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Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie J, Aeilts A, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE. Association of ESR1 germline variants with TP53 somatic variants in breast tumors in a genome-wide study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299442. [PMID: 38106140 PMCID: PMC10723566 DOI: 10.1101/2023.12.06.23299442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency of TP53 somatic mutations than other subtypes. PIK3CA mutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. Methods A genome-wide association study was conducted using breast cancer mutation status of TP53 and PIK3CA and functional mutation categories including TP53 gain of function (GOF) and loss of function mutations and PIK3CA activating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC. Results The discovery Germline x Mutation (GxM) association study found five variants associated with one or more TP53 phenotypes with P values <1×10-6, 33 variants associated with one or more TP53 phenotypes with P values <1×10-5, and 44 variants associated with one or more PIK3CA phenotypes with P values <1×10-5. In the multi-ancestry and Malaysian validation studies, germline ESR1 locus variant, rs9383938, was associated with the presence of TP53 mutations overall (P values 6.8×10-5 and 9.8×10-8, respectively) and TP53 GOF mutations (P value 8.4×10-6). Multiple variants showed suggestive evidence of association with PIK3CA mutation status in the validation studies, but none were significant after correction for multiple comparisons. Conclusions We found evidence that germline variants were associated with TP53 and PIK3CA mutation status in breast cancers. Variants near the estrogen receptor alpha gene, ESR1, were significantly associated with overall TP53 mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.
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Affiliation(s)
- Nijole P. Tjader
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Abigail J. Beer
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Johnny Ramroop
- The City College of New York, City University of New York, New York, NY, USA
| | - Mei-Chee Tai
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Jie Ping
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Tanish Gandhi
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Medical School, Columbus, OH, 43210, USA
| | - Cara Dauch
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Wexner Medical Center, Clinical Trials Office, Columbus, OH 43210, USA
| | - Susan L. Neuhausen
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Elad Ziv
- University of California, Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA
- University of California, Department of Medicine, San Francisco, San Francisco, CA, USA
- University of California San Francisco, Institute for Human Genetics, San Francisco, CA, USA
| | - Nereida Sotelo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Shreya Ghanekar
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Owen Meadows
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Monica Paredes
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jessica Gillespie
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Amber Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Heather Hampel
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Guochong Jia
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B. Ambrosone
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - John D. Carpten
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Integrative Translational Sciences, City of Hope, Duarte, CA
| | - Song Yao
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Patrick Stevens
- The Ohio State University Comprehensive Cancer Center, Bioinformatics Shared Resource, Columbus, OH, USA
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Jia Wern Pan
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Paolo Fadda
- The Ohio State University Comprehensive Cancer Center, Genomics Shared Resource, Columbus, OH, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Joseph Paul McElroy
- The Ohio State University Center for Biostatistics, Department of Biomedical Informatics, Columbus, OH, USA
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
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Jablonski KP, Beerenwinkel N. Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. Bioinformatics 2023; 39:btad522. [PMID: 37610338 PMCID: PMC10471899 DOI: 10.1093/bioinformatics/btad522] [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: 11/12/2022] [Revised: 07/04/2023] [Accepted: 08/22/2023] [Indexed: 08/24/2023] Open
Abstract
MOTIVATION Gene set enrichment methods are a common tool to improve the interpretability of gene lists as obtained, for example, from differential gene expression analyses. They are based on computing whether dysregulated genes are located in certain biological pathways more often than expected by chance. Gene set enrichment tools rely on pre-existing pathway databases such as KEGG, Reactome, or the Gene Ontology. These databases are increasing in size and in the number of redundancies between pathways, which complicates the statistical enrichment computation. RESULTS We address this problem and develop a novel gene set enrichment method, called pareg, which is based on a regularized generalized linear model and directly incorporates dependencies between gene sets related to certain biological functions, for example, due to shared genes, in the enrichment computation. We show that pareg is more robust to noise than competing methods. Additionally, we demonstrate the ability of our method to recover known pathways as well as to suggest novel treatment targets in an exploratory analysis using breast cancer samples from TCGA. AVAILABILITY AND IMPLEMENTATION pareg is freely available as an R package on Bioconductor (https://bioconductor.org/packages/release/bioc/html/pareg.html) as well as on https://github.com/cbg-ethz/pareg. The GitHub repository also contains the Snakemake workflows needed to reproduce all results presented here.
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Affiliation(s)
- Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel 4058, Switzerland
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3
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[Expression pattern of the histone lysine demethylase family and its potential role in bladder cancer: a multi-omics analysis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:1822-1831. [PMID: 36651250 PMCID: PMC9878407 DOI: 10.12122/j.issn.1673-4254.2022.12.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To investigate the expression patterns of 19 histone lysine demethylases (KDMs) and their role in bladder cancer. METHODS In this study, UALCAN and GSCALite were used to analyze the transcriptional expression, methylation level and somatic variation of KDMs in bladder cancer samples from TCGA. Kaplan Meier-Plotter and Assistant for clinical bioinformatics were used to investigate the effect of KDMs expression on the prognosis of BLCA samples. The immune infiltration and drug sensitivity of KDMs in bladder cancer were analyzed by Timer and GSCALite. RESULTS The KDMs did not show consistent expressions patterns in bladder cancer, where the expressions of KDM1A/1B/2B/4A/4B/5B/5C were significantly upregulated while those of KDM3B/6B/7C were significantly downregulated. Methylation data analysis showed that methylation levels of KDM1A/3B/4A/4B/4C/5A/5B/5C/7B were significantly downregulated and that of KDM7C was upregulated. The transcription levels of 14 KDMs had significant negative correlations with their methylation levels, and among them KDM1A showed the strongest correlation. Mutation analysis revealed that KDM6A had the highest frequency of nonsynonymous mutations with the largest variety, and these mutations were complementary to nonsynonymous mutations of the other KDMs. Survival analysis showed that KDM3A/4C/5D/6A/7B were protective for OS while KDM3B/5B/5C adversely affected RFS of BLCA patients. Further comprehensive prognostic modeling confirmed that KDM4C/6A/7B were potential prognostic biomarkers of bladder cancer, and their expressions were positively correlated with immune infiltration in BLCA patients. KDM2B/3B/4B/4C/5A were negatively correlated with the sensitivity to most anticancer drugs, while KDM2B/4B were positively correlated with the sensitivity to 4 anticancer drugs. CONCLUSION The expression patterns of the KDMs in bladder cancer highlight a high mutation complementarity and a negative correlation between over-expression and hypomethylation level closely related with the prognosis, immune infiltration and drug sensitivity.
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Wang D, Gao S, Qian H, Yuan P, Zhang B. Prognostic Value of Copy Number Alteration Burden in Early-Stage Breast Cancer and the Construction of an 11-Gene Copy Number Alteration Model. Cancers (Basel) 2022; 14:cancers14174145. [PMID: 36077687 PMCID: PMC9454926 DOI: 10.3390/cancers14174145] [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: 07/23/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The increasing burden of breast cancer has prompted a wide range of researchers to search for new prognostic markers. Considering that tumor mutation burden (TMB) is low and copy number alteration burden (CNAB) is high in breast cancer, we built a CNAB-based model using a public database and validated it with a Chinese population. We collected formalin-fixed, paraffin-embedded (FFPE) tissue samples from 31 breast cancer patients who were treated between 2010 and 2014 at the National Cancer Center (CICAMS). METABRIC and TCGA data were downloaded via cBioPortal. In total, 2295 patients with early-stage breast cancer were enrolled in the study, including 1427 in the METABRIC cohort, 837 in the TCGA cohort, and 31 in the CICAMS cohort. Based on the ROC curve, we consider 2.2 CNA/MBp as the threshold for the CNAB-high and CNAB-low groupings. In both the TCGA cohort and the CICAMS cohort, CNAB-high had a worse prognosis than CNAB-low. We further simplified this model by establishing a prognostic nomogram for early breast cancer patients by 11 core genes, and this nomogram was highly effective in both the TCGA cohort and the CICAMS cohort. We hope that this model will subsequently help clinicians with prognostic assessments.
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Affiliation(s)
- Dingyuan Wang
- Department of Breast 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
| | - Songlin Gao
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Correspondence: (P.Y.); (B.Z.)
| | - Bailin Zhang
- Department of Breast 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
- Correspondence: (P.Y.); (B.Z.)
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Jin L, Qu K, Hanif Q, Zhang J, Liu J, Chen N, Suolang Q, Lei C, Huang B. Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures. Front Genet 2022; 13:833475. [PMID: 35422847 PMCID: PMC9001881 DOI: 10.3389/fgene.2022.833475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/04/2022] [Indexed: 12/14/2022] Open
Abstract
Dengchuan cattle are the only dairy yellow cattle and endangered cattle among Yunnan native cattle breeds. However, its genetic background remains unclear. Here, we performed whole-genome sequencing of ten Dengchuan cattle. Integrating our data with the publicly available data, Dengchuan cattle were observed to be highly interbred than other cattle in the dataset. Furthermore, the positive selective signals were mainly manifested in candidate genes and pathways related to milk production, disease resistance, growth and development, and heat tolerance. Notably, five genes (KRT39, PGR, KRT40, ESR2, and PRKACB) were significantly enriched in the estrogen signaling pathway. Moreover, the missense mutation in the PGR gene (c.190T > C, p.Ser64Pro) showed a homozygous mutation pattern with higher frequency (83.3%) in Dengchuan cattle. In addition, a large number of strong candidate regions matched genes and QTLs related to milk yield and composition. Our research provides a theoretical basis for analyzing the genetic mechanism underlying Dengchuan cattle with excellent lactation and adaptability, crude feed tolerance, good immune performance, and small body size and also laid a foundation for genetic breeding research of Dengchuan cattle in the future.
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Affiliation(s)
- Liangliang Jin
- Yunnan Academy of Grassland and Animal Science, Kunming, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quji Suolang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
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6
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Varghese B, Del Gaudio N, Cobellis G, Altucci L, Nebbioso A. KDM4 Involvement in Breast Cancer and Possible Therapeutic Approaches. Front Oncol 2021; 11:750315. [PMID: 34778065 PMCID: PMC8581295 DOI: 10.3389/fonc.2021.750315] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer death in women, although recent scientific and technological achievements have led to significant improvements in progression-free disease and overall survival of patients. Genetic mutations and epigenetic modifications play a critical role in deregulating gene expression, leading to uncontrolled cell proliferation and cancer progression. Aberrant histone modifications are one of the most frequent epigenetic mechanisms occurring in cancer. In particular, methylation and demethylation of specific lysine residues alter gene accessibility via histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The KDM family includes more than 30 members, grouped into six subfamilies and two classes based on their sequency homology and catalytic mechanisms, respectively. Specifically, the KDM4 gene family comprises six members, KDM4A-F, which are associated with oncogene activation, tumor suppressor silencing, alteration of hormone receptor downstream signaling, and chromosomal instability. Blocking the activity of KDM4 enzymes renders them "druggable" targets with therapeutic effects. Several KDM4 inhibitors have already been identified as anticancer drugs in vitro in BC cells. However, no KDM4 inhibitors have as yet entered clinical trials due to a number of issues, including structural similarities between KDM4 members and conservation of the active domain, which makes the discovery of selective inhibitors challenging. Here, we summarize our current knowledge of the molecular functions of KDM4 members in BC, describe currently available KDM4 inhibitors, and discuss their potential use in BC therapy.
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Affiliation(s)
- Benluvankar Varghese
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Gilda Cobellis
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Biogem Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
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7
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Coronel-Hernández J, Pérez-Yépez EA, Delgado-Waldo I, Contreras-Romero C, Jacobo-Herrera N, Cantú-De León D, Pérez-Plasencia C. Aberrant Metabolism as Inductor of Epigenetic Changes in Breast Cancer: Therapeutic Opportunities. Front Oncol 2021; 11:676562. [PMID: 34692471 PMCID: PMC8531643 DOI: 10.3389/fonc.2021.676562] [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: 03/05/2021] [Accepted: 09/08/2021] [Indexed: 12/23/2022] Open
Abstract
Aberrant metabolism is arising interest in the scientific community not only because of the role it plays in the development and establishment of the tumor mass but also the possibility of drug poisoning of key enzymes overexpressed in tumor cells. Moreover, tumor metabolism provides key molecules to maintain the epigenetic changes that are also an undisputed characteristic of each tumor type. This metabolic change includes the Warburg effect and alterations in key pathways involved in glutaminolysis, pentose phosphate, and unsaturated fatty acid biosynthesis. Modifications in all these pathways have consequences that impact genetics and epigenetics processes such as DNA methylation patterns, histone post-translational modifications, triggering oncogenes activation, and loss in tumor suppressor gene expression to lead the tumor establishment. In this review, we describe the metabolic rearrangement and its association with epigenetic regulation in breast cancer, as well as its implication in biological processes involved in cancer progression. A better understanding of these processes could help to find new targets for the diagnosis, prognosis, and treatment of this human health problem.
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Affiliation(s)
| | - Eloy Andrés Pérez-Yépez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico.,Cátedra-CONACYT, Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico City, Mexico
| | | | | | - Nadia Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán, Mexico City, Mexico
| | - David Cantú-De León
- Unidad de Investigación en Cáncer, Instituto Nacional de Cancerología , Mexico City, Mexico
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico.,Laboratorio de Genómica Funcional, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
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8
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Li W, Wu H, Sui S, Wang Q, Xu S, Pang D. Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way. Front Cell Dev Biol 2021; 9:736935. [PMID: 34595180 PMCID: PMC8476812 DOI: 10.3389/fcell.2021.736935] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
Histone modifications (HMs) contribute to maintaining genomic stability, transcription, DNA repair, and modulating chromatin in cancer cells. Furthermore, HMs are dynamic and reversible processes that involve interactions between numerous enzymes and molecular components. Aberrant HMs are strongly associated with tumorigenesis and progression of breast cancer (BC), although the specific mechanisms are not completely understood. Moreover, there is no comprehensive overview of abnormal HMs in BC, and BC therapies that target HMs are still in their infancy. Therefore, this review summarizes the existing evidence regarding HMs that are involved in BC and the potential mechanisms that are related to aberrant HMs. Moreover, this review examines the currently available agents and approved drugs that have been tested in pre-clinical and clinical studies to evaluate their effects on HMs. Finally, this review covers the barriers to the clinical application of therapies that target HMs, and possible strategies that could help overcome these barriers and accelerate the use of these therapies to cure patients.
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Affiliation(s)
- Wei Li
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Hao Wu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shiyao Sui
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Qin Wang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shouping Xu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Da Pang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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9
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Xue L, Li C, Ren J, Wang Y. KDM4C contributes to cytarabine resistance in acute myeloid leukemia via regulating the miR-328-3p/CCND2 axis through MALAT1. Ther Adv Chronic Dis 2021; 12:2040622321997259. [PMID: 34394903 PMCID: PMC8358730 DOI: 10.1177/2040622321997259] [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: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022] Open
Abstract
Aims Acute myeloid leukemia (AML) is an aggressive hematologic neoplasm, in which relapse due to drug resistance is the main cause for treatment failure and the disease progression. In this study, we aimed to investigate the molecular mechanism of KDM4C-dependent MALAT1/miR-328-3p/CCND2 axis in cytarabine (Ara-C) resistance in the context of AML. Methods Bioinformatics analysis was performed to predict the targeting relationships among KDM4C, MALAT1, miR-328-3p, and CCND2 in AML, which were validated with chromatin immunoprecipitation and dual-luciferase reporter assay. Methylation-specific polymerase chain reaction was conducted to detect the methylation of MALAT1 promoter. After conducting gain- and loss-of-function assays, we investigated the effect of KDM4C on cell Ara-C resistance. A NOD/SCID mouse model was established to further investigate the roles of KDM4C/MALAT1/miR-328-3p/CCND2 in Ara-C resistant AML cells. Results KDM4C expression was upregulated in AML. KDM4C upregulation promoted the demethylation in the promoter region of MALAT1 to increase its expression, MALAT1 targeted and inhibited miR-328-3p expression, enhancing the Ara-C resistance of HL-60/A. miR-328-3p targeted and suppressed the expression of CCND2 in HL-60/A to inhibit the Ara-C resistance. Mechanistically, KDM4C regulated miR-328-3p/CCND2 through MALAT1, resulting in Ara-C resistance in AML. Findings in an in vivo xenograft NOD/SCID mouse model further confirmed the contribution of KDM4C/MALAT1/miR-328-3p/CCND2 in the Ara-C resistant AML. Conclusion Our study demonstrated that KDM4C may up-regulate MALAT1 expression, which decreases the expression of miR-328-3p. The downregulation of miR-328-3p increased the level of CCND2, which induced the Ara-C resistance in AML.
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Affiliation(s)
- Lu Xue
- Department of Pediatrics Hematology, The First Hospital of Jilin University, Changchun, P.R. China
| | - Chunhuai Li
- Department of Pediatrics Hematology, The First Hospital of Jilin University, Changchun, P.R. China
| | - Jin Ren
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, P.R. China
| | - Yue Wang
- Department of Pediatrics Hematology, The First Hospital of Jilin University, No. 1, Xinmin Street, Chaoyang District, Changchun, Jilin Province 130021, P.R. China
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10
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Rong Z, Xu J, Shi S, Tan Z, Meng Q, Hua J, Liu J, Zhang B, Wang W, Yu X, Liang C. Circular RNA in pancreatic cancer: a novel avenue for the roles of diagnosis and treatment. Am J Cancer Res 2021; 11:2755-2769. [PMID: 33456571 PMCID: PMC7806488 DOI: 10.7150/thno.56174] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer (PC), an important cause of cancer-related deaths worldwide, is one of the most malignant cancers characterized by a dismal prognosis. Circular RNAs (circRNAs), a class of endogenous ncRNAs with unique covalently closed loops, have attracted great attention in regard to various diseases, especially cancers. Compelling studies have suggested that circRNAs are aberrantly expressed in different cancer tissues and cell types, including PC. More specifically, circRNAs can modify the proliferation, progression, tumorigenesis and chemosensitivity of PC, and some circRNAs could serve as biomarkers for diagnosis and prognosis. Herein, we summarize what is currently known to be related to the biogenesis, functions and potential roles of human circRNAs in PC and their application prospects for PC clinical treatments.
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Histone Demethylase KDM4C Is Required for Ovarian Cancer Stem Cell Maintenance. Stem Cells Int 2020; 2020:8860185. [PMID: 32908544 PMCID: PMC7475738 DOI: 10.1155/2020/8860185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/24/2020] [Accepted: 08/07/2020] [Indexed: 01/06/2023] Open
Abstract
Ovarian cancer is a highly deadly disease, which is often diagnosed at a late stage with metastases. However, most ovarian cancers relapse after surgery combined with platinum-based chemotherapy. Cancer stem cells (CSCs) are stem-like cells that possess high tumorigenic capability and display higher resistant capability against current therapies. However, our knowledge of ovarian CSCs and their molecular mechanism remains sparse. In the current study, we found that KDM4C, a histone demethylase, was required for ovarian cancer stem cell (CSC) maintenance. Depletion of KDM4C significantly reduced the CSC population and sphere formation in vitro. Moreover, we found that KDM4C can regulate the expression of stem cell factor OCT-4 via binding to its promoter. These data indicate that KDM4C is relevant for ovarian CSC maintenance and underscore its importance as a potential therapeutic target.
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Hwang JW, Desterke C, Féraud O, Richard S, Ferlicot S, Verkarre V, Patard JJ, Loisel-Duwattez J, Foudi A, Griscelli F, Bennaceur-Griscelli A, Turhan AG. iPSC-Derived Embryoid Bodies as Models of c- Met-Mutated Hereditary Papillary Renal Cell Carcinoma. Int J Mol Sci 2019; 20:ijms20194867. [PMID: 31575031 PMCID: PMC6801716 DOI: 10.3390/ijms20194867] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Hereditary cancers with cancer-predisposing mutations represent unique models of human oncogenesis, as a driving oncogenic event is present in germline. Currently, there are no satisfactory models to study these malignancies. We report the generation of IPSC from the somatic cells of a patient with hereditary c-met-mutated papillary renal cell carcinoma (PRCC). From these cells we have generated spontaneous aggregates organizing in structures which expressed kidney markers such as PODXL and Six2. These structures expressed PRCC markers both in vitro and in vivo in NSG mice. Gene-expression profiling showed striking molecular similarities with signatures found in a large cohort of PRCC tumor samples. This analysis, applied to primary cancers with and without c-met mutation, showed overexpression of the BHLHE40 and KDM4C only in the c-met-mutated PRCC tumors, as predicted by c-met-mutated embryoid bodies transcriptome. These data therefore represent the first proof of concept of “hereditary renal cancer in a dish” model using c-met-mutated iPSC-derived embryoid bodies, opening new perspectives for discovery of novel predictive progression markers and for drug-screening for future precision-medicine strategies.
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Affiliation(s)
- Jin Wook Hwang
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
| | - Christophe Desterke
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
| | - Olivier Féraud
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
| | - Stephane Richard
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR, labellisé par l'INCa, et Service d'Urologie, AP-HP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; Génétique Oncologique EPHE, PSL Université, INSERM UMR 1186, Gustave Roussy, Faculté de Médecine et Université Paris-Sud, 94800 Villejuif, France.
| | - Sophie Ferlicot
- INSERM, UMR 1186, Gustave Roussy, Paris-Sud University, Paris-Saclay University, 94800 Villejuif, France.
- Department of Pathology, Bicêtre Hospital, AP-HP, 94270 Le Kremlin-Bicêtre, France.
| | - Virginie Verkarre
- Service d'Anatomie Pathologique, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France.
- Faculté de médecine, Université Paris Descartes, 75006 Paris, France.
| | - Jean Jacques Patard
- Service d'Urologie, Centre Hospitalier de Mont de Marsan, 40024 Mont de Marsan, France.
| | - Julien Loisel-Duwattez
- INSERM U1195, Université Paris Sud, Faculté de Médecine, APHP, Service de Neurologie, Hôpital Bicêtre, 94276 le Kremlin Bicêtre, France.
| | - Adlen Foudi
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
- ATIP Avenir INSERM UMR-S 935, Université Paris Sud, 94800 Villejuif, France.
| | - Frank Griscelli
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
- INGESTEM National IPSC Infrastructure, 94800 Villejuif, France.
- Paris Descartes University, Faculty Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France.
| | - Annelise Bennaceur-Griscelli
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
- INGESTEM National IPSC Infrastructure, 94800 Villejuif, France.
- Division of Hematology, Paris Sud University Hospitals, Le Kremlin Bicêtre 75006, 94800 Villejuif, France.
| | - Ali G Turhan
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, 94800 Villejuif, France.
- INGESTEM National IPSC Infrastructure, 94800 Villejuif, France.
- Division of Hematology, Paris Sud University Hospitals, Le Kremlin Bicêtre 75006, 94800 Villejuif, France.
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Immune profiles in primary squamous cell carcinoma of the head and neck. Oral Oncol 2019; 96:77-88. [PMID: 31422218 DOI: 10.1016/j.oraloncology.2019.06.032] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES In this study we describe the tumor microenvironment, the signaling pathways and genetic alterations associated with the presence or absence of CD8+ T-cell infiltration in primary squamous cell carcinoma of the head and neck (SCCHN) tumors. MATERIALS AND METHODS Two SCCHN multi-analyte cohorts were utilized, the Cancer Genome Atlas (TCGA) and the Chicago Head and Neck Genomics (CHGC) cohort. A well-established chemokine signature classified SCCHN tumors into high and low CD8+ T-cell inflamed phenotypes (TCIP-H, TCIP-L respectively). Gene set enrichment and iPANDA analyses were conducted to dissect differences in signaling pathways, somatic mutations and copy number aberrations for TCIP-H versus TCIP-L tumors, stratified by HPV status. RESULTS TCIP-H SCCHN tumors were enriched in multiple immune checkpoints irrespective of HPV-status. HPV-positive tumors were enriched in markers of T-regulatory cells (Tregs) and HPV-negative tumors in protumorigenic M2 macrophages. TCIP-L SCCHN tumors were enriched for the β-catenin/WNT and Hedgehog signaling pathways, had frequent mutations in NSD1, amplifications in EGFR and YAP1, as well as CDKN2A deletions. TCIP-H SCCHN tumors were associated with the MAPK/ERK, JAK/STAT and mTOR/AKT signaling pathways, and were enriched in CASP8, EP300, EPHA2, HRAS mutations, CD274, PDCD1LG2, JAK2 amplifications. CONCLUSIONS Our findings support that combinatorial immune checkpoint blockade and depletion strategies targeting Tregs in HPV-positive and M2 macrophages in HPV-negative tumors may lead to improved antitumor immune responses in patients with TCIP-H SCCHN. We highlight novel pathways and genetic events that may serve as candidate biomarkers and novel targeted therapies to enhance the efficacy of immunotherapy in SCCHN patients.
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Garcia J, Lizcano F. Kdm4c is Recruited to Mitotic Chromosomes and Is Relevant for Chromosomal Stability, Cell Migration and Invasion of Triple Negative Breast Cancer Cells. BREAST CANCER-BASIC AND CLINICAL RESEARCH 2018; 12:1178223418773075. [PMID: 30083054 PMCID: PMC6073829 DOI: 10.1177/1178223418773075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/04/2018] [Indexed: 01/23/2023]
Abstract
Members of the jumonji-containing lysine demethylase protein family have been associated with cancer development, although their specific roles in the evolution of tumor cells remain unknown. This work examines the effects of lysine demethylase 4C (KDM4C) knockdown on the behavior of a triple-negative breast cancer cell line. KDM4C expression was knocked-down by siRNA and analyzed by Western blot and immunofluorescence. HCC38 cell proliferation was examined by MTT assay, while breast cancer cells’ migration and invasion were tested in Transwell format by chemotaxis. Immunofluorescence assays showed that KDM4C, which is a key protein for modulating histone demethylation and chromosome stability through the distribution of genetic information, is located at the chromosomes during mitosis. Proliferation assays demonstrated that KDM4C is important for cell survival, while Transwell migration and invasion assays indicated that this protein is relevant for cancer progression. These data indicate that KDM4C is relevant for breast cancer progression and highlight its importance as a potential therapeutic target.
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Affiliation(s)
- Jeison Garcia
- Doctorate in Biociences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
| | - Fernando Lizcano
- Doctorate in Biociences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
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