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Zhao Y, Liu Z, Deng K, Qu H, Zhang Q, Zhou P, Yang M, Yang X, Wang H, Li R, Xia J. Identification of TAP1 as a T-cell related therapeutic target in gastric cancer by mediating oxalipliatin-related synergistic enhancement of immunotherapy. Int Immunopharmacol 2024; 132:111998. [PMID: 38593510 DOI: 10.1016/j.intimp.2024.111998] [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: 10/14/2023] [Revised: 11/30/2023] [Accepted: 03/31/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Given the intricate molecular complexities and heterogeneity inherent in T-cell immunotherapy of gastric cancer (GC), elucidative T-cell-related biomarkers were imperative needed for facilitating the prediction of GC patient prognosis and identify potential synergistic therapeutic targets. METHODS We conducted COX regression analysis in TISIDB, TCGA-STAD, and GEO databases to identify 19 GC T-cell-mediated sensitivity tumor killing (TTK) genes (key GCTTKs). Based on key GCTTKs, we constructed two TTK patterns and analyzed their metabolic pathways, mutation features, clinical data distribution, immune cell infiltration, and prognosis. LASSO regression was performed to develop a T-cell-mediated GC Prognosis (TGCP) model. We validated the TGCP model in GC patients. TAP1 was further selected for investigation of its biological functions and molecular mechanisms. We assessed the potential of TAP1 as a promising therapeutic target for GC using Patient-derived organoids (PDOs)-derived xenografts (PDOXs) models of GC. RESULTS The TTK patterns display notable disparities. The TGCP model showcases its proficiency in predicting immune response efficacy, effectively distinguishes immunotherapy difference GC patients. Our findings find further confirmation in PDOX models, affirming TAP1 can enhance immunotherapy facilitated by PDL1 inhibitors. Furthermore, Oxaliplatin, by promoting TAP1 expression, augments PDL1 expression, thereby enhancing the efficacy of immunotherapy. CONCLUSIONS We constructed a TGCP model, which demonstrates satisfactory predictive accuracy. Out of 9 prognostic genes, TAP1 was validated as a synergistic target for Oxaliplatin and PDL1 inhibitors, offering a genetic-level explanation for the synergy observed in GC treatment involving Oxaliplatin in combination with PDL1 inhibitors.
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Affiliation(s)
- Yupeng Zhao
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Ziyuan Liu
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Kaiyuan Deng
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Huiheng Qu
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Qing Zhang
- Affiliated WuXi Clinical College of Nantong University, Wuxi, PR China
| | - Peng Zhou
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Mengqi Yang
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China
| | - Xiao Yang
- Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Hao Wang
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China
| | - Ranran Li
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
| | - Jiazeng Xia
- Department of General Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, PR China; Department of General Surgery, Jiangnan University Medical Center, Wuxi, PR China; Affiliated WuXi Clinical College of Nantong University, Wuxi, PR China.
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Song Y, Xue M, Wang F, Tang Q, Luo Y, Zheng M, Wang Y, Xue P, Dong N, Sun R, Fang M. Study on the Characteristics of Coarse Feeding Tolerance of Ding'an Pigs: Phenotypic and Candidate Genes Identification. Genes (Basel) 2024; 15:599. [PMID: 38790227 PMCID: PMC11121715 DOI: 10.3390/genes15050599] [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: 03/25/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Ding'an (DA) pig, a prominent local breed in Hainan Province, exhibits notable advantages in coarse feeding tolerance and high-quality meat. To explore the potential genetic mechanism of coarse feeding tolerance in DA pigs, 60-day-old full sibling pairs of DA and DLY (Duroc-Landrace-Yorkshire) pigs were subjected to fed normal (5%) and high (10%) crude fiber diets for 56 days, respectively. The findings showed that increasing the crude fiber level had no impact on the apparent digestibility of crude fiber, intramuscular fat, and marbling scores in DA pigs, whereas these factors were significantly reduced in DLY pigs (p < 0.05). Through differential expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA) of the colonic mucosal transcriptome data, 65 and 482 candidate genes with coarse feeding tolerance in DA pigs were identified, respectively. Joint analysis screened four key candidate genes, including LDHB, MLC1, LSG1, and ESM1, potentially serving as key regulated genes for coarse feeding tolerance. Functional analysis revealed that the most significant pathway enriched in differential genes associated with coarse feeding tolerance in Ding'an pigs was the signaling receptor binding. The results hold substantial significance for advancing our understanding of the genetic mechanisms governing coarse feeding tolerance in Ding'an pigs.
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Affiliation(s)
- Yanxia Song
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Feng Wang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571100, China; (F.W.); (R.S.)
| | - Qiguo Tang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Meili Zheng
- Beijing General Station of Animal Husbandry, Beijing 100107, China;
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Pengxiang Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Ningqi Dong
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Ruiping Sun
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571100, China; (F.W.); (R.S.)
| | - Meiying Fang
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
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Pandey S, Anang V, Schumacher MM. Mitochondria driven innate immune signaling and inflammation in cancer growth, immune evasion, and therapeutic resistance. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 386:223-247. [PMID: 38782500 DOI: 10.1016/bs.ircmb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Mitochondria play an important and multifaceted role in cellular function, catering to the cell's energy and biosynthetic requirements. They modulate apoptosis while responding to diverse extracellular and intracellular stresses including reactive oxygen species (ROS), nutrient and oxygen scarcity, endoplasmic reticulum stress, and signaling via surface death receptors. Integral components of mitochondria, such as mitochondrial DNA (mtDNA), mitochondrial RNA (mtRNA), Adenosine triphosphate (ATP), cardiolipin, and formyl peptides serve as major damage-associated molecular patterns (DAMPs). These molecules activate multiple innate immune pathways both in the cytosol [such as Retionoic Acid-Inducible Gene-1 (RIG-1) and Cyclic GMP-AMP Synthase (cGAS)] and on the cell surface [including Toll-like receptors (TLRs)]. This activation cascade leads to the release of various cytokines, chemokines, interferons, and other inflammatory molecules and oxidative species. The innate immune pathways further induce chronic inflammation in the tumor microenvironment which either promotes survival and proliferation or promotes epithelial to mesenchymal transition (EMT), metastasis and therapeutic resistance in the cancer cell's. Chronic activation of innate inflammatory pathways in tumors also drives immunosuppressive checkpoint expression in the cancer cells and boosts the influx of immune-suppressive populations like Myeloid-Derived Suppressor Cells (MDSCs) and Regulatory T cells (Tregs) in cancer. Thus, sensing of cellular stress by the mitochondria may lead to enhanced tumor growth. In addition to that, the tumor microenvironment also becomes a source of immunosuppressive cytokines. These cytokines exert a debilitating effect on the functioning of immune effector cells, and thus foster immune tolerance and facilitate immune evasion. Here we describe how alteration of the mitochondrial homeostasis and cellular stress drives innate inflammatory pathways in the tumor microenvironment.
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Affiliation(s)
- Sanjay Pandey
- Department of Radiation Oncology, Montefiore Medical Center, Bronx, NY, United States.
| | - Vandana Anang
- International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Michelle M Schumacher
- Department of Radiation Oncology, Montefiore Medical Center, Bronx, NY, United States; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
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4
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Duvivier L, Gerard L, Diaz A, Gillet JP. Linking ABC transporters to the hallmarks of cancer. Trends Cancer 2024; 10:124-134. [PMID: 37884430 DOI: 10.1016/j.trecan.2023.09.013] [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: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Human ATP-binding cassette (ABC) transporters are ubiquitously expressed and transport a broad range of endogenous and xenobiotic substrates across extra- and intracellular membranes. Mutations in ABC genes cause 21 monogenic diseases, and polymorphisms in these genes are associated with susceptibility to complex diseases. ABC transporters also play a major role in drug bioavailability, and they mediate multidrug resistance in cancer. At least 13 ABC transporters were shown to be involved in drug resistance in vitro. In the past decade, efforts have been made to elucidate their roles in tumor biology. Herein, we explore their involvement in tumorigenesis, focusing on the hallmarks of cells as they make their way from normalcy to neoplastic growth states.
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Affiliation(s)
- Laurent Duvivier
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, Namur, Belgium
| | - Louise Gerard
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, Namur, Belgium
| | - Adriana Diaz
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, Namur, Belgium
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, Namur, Belgium.
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Lee Y, Moon S, Seok JY, Lee JH, Nam S, Chung YS. Characterization of the genomic alterations in poorly differentiated thyroid cancer. Sci Rep 2023; 13:19154. [PMID: 37932340 PMCID: PMC10628257 DOI: 10.1038/s41598-023-46466-5] [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: 07/26/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Poorly differentiated thyroid carcinoma (PDTC) is a subtype of thyroid cancer that has a high rate of metastasis or recurrence and a relatively poor prognosis. However, there are few studies that have been conducted on PDTC at the whole protein-coding gene scale. Here, we performed genomic profiling of 15 patients with PDTC originated from follicular thyroid carcinoma using whole exome sequencing and also performed gene functional enrichment analysis of differentially expressed genes (DEGs) for three patients. Further, we investigated genetic variants associated with PDTC progression and the characteristics of clinical pathology. We revealed somatic genomic alterations in the RAF1, MAP2K2, and AKT2 genes that were not reported in previous studies. We confirmed frequent occurrences in the RAS gene in patients with PDTC; the genetic alterations were associated with the RAS-RAF-MEK-ERK/JNK, PI3K-AKT-mTOR signaling pathways, and the cell cycle. DEG analysis showed that immune response was lower in cancer tissues than in normal tissues. Through the association analysis of somatic mutations and the characteristics of clinical pathology from patients with PDTC, the somatic mutations of ABCA12, CLIP1, and ATP13A3 were significantly associated with a vascular invasion phenotype. By providing molecular genetic insight on PDTC, this study may contribute to the discovery of novel therapeutic target candidates.
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Affiliation(s)
- Yeeun Lee
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea
| | - SeongRyeol Moon
- A.I. Structural Design Team, Division of Biodrug Analysis, New Drug Development Center, OSONG Medical Innovation Foundation, Cheongju-si, 28160, Chungcheongbuk-do, Korea
| | - Jae Yeon Seok
- Department of Pathology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin Severance Hospital 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Korea
| | - Joon-Hyop Lee
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea.
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, 21999, Korea.
| | - Yoo Seung Chung
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea.
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Blander JM, Yee Mon KJ, Jha A, Roycroft D. The show and tell of cross-presentation. Adv Immunol 2023; 159:33-114. [PMID: 37996207 DOI: 10.1016/bs.ai.2023.08.002] [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: 11/25/2023]
Abstract
Cross-presentation is the culmination of complex subcellular processes that allow the processing of exogenous proteins and the presentation of resultant peptides on major histocompatibility class I (MHC-I) molecules to CD8 T cells. Dendritic cells (DCs) are a cell type that uniquely specializes in cross-presentation, mainly in the context of viral or non-viral infection and cancer. DCs have an extensive network of endovesicular pathways that orchestrate the biogenesis of an ideal cross-presentation compartment where processed antigen, MHC-I molecules, and the MHC-I peptide loading machinery all meet. As a central conveyor of information to CD8 T cells, cross-presentation allows cross-priming of T cells which carry out robust adaptive immune responses for tumor and viral clearance. Cross-presentation can be canonical or noncanonical depending on the functional status of the transporter associated with antigen processing (TAP), which in turn influences the vesicular route of MHC-I delivery to internalized antigen and the cross-presented repertoire of peptides. Because TAP is a central node in MHC-I presentation, it is targeted by immune evasive viruses and cancers. Thus, understanding the differences between canonical and noncanonical cross-presentation may inform new therapeutic avenues against cancer and infectious disease. Defects in cross-presentation on a cellular and genetic level lead to immune-related disease progression, recurrent infection, and cancer progression. In this chapter, we review the process of cross-presentation beginning with the DC subsets that conduct cross-presentation, the signals that regulate cross-presentation, the vesicular trafficking pathways that orchestrate cross-presentation, the modes of cross-presentation, and ending with disease contexts where cross-presentation plays a role.
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Affiliation(s)
- J Magarian Blander
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, United States; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, United States; Immunology and Microbial Pathogenesis Programs, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States.
| | - Kristel Joy Yee Mon
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Atimukta Jha
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Dylan Roycroft
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
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Ephraim R, Fraser S, Devereaux J, Stavely R, Feehan J, Eri R, Nurgali K, Apostolopoulos V. Differential Gene Expression of Checkpoint Markers and Cancer Markers in Mouse Models of Spontaneous Chronic Colitis. Cancers (Basel) 2023; 15:4793. [PMID: 37835487 PMCID: PMC10571700 DOI: 10.3390/cancers15194793] [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: 09/04/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The presence of checkpoint markers in cancer cells aids in immune escape. The identification of checkpoint markers and early cancer markers is of utmost importance to gain clarity regarding the relationship between colitis and progressive inflammation leading to cancer. Herein, the gene expression levels of checkpoint makers, cancer-related pathways, and cancer genes in colon tissues of mouse models of chronic colitis (Winnie and Winnie-Prolapse mice) using next-generation sequencing are determined. Winnie mice are a result of a Muc2 missense mutation. The identification of such genes and their subsequent expression and role at the protein level would enable novel markers for the early diagnosis of cancer in IBD patients. The differentially expressed genes in the colonic transcriptome were analysed based on the Kyoto Encyclopedia of Genes and Genomes pathway. The expression of several oncogenes is associated with the severity of IBD, with Winnie-Prolapse mice expressing a large number of key genes associated with development of cancer. This research presents a number of new targets to evaluate for the development of biomarkers and therapeutics.
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Affiliation(s)
- Ramya Ephraim
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Sarah Fraser
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Jeannie Devereaux
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Rhian Stavely
- Pediatric Surgery Research Laboratories, Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Rajaraman Eri
- STEM/School of Science, RMIT University, Melbourne, VIC 3001, Australia;
| | - Kulmira Nurgali
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Department of Medicine Western Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Regenerative Medicine and Stem Cells Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
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Neves RL, Marem A, Carmona B, Arata JG, Cyrillo Ramos MP, Justo GZ, Machado de Melo FH, Oliveira V, Icimoto MY. Expression of thimet oligopeptidase (THOP) modulated by oxidative stress in human multidrug resistant (MDR) leukemia cells. Biochimie 2023; 212:21-30. [PMID: 36997147 DOI: 10.1016/j.biochi.2023.03.013] [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: 08/22/2022] [Revised: 03/03/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023]
Abstract
Thimet oligopeptidase (THOP) is a cytosolic metallopeptidase known to regulate the fate of post-proteasomal peptides, protein turnover and peptide selection in the antigen presentation machinery (APM) system. Oxidative stress influences THOP expression and regulates its proteolytic activity, generating variable cytosolic peptide levels, possibly affecting the immune evasion of tumor cells. In the present work, we examined the association between THOP expression/activity and stress oxidative resistance in human leukemia cells using the K562 cell line, a chronic myeloid leukemia (CML), and the multidrug-resistant (MDR) Lucena 1 (K562-derived MDR cell line) as model. The Lucena 1 phenotype was validated under vincristine treatment and the relative THOP1 mRNA levels and protein expression compared to K562 cell line. Our data demonstrated increased THOP1 gene and protein levels in K562 cells in contrast to the oxidative-resistant Lucena 1, even after H2O2 treatment, suggesting an oxidative stress dependence in THOP regulation. Further, it was observed higher basal levels of reactive oxygen species (ROS) in K562 compared to Lucena 1 cell line using DHE fluorescent probe. Since THOP activity is dependent on its oligomeric state, we also compared its proteolytic activity under reducing agent treatment, which demonstrated that its function modulation with respect to changes in redox state. Finally, the mRNA expression and FACS analyses demonstrated a reduced expression of MHC I only in K562 cell line. In conclusion, our results highlight THOP redox modulation, which could influence antigen presentation in multidrug resistant leukemia cells.
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Affiliation(s)
- Raquel Leão Neves
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Alyne Marem
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Bruno Carmona
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Júlia Galanakis Arata
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Giselle Zenker Justo
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil; Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | | | - Vitor Oliveira
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil.
| | - Marcelo Yudi Icimoto
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil; Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, United States.
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Chen X, Lu Q, Zhou H, Liu J, Nadorp B, Lasry A, Sun Z, Lai B, Rona G, Zhang J, Cammer M, Wang K, Al-Santli W, Ciantra Z, Guo Q, You J, Sengupta D, Boukhris A, Zhang H, Liu C, Cresswell P, Dahia PLM, Pagano M, Aifantis I, Wang J. A membrane-associated MHC-I inhibitory axis for cancer immune evasion. Cell 2023; 186:3903-3920.e21. [PMID: 37557169 PMCID: PMC10961051 DOI: 10.1016/j.cell.2023.07.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/30/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of T cell immunity involving aberrant major histocompatibility complex class I (MHC-I) antigen presentation (AP). To map such mechanisms of resistance, we identified key MHC-I regulators using specific peptide-MHC-I-guided CRISPR-Cas9 screens in AML. The top-ranked negative regulators were surface protein sushi domain containing 6 (SUSD6), transmembrane protein 127 (TMEM127), and the E3 ubiquitin ligase WWP2. SUSD6 is abundantly expressed in AML and multiple solid cancers, and its ablation enhanced MHC-I AP and reduced tumor growth in a CD8+ T cell-dependent manner. Mechanistically, SUSD6 forms a trimolecular complex with TMEM127 and MHC-I, which recruits WWP2 for MHC-I ubiquitination and lysosomal degradation. Together with the SUSD6/TMEM127/WWP2 gene signature, which negatively correlates with cancer survival, our findings define a membrane-associated MHC-I inhibitory axis as a potential therapeutic target for both leukemia and solid cancers.
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Affiliation(s)
- Xufeng Chen
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Qiao Lu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Hua Zhou
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jia Liu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Bettina Nadorp
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Audrey Lasry
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Zhengxi Sun
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Baoling Lai
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gergely Rona
- The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jiangyan Zhang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Michael Cammer
- Microscopy Core, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Wafa Al-Santli
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Zoe Ciantra
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Qianjin Guo
- Department of Medicine, Division of Hematology and Medical Oncology, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jia You
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Debrup Sengupta
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Ahmad Boukhris
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | | | - Cheng Liu
- Eureka Therapeutics Inc., Emeryville, CA 94608, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Patricia L M Dahia
- Department of Medicine, Division of Hematology and Medical Oncology, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michele Pagano
- The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
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10
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Wang Y, Jasinski-Bergner S, Wickenhauser C, Seliger B. Cancer Immunology: Immune Escape of Tumors-Expression and Regulation of HLA Class I Molecules and Its Role in Immunotherapies. Adv Anat Pathol 2023; 30:148-159. [PMID: 36517481 DOI: 10.1097/pap.0000000000000389] [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: 12/23/2022]
Abstract
The addition of "avoiding immune destruction" to the hallmarks of cancer demonstrated the importance of cancer immunology and in particular the role of immune surveillance and escape from malignancies. However, the underlying mechanisms contributing to immune impairment and immune responses are diverse. Loss or reduced expression of the HLA class I molecules are major characteristics of human cancers resulting in an impaired recognition of tumor cells by CD8 + cytotoxic T lymphocytes. This is of clinical relevance and associated with worse patients outcome and limited efficacy of T-cell-based immunotherapies. Here, we summarize the role of HLA class I antigens in cancers by focusing on the underlying molecular mechanisms responsible for HLA class I defects, which are caused by either structural alterations or deregulation at the transcriptional, posttranscriptional, and posttranslational levels. In addition, the influence of HLA class I abnormalities to adaptive and acquired immunotherapy resistances will be described. The in-depth knowledge of the different strategies of malignancies leading to HLA class I defects can be applied to design more effective cancer immunotherapies.
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Affiliation(s)
| | - Simon Jasinski-Bergner
- Institute of Medical Immunology
- Institute for Translational Immunology, Medical School "Theodor Fontane", Brandenburg, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale)
| | - Barbara Seliger
- Institute of Medical Immunology
- Department of Good Manufacturing Practice (GMP) Development & Advanced Therapy Medicinal Products (ATMP) Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, GermanyLeipzig, Germany
- Institute for Translational Immunology, Medical School "Theodor Fontane", Brandenburg, Germany
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11
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Micevic G, Bosenberg MW, Yan Q. The Crossroads of Cancer Epigenetics and Immune Checkpoint Therapy. Clin Cancer Res 2023; 29:1173-1182. [PMID: 36449280 PMCID: PMC10073242 DOI: 10.1158/1078-0432.ccr-22-0784] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/02/2022]
Abstract
Immune checkpoint inhibitors (ICI) have significantly improved treatment outcomes for several types of cancer over the past decade, but significant challenges that limit wider effectiveness of current immunotherapies remain to be addressed. Certain "cold" tumor types, such as pancreatic cancer, exhibit very low response rates to ICI due to intrinsically low immunogenicity. In addition, many patients who initially respond to ICI lack a sustained response due to T-cell exhaustion. Several recent studies show that epigenetic modifiers, such as SETDB1 and LSD1, can play critical roles in regulating both tumor cell-intrinsic immunity and T-cell exhaustion. Here, we review the evidence showing that multiple epigenetic regulators silence the expression of endogenous antigens, and their loss induces viral mimicry responses bolstering the response of "cold" tumors to ICI in preclinical models. Similarly, a previously unappreciated role for epigenetic enzymes is emerging in the establishment and maintenance of stem-like T-cell populations that are critical mediators of response to ICI. Targeting the crossroads of epigenetics and immune checkpoint therapy has tremendous potential to improve antitumor immune responses and herald the next generation of sustained responses in immuno-oncology.
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Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
| | - Marcus W. Bosenberg
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520
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12
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Lasorsa F, di Meo NA, Rutigliano M, Milella M, Ferro M, Pandolfo SD, Crocetto F, Tataru OS, Autorino R, Battaglia M, Ditonno P, Lucarelli G. Immune Checkpoint Inhibitors in Renal Cell Carcinoma: Molecular Basis and Rationale for Their Use in Clinical Practice. Biomedicines 2023; 11:biomedicines11041071. [PMID: 37189689 DOI: 10.3390/biomedicines11041071] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Renal cell carcinoma (RCC) is the seventh most common cancer in men and the ninth most common cancer in women worldwide. There is plenty of evidence about the role of the immune system in surveillance against tumors. Thanks to a better understanding of immunosurveillance mechanisms, immunotherapy has been introduced as a promising cancer treatment in recent years. Renal cell carcinoma (RCC) has long been thought chemoresistant but highly immunogenic. Considering that up to 30% of the patients present metastatic disease at diagnosis, and around 20–30% of patients undergoing surgery will suffer recurrence, we need to identify novel therapeutic targets. The introduction of immune checkpoint inhibitors (ICIs) in the clinical management of RCC has revolutionized the therapeutic approach against this tumor. Several clinical trials have shown that therapy with ICIs in combination or ICIs and the tyrosine kinase inhibitor has a very good response rate. In this review article we summarize the mechanisms of immunity modulation and immune checkpoints in RCC and discuss the potential therapeutic strategies in renal cancer treatment.
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Affiliation(s)
- Francesco Lasorsa
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Nicola Antonio di Meo
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Monica Rutigliano
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Martina Milella
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Savio Domenico Pandolfo
- Department of Neurosciences and Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Felice Crocetto
- Department of Neurosciences and Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Octavian Sabin Tataru
- The Institution Organizing University Doctoral Studies (I.O.S.U.D.), George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 540139 Târgu Mureș, Romania
| | - Riccardo Autorino
- Department of Urology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Michele Battaglia
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Pasquale Ditonno
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppe Lucarelli
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy
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13
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Kalla R, Adams AT, Nowak JK, Bergemalm D, Vatn S, Ventham NT, Kennedy NA, Ricanek P, Lindstrom J, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjørn C, Richmond R, Relton C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome. J Crohns Colitis 2023; 17:170-184. [PMID: 36029471 PMCID: PMC10024547 DOI: 10.1093/ecco-jcc/jjac127] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Epigenetic alterations may provide valuable insights into gene-environment interactions in the pathogenesis of inflammatory bowel disease [IBD]. METHODS Genome-wide methylation was measured from peripheral blood using the Illumina 450k platform in a case-control study in an inception cohort (295 controls, 154 Crohn's disease [CD], 161 ulcerative colitis [UC], 28 IBD unclassified [IBD-U)] with covariates of age, sex and cell counts, deconvoluted by the Houseman method. Genotyping was performed using Illumina HumanOmniExpressExome-8 BeadChips and gene expression using the Ion AmpliSeq Human Gene Expression Core Panel. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. RESULTS A total of 137 differentially methylated positions [DMPs] were identified in IBD, including VMP1/MIR21 [p = 9.11 × 10-15] and RPS6KA2 [6.43 × 10-13], with consistency seen across Scandinavia and the UK. Dysregulated loci demonstrate strong genetic influence, notably VMP1 [p = 1.53 × 10-15]. Age acceleration is seen in IBD [coefficient 0.94, p < 2.2 × 10-16]. Several immuno-active genes demonstrated highly significant correlations between methylation and gene expression in IBD, in particular OSM: IBD r = -0.32, p = 3.64 × 10-7 vs non-IBD r = -0.14, p = 0.77]. Multi-omic integration of the methylome, genome and transcriptome also implicated specific pathways that associate with immune activation, response and regulation at disease inception. At follow-up, a signature of three DMPs [TAP1, TESPA1, RPTOR] were associated with treatment escalation to biological agents or surgery (hazard ratio of 5.19 [CI: 2.14-12.56], logrank p = 9.70 × 10-4). CONCLUSION These data demonstrate consistent epigenetic alterations at diagnosis in European patients with IBD, providing insights into the pathogenetic importance and translational potential of epigenetic mapping in complex disease.
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Affiliation(s)
- Rahul Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Alex T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jan K Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simen Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, Exeter, UK
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Johan Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marie Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - Mauro D’Amato
- CIC bioGUNE – BRTA, Derio, SpainIKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Christine Olbjørn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Rebecca Richmond
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jack Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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14
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Starska-Kowarska K. The Role of Different Immunocompetent Cell Populations in the Pathogenesis of Head and Neck Cancer-Regulatory Mechanisms of Pro- and Anti-Cancer Activity and Their Impact on Immunotherapy. Cancers (Basel) 2023; 15:1642. [PMID: 36980527 PMCID: PMC10046400 DOI: 10.3390/cancers15061642] [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: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most aggressive and heterogeneous groups of human neoplasms. HNSCC is characterized by high morbidity, accounting for 3% of all cancers, and high mortality with ~1.5% of all cancer deaths. It was the most common cancer worldwide in 2020, according to the latest GLOBOCAN data, representing the seventh most prevalent human malignancy. Despite great advances in surgical techniques and the application of modern combinations and cytotoxic therapies, HNSCC remains a leading cause of death worldwide with a low overall survival rate not exceeding 40-60% of the patient population. The most common causes of death in patients are its frequent nodal metastases and local neoplastic recurrences, as well as the relatively low response to treatment and severe drug resistance. Much evidence suggests that the tumour microenvironment (TME), tumour infiltrating lymphocytes (TILs) and circulating various subpopulations of immunocompetent cells, such regulatory T cells (CD4+CD25+Foxp3+Tregs), cytotoxic CD3+CD8+ T cells (CTLs) and CD3+CD4+ T helper type 1/2/9/17 (Th1/Th2/Th9/Th17) lymphocytes, T follicular helper cells (Tfh) and CD56dim/CD16bright activated natural killer cells (NK), carcinoma-associated fibroblasts (CAFs), myeloid-derived suppressor cells (MDSCs), tumour-associated neutrophils (N1/N2 TANs), as well as tumour-associated macrophages (M1/M2 phenotype TAMs) can affect initiation, progression and spread of HNSCC and determine the response to immunotherapy. Rapid advances in the field of immuno-oncology and the constantly growing knowledge of the immunosuppressive mechanisms and effects of tumour cancer have allowed for the use of effective and personalized immunotherapy as a first-line therapeutic procedure or an essential component of a combination therapy for primary, relapsed and metastatic HNSCC. This review presents the latest reports and molecular studies regarding the anti-tumour role of selected subpopulations of immunocompetent cells in the pathogenesis of HNSCC, including HPV+ve (HPV+) and HPV-ve (HPV-) tumours. The article focuses on the crucial regulatory mechanisms of pro- and anti-tumour activity, key genetic or epigenetic changes that favour tumour immune escape, and the strategies that the tumour employs to avoid recognition by immunocompetent cells, as well as resistance mechanisms to T and NK cell-based immunotherapy in HNSCC. The present review also provides an overview of the pre- and clinical early trials (I/II phase) and phase-III clinical trials published in this arena, which highlight the unprecedented effectiveness and limitations of immunotherapy in HNSCC, and the emerging issues facing the field of HNSCC immuno-oncology.
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Affiliation(s)
- Katarzyna Starska-Kowarska
- Department of Physiology, Pathophysiology and Clinical Immunology, Department of Clinical Physiology, Medical University of Lodz, Żeligowskiego 7/9, 90-752 Lodz, Poland; ; Tel.: +48-604-541-412
- Department of Otorhinolaryngology, EnelMed Center Expert, Drewnowska 58, 91-001 Lodz, Poland
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15
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Zhu R, Chen YT, Wang BW, You YY, Wang XH, Xie HT, Jiang FG, Zhang MC. TAP1, a potential immune-related prognosis biomarker with functional significance in uveal melanoma. BMC Cancer 2023; 23:146. [PMID: 36774490 PMCID: PMC9921415 DOI: 10.1186/s12885-023-10527-9] [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: 10/04/2022] [Accepted: 01/09/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND TAP1 is an immunomodulation-related protein that plays different roles in various malignancies. This study investigated the transcriptional expression profile of TAP1 in uveal melanoma (UVM), revealed its potential biological interaction network, and determined its prognostic value. METHODS CIBERSORT and ESTIMATE bioinformatic methods were used on data sourced from The Cancer Genome Atlas database (TCGA) to determine the correlation between TAP1 expression, UVM prognosis, biological characteristics, and immune infiltration. Gene set enrichment analysis (GSEA) was used to discover the signaling pathways associated with TAP1, while STRING database and CytoHubba were used to construct protein-protein interaction (PPI) and competing endogenous RNA (ceRNA) networks, respectively. An overall survival (OS) prognostic model was constructed to test the predictive efficacy of TAP1, and its effect on the in vitro proliferation activity and metastatic potential of UVM cell line C918 cells was verified by RNA interference. RESULTS There was a clear association between TAP1 expression and UVM patient prognosis. Upregulated TAP1 was strongly associated with a shorter survival time, higher likelihood of metastasis, and higher mortality outcomes. According to GSEA analysis, various immunity-related signaling pathways such as primary immunodeficiency were enriched in the presence of elevated TAP1 expression. A PPI network and a ceRNA network were constructed to show the interactions among mRNAs, miRNAs, and lncRNAs. Furthermore, TAP1 expression showed a significant positive correlation with immunoscore, stromal score, CD8+ T cells, and dendritic cells, whereas the correlation with B cells and neutrophils was negative. The Cox regression model and calibration plots confirmed a strong agreement between the estimated OS and actual observed patient values. In vitro silencing of TAP1 expression in C918 cells significantly inhibited cell proliferation and metastasis. CONCLUSIONS This study is the first to demonstrate that TAP1 expression is positively correlated with clinicopathological factors and poor prognosis in UVM. In vitro experiments also verified that TAP1 is associated with C918 cell proliferation, apoptosis, and metastasis. These results suggest that TAP1 may function as an oncogene, prognostic marker, and importantly, as a novel therapeutic target in patients with UVM.
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Affiliation(s)
- Ru Zhu
- grid.33199.310000 0004 0368 7223Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yu-Ting Chen
- grid.33199.310000 0004 0368 7223Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Bo-Wen Wang
- grid.33199.310000 0004 0368 7223Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Ya-Yan You
- grid.33199.310000 0004 0368 7223Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xing-Hua Wang
- grid.33199.310000 0004 0368 7223Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Hua-Tao Xie
- grid.33199.310000 0004 0368 7223Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Fa-Gang Jiang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Ming-Chang Zhang
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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16
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Tu Z, Li K, Ji Q, Huang Y, Lv S, Li J, Wu L, Huang K, Zhu X. Pan-cancer analysis: predictive role of TAP1 in cancer prognosis and response to immunotherapy. BMC Cancer 2023; 23:133. [PMID: 36759763 PMCID: PMC9912572 DOI: 10.1186/s12885-022-10491-w] [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: 06/09/2022] [Accepted: 12/26/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Transporter associated with antigen processing 1 (TAP1) is a molecule involved in processing and presentation of major histocompatibility complex class I restricted antigens, including tumor-associated antigens. TAP1 participates in tumor immunity, and is aberrantly expressed in multiple cancer types; METHODS: Transcriptome profiles were obtained from The Cancer Genome Atlas and Genotype-Tissue Expression databases. Genetic alterations, protein distribution, and interaction information for TAP1 were downloaded from cBioPortal, Human Protein Atlas and Compartmentalized Protein-Protein Interaction, respectively. Single-cell analyses of TAP1 across cancers were conducted via the Tumor Immune Single-cell Hub website. Gene set enrichment analysis was employed to investigate TAP1-associated functional mechanisms and processes. Immune cell infiltration was explored using Tumor Immune Estimation Resource 2.0. Pan-cancer correlations between TAP1 expression and immunotherapy biomarkers were explored using the Spearman's correlation test. Associations with immunotherapy responses were also investigated using clinicopathological and prognostic information from cohorts of patients with cancer receiving immune checkpoint inhibitors. RESULTS TAP1 expression was elevated in most cancer types and exhibited distinct prognostic value. Immune cells expressed more TAP1 than malignant cells within most tumors. TAP1 expression was significantly correlated with immune-related pathways, T-lymphocyte infiltration, and immunotherapeutic biomarkers. Clinical cohort validation revealed a significant correlation with immune therapeutic effects and verified the prognostic role of TAP1 in immunotherapy. Western blot assay indicated that TAP1 is upregulated in glioblastoma compared with adjacent normal brain tissues. CONCLUSION TAP1 is a robust tumor prognostic biomarker and a novel predictor of clinical prognosis and immunotherapeutic responses in various cancer types.
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Affiliation(s)
- Zewei Tu
- grid.412455.30000 0004 1756 5980Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Jiangxi 330006 Nanchang, P. R. China ,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Jiangxi 330006 Nanchang, P. R. China ,grid.260463.50000 0001 2182 8825Institute of Neuroscience, Nanchang University, Jiangxi 330006 Nanchang, P. R. China ,JXHC Key Laboratory of Neurological Medicine, Jiangxi 330006 Nanchang, P. R. China
| | - Kuangxun Li
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Jiangxi 330006 Nanchang, P. R. China ,grid.260463.50000 0001 2182 8825Institute of Neuroscience, Nanchang University, Jiangxi 330006 Nanchang, P. R. China ,JXHC Key Laboratory of Neurological Medicine, Jiangxi 330006 Nanchang, P. R. China ,grid.260463.50000 0001 2182 8825Queen Mary School, University of Nanchang, Jiangxi 330006 Nanchang, P. R. China
| | - Qiankun Ji
- grid.412455.30000 0004 1756 5980Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Jiangxi 330006 Nanchang, P. R. China ,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Jiangxi 330006 Nanchang, P. R. China ,grid.260463.50000 0001 2182 8825Institute of Neuroscience, Nanchang University, Jiangxi 330006 Nanchang, P. R. China ,JXHC Key Laboratory of Neurological Medicine, Jiangxi 330006 Nanchang, P. R. China
| | - Yuyang Huang
- grid.260463.50000 0001 2182 8825Queen Mary School, University of Nanchang, Jiangxi 330006 Nanchang, P. R. China
| | - Shigang Lv
- grid.412455.30000 0004 1756 5980Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Jiangxi 330006 Nanchang, P. R. China
| | - Jingying Li
- grid.412455.30000 0004 1756 5980Department of Comprehensive Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Lei Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Jiangxi, 330006, Nanchang, P. R. China. .,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Jiangxi, 330006, Nanchang, P. R. China. .,Institute of Neuroscience, Nanchang University, Jiangxi, 330006, Nanchang, P. R. China. .,JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, P. R. China.
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Jiangxi, 330006, Nanchang, P. R. China. .,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Jiangxi, 330006, Nanchang, P. R. China. .,Institute of Neuroscience, Nanchang University, Jiangxi, 330006, Nanchang, P. R. China. .,JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, P. R. China.
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Jiangxi, 330006, Nanchang, P. R. China. .,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Jiangxi, 330006, Nanchang, P. R. China. .,Institute of Neuroscience, Nanchang University, Jiangxi, 330006, Nanchang, P. R. China. .,JXHC Key Laboratory of Neurological Medicine, Jiangxi, 330006, Nanchang, P. R. China.
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17
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Pang T, Tang Q, Wei J, Li J, Ma L, Qin Q, Ma J, He H, Chen Y. Construction of a novel immune-related prognostic-predicting model of gastric cancer. Gene 2023; 852:147032. [PMID: 36403868 DOI: 10.1016/j.gene.2022.147032] [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: 09/28/2021] [Revised: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022]
Abstract
Gastric cancer (GC) is a common primary stomach tumor of the central nervous system with a poor prognosis. In this study, 274 differentially expressed immune-related genes (DEIRGs) were identified among six cell subpopulations in GSE112302 single-cell RNA sequencing (scRNA-seq) data of GC. Those DEIRGs were able to divide GC patients into three distinct subtypes with different overall survivals and tumor microenvironment. By univariate Cox and LASSO regression analyses, eight immune-related genes, including CTGF, CXCL3, CXCR4, NRP1, OAS1, SP1, STC1 and TAP1, were identified as GC prognostic signatures. Accordingly, a risk score model for predicting GC prognosis was constructed in TCGA-GC training cohort and validated in the external GSE66229 dataset. Moreover, a nomogram for predicting the survival of GC patients was also established based on independent prognostic factors (age, grade, cancer status and risk score) identified by univariate and multivariate Cox regression analyses. In addition, Gene Set Variation Analysis (GSVA) analysis indicated that the prognostic immune signatures may regulate GC via inflammation and cell proliferation related pathways, such as DNA replication, complement and coagulation cascades, focal adhesion and TGF-β signaling pathway.
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Affiliation(s)
- Ting Pang
- Faculty of Pharmacy, Guangxi Agricultural Vocational and Technical University, Nanning 530007, China; Faculty of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530022, China
| | - Qiulian Tang
- Guangxi International Zhuang Medical Hospital, Nanning 530003, China
| | - Jiangcun Wei
- Faculty of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530022, China; Guangxi International Zhuang Medical Hospital, Nanning 530003, China
| | - Junxuan Li
- Faculty of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530022, China.
| | - Liuhui Ma
- Faculty of Pharmacy, Guangxi Agricultural Vocational and Technical University, Nanning 530007, China
| | - Qingxia Qin
- Faculty of Pharmacy, Guangxi Agricultural Vocational and Technical University, Nanning 530007, China
| | - Jiabao Ma
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Huan He
- Faculty of Pharmacy, Guangxi Agricultural Vocational and Technical University, Nanning 530007, China.
| | - Yong Chen
- Faculty of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530022, China.
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18
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Zhu D, Ouyang X, Zhang Y, Yu X, Su K, Li L. A promising new cancer marker: Long noncoding RNA EGFR-AS1. Front Oncol 2023; 13:1130472. [PMID: 36910672 PMCID: PMC9999470 DOI: 10.3389/fonc.2023.1130472] [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: 12/23/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Cancer consists of a group of diseases with the salient properties of an uncontrolled cell cycle, metastasis, and evasion of the immune response, mainly driven by the genomic instability of somatic cells and the physicochemical environment. Long noncoding RNAs (lncRNAs) are defined as noncoding RNAs with a length of more than 200 nucleotides. LncRNA dysregulation participates in diverse disease types and is tightly associated with patient clinical features, such as age, disease stage, and prognosis. In addition, an increasing number of lncRNAs have been confirmed to regulate a series of biological and pathological processes through numerous mechanisms. The lncRNA epidermal growth factor receptor antisense RNA 1 (EGFR-AS1) was recently discovered to be aberrantly expressed in many types of diseases, particularly in cancers. A high level of EGFR-AS1 was demonstrated to correlate with multiple patient clinical characteristics. More importantly, EGFR-AS1 was found to be involved in the mediation of various cellular activities, including cell proliferation, invasion, migration, chemosensitivity, and stemness. Therefore, EGFR-AS1 is a promising marker for cancer management. In this review, we introduce the expression profile, molecular mechanisms, biological functions, and clinical value of EGFR-AS1 in cancers.
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Affiliation(s)
- Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxi Ouyang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanhong Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaopeng Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kunkai Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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19
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Korotaeva AA, Borunova AA, Kuzevanova AY, Zabotina TN, Alimov AA. [Molecular mechanisms of impaired antigenic presentation as a cause of tumor escape from immune surveillance]. Arkh Patol 2023; 85:76-83. [PMID: 38010642 DOI: 10.17116/patol20238506176] [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: 11/29/2023]
Abstract
The review summarizes data on the features of antigen presentation in tumor cells. The molecular mechanisms of the antitumor immune response are considered with an emphasis on the ability of tumor cells to avoid the action of immune surveillance. The features of expression of MHC molecules depending on treatment regimens are provided. Ways to improve existing and create new treatment regimens aimed at elimination of tumor cells because of antitumor immune response are discussed.
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Affiliation(s)
- A A Korotaeva
- Research Centre for Medical Genetics, Moscow, Russia
| | - A A Borunova
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | | | - T N Zabotina
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - A A Alimov
- Research Centre for Medical Genetics, Moscow, Russia
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20
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Wang X, Yang X, Wang Y, Chen Y, Yang Y, Shang S, Wang W, Wang Y. Combination of Expanded Allogeneic NK Cells and T Cell-Based Immunotherapy Exert Enhanced Antitumor Effects. Cancers (Basel) 2022; 15:cancers15010251. [PMID: 36612246 PMCID: PMC9818244 DOI: 10.3390/cancers15010251] [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: 11/30/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Immunotherapies based on immune checkpoint blockade, neoantigen-reactive tumor-infiltrating lymphocytes and T cell receptor-engineered T cells (TCR-T) have achieved favorable clinical outcomes in tumor treatment. However, sustained immune response and tumor regression have been observed only in a few patients due to immune escape. Natural killer (NK) cells can mediate direct tumor lysis and target cancer cells with low or no expression of human leukocyte antigen class I (HLA-I) that are no longer recognized by T cells during immune escape. Therefore, the combination of T cell-based immunotherapy and NK cell therapy is a promising strategy for improving antitumor response and response rate. However, allogeneic NK cells for adoptive cell therapy have been limited by both the required cell number and quality. Here, we developed an efficient manufacturing system that relies on genetically modified K562 cells for the expansion of high-quality NK cells derived from peripheral blood mononuclear cells. NK cells with the optimal expansion and activity were identified by comparing the different culture systems. Furthermore, we demonstrated that the cooperation of NK cells with tumor-reactive T cells or with NY-ESO-1-specific TCR-T cells further enhanced tumors lysis, especially against tumors with downregulated HLA-I expression. The advantages of HLA-mismatch and non-rejection by other allogeneic immune cells demonstrated the potential of "off-the-shelf" NK cells with the capacity to target tumors for immunotherapy. Our results indicate that the combination strategy based on T cell and allogeneic NK cell immunotherapy might have potential for overcoming the barrier of immune incompetence caused by HLA-I downregulation.
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Affiliation(s)
- Xiao Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xuejiao Yang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yueping Wang
- Institute of Interdisciplinary Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yunshuo Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ying Yang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Siqi Shang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wenbo Wang
- Department of Oncology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China
- LeaLing Biopharma Company, Ltd., Suzhou 215000, China
- Correspondence: (W.W.); (Y.W.)
| | - Yueying Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence: (W.W.); (Y.W.)
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21
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Wang ZD, Tian X, Wang Y, Wang JJ, Ye SQ, Huang YQ, Qu YY, Chang K, Shi GH, Ye DW, Gu CY. The expression and prognostic value of transporter 1, ATP binding cassette subfamily B member in clear cell renal cell cancer with experimental validation. Front Oncol 2022; 12:1013790. [PMID: 36419887 PMCID: PMC9676953 DOI: 10.3389/fonc.2022.1013790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2023] Open
Abstract
Transporter associated with antigen processing 1(TAP1) serves as a protein to transport antigenic peptides from the surface of the endoplasmic reticulum to the lumen of the endoplasmic reticulum when the antigens are presented by major histocompatibility complex type I (MHC-I), which has been identified to play a critical role in antigen presentation in innate immunity. In tumors, the role of TAP1 seems to remain controversial. On the one hand, given the role of TAP1 in antigen presentation, it is indicated that high TAP1 expression corresponds to the emergence of more neoantigens epitopes that facilitate the recognition for phagocytes, T cells and other cells. On the other hand, the genetic ablation of transporter associated with antigen processing (TAP) results in the presentation of new class I-restricted epitopes encoded in house-keeping products. Opposite result has been revealed by studies in other tumors suggest, which implies a more complex function of TAP1. Therefore, it's significant to clarify the role of TAP1 in clear cell renal cell carcinoma (ccRCC). In this study, we found the elevated expression levels in mRNA and protein of TAP1 in ccRCC tissues, which indicated a relatively worse prognosis. Transwell assay and Scratch assay in vitro demonstrated the promotive role of TAP1 in ccRCC migration as well as a significant role in metastasis. And the increased expression of TAP1 resulted in more immune cells infiltrated in cancer tissues. TAP1 was also demonstrated to be related to immune regulator genes, as gene set enrichment analysis (GSEA) indicated its significant role in immune regulation. The results of CancerSEA indicated the positive association of the high-level TAP1 expression with epithelial-mesenchymal transition (EMT) and the inverse association with Cell Cycle. The effective drugs were also predicted based on TAP1 expression, of which the high level was indeed associated with resistance to multiple drugs, but some effective drugs still identified based on high TAP1 expression. According to the analysis of various databases, the role of TAP1 in ccRCC was explored, especially in relationship of TAP1 with tumor microenvironment. These results indicate that TAP1 can serve as a potential target for treatment of ccRCC.
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Affiliation(s)
- Zhen-Da Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun-Jie Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Qi Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong-Qiang Huang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng-Yuan Gu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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22
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Gerber HP, Presta LG. TCR mimic compounds for pHLA targeting with high potency modalities in oncology. Front Oncol 2022; 12:1027548. [PMID: 36338746 PMCID: PMC9635445 DOI: 10.3389/fonc.2022.1027548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/29/2022] [Indexed: 12/02/2022] Open
Abstract
pHLA complexes represent the largest class of cell surface markers on cancer cells, making them attractive for targeted cancer therapies. Adoptive cell therapies expressing TCRs that recognize tumor specific pHLAs take advantage of the unique selectivity and avidity of TCR: pHLA interactions. More recently, additional protein binding domains binding to pHLAs, known as TCR mimics (TCRm), were developed for tumor targeting of high potency therapeutic modalities, including bispecifics, ADCs, CAR T and -NK cells. TCRm compounds take advantage of the exquisite tumor specificity of certain pHLA targets, including cell lineage commitment markers and cancer testis antigens (CTAs). To achieve meaningful anti-tumor responses, it is critical that TCRm compounds integrate both, high target binding affinities and a high degree of target specificity. In this review, we describe the most advanced approaches to achieve both criteria, including affinity- and specificity engineering of TCRs, antibodies and alternative protein scaffolds. We also discuss the status of current TCRm based therapeutics developed in the clinic, key challenges, and emerging trends to improve treatment options for cancer patients treated with TCRm based therapeutics in Oncology.
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23
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Mining Potential Drug Targets and Constructing Diagnostic Models for Heart Failure Based on miRNA-mRNA Networks. Mediators Inflamm 2022; 2022:9652169. [PMID: 36204659 PMCID: PMC9532133 DOI: 10.1155/2022/9652169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Heart failure (HF) is a globally prevalent cardiovascular disease, but effective drug targets and diagnostic models are still lacking. This study was designed to investigate effective drug targets and diagnostic models for HF in terms of miRNA targets, hoping to contribute to the understanding and treatment of HF. Using HF miRNA and gene expression profile data from the GEO database, we analyzed differentially expressed miRNAs/gene identification in HF using Limma and predicted miRNA targets by the online TargetScan database. Subsequently, gene set enrichment analysis and annotation were performed using WebGestaltR package. Protein-protein interactions were identified using the STRING database. The proximity of drugs to treat HF was also calculated and predicted for potential target therapeutic drug. In addition, further drug identification was performed by molecular docking. Finally, diagnostic models were constructed based on differential miRNAs. The GEO dataset was used to screen 66 differentially expressed miRNAs, incorporating 56 downregulated miRNAs and 10 upregulated miRNAs. The JAK-STAT signaling pathway, MAPK signaling pathway, p53 signaling pathway, Prolactin signaling pathway, and TGF-beta signaling pathway were enriched, as shown by KEGG enrichment analysis on the target genes. In addition, we found that 83 genes were upregulated and 92 genes were downregulated in HF patients vs. healthy individuals. Based on the inflammation-related score, hypoxia-related score, and energy metabolism-related score, we identified key miRNA-mRNA pairs and constructed an interaction network. Following that, TAP1, which had the highest expression and network connectivity in acute HF with crystal and molecular docking studies, was selected as a key candidate gene in the network. And the compound DB04847 was selected to produce a large number of favorable interactions with TAP1 protein. Finally, we constructed two diagnostic models based on the differential miRNAs hsa-miR-6785-5p and hsa-miR-4443. In conclusion, we identified TAP1, a key candidate gene in the diagnosis and treatment of HF, and determined that compound DB04847 is highly likely to be a potential inhibitor of TAP1. The TAP1 gene was also found to be regulated by hsa-miR-6785-5p and hsa-miR-4443, and a diagnostic model was constructed. This provides a new promising direction to improve the diagnosis, prognosis, and treatment outcome and guide more effective immunotherapy strategies of HF.
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24
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MTFR2 shapes a barrier of immune microenvironment in hepatocellular carcinoma. iScience 2022; 26:105095. [PMID: 36713263 PMCID: PMC9881049 DOI: 10.1016/j.isci.2022.105095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/31/2022] [Accepted: 09/04/2022] [Indexed: 02/01/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death in the world. Mitochondrial fission regulator 2 (MTFR2) is involved in the development of various cancers. However, the roles of MTFR2 in HCC remain unknown. In this study, we conducted a comprehensive analysis of MTFR2 in HCC, which was generated from integrative MTFR2 analyses of eight HCC cell lines, and three datasets (public dataset, real-world dataset, and immunotherapy dataset) derived from bulk HCC tissues, survival, and immunotherapy data. We demonstrated that the expression level of MTFR2 is upregulated in HCC, leading to poor prognosis. MTFR2 is positively correlated with the level of immune cell infiltration, multiple immune checkpoints and immunotherapy response prediction pathways, and acts as an important role in cancer-immunity cycle. In conclusion, our work indicates that MTFR2 can shape a barrier of immune microenvironment and result in poor prognosis in hepatocellular carcinoma, but the immune barrier may be broken by immunotherapy.
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25
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Selvin T, Fasterius E, Jarvius M, Fryknäs M, Larsson R, Andersson CR. Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model. Sci Rep 2022; 12:11960. [PMID: 35831404 PMCID: PMC9279337 DOI: 10.1038/s41598-022-16077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.
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Affiliation(s)
- Tove Selvin
- Department of Medical Sciences, Uppsala University, 75185, Uppsala, Sweden.
| | - Erik Fasterius
- National Bioinformatics Infrastructure Sweden (NBIS), Stockholm University, Stockholm, Sweden
| | - Malin Jarvius
- Department of Medical Sciences, Uppsala University, 75185, Uppsala, Sweden.,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Mårten Fryknäs
- Department of Medical Sciences, Uppsala University, 75185, Uppsala, Sweden
| | - Rolf Larsson
- Department of Medical Sciences, Uppsala University, 75185, Uppsala, Sweden
| | - Claes R Andersson
- Department of Medical Sciences, Uppsala University, 75185, Uppsala, Sweden.
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26
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Jiang L, Chen S, Pan Q, Zheng J, He J, Sun J, Han Y, Yang J, Zhang N, Fu G, Gao F. The feasibility of proteomics sequencing based immune-related prognostic signature for predicting clinical outcomes of bladder cancer patients. BMC Cancer 2022; 22:676. [PMID: 35725413 PMCID: PMC9210750 DOI: 10.1186/s12885-022-09783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Background Bladder cancer (BCa) shows its potential immunogenity in current immune-checkpoint inhibitor related immunotherapies. However, its therapeutic effects are improvable and could be affected by tumor immune microenvironment. Hence it is interesting to find some more prognostic indicators for BCa patients concerning immunotherapies. Methods In the present study, we retrospect 129 muscle-invasive BCa (MIBC) patients with radical cystectomy in Shanghai General Hospital during 2007 to 2018. Based on the results of proteomics sequencing from 9 pairs of MIBC tissue from Shanghai General Hospital, we focused on 13 immune-related differential expression proteins and their related genes. An immune-related prognostic signature (IRPS) was constructed according to Cancer Genome Atlas (TCGA) dataset. The IRPS was verified in ArrayExpress (E-MTAB-4321) cohort and Shanghai General Hospital (General) cohort, separately. A total of 1010 BCa patients were involved in the study, including 405 BCa patients in TCGA cohort, 476 BCa patients in E-MTAB-4321 cohort and 129 MIBC patients in General cohort. Result It can be indicated that high IRPS score was related to poor 5-year overall survival and disease-free survival. The IRPS score was also evaluated its immune infiltration. We found that the IRPS score was adversely associated with GZMB, IFN-γ, PD-1, PD-L1. Additionally, higher IRPS score was significantly associated with more M2 macrophage and resting mast cell infiltration. Conclusion The study revealed a novel BCa prognostic signature based on IRPS score, which may be useful for BCa immunotherapies. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09783-y.
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Affiliation(s)
- Liren Jiang
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China
| | - Siteng Chen
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Pan
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zheng
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China
| | - Jin He
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China
| | - Juanjuan Sun
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China
| | - Yaqin Han
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China
| | - Jiji Yang
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China
| | - Ning Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin 2nd Road, Shanghai, 200020, China.
| | - Guohui Fu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 280, South Chong-Qing Road, Shanghai, 200025, China.
| | - Feng Gao
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100, Hai Ning Road, Shanghai, 200080, China.
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Mercier R, LaPointe P. The role of cellular proteostasis in anti-tumor immunity. J Biol Chem 2022; 298:101930. [PMID: 35421375 PMCID: PMC9108985 DOI: 10.1016/j.jbc.2022.101930] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/25/2022] Open
Abstract
Immune checkpoint blockade therapy is perhaps the most important development in cancer treatment in recent memory. It is based on decades of investigation into the biology of immune cells and the role of the immune system in controlling cancer growth. While the molecular circuitry that governs the immune system in general - and anti-tumor immunity in particular - is intensely studied, far less attention has been paid to the role of cellular stress in this process. Proteostasis, intimately linked to cell stress responses, refers to the dynamic regulation of the cellular proteome and is maintained through a complex network of systems that govern the synthesis, folding, and degradation of proteins in the cell. Disruption of these systems can result in the loss of protein function, altered protein function, the formation of toxic aggregates, or pathologies associated with cell stress. However, the importance of proteostasis extends beyond its role in maintaining proper protein function; proteostasis governs how tolerant cells may be to mutations in protein coding genes and the overall half-life of proteins. Such gene expression changes may be associated with human diseases including neurodegenerative diseases, metabolic disease, and cancer and manifest at the protein level against the backdrop of the proteostasis network in any given cellular environment. In this review, we focus on the role of proteostasis in regulating immune responses against cancer as well the role of proteostasis in determining immunogenicity of cancer cells.
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Affiliation(s)
- Rebecca Mercier
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada.
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Regulation of the antigen presentation machinery in cancer and its implication for immune surveillance. Biochem Soc Trans 2022; 50:825-837. [PMID: 35343573 PMCID: PMC9162455 DOI: 10.1042/bst20210961] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 12/20/2022]
Abstract
Evading immune destruction is one of the hallmarks of cancer. A key mechanism of immune evasion deployed by tumour cells is to reduce neoantigen presentation through down-regulation of the antigen presentation machinery. MHC-I and MHC-II proteins are key components of the antigen presentation machinery responsible for neoantigen presentation to CD8+ and CD4+ T lymphocytes, respectively. Their expression in tumour cells is modulated by a complex interplay of genomic, transcriptomic and post translational factors involving multiple intracellular antigen processing pathways. Ongoing research investigates mechanisms invoked by cancer cells to abrogate MHC-I expression and attenuate anti-tumour CD8+ cytotoxic T cell response. The discovery of MHC-II on tumour cells has been less characterized. However, this finding has triggered further interest in utilising tumour-specific MHC-II to harness sustained anti-tumour immunity through the activation of CD4+ T helper cells. Tumour-specific expression of MHC-I and MHC-II has been associated with improved patient survival in most clinical studies. Thus, their reactivation represents an attractive way to unleash anti-tumour immunity. This review provides a comprehensive overview of physiologically conserved or novel mechanisms utilised by tumour cells to reduce MHC-I or MHC-II expression. It outlines current approaches employed at the preclinical and clinical trial interface towards reversing these processes in order to improve response to immunotherapy and survival outcomes for patients with cancer.
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Chen R, Zhang H, Wu W, Li S, Wang Z, Dai Z, Liu Z, Zhang J, Luo P, Xia Z, Cheng Q. Antigen Presentation Machinery Signature-Derived CALR Mediates Migration, Polarization of Macrophages in Glioma and Predicts Immunotherapy Response. Front Immunol 2022; 13:833792. [PMID: 35418980 PMCID: PMC8995475 DOI: 10.3389/fimmu.2022.833792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Immunogenicity, influenced by tumor antigenicity and antigen presenting efficiency, critically determines the effectiveness of immune checkpoint inhibitors. The role of immunogenicity has not been fully elucidated in gliomas. In this study, a large-scale bioinformatics analysis was performed to analyze the prognostic value and predictive value of antigen presentation machinery (APM) signature in gliomas. ssGSEA algorithm was used for development of APM signature and LASSO regression analysis was used for construction of APM signature-based risk score. APM signature and risk score showed favorable performance in stratifying survival and predicting tumorigenic factors of glioma patients. APM signature and risk score were also associated with different genomic features in both training cohort TCGA and validating cohort CGGA. Furthermore, APM signature-based risk score was independently validated in three external cohorts and managed to predict immunotherapy response. A prognostic nomogram was constructed based on risk score. Risk score-derived CALR was found to mediate the invasion and polarization of macrophages based on the coculture of HMC3 and U251 cells. CALR could significantly predict immunotherapy response. In conclusion, APM signature and APM signature-based risk score could help promote the clinical management of gliomas.
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Affiliation(s)
- Rui Chen
- Department of Neurosurgery, Affiliated Nanhua Hospital, University of South China, Hengyang, China
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wantao Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuyu Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiwei Xia
- Department of Neurology, Hunan Aerospace Hospital, Changsa, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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30
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Yin Y, Jiang R, Shen M, Li Z, Yan N, Feng J, Jiang H, Lv J, Shi L, Wang L, Liu X, Zhang K, Chen D. Prediction of occult tumor progression via platelet RNAs in a mouse melanoma model: a potential new platform for early detection of cancer. J Transl Med 2022; 20:71. [PMID: 35123499 PMCID: PMC8817485 DOI: 10.1186/s12967-022-03268-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Cancer screening provides the opportunity to detect cancer early, ideally before symptom onset and metastasis, and offers an increased opportunity for a better prognosis. The ideal biomarkers for cancer screening should discriminate individuals who have not developed invasive cancer yet but are destined to do so from healthy subjects. However, most cancers lack effective screening recommendations. Therefore, further studies on novel screening strategies are urgently required. Methods We used a simple suboptimal inoculation melanoma mouse model to obtain ‘pre-diagnostic samples’ of mice with macroscopic melanomas. High-throughput sequencing and bioinformatic analysis were employed to identify differentially expressed RNAs in platelet signatures of mice injected with a suboptimal number of melanoma cells (eDEGs) compared with mice with macroscopic melanomas and negative controls. Moreover, 36 genes selected from the eDEGs via bioinformatics analysis were verified in a mouse validation cohort via quantitative real-time PCR. LASSO regression was utilized to generate the prediction models with gene expression signatures as the best predictors for occult tumor progression in mice. Results These RNAs identified from eDEGs of mice injected with a suboptimal number of cancer cells were strongly enriched in pathways related to immune response and regulation. The prediction models generated by 36 gene qPCR verification data showed great diagnostic efficacy and predictive value in our murine validation cohort, and could discriminate mice with occult tumors from control group (area under curve (AUC) of 0.935 (training data) and 0.912 (testing data)) (gene signature including Cd19, Cdkn1a, S100a9, Tap1, and Tnfrsf1b) and also from macroscopic tumor group (AUC of 0.920 (training data) and 0.936 (testing data)) (gene signature including Ccr7, Cd4, Kmt2d, and Ly6e). Conclusions Our proof-of-concept study provides evidence for potential clinical relevance of blood platelets as a platform for liquid biopsy-based early detection of cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03268-z.
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Mantel I, Sadiq BA, Blander JM. Spotlight on TAP and its vital role in antigen presentation and cross-presentation. Mol Immunol 2022; 142:105-119. [PMID: 34973498 PMCID: PMC9241385 DOI: 10.1016/j.molimm.2021.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/18/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023]
Abstract
In the late 1980s and early 1990s, the hunt for a transporter molecule ostensibly responsible for the translocation of peptides across the endoplasmic reticulum (ER) membrane yielded the successful discovery of transporter associated with antigen processing (TAP) protein. TAP is a heterodimer complex comprised of TAP1 and TAP2, which utilizes ATP to transport cytosolic peptides into the ER across its membrane. In the ER, together with other components it forms the peptide loading complex (PLC), which directs loading of high affinity peptides onto nascent major histocompatibility complex class I (MHC-I) molecules that are then transported to the cell surface for presentation to CD8+ T cells. TAP also plays a crucial role in transporting peptides into phagosomes and endosomes during cross-presentation in dendritic cells (DCs). Because of the critical role that TAP plays in both classical MHC-I presentation and cross-presentation, its expression and function are often compromised by numerous types of cancers and viruses to evade recognition by cytotoxic CD8 T cells. Here we review the discovery and function of TAP with a major focus on its role in cross-presentation in DCs. We discuss a recently described emergency route of noncanonical cross-presentation that is mobilized in DCs upon TAP blockade to restore CD8 T cell cross-priming. We also discuss the various strategies employed by cancer cells and viruses to target TAP expression or function to evade immunosurveillance - along with some strategies by which the repertoire of peptides presented by cells which downregulate TAP can be targeted as a therapeutic strategy to mobilize a TAP-independent CD8 T cell response. Lastly, we discuss TAP polymorphisms and the role of TAP in inherited disorders.
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Affiliation(s)
- Ian Mantel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, New York, NY, 10021, USA; Joan and Sanford I. Weill Department of Medicine, New York, NY, 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, 10021, USA
| | - Barzan A Sadiq
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, New York, NY, 10021, USA; Joan and Sanford I. Weill Department of Medicine, New York, NY, 10021, USA
| | - J Magarian Blander
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, New York, NY, 10021, USA; Joan and Sanford I. Weill Department of Medicine, New York, NY, 10021, USA; Department of Microbiology and Immunology, New York, NY, 10021, USA; Sandra and Edward Meyer Cancer Center, New York, NY, 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, 10021, USA.
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Li X, Zeng S, Ding Y, Nie Y, Yang M. Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells. Front Mol Biosci 2021; 8:763958. [PMID: 34957213 PMCID: PMC8702961 DOI: 10.3389/fmolb.2021.763958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/19/2021] [Indexed: 01/22/2023] Open
Abstract
Transporter associated with antigen processing 1 (TAP1) is a protein related immune regulation and plays a role in several malignant tumors. However, the effect of TAP1 on immune infiltration, immunotherapy, and metastasis in different cancers has not been reported till date. The cancer genome atlas database, the tumor immune estimation resource database, and the estimation of stromal and immune cells in malignant tumors using expression (ESTIMATE) algorithm were used to determine the correlation between TAP1 expression and the prognosis of a variety of cancers, immune infiltration, immune checkpoint genes, DNA methylation, and neoantigens. Various enrichment analyses were used to study the correlation between TAP1 and key transcription factors using the Kyoto encyclopedia of genes and genomes (KEGG) pathway in ovarian cancer. Immunological methods were used to evaluate the expression of TAP1 protein in ovarian and cervical cancer, and Kaplan-Meier analysis was used to analyze the prognostic value of TAP1. RNA interference (RNAi) was used to verify the effect of TAP1 on ovarian cancer. Compared with normal tissues, cancer tissues showed a significant increase in the expression of TAP1, and TAP1 expression was related to the poor prognosis of cancers such as ovarian cancer. The expression level of TAP1 was correlated with immune checkpoint genes, DNA methylation, tumor mutation burden, microsatellite instability, and neoantigens in various cancers. Our results showed that TAP1 was upregulated in ovarian cancer cell lines and was associated with poor prognosis. Further, we verified the expression of TAP1-related transcription factors (MEF2A and LEF1) and found that TAP1 was closely related to ovarian cancer metastasis in vitro and in vivo. These results indicated that TAP1 could be used as a biomarker for the diagnosis and prognosis of cancer and as a new therapeutic target.
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Affiliation(s)
- Xiaoxue Li
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shiyu Zeng
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yiling Ding
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yanting Nie
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Mengyuan Yang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, China
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Tan Q, Liu H, Xu J, Mo Y, Dai F. Integrated analysis of tumor-associated macrophage infiltration and prognosis in ovarian cancer. Aging (Albany NY) 2021; 13:23210-23232. [PMID: 34633990 PMCID: PMC8544311 DOI: 10.18632/aging.203613] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022]
Abstract
Ovarian cancer (OC) is a frequently lethal gynecologic malignancy, characterized by a poor prognosis and high recurrence rate. The immune microenvironment has been implicated in the progression of OC. We characterized the immune landscape in primary and malignant OC ascites using single-cell and bulk transcriptome raw OC data acquired from the Gene Expression Omnibus and The Cancer Genome Atlas databases. We then used the CIBERSORT deconvolution algorithm, weighted gene co-expression network analysis, univariate and multivariate Cox analyses, and the LASSO algorithm to develop a tumor-associated macrophage-related gene (TAMRG) prognostic signature, which enabled us to stratify and predict overall survival (OS) of OC patients. In addition, inter- and intra-patient heterogeneity of infiltrating immune cells was characterized at single-cell resolution. Tumor-infiltrating macrophages with an M2 phenotype exhibited immunosuppressive activity. M1 macrophages positively correlated with OS, whereas activated mast cells, neutrophils, M2 macrophages, and activated memory CD4+ T cells were all negatively correlated with OS. A total of 219 TAMRGs were identified, and a novel 6-gene signature (TAP1, CD163, VSIG4, IGKV4-1, CD3E, and MS4A7) with independent prognostic value was established. These results show that a TAMRG-based signature may be a promising prognostic and therapeutic target in OC.
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Affiliation(s)
- Qianxia Tan
- Department of Gynecology and Obstetrics, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Huining Liu
- Department of Gynecology and Obstetrics, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Jie Xu
- Department of Nephrology, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Yanqun Mo
- Department of Gynecology and Obstetrics, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Furong Dai
- Department of Gynecology and Obstetrics, Xiangya Hospital Central South University, Changsha, Hunan, China
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Establishment of an Immune-Related Gene Signature for Risk Stratification for Patients with Glioma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:2191709. [PMID: 34497663 PMCID: PMC8420975 DOI: 10.1155/2021/2191709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/14/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Glioma is a frequently seen primary malignant intracranial tumor, characterized by poor prognosis. The study is aimed at constructing a prognostic model for risk stratification in patients suffering from glioma. Weighted gene coexpression network analysis (WGCNA), integrated transcriptome analysis, and combining immune-related genes (IRGs) were used to identify core differentially expressed IRGs (DE IRGs). Subsequently, univariate and multivariate Cox regression analyses were utilized to establish an immune-related risk score (IRRS) model for risk stratification for glioma patients. Furthermore, a nomogram was developed for predicting glioma patients' overall survival (OS). The turquoise module (cor = 0.67; P < 0.001) and its genes (n = 1092) were significantly pertinent to glioma progression. Ultimately, multivariate Cox regression analysis constructed an IRRS model based on VEGFA, SOCS3, SPP1, and TGFB2 core DE IRGs, with a C-index of 0.811 (95% CI: 0.786-0.836). Then, Kaplan-Meier (KM) survival curves revealed that patients presenting high risk had a dismal outcome (P < 0.0001). Also, this IRRS model was found to be an independent prognostic indicator of gliomas' survival prediction, with HR of 1.89 (95% CI: 1.252-2.85) and 2.17 (95% CI: 1.493-3.14) in the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) datasets, respectively. We established the IRRS prognostic model, capable of effectively stratifying glioma population, convenient for decision-making in clinical practice.
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Segami K, Aoyama T, Hiroshima Y, Komori K, Hashimoto I, Watanabe H, Kano K, Nagasawa S, Nakazono M, Maezawa Y, Fujikawa H, Numata M, Yamada T, Tamagawa H, Yamamoto N, Ogata T, Siozawa M, Yukawa N, Morinaga S, Rino Y, Masuda M, Miyagi Y, Saeki H, Oshima T. Clinical Significance of TAP1 and DLL4 Expression in Patients With Locally Advanced Gastric Cancer. In Vivo 2021; 35:2771-2777. [PMID: 34410967 DOI: 10.21873/invivo.12562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/20/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND/AIM Cancer stem cells (CSCs) are reported to associated with cancer metastasis, relapse, and chemoresistance. This study examined the clinical significance of the expression of two CSC markers, the transporter associated with antigen processing 1 (TAP1) and the Delta-like 4 (DLL4) protein, in patients with locally advanced GC. PATIENTS AND METHODS This study was performed using samples obtained from 413 pathological stage II/III GC patients after curative gastrectomy. We examined TAP1 and DLL4 expression using immunohistochemical analysis with tissue microarray and examined the association between TAP1 or DLL4 expression, clinicopathological factors and survival. RESULTS High TAP1 expression was associated with better overall survival compared to low TAP1 expression (p=0.004). Furthermore, in multivariate analysis, high TAP1 expression was defined as a predictive factor for good survival. There was no significant difference between DLL4 expression and clinicopathological features and overall survival. CONCLUSION TAP1 expression may be a useful prognostic marker in patients with locally advanced GC.
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Affiliation(s)
- Kenki Segami
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan.,Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Toru Aoyama
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | | | - Keisuke Komori
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Itaru Hashimoto
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Hayato Watanabe
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Kazuki Kano
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | | | - Masato Nakazono
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Yukio Maezawa
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Hirohito Fujikawa
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Masakatsu Numata
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Takanobu Yamada
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Hiroshi Tamagawa
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Naoto Yamamoto
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Takashi Ogata
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Manabu Siozawa
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Norio Yukawa
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Soichiro Morinaga
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Yasushi Rino
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Munetaka Masuda
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Yohei Miyagi
- Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Hiroshi Saeki
- Department of Gastrointestinal Surgery, Gunma University, Gunma, Japan
| | - Takashi Oshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan;
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Murtadha AH, Azahar IIM, Sharudin NA, Has ATC, Mokhtar NF. Influence of nNav1.5 on MHC class I expression in breast cancer. J Biosci 2021. [DOI: 10.1007/s12038-021-00196-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mohanty V, Wang F, Mills GB, Chen K. Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers. Cell Rep Med 2021; 2:100349. [PMID: 34337565 PMCID: PMC8324495 DOI: 10.1016/j.xcrm.2021.100349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/11/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022]
Abstract
Uncoupling of mRNA expression from copy number (UECN) might be a strategy for cancer cells to a tolerate high degree of aneuploidy. To test the extent and role of UECN across cancers, we perform integrative multiomic analysis of The Cancer Genome Atlas (TCGA) dataset, encompassing ∼5,000 individual tumors. We find UECN is common in cancers and is associated with increased oncogenic signaling, proliferation, and immune suppression. UECN appears to be orchestrated by complex regulatory changes, with transcription factors (TFs) playing a prominent role. To further dissect the regulatory mechanisms, we develop a systems-biology approach to identify candidate TFs, which could serve as targets to disrupt UECN and reduce tumor fitness. Applying our approach to TCGA data, we identify 21 putative targets, 42.8% of which are validated by independent sources. Together, our study indicates that UECN is likely an important mechanism in development of aneuploid tumors and might be therapeutically targetable.
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Affiliation(s)
- Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B. Mills
- Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health University, Portland, OR 97201, USA
| | - CTD2 Research Network
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health University, Portland, OR 97201, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Abstract
Next-generation sequencing technologies have revolutionized our ability to catalog the landscape of somatic mutations in tumor genomes. These mutations can sometimes create so-called neoantigens, which allow the immune system to detect and eliminate tumor cells. However, efforts that stimulate the immune system to eliminate tumors based on their molecular differences have had less success than has been hoped for, and there are conflicting reports about the role of neoantigens in the success of this approach. Here we review some of the conflicting evidence in the literature and highlight key aspects of the tumor-immune interface that are emerging as major determinants of whether mutation-derived neoantigens will contribute to an immunotherapy response. Accounting for these factors is expected to improve success rates of future immunotherapy approaches.
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Affiliation(s)
- Andrea Castro
- Biomedical Informatics Program, University of California San Diego, La Jolla, California 92093, USA
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
| | - Maurizio Zanetti
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- The Laboratory of Immunology, Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
- The Laboratory of Immunology, Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
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Mao R, Liu K, Zhao N, Guo P, Wu Y, Wang Z, Liu Y, Zhang T. Clinical significance and prognostic role of an immune-related gene signature in gastric adenocarcinoma. Aging (Albany NY) 2021; 13:17734-17767. [PMID: 34247148 PMCID: PMC8312416 DOI: 10.18632/aging.203266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/11/2021] [Indexed: 12/13/2022]
Abstract
Limited progress has been made in the treatment of gastric adenocarcinoma (GAC) in recent years, but the potential of immunotherapy in GAC is worthy of consideration. The purpose of this study was to develop a reliable, personalized signature based on immune genes to predict the prognosis of GAC. Here, we identified two groups of patients with significantly different prognoses by performing unsupervised clustering analysis of The Cancer Genome Atlas (TCGA) database based on 881 immune genes. The immune signature was constructed with a training set composed of 350 GAC samples from the TCGA and subsequently validated with 431 samples from GSE84437, 432 samples from GSE26253, and 145 GAC samples from real-time quantitative reverse transcription polymerase chain reaction data. This classification system can also be used to predict prognosis in different clinical subgroups. Further analysis suggested that high-risk patients were characterized by low immune scores, distinctive immune cell proportions, different immune checkpoint profiles, and a low tumor mutational burden. Ultimately, the signature was identified as an independent prognostic factor. In general, the signature can accurately predict recurrence and overall survival in patients with GAC and may serve as a powerful prognostic tool to further optimize cancer immunotherapy.
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Affiliation(s)
- Rui Mao
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China.,Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China
| | - Kehao Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China
| | - Nana Zhao
- Department of Operating Room, The Third People's Hospital of Chengdu, Chengdu 610031, China
| | - Pengsen Guo
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China
| | - Yingxin Wu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China
| | - Zheng Wang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yanjun Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China.,Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China
| | - Tongtong Zhang
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University and The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu 610031, China.,Affiliated Hospital of Southwest Jiaotong University, Chengdu 610036, China.,Medical Research Center, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, The Second Chengdu Hospital Affiliated to Chongqing Medical University, Chengdu 610031, China
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Tabassum A, Samdani MN, Dhali TC, Alam R, Ahammad F, Samad A, Karpiński TM. Transporter associated with antigen processing 1 (TAP1) expression and prognostic analysis in breast, lung, liver, and ovarian cancer. J Mol Med (Berl) 2021; 99:1293-1309. [PMID: 34047812 PMCID: PMC8367907 DOI: 10.1007/s00109-021-02088-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/15/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022]
Abstract
Abstract Transporter associated with antigen processing 1 (TAP1) is a transporter protein that represent tumor antigen in the MHC I or HLA complex. Any defect in the TAP1 gene resulting in inadequate tumor tracking. TAP1 influences multidrug resistance (MDR) in human cancer cell lines and hinders the treatment during chemotherapeutic. The association of TAP1 in cancer progression remains mostly unknown and further study of the gene in relation with cancer need to conduct. Thus, the study has designed to analyze the association between the TAP1 with cancer by computationally. The expression pattern of the gene has determined by using ONCOMINE, GENT2, and GEPIA2 online platforms. The protein level of TAP1 was examined by the help of Human Protein Atlas. Samples with different clinical outcomes were investigated to evaluate the expression and promoter methylation in cancer vs. normal tissues by using UALCAN server. The copy number alteration, mutation frequency, and expression level of the gene in different cancer were analyzed by using cBioPortal server. The PrognoScan and KM plotter platforms were used to perform the survival analysis and represented graphically. Additionally, pathway and gene ontology (GO) features correlated to the TAP1 gene were analyzed and presented by bar charts. After arranging the data in a single panel like correlating expression to prognosis, mutational and alterations characteristic, and pathways analysis, we observed some interesting insights that emphasized the importance of the gene in cancer progression. The study found the relationship between the TAP1 expression pattern and prognosis in different cancer tissues and shows how TAP1 affects the clinical characteristics. The analytical data presented in the study is vital to learn about the effect of TAP1 in tumor tissue, where previously studies showing contradicting expression of TAP1 in cancer tissue. The analyzed data can also be utilized further to evade the threats against chemotherapy. Overall, the study provided a new aspect to consider the role of TAP1 gene in cancer progression and survival status. Key messages • This study demonstrated, for the first time, a correlation between the TAP1 gene and tumor progression. • An upregulation of TAP1 mRNA was demonstrated in various cancer types. • This study reported a significant negative correlation for TAP1 gene expression and the survival rate in different cancer types. Supplementary Information The online version contains supplementary material available at 10.1007/s00109-021-02088-w.
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Affiliation(s)
- Anika Tabassum
- Biochemistry Department, School of Life Sciences, Independent University, Dhaka, 1229, Bangladesh
| | - Md Nazmus Samdani
- Department of Pharmacy, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tarak Chandra Dhali
- Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Rahat Alam
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Foysal Ahammad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh. .,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh. .,Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, 21589, Saudi Arabia.
| | - Abdus Samad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh. .,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| | - Tomasz M Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712, Poznań, Poland.
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Blair TC, Alice AF, Zebertavage L, Crittenden MR, Gough MJ. The Dynamic Entropy of Tumor Immune Infiltrates: The Impact of Recirculation, Antigen-Specific Interactions, and Retention on T Cells in Tumors. Front Oncol 2021; 11:653625. [PMID: 33968757 PMCID: PMC8101411 DOI: 10.3389/fonc.2021.653625] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Analysis of tumor infiltration using conventional methods reveals a snapshot view of lymphocyte interactions with the tumor environment. However, lymphocytes have the unique capacity for continued recirculation, exploring varied tissues for the presence of cognate antigens according to inflammatory triggers and chemokine gradients. We discuss the role of the inflammatory and cellular makeup of the tumor environment, as well as antigen expressed by cancer cells or cross-presented by stromal antigen presenting cells, on recirculation kinetics of T cells. We aim to discuss how current cancer therapies may manipulate lymphocyte recirculation versus retention to impact lymphocyte exclusion in the tumor.
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Affiliation(s)
- Tiffany C Blair
- Molecular Microbiology and Immunology, Oregon Health and Sciences University (OHSU), Portland, OR, United States.,Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Alejandro F Alice
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Lauren Zebertavage
- Molecular Microbiology and Immunology, Oregon Health and Sciences University (OHSU), Portland, OR, United States.,Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Marka R Crittenden
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States.,The Oregon Clinic, Portland, OR, United States
| | - Michael J Gough
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
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Dhatchinamoorthy K, Colbert JD, Rock KL. Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation. Front Immunol 2021; 12:636568. [PMID: 33767702 PMCID: PMC7986854 DOI: 10.3389/fimmu.2021.636568] [Citation(s) in RCA: 372] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Major histocompatibility class I (MHC I) molecules bind peptides derived from a cell's expressed genes and then transport and display this antigenic information on the cell surface. This allows CD8 T cells to identify pathological cells that are synthesizing abnormal proteins, such as cancers that are expressing mutated proteins. In order for many cancers to arise and progress, they need to evolve mechanisms to avoid elimination by CD8 T cells. MHC I molecules are not essential for cell survival and therefore one mechanism by which cancers can evade immune control is by losing MHC I antigen presentation machinery (APM). Not only will this impair the ability of natural immune responses to control cancers, but also frustrate immunotherapies that work by re-invigorating anti-tumor CD8 T cells, such as checkpoint blockade. Here we review the evidence that loss of MHC I antigen presentation is a frequent occurrence in many cancers. We discuss new insights into some common underlying mechanisms through which some cancers inactivate the MHC I pathway and consider some possible strategies to overcome this limitation in ways that could restore immune control of tumors and improve immunotherapy.
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43
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HLA class I loss in colorectal cancer: implications for immune escape and immunotherapy. Cell Mol Immunol 2021; 18:556-565. [PMID: 33473191 PMCID: PMC8027055 DOI: 10.1038/s41423-021-00634-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/23/2020] [Indexed: 01/30/2023] Open
Abstract
T cell-mediated immune therapies have emerged as a promising treatment modality in different malignancies including colorectal cancer (CRC). However, only a fraction of patients currently respond to treatment. Understanding the lack of responses and finding biomarkers with predictive value is of great importance. There is evidence that CRC is a heterogeneous disease and several classification systems have been proposed that are based on genomic instability, immune cell infiltration, stromal content and molecular subtypes of gene expression. Human leukocyte antigen class I (HLA-I) plays a pivotal role in presenting processed antigens to T lymphocytes, including tumour antigens. These molecules are frequently lost in different types of cancers, including CRC, resulting in tumour immune escape from cytotoxic T lymphocytes during the natural history of cancer development. The aim of this review is to (i) summarize the prevalence and molecular mechanisms behind HLA-I loss in CRC, (ii) discuss HLA-I expression/loss in the context of the newly identified CRC molecular subtypes, (iii) analyze the HLA-I phenotypes of CRC metastases disseminated via blood or the lymphatic system, (iv) discuss strategies to recover/circumvent HLA-I expression/loss and finally (v) review the role of HLA class II (HLA-II) in CRC prognosis.
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44
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Mpakali A, Stratikos E. The Role of Antigen Processing and Presentation in Cancer and the Efficacy of Immune Checkpoint Inhibitor Immunotherapy. Cancers (Basel) 2021; 13:E134. [PMID: 33406696 PMCID: PMC7796214 DOI: 10.3390/cancers13010134] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
Recent clinical successes of cancer immunotherapy using immune checkpoint inhibitors (ICIs) are rapidly changing the landscape of cancer treatment. Regardless of initial impressive clinical results though, the therapeutic benefit of ICIs appears to be limited to a subset of patients and tumor types. Recent analyses have revealed that the potency of ICI therapies depends on the efficient presentation of tumor-specific antigens by cancer cells and professional antigen presenting cells. Here, we review current knowledge on the role of antigen presentation in cancer. We focus on intracellular antigen processing and presentation by Major Histocompatibility class I (MHCI) molecules and how it can affect cancer immune evasion. Finally, we discuss the pharmacological tractability of manipulating intracellular antigen processing as a complementary approach to enhance tumor immunogenicity and the effectiveness of ICI immunotherapy.
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Affiliation(s)
- Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15784 Athens, Greece
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45
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DiNatale RG, Hakimi AA, Chan TA. Genomics-based immuno-oncology: bridging the gap between immunology and tumor biology. Hum Mol Genet 2020; 29:R214-R225. [PMID: 33029628 PMCID: PMC7574960 DOI: 10.1093/hmg/ddaa203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
The first hypotheses about how the immune system affects cancers were proposed in the early 20th century. These early concepts about cancer immunosurveillance were further developed in the decades that followed, but a detailed understanding of cancer immunity remained elusive. It was only recently, through the advent of high-throughput technologies, that scientists gained the ability to profile tumors with a resolution that allowed for granular assessment of both tumor cells and the tumor microenvironment. The advent of immune checkpoint inhibitors (ICIs), which have proven to be effective cancer therapies in many malignancies, has spawned great interest in developing biomarkers for efficacy, an endeavor that highlighted the value of dissecting tumor immunity using large-scale methods. Response to ICI therapy has been shown to be a highly complex process, where the dynamics of tumor and immune cells is key to success. The need to understand the biologic mechanisms at the tumor-immune interface has given rise to the field of cancer immunogenomics, a discipline that aims to bridge the gap between cancer genomics and classical immunology. We provide a broad overview of this emerging branch of translational science, summarizing common platforms used and recent discoveries in the field, which are having direct clinical implications. Our discussion will be centered around the genetic foundations governing tumor immunity and molecular determinants associated with clinical benefit from ICI therapy. We emphasize the importance of molecular diversity as a driver of anti-tumor immunity and discuss how these factors can be probed using genomic approaches.
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Affiliation(s)
- Renzo G DiNatale
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - A Ari Hakimi
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
- Lerner Research Institute and Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA
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46
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Xing Q, Liu S, Jiang S, Li T, Wang Z, Wang Y. Prognostic model of 10 immune-related genes and identification of small molecule drugs in bladder urothelial carcinoma (BLCA). Transl Androl Urol 2020; 9:2054-2070. [PMID: 33209669 PMCID: PMC7658175 DOI: 10.21037/tau-20-696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background We aimed to establish an immune-related gene (IRG) based signature that could provide guidance for clinical bladder cancer (BC) prognostic surveillance. Methods Differentially expressed IRGs and transcription factors (TFs) between BCs and normal tissues were extracted from transcriptome data downloaded from the TCGA database. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out to identify related pathways based on differently expressed IRGs. Then, univariate Cox regression analysis was performed to investigate IRGs with prognostic values and LASSO penalized Cox regression analysis was utilized to develop the prognostic index (PI) model. Results A total of 411 BC tissue samples and 19 normal bladder tissues in the TCGA database were enrolled in this study and 259 differentially expressed IRGs were identified. Networks between TFs and IRGs were also provided to seek the upstream regulators of differentially expressed IRGs. By means of univariate Cox regression analysis, 57 IRGs were analyzed with prognostic values and 10 IRGs were finally identified by LASSO penalized Cox regression analysis to construct the PI model. This model could significantly classified BC patients into high-risk group and low-risk group in terms of OS (P=9.923e-07) and its AUC reached 0.711. By means of univariate and multivariate COX regression analysis, this PI was proven to be a valuable independent prognostic factor (HR =1.119, 95% CI =1.066-1.175, P<0.001). CMap database analysis was also utilized to screen out 10 small molecules drugs with the potential for the treatment of BC. Conclusions Our study successfully provided a novel PI based on IRGs with the potential to predict the prognosis of BC and screened out 10 small molecules drugs with the potential to treat BC. Besides, networks between TFs and IRGs were also displayed to seek its upstream regulators for future researches.
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Affiliation(s)
- Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shouyong Liu
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Silin Jiang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tao Li
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Zengjun Wang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Wang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, China
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47
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Li Y, Burgman B, McGrail DJ, Sun M, Qi D, Shukla SA, Wu E, Capasso A, Lin SY, Wu CJ, Eckhardt SG, Mills GB, Li B, Sahni N, Yi SS. Integrated Genomic Characterization of the Human Immunome in Cancer. Cancer Res 2020; 80:4854-4867. [PMID: 32855206 DOI: 10.1158/0008-5472.can-20-0384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/10/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022]
Abstract
Alterations in immune-related pathways are common hallmarks of cancer. A comprehensive understanding of how cancer mutations rewire immune signaling networks and functional output across cancer types is instrumental to realize the full potential of immunotherapy. Here, we systematically interrogated somatic mutations involved in immune signaling that alter immune responses in patients with cancer. To do so, we developed a Network-based Integrative model to Prioritize Potential immune respondER genes (NIPPER). Identified mutations were enriched in essential protein domains and genes identified by NIPPER were associated with responsiveness to multiple immunotherapy modalities. These genes were used to devise an interactome network propagation framework integrated with drug-associated gene signatures to identify potential immunomodulatory drug candidates. Together, our systems-level analysis results help interpret the heterogeneous immune responses among patients and serve as a resource for future functional studies and targeted therapeutics. SIGNIFICANCE: This study demonstrates that integration of multi-omics data can help identify critical molecular determinants for effective targeted therapeutics.
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Affiliation(s)
- Yongsheng Li
- Department of Oncology, The University of Texas at Austin, Dell Medical School, Livestrong Cancer Institutes, Austin, Texas
| | - Brandon Burgman
- Department of Oncology, The University of Texas at Austin, Dell Medical School, Livestrong Cancer Institutes, Austin, Texas.,Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, Texas
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dan Qi
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, Texas
| | - Sachet A Shukla
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Erxi Wu
- Department of Oncology, The University of Texas at Austin, Dell Medical School, Livestrong Cancer Institutes, Austin, Texas.,Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, Texas.,Departments of Surgery and Pharmaceutical Sciences, Texas A & M University Health Science Center, Colleges of Medicine and Pharmacy, Temple, Texas
| | - Anna Capasso
- Department of Oncology, The University of Texas at Austin, Dell Medical School, Livestrong Cancer Institutes, Austin, Texas.,Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, Texas
| | - Shiaw-Yih Lin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Catherine J Wu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - S Gail Eckhardt
- Department of Oncology, The University of Texas at Austin, Dell Medical School, Livestrong Cancer Institutes, Austin, Texas.,Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, Texas
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health & Science University, Portland, Oregon.,Precision Oncology, Knight Cancer Institute, Portland, Oregon
| | - Bo Li
- Lyda Hill Department of Bioinformatics, Department of Immunology, UT Southwestern Medical Center, Dallas, Texas.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas.,Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, Texas
| | - S Stephen Yi
- Department of Oncology, The University of Texas at Austin, Dell Medical School, Livestrong Cancer Institutes, Austin, Texas. .,Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, Texas.,Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas.,Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, Texas
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48
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Downregulation of TAP1 in Tumor-Free Tongue Contralateral to Squamous Cell Carcinoma of the Oral Tongue, an Indicator of Better Survival. Int J Mol Sci 2020; 21:ijms21176220. [PMID: 32867395 PMCID: PMC7503265 DOI: 10.3390/ijms21176220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 01/30/2023] Open
Abstract
Oral cancers are surrounded by epithelium that histologically might seem normal, but genetically has aberrations. In patients with squamous cell carcinoma of the oral tongue (SCCOT), it is therefore important to study not only the tumor but also the clinically tumor-free contralateral tongue tissue that remains in the patient after treatment to map changes of prognostic and/or diagnostic value. The transporter associated with antigen processing (TAP) dimer is a key factor in the process of activating cytotoxic T cells. By downregulating the expression of TAP, tumor cells can escape cytotoxic T cell recognition. Biopsies from tumor and clinically tumor-free contralateral tongue tissue in 21 patients with SCCOT were analyzed together with tongue biopsies from 14 healthy individuals, which served as the control group. Dividing patients into TAP1-high and TAP1-low groups according to the median TAP1 level in tumor-free samples showed that patients with lower TAP1 mRNA levels in tumor-free samples had better overall (p = 0.003) and disease-free survival (p = 0.002). The results showing that TAP1 levels in tumor-free tongue tissue contralateral to the SCCOT correlate with survival is an important contribution to early diagnosis and follow up of SCCOT.
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49
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A few good peptides: MHC class I-based cancer immunosurveillance and immunoevasion. Nat Rev Immunol 2020; 21:116-128. [PMID: 32820267 DOI: 10.1038/s41577-020-0390-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
The remarkable success of immune checkpoint inhibitors demonstrates the potential of tumour-specific CD8+ T cells to prevent and treat cancer. Although the number of lives saved by immunotherapy mounts, only a relatively small fraction of patients are cured. Here, we review two of the factors that limit the application of CD8+ T cell immunotherapies: difficulties in identifying tumour-specific peptides presented by MHC class I molecules and the ability of tumour cells to impair antigen presentation as they evolve under T cell selection. We describe recent advances in understanding how peptides are generated from non-canonical translation of defective ribosomal products, relate this to the dysregulated translation that is a feature of carcinogenesis and propose dysregulated translation as an important new source of tumour-specific peptides. We discuss how the synthesis and function of components of the antigen-processing and presentation pathway, including the recently described immunoribosome, are manipulated by tumours for immunoevasion and point to common druggable targets that may enhance immunotherapy.
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50
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Systematic analysis of the ABC transporter family in hepatocellular carcinoma reveals the importance of ABCB6 in regulating ferroptosis. Life Sci 2020; 257:118131. [PMID: 32710948 DOI: 10.1016/j.lfs.2020.118131] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/11/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023]
Abstract
AIMS ATP-binding cassette (ABC) transporters constitute one of the largest families of membrane proteins in most organisms; however, their functions in hepatocellular carcinoma (HCC) remain unclear. MAIN METHODS A set of bioinformatic tools was integrated to analyze the expression of 49 members of the ABC transporter family. The function of members which had prognostic values in HCC was explored by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. KEY FINDINGS ABCA8 and ABCA9 were significantly down-regulated in HCC. Prognostic analysis indicated that HCC patients with low expression of ABCA8 and ABCA9 had significantly shorter survival time. On the contrary, ABCB6 was over-expressed in the disease and high expression of ABCB6 was associated with worse prognosis. Co-expression analysis, and subsequently GO and KEGG analysis indicated that ABCA8 and ABCA9 might participate in the catabolic processes of multiple metabolites, while ABCB6 might regulate ferroptosis. SIGNIFICANCE This study reveals a previously unrecognized function of ABCB6 in HCC, by regulating ferroptosis. Since ABCB6 is over-expressed in HCC and ferroptosis involves in cancer development, ABCB6 might be a promising therapeutic target in the disease.
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