland
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Jihwan Park
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Xin Sheng
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Allison Vassalotti
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19014, USA.
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47
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Li HT, Jang HJ, Rohena-Rivera K, Liu M, Gujar H, Kulchycki J, Zhao S, Billet S, Zhou X, Weisenberger DJ, Gill I, Jones PA, Bhowmick NA, Liang G. RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer. Cell Rep 2023; 42:112016. [PMID: 36662621 PMCID: PMC10034851 DOI: 10.1016/j.celrep.2023.112016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Tumors with mutations in chromatin regulators present attractive targets for DNA hypomethylating agent 5-aza-2'-deoxycytidine (DAC) therapy, which further disrupts cancer cells' epigenomic fidelity and reactivates transposable element (TE) expression to drive viral mimicry responses. SETD2 encodes a histone methyltransferase (H3K36me3) and is prevalently mutated in advanced kidney cancers. Here, we show that SETD2-mutant kidney cancer cells are especially sensitive in vitro and in vivo to DAC treatment. We find that the viral mimicry response are direct consequences of mis-splicing events, such as exon inclusions or extensions, triggered by DAC treatment in an SETD2-loss context. Comprehensive epigenomic analysis reveals H3K9me3 deposition, rather than DNA methylation dynamics, across intronic TEs might contribute to elevated mis-splicing rates. Through epigenomic and transcriptomic analyses, we show that SETD2-deficient kidney cancers are prone to mis-splicing, which can be therapeutically exacerbated with DAC treatment to increase viral mimicry activation and provide synergy with combinatorial immunotherapy approaches.
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Affiliation(s)
- Hong-Tao Li
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - H Josh Jang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Krizia Rohena-Rivera
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Minmin Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Hemant Gujar
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Justin Kulchycki
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Shuqing Zhao
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Sandrin Billet
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xinyi Zhou
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Inderbir Gill
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter A Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Neil A Bhowmick
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA.
| | - Gangning Liang
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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48
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Brochier W, Bricard O, Coulie PG. Facts and Hopes in Cancer Antigens Recognized by T Cells. Clin Cancer Res 2023; 29:309-315. [PMID: 36044396 DOI: 10.1158/1078-0432.ccr-21-3798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/13/2022] [Accepted: 08/15/2022] [Indexed: 01/19/2023]
Abstract
T cells are key effectors of our immune response against tumors and exert their antitumor effects upon recognizing a variety of tumor-specific peptides presented by HLA molecules on the surface of tumor cells. The identification of the tumor-specific antigens of a given tumor is not required for immune checkpoint therapy (ICT), which mainly reactivates existing tumor-specific T cells together with T cells of unknown specificities. To decrease the activation of non-tumor-specific T cells, active or passive immunizations against tumor-specific antigens are considered. These immunizations require the identification of at least some of the tumor-specific antigens displayed on the tumor cells of a patient. While this has become an easy task for tumors with a large number of mutations generating neoantigens, it remains difficult for the remainder. Here, we review some facts about human tumor-specific or tumor-associated antigens, as well as some hopes for their future use in cancer immunotherapy.
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Affiliation(s)
| | - Orian Bricard
- de Duve Institute, UCLouvain, Brussels, Belgium.,Immunology Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Pierre G Coulie
- de Duve Institute, UCLouvain, Brussels, Belgium.,Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Wavre, Belgium
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49
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Alldredge J, Kumar V, Nguyen J, Sanders BE, Gomez K, Jayachandran K, Zhang J, Schwarz J, Rahmatpanah F. Endogenous Retrovirus RNA Expression Differences between Race, Stage and HPV Status Offer Improved Prognostication among Women with Cervical Cancer. Int J Mol Sci 2023; 24:1492. [PMID: 36675007 PMCID: PMC9864224 DOI: 10.3390/ijms24021492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Endogenous human retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the human genome. Using publicly available RNA-seq data from 63 cervical cancer patients, we investigated the expression of ERVs in cervical cancers. Four aspects of cervical cancer were investigated: patient ancestral background, tumor HPV type, tumor stage and patient survival. Between the racial subgroups, 74 ERVs were significantly differentially expressed, with Black Americans having 30 upregulated and 44 downregulated (including MER21C, HERV9-int, and HERVH-int) ERVs when compared to White Americans. We found that 3313 ERVs were differentially expressed between HPV subgroups, including MER41A, HERVH-int and HERVK9. There were 28 downregulated (including MLT1D and HERVH-int) and 61 upregulated (including MER41A) ERVs in locally advanced-stage compared to early-stage samples. Tissue microarrays of cervical cancer patients were used to investigate the protein expression of ERVs with protein coding potential (i.e., HERVK and ERV3). Significant differences in protein expression of ERV3 (p = 0.000905) were observed between early-stage and locally advanced-stage tumors. No significant differential expression at the protein level was found for HERVK7 (p = 0.243). We also investigated a prognostic model, supplementing a baseline prediction model using FIGO stage, age and HPV positivity with ERVs data. The expression levels of all ERVs in the HERVd were input into a Lasso-Cox proportional hazards model, developing a predictive 67-ERV panel. When ERVs expression levels were supplemented with the clinical data, a significant increase in prognostic power (p = 9.433 × 10-15) relative to that obtained with the clinical parameters alone (p = 0.06027) was observed. In summary, ERV RNA expression in cervical cancer tumors is significantly different among racial cohorts, HPV subgroups and disease stages. The combination of the expression of certain ERVs in cervical cancers with clinical factors significantly improved prognostication compared to clinical factors alone; therefore, ERVs may serve as future prognostic biomarkers and therapeutic targets. Novelty and Impact: When endogenous retroviral (ERV) expression signatures were combined with currently employed clinical prognosticators of relapse of cervical cancer, the combination outperformed prediction models based on clinical prognosticators alone. ERV expression signatures in tumor biopsies may therefore be useful to help identify patients at greater risk of recurrence. The novel ERV expression signatures or adjacent genes possibly impacted by ERV expression described here may also be targets for the development of future therapeutic interventions.
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Affiliation(s)
- Jill Alldredge
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Vinay Kumar
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - James Nguyen
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Brooke E. Sanders
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Karina Gomez
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Kay Jayachandran
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jin Zhang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Julie Schwarz
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Farah Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
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50
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Liu T, Li S, Xia C, Xu D. TERT promoter mutations and methylation for telomerase activation in urothelial carcinomas: New mechanistic insights and clinical significance. Front Immunol 2023; 13:1071390. [PMID: 36713366 PMCID: PMC9877314 DOI: 10.3389/fimmu.2022.1071390] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Telomerase, an RNA-dependent DNA polymerase synthesizing telomeric TTAGGG sequences, is primarily silent in normal human urothelial cells (NHUCs), but widely activated in urothelial cell-derived carcinomas or urothelial carcinomas (UCs) including UC of the bladder (UCB) and upper track UC (UTUC). Telomerase activation for telomere maintenance is required for the UC development and progression, and the key underlying mechanism is the transcriptional de-repression of the telomerase reverse transcriptase (TERT), a gene encoding the rate-limiting, telomerase catalytic component. Recent mechanistic explorations have revealed important roles for TERT promoter mutations and aberrant methylation in activation of TERT transcription and telomerase in UCs. Moreover, these TERT-featured genomic and epigenetic alterations have been evaluated for their usefulness in non-invasive UC diagnostics, recurrence monitoring, outcome prediction and response to treatments such as immunotherapy. Importantly, the detection of the mutated TERT promoter and TERT mRNA as urinary biomarkers holds great promise for urine-based UC liquid biopsy. In the present article, we review recent mechanistic insights into altered TERT promoter-mediated telomerase activation in UCs and discuss potential clinical implications. Specifically, we compare differences in senescence and transformation between NHUCs and other types of epithelial cells, address the interaction between TERT promoter mutations and other factors to affect UC progression and outcomes, evaluate the impact of TERT promoter mutations and TERT-mediated activation of human endogenous retrovirus genes on UC immunotherapy including Bacillus Calmette-Guérin therapy and immune checkpoint inhibitors. Finally, we suggest the standardization of a TERT assay and evaluation system for UC clinical practice.
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Affiliation(s)
- Tiantian Liu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shihong Li
- Department of Pathology, Maternal and Child Health Hospital of Liaocheng, Liaocheng, China
| | - Chuanyou Xia
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China,*Correspondence: Chuanyou Xia, ; Dawei Xu,
| | - Dawei Xu
- Department of Medicine, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden,*Correspondence: Chuanyou Xia, ; Dawei Xu,
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