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Lee CR, Suh J, Jang D, Jin BY, Cho J, Lee M, Sim H, Kang M, Lee J, Park JH, Lee KH, Hwang GS, Moon KC, Song C, Ku JH, Kwak C, Kim HH, Cho SY, Choi M, Jeong CW. Comprehensive molecular characterization of TFE3-rearranged renal cell carcinoma. Exp Mol Med 2024; 56:1807-1815. [PMID: 39085357 PMCID: PMC11372160 DOI: 10.1038/s12276-024-01291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 08/02/2024] Open
Abstract
TFE3-rearranged renal cell cancer (tRCC) is a rare form of RCC that involves chromosomal translocation of the Xp11.2 TFE3 gene. Despite its early onset and poor prognosis, the molecular mechanisms of the pathogenesis of tRCC remain elusive. This study aimed to identify novel therapeutic targets for patients with primary and recurrent tRCC. We collected 19 TFE3-positive RCC tissues that were diagnosed by immunohistochemistry and subjected them to genetic characterization to examine their genomic and transcriptomic features. Tumor-specific signatures were extracted using whole exome sequencing (WES) and RNA sequencing (RNA-seq) data, and the functional consequences were analyzed in a cell line with TFE3 translocation. Both a low burden of somatic single nucleotide variants (SNVs) and a positive correlation between the number of somatic variants and age of onset were observed. Transcriptome analysis revealed that four samples (21.1%) lacked the expected fusion event and clustered with the genomic profiles of clear cell RCC (ccRCC) tissues. The fusion event also demonstrated an enrichment of upregulated genes associated with mitochondrial respiration compared with ccRCC expression profiles. Comparison of the RNA expression profile with the TFE3 ChIP-seq pattern data indicated that PPARGC1A is a metabolic regulator of the oncogenic process. Cell proliferation was reduced when PPARGC1A and its related metabolic pathways were repressed by its inhibitor SR-18292. In conclusion, we demonstrate that PPARGC1A-mediated mitochondrial respiration can be considered a potential therapeutic target in tRCC. This study identifies an uncharacterized genetic profile of an RCC subtype with unique clinical features and provides therapeutic options specific to tRCC.
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Affiliation(s)
- Cho-Rong Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jungyo Suh
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dongjun Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bo-Yeong Jin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jaeso Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moses Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Minyong Kang
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
- Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
- Department of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Ju Hyun Park
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kyoung-Hwa Lee
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Songdo Bio-Engineering, Incheon Jaeneung University, Incheon, Republic of Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
- Department of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Cheryn Song
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ja Hyeon Ku
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Cheol Kwak
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyeon Hoe Kim
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Yup Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biochemistry, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Chang Wook Jeong
- Department of Urology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Lundgaard AT, Burdet F, Siggaard T, Westergaard D, Vagiaki D, Cantwell L, Röder T, Vistisen D, Sparsø T, Giordano GN, Ibberson M, Banasik K, Brunak S. BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus. PLoS Comput Biol 2023; 19:e1011403. [PMID: 37590326 PMCID: PMC10464978 DOI: 10.1371/journal.pcbi.1011403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 08/29/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Novel biomarkers are key to addressing the ongoing pandemic of type 2 diabetes mellitus. While new technologies have improved the potential of identifying such biomarkers, at the same time there is an increasing need for informed prioritization to ensure efficient downstream verification. We have built BALDR, an automated pipeline for biomarker comparison and prioritization in the context of diabetes. BALDR includes protein, gene, and disease data from major public repositories, text-mining data, and human and mouse experimental data from the IMI2 RHAPSODY consortium. These data are provided as easy-to-read figures and tables enabling direct comparison of up to 20 biomarker candidates for diabetes through the public website https://baldr.cpr.ku.dk.
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Affiliation(s)
- Agnete T. Lundgaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Frédéric Burdet
- Vital-IT, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Troels Siggaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Danai Vagiaki
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Lisa Cantwell
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Timo Röder
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Dorte Vistisen
- Clinical Epidemiological Research, Steno Diabetes Center Copenhagen, Herlev, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sparsø
- Bioinformatics and Data Mining, Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Giuseppe N. Giordano
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Clinical Research Centre, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mark Ibberson
- Vital-IT, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
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Li M, Long X, Bu W, Zhang G, Deng G, Liu Y, Su J, Huang K. Immune-related risk score: An immune-cell-pair-based prognostic model for cutaneous melanoma. Front Immunol 2023; 14:1112181. [PMID: 36875110 PMCID: PMC9975150 DOI: 10.3389/fimmu.2023.1112181] [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] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
Background Melanoma is among the most malignant immunologic tumor types and is associated with high mortality. However, a considerable number of melanoma patients cannot benefit from immunotherapy owing to individual differences. This study attempts to build a novel prediction model of melanoma that fully considers individual differences in the tumor microenvironment. Methods An immune-related risk score (IRRS) was constructed based on cutaneous melanoma data from The Cancer Genome Atlas (TCGA). Single-sample gene set enrichment analysis (ssGSEA) was used to calculate immune enrichment scores of 28 immune cell signatures. We performed pairwise comparisons to obtain scores for cell pairs based on the difference in the abundance of immune cells within each sample. The resulting cell pair scores, in the form of a matrix of relative values of immune cells, formed the core of the IRRS. Results The area under the curve (AUC) for the IRRS was over 0.700, and when the IRRS was combined with clinical information, the AUC reached 0.785, 0.817, and 0.801 for the 1-, 3-, and 5-year survival, respectively. Differentially expressed genes between the two groups were enriched in staphylococcal infection and estrogen metabolism pathway. The low IRRS group showed a better immunotherapeutic response and exhibited more neoantigens, richer T-cell receptor and B-cell receptor diversity, and higher tumor mutation burden. Conclusion The IRRS enables a good prediction of prognosis and immunotherapy effect, based on the difference in the relative abundance of different types of infiltrating immune cells, and could provide support for further research in melanoma.
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Affiliation(s)
- Mingjia Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Peking University First Hospital, Peking University, Beijing, China
| | - Xinrui Long
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wenbo Bu
- Department of Dermatological Surgery, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Peking Union Medical College, Nanjing, China
| | - Guanxiong Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Guangtong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuancheng Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Kai Huang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, China.,Hunan Engineering Research Center of Skin Health and Disease, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, 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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Kumbrink J, Bohlmann L, Mamlouk S, Redmer T, Peilstöcker D, Li P, Lorenzen S, Algül H, Kasper S, Hempel D, Kaiser F, Michl M, Bartsch H, Neumann J, Klauschen F, von Bergwelt-Baildon M, Modest DP, Stahler A, Stintzing S, Jung A, Kirchner T, Schäfer R, Heinemann V, Holch JW. Serial Analysis of Gene Mutations and Gene Expression during First-Line Chemotherapy against Metastatic Colorectal Cancer: Identification of Potentially Actionable Targets within the Multicenter Prospective Biomarker Study REVEAL. Cancers (Basel) 2022; 14:cancers14153631. [PMID: 35892888 PMCID: PMC9367450 DOI: 10.3390/cancers14153631] [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: 06/24/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The emergence of resistant cells remains a major obstacle for chemotherapy treatment of metastatic colorectal cancers. Improvement of the therapeutic response requires a thorough understanding of the mechanisms of resistance as well as informative biomarkers. In the REVEAL study, we have systematically compared the mutational patterns and expression profiles of primary tumor specimens before and after first-line chemotherapy treatment in the metastatic situation. In addition, we analyzed liquid biopsies pre, during, and after treatment. Alterations in gene expression appeared as the major drivers of chemotherapy resistance. We identified a gene expression signature differentiating primary tumors and metastases and validated this signature in two independent patient cohorts. Moreover, we evaluated the expression of two signature genes, SFRP2 and SPP1, as prognostic and potentially druggable biomarkers. Abstract Most metastatic colorectal cancer (mCRC) patients succumb to refractory disease due to secondary chemotherapy resistance. To elucidate the molecular changes associated with secondary resistance, we recruited 64 patients with mCRC and hepatic metastases before standard first-line chemotherapy between 2014 and 2018. We subjected DNA from primary tumor specimens (P), hepatic metastasis specimens after treatment (M), and liquid biopsies (L) taken prior to (pre), during (intra), and after (post) treatment to next generation sequencing. We performed Nanostring expression analysis in P and M specimens. Comparative bioinformatics and statistical analysis revealed typical mutational patterns with frequent alterations in TP53, APC, and KRAS in P specimens (n = 48). P and pre-L (n = 42), as well as matched P and M (n = 30), displayed a similar mutation spectrum. In contrast, gene expression profiles classified P (n = 31) and M (n = 23), distinguishable by up-regulation of immune/cytokine receptor and autophagy programs. Switching of consensus molecular subtypes from P to M occurred in 58.3% of cases. M signature genes SFRP2 and SPP1 associated with inferior survival, as validated in an independent cohort. Molecular changes during first-line treatment were detectable by expression profiling rather than by mutational tumor and liquid biopsy analyses. SFRP2 and SPP1 may serve as biomarkers and/or actionable targets.
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Affiliation(s)
- Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Correspondence:
| | - Lisa Bohlmann
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Soulafa Mamlouk
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Pathology, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Torben Redmer
- Institute of Medical Biochemistry, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;
| | - Daniela Peilstöcker
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Pan Li
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Sylvie Lorenzen
- Klinik und Poliklinik für Innere Medizin III, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany;
| | - Hana Algül
- School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- Comprehensive Cancer Center Munich, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Stefan Kasper
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, 45147 Essen, Germany;
| | - Dirk Hempel
- Steinbeishochschule Berlin, 12489 Berlin, Germany;
- Steinbeis Transfer Institute Clinical Hematology-Oncology, 86609 Donauwörth, Germany
| | | | - Marlies Michl
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
- Comprehensive Cancer Center, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Harald Bartsch
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Jens Neumann
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Frederick Klauschen
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Michael von Bergwelt-Baildon
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
| | - Dominik Paul Modest
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Arndt Stahler
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sebastian Stintzing
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Andreas Jung
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Reinhold Schäfer
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- Charité Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Volker Heinemann
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
- Comprehensive Cancer Center, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Julian W. Holch
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
- Comprehensive Cancer Center, University Hospital, LMU Munich, 81377 Munich, Germany
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Venkatraman S, Meller J, Hongeng S, Tohtong R, Chutipongtanate S. Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy. Vaccines (Basel) 2020; 8:E735. [PMID: 33291616 PMCID: PMC7761936 DOI: 10.3390/vaccines8040735] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
The study of immune evasion has gained a well-deserved eminence in cancer research by successfully developing a new class of therapeutics, immune checkpoint inhibitors, such as pembrolizumab and nivolumab, anti-PD-1 antibodies. By aiming at the immune checkpoint blockade (ICB), these new therapeutics have advanced cancer treatment with notable increases in overall survival and tumor remission. However, recent reports reveal that 40-60% of patients fail to benefit from ICB therapy due to acquired resistance or tumor relapse. This resistance may stem from increased expression of co-inhibitory immune checkpoints or alterations in the tumor microenvironment that promotes immune suppression. Because these mechanisms are poorly elucidated, the transcription factors that regulate immune checkpoints, known as "master regulators", have garnered interest. These include AP-1, IRF-1, MYC, and STAT3, which are known to regulate PD/PD-L1 and CTLA-4. Identifying these and other potential master regulators as putative therapeutic targets or biomarkers can be facilitated by mining cancer literature, public datasets, and cancer genomics resources. In this review, we describe recent advances in master regulator identification and characterization of the mechanisms underlying immune checkpoints regulation, and discuss how these master regulators of immune checkpoint molecular expression can be targeted as a form of auxiliary therapeutic strategy to complement traditional immunotherapy.
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Affiliation(s)
- Simran Venkatraman
- Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Jarek Meller
- Departments of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Rutaiwan Tohtong
- Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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6
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Ru B, Sun J, Kang Q, Tong Y, Zhang J. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. Bioinformatics 2019; 35:1805-1812. [PMID: 30358822 DOI: 10.1093/bioinformatics/bty836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/24/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Chromatin regulators (CRs) are frequently dysregulated to reprogram the epigenetic landscape of the cancer genome. However, the underpinnings of the dysregulation of CRs and their downstream effectors remain to be elucidated. RESULTS Here, we designed an integrated framework based on multi-omics data to identify candidate master regulatory CRs affected by genomic alterations across eight cancer types in The Cancer Genome Atlas. Most of them showed consistent activated or repressed (i.e. oncogenic or tumor-suppressive) roles in cancer initiation and progression. In order to further explore the insight mechanism of the dysregulated CRs, we developed an R package ModReg based on differential connectivity to identify CRs as modulators of transcription factors (TFs) involved in tumorigenesis. Our analysis revealed that the connectivity between TFs and their target genes (TGs) tended to be disrupted in the patients who had a high expression of oncogenic CRs or low-expression of tumor-suppressive CRs. As a proof-of-principle study, 14 (82.4%) of the top-ranked 17 driver CRs in liver cancer were able to be validated by literature mining or experiments including shRNA knockdown and dCas9-based epigenetic editing. Moreover, we confirmed that CR SIRT7 physically interacted with TF NFE2L2, and positively modulated the transcriptional program of NFE2L2 by affecting ∼64% of its TGs. AVAILABILITY AND IMPLEMENTATION ModReg is freely accessible at http://cis.hku.hk/software/ModReg.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Gallo Cantafio ME, Grillone K, Caracciolo D, Scionti F, Arbitrio M, Barbieri V, Pensabene L, Guzzi PH, Di Martino MT. From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. High Throughput 2018; 7:ht7040033. [PMID: 30373182 PMCID: PMC6306876 DOI: 10.3390/ht7040033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023] Open
Abstract
Integration of multi-omics data from different molecular levels with clinical data, as well as epidemiologic risk factors, represents an accurate and promising methodology to understand the complexity of biological systems of human diseases, including cancer. By the extensive use of novel technologic platforms, a large number of multidimensional data can be derived from analysis of health and disease systems. Comprehensive analysis of multi-omics data in an integrated framework, which includes cumulative effects in the context of biological pathways, is therefore eagerly awaited. This strategy could allow the identification of pathway-addiction of cancer cells that may be amenable to therapeutic intervention. However, translation into clinical settings requires an optimized integration of omics data with clinical vision to fully exploit precision cancer medicine. We will discuss the available technical approach and more recent developments in the specific field.
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Affiliation(s)
- Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | | | - Vito Barbieri
- Medical Oncology Unit, Mater Domini Hospital, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Licia Pensabene
- Department of Medical and Surgical Sciences Pediatric Unit, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Pietro Hiram Guzzi
- Department of Medical and Surgical Sciences, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
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