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Deng H, Wen C, Jiang S, Yu Y, Zhao J, Zhang B. Single-cell analysis reveals one cancer-associated fibroblasts subtype linked to metastasis in breast cancer: MXRA5 as a potential novel marker for prognosis. Am J Cancer Res 2024; 14:526-544. [PMID: 38455411 PMCID: PMC10915337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/21/2024] [Indexed: 03/09/2024] Open
Abstract
Cancer-associated fibroblasts (CAFs) are prevalent in the tumor microenvironment of breast cancer, comprising a group of cell subpopulations with spatial, phenotypic, and functional heterogeneity. Due to the lack of specific markers for CAF subpopulations, their specific mechanisms in breast cancer remain unclear. We identified eight distinct CAF phenotypes in breast cancer using multiple single-cell RNA sequencing datasets and determined distinct transcription factors (TFs) of CAFs through SCENIC analysis. Our study highlights one CAF subtype in breast cancer, FN1+CAF2, associated with metastasis and macrophage polarization. We observed elevated FN1 expression in the stromal tissue of breast cancer patients. Furthermore, FN1 knockdown in CAFs reduced the migration ability of breast cancer cells. We identified a regulatory gene, MXRA5, in CAF2, which may play crucial roles in breast cancer. Our results indicated upregulated MXRA5 expression in breast cancer tissues and CAFs from patients with lymph node metastasis in the following experiment. Overall, our study reveals that the FN1+CAF2 subtype is associated with metastasis and suggests that MXRA5 may be a novel marker mediating the effects of CAF2 on breast cancer metastasis. This study enriches our understanding of CAF heterogeneity and offers new insights for treating breast cancer metastasis.
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Affiliation(s)
- Huifang Deng
- Department of Thyroid and Breast Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Chengxu Wen
- Department of Thyroid and Breast Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Shangxuan Jiang
- Department of Thyroid and Breast Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Yuanhang Yu
- Department of Thyroid and Breast Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
| | - Jianguo Zhao
- Department of Thyroid and Breast Surgery, Wuhan No. 1 HospitalWuhan 430022, Hubei, China
| | - Bo Zhang
- Department of Thyroid and Breast Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, Hubei, China
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Postel MD, Darabi S, Howe JR, Liang WS, Craig DW, Demeure MJ. Multiomic sequencing of paired primary and metastatic small bowel carcinoids. F1000Res 2023; 12:417. [PMID: 37954063 PMCID: PMC10632590 DOI: 10.12688/f1000research.130251.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 11/14/2023] Open
Abstract
Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.
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Affiliation(s)
- Mackenzie D. Postel
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Sourat Darabi
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
| | - James R. Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - David W. Craig
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michael J. Demeure
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
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Andus I, Prall F, Linnebacher M, Linnebacher CS. Establishment, characterization, and drug screening of low-passage patient individual non-small cell lung cancer in vitro models including the rare pleomorphic subentity. Front Oncol 2023; 13:1089681. [PMID: 37228492 PMCID: PMC10203569 DOI: 10.3389/fonc.2023.1089681] [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: 11/04/2022] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction For pre-clinical drug development and precision oncology research, robust cancer cell models are essential. Patient-derived models in low passages retain more genetic and phenotypic characteristics of their original tumors than conventional cancer cell lines. Subentity, individual genetics, and heterogeneity greatly influence drug sensitivity and clinical outcome. Materials and methods Here, we report on the establishment and characterization of three patient-derived cell lines (PDCs) of different subentities of non-small cell lung cancer (NSCLC): adeno-, squamous cell, and pleomorphic carcinoma. The in-depth characterization of our PDCs included phenotype, proliferation, surface protein expression, invasion, and migration behavior as well as whole-exome and RNA sequencing. Additionally, in vitro drug sensitivity towards standard-of-care chemotherapeutic regimens was evaluated. Results The pathological and molecular properties of the patients' tumors were preserved in the PDC models HROLu22, HROLu55, and HROBML01. All cell lines expressed HLA I, while none were positive for HLA II. The epithelial cell marker CD326 and the lung tumor markers CCDC59, LYPD3, and DSG3 were also detected. The most frequently mutated genes included TP53, MXRA5, MUC16, and MUC19. Among the most overexpressed genes in tumor cells compared to normal tissue were the transcription factors HOXB9, SIM2, ZIC5, SP8, TFAP2A, FOXE1, HOXB13, and SALL4; the cancer testis antigen CT83; and the cytokine IL23A. The most downregulated genes on the RNA level encode the long non-coding RNA LANCL1-AS1, LINC00670, BANCR, and LOC100652999; the regulator of angiogenesis ANGPT4; the signaling molecules PLA2G1B and RS1; and the immune modulator SFTPD. Furthermore, neither pre-existing therapy resistances nor drug antagonistic effects could be observed. Conclusion In summary, we successfully established three novel NSCLC PDC models from an adeno-, a squamous cell, and a pleomorphic carcinoma. Of note, NSCLC cell models of the pleomorphic subentity are very rare. The detailed characterization including molecular, morphological, and drug-sensitivity profiling makes these models valuable pre-clinical tools for drug development applications and research on precision cancer therapy. The pleomorphic model additionally enables research on a functional and cell-based level of this rare NCSLC subentity.
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Affiliation(s)
- Ingo Andus
- Patient Models for Precision Medicine, Department of General Surgery, University Medical Center Rostock, Rostock, Germany
| | - Friedrich Prall
- Institute of Pathology, University Medical Center Rostock, Rostock, Germany
| | - Michael Linnebacher
- Molecular Oncology and Immunotherapy, Department of General Surgery, University Medical Center Rostock, Rostock, Germany
| | - Christina S. Linnebacher
- Patient Models for Precision Medicine, Department of General Surgery, University Medical Center Rostock, Rostock, Germany
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Peng SQ, Zhu XR, Zhao MZ, Zhang YF, Wang AR, Chen MB, Ye ZY. Identification of matrix-remodeling associated 5 as a possible molecular oncotarget of pancreatic cancer. Cell Death Dis 2023; 14:157. [PMID: 36828810 PMCID: PMC9958022 DOI: 10.1038/s41419-023-05684-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023]
Abstract
Pancreatic cancer has an extremely poor prognosis. Here we examined expression, potential functions and underlying mechanisms of MXRA5 (matrix remodeling associated 5) in pancreatic cancer. Bioinformatics studies revealed that MXRA5 transcripts are significantly elevated in pancreatic cancer tissues, correlating with the poor overall survival, high T-stage, N1 and pathologic stage of the patients. MXRA5 mRNA and protein expression is significantly elevated in microarray pancreatic cancer tissues and different pancreatic cancer cells. In primary and immortalized (BxPC-3 and PANC-1 lines) pancreatic cancer cells, shRNA-induced MXRA5 silencing or CRISPR/Cas9-mediated MXRA5 knockout suppressed cell survival, proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT), while provoking cell apoptosis. Conversely, forced overexpression of MXRA5 further promoted pancreatic cancer cell progression and EMT. Bioinformatics studies and the protein chip analyses revealed that differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in MXRA5-overexpressed primary pancreatic cancer cells were enriched in the PI3K-Akt-mTOR cascade. Indeed, Akt-mTOR activation in primary human pancreatic cancer cells was inhibited by MXRA5 shRNA or knockout, but was augmented following MXRA5 overexpression. In vivo, the growth of MXRA5 KO PANC-1 xenografts was largely inhibited in nude mice. Moreover, intratumoral injection of adeno-associated virus-packed MXRA5 shRNA potently inhibited primary pancreatic cancer cell growth in nude mice. Akt-mTOR activation was also largely inhibited in the MXRA5-depleted pancreatic cancer xenografts. Contrarily MXRA5 overexpression promoted primary pancreatic cancer cell growth in nude mice. Together, overexpressed MXRA5 is important for pancreatic cancer cell growth possibly through promoting EMT and Akt-mTOR activation. MXRA5 could be a potential therapeutic oncotarget for pancreatic cancer.
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Affiliation(s)
- Shi-Qing Peng
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Xiao-Ren Zhu
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Ming-Zhi Zhao
- Clinical Research Center of Neurological Disease and Department of Orthopaedics, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi-Fan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - An-Ran Wang
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Min-Bin Chen
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China.
| | - Zhen-Yu Ye
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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Gao Y, Shen L, Dong T, Yang X, Cui H, Guo Y, Ma Y, Kong P, Cheng X, Zhang L, Cui Y. An N-glycoproteomic site-mapping analysis reveals glycoprotein alterations in esophageal squamous cell carcinoma. J Transl Med 2022; 20:285. [PMID: 35752862 PMCID: PMC9233802 DOI: 10.1186/s12967-022-03489-2] [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: 01/14/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Aberrant glycosylation has been recognized as a hallmark of cancer and N-glycosylation is one of the main types of glycosylation in eukaryotes. Although N-glycoproteomics has made contributions to the discovery of biomarkers in a variety of cancers, less is known about the abnormal glycosylation signatures in esophageal squamous cell carcinoma (ESCC). Methods In this study, we reported the proteomics and N-glycoproteomic site-mapping analysis of eight pairs of ESCC tissues and adjacent normal tissues. With zic-HILIC enrichment, TMT-based isobaric labeling, LC–MS/MS analysis, differentially expressed N-glycosylation was quantitatively characterized. Lectin affinity enrichment combined with western blot was used to validate the potential biomarkers in ESCC. Results A series of differentially expressed glycoproteins (e.g., LAMP2, PLOD2) and enriched signaling pathways (e.g., metabolism-related pathway, ECM-receptor interaction, focal adhesion) were identified. Besides that, seven significantly enriched motifs were found from the identified N-glycosylation sites. Three clusters were identified after conducting the dynamic profiling analysis of glycoprotein change during lymph node metastasis progression. Further validation found that the elevated fucosylation level of ITGB1, CD276 contributed to the occurrence and development of ESCC, which might be the potential biomarkers in ESCC. Conclusion In summary, we characterized the N-glycosylation and N-glycoprotein alterations associated with ESCC. The typical changes in glycoprotein expression and glycosylation occupancy identified in our study will not only be used as ESCC biomarkers but also improve the understanding of ESCC biology. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03489-2.
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Affiliation(s)
- Yingzhen Gao
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Liuyi Shen
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Tianyue Dong
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Xin Yang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Heyang Cui
- Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518035, People's Republic of China
| | - Yanlin Guo
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Yanchun Ma
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Ling Zhang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China. .,Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518035, People's Republic of China.
| | - Yongping Cui
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China. .,Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518035, People's Republic of China.
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Cao J, Liu Z, Liu J, Li C, Zhang G, Shi R. Bioinformatics Analysis and Identification of Genes and Pathways in Ischemic Cardiomyopathy. Int J Gen Med 2021; 14:5927-5937. [PMID: 34584445 PMCID: PMC8464396 DOI: 10.2147/ijgm.s329980] [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: 07/27/2021] [Accepted: 09/08/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Ischemic cardiomyopathy (ICM) is considered to be the most common cause of heart failure, with high prevalence and mortality. This study aimed to investigate the different expressed genes (DEGs) and pathways in the pathogenesis of ICM using bioinformatics analysis. Methods The control and ICM datasets GSE116250, GSE46224 and GSE5406 were collected from the gene expression omnibus (GEO) database. DEGs were identified using limma package of R software, and co-expressed genes were identified using Venn diagrams. Then, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore the biological functions and signaling pathways. Protein-protein interaction (PPI) networks were assembled with Cytoscape software to identify hub genes related to the pathogenesis of ICM. RT-PCR of Heart tissues (n=2 for non-failing controls and n=4 for ischemic cardiomyopathy patients) was used to validate the bioinformatic results. Results A total of 844 DEGs were screened from GSE116250, of which 447 were up-regulated genes and 397 were down-regulated genes, respectively. A total of 99 DEGs were singled out from GSE46224, of which 58 were up-regulated genes and 41 were down-regulated genes, respectively. Thirty DEGs were screened from GSE5406, including 10 genes with up-regulated expression and 20 genes with down-regulated expression. Five up-regulated and 3 down-regulated co-expressed DEGs were intersected in three datasets. GO and KEGG pathway analyses revealed that DEGs are mainly enriched in collagen fibril organization, protein digestion and absorption, AGE-RAGE signaling pathway and other related pathways. Collagen alpha-1(III) chain (COL3A1), collagen alpha-2(I) chain (COL1A2) and lumican (LUM) are the three hub genes in all three datasets through PPI network analysis. The expression of 5 DEGs (SERPINA3, FCN3, COL3A1, HBB, MXRA5) in heart tissues by qRT-PCR results was consistent with our GEO analysis, while expression of 3 DEGs (ASPN, LUM, COL1A2) was opposite with GEO analysis. Conclusion These findings from this bioinformatics network analysis investigated key hub genes, which contributed to better understanding the mechanism and new therapeutic targets of ICM.
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Affiliation(s)
- Jing Cao
- Department of Cardiovascular Medicine, Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhaoya Liu
- Department of Geriatrics, Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jie Liu
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Chan Li
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Guogang Zhang
- Department of Cardiovascular Medicine, Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Ruizheng Shi
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
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Jiang Y, Zhang X, Zhang X, Zhao K, Zhang J, Yang C, Chen Y. Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Pterygium by MeRIP Sequencing. Front Cell Dev Biol 2021; 9:670528. [PMID: 34249924 PMCID: PMC8267473 DOI: 10.3389/fcell.2021.670528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/04/2021] [Indexed: 01/08/2023] Open
Abstract
Aim Pterygium is a common ocular surface disease, which is affected by a variety of factors. Invasion of the cornea can cause severe vision loss. N6-methyladenosine (m6A) is a common post-transcriptional modification of eukaryotic mRNA, which can regulate mRNA splicing, stability, nuclear transport, and translation. To our best knowledge, there is no current research on the mechanism of m6A in pterygium. Methods We obtained 24 pterygium tissues and 24 conjunctival tissues from each of 24 pterygium patients recruited from Shanghai Yangpu Hospital, and the level of m6A modification was detected using an m6A RNA Methylation Quantification Kit. Expression and location of METTL3, a key m6A methyltransferase, were identified by immunostaining. Then we used m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq), RNA sequencing (RNA-seq), and bioinformatics analyses to compare the differential expression of m6A methylation in pterygium and normal conjunctival tissue. Results We identified 2,949 dysregulated m6A peaks in pterygium tissue, of which 2,145 were significantly upregulated and 804 were significantly downregulated. The altered m6A peak of genes were found to play a key role in the Hippo signaling pathway and endocytosis. Joint analyses of MeRIP-seq and RNA-seq data identified 72 hypermethylated m6A peaks and 15 hypomethylated m6A peaks in mRNA. After analyzing the differentially methylated m6A peaks and synchronously differentially expressed genes, we searched the Gene Expression Omnibus database and identified five genes related to the development of pterygium (DSP, MXRA5, ARHGAP35, TMEM43, and OLFML2A). Conclusion Our research shows that m6A modification plays an important role in the development of pterygium and can be used as a potential new target for the treatment of pterygium in the future.
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Affiliation(s)
- Yaping Jiang
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Zhang
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyan Zhang
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai, China
| | - Kun Zhao
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuanxi Yang
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
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MXRA5 Is a Novel Immune-Related Biomarker That Predicts Poor Prognosis in Glioma. DISEASE MARKERS 2021; 2021:6680883. [PMID: 34211612 PMCID: PMC8211501 DOI: 10.1155/2021/6680883] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
Background Glioma is the most common primary intracranial tumor and is associated with poor prognosis. Identifying effective biomarkers for glioma is particularly important. MXRA5, a secreted glycoprotein, is involved in cell adhesion and extracellular matrix remodeling and has been reported to be expressed in many cancers. However, the role and mechanism of action of MXRA5 in gliomas remain unclear. This study was aimed at investigating the role of MXRA5 at the transcriptome level and its clinical prognostic value. Methods In this study, RNA microarray data of 301 glioma patients from the Chinese Glioma Genome Atlas (CGGA) were collected as a training cohort and RNA-seq data of 702 glioma samples from The Cancer Genome Atlas (TCGA) were used for validation. We analyzed the clinical and molecular characteristics as well as the prognostic value of MXRA5 in glioma. In addition, the expression level of MXRA was evaluated in 28 glioma tissue samples. Results We found that MXRA5 expression was significantly upregulated in high-grade gliomas and IDH wild-type gliomas compared to controls. Receiver operating characteristic (ROC) analysis showed that MXRA5 is a potential marker of the mesenchymal subtype of glioblastoma multiforme (GBM). We found that MXRA5 expression is highly correlated with immune checkpoint molecule expression levels and tumor-associated macrophage infiltration. High MXRA5 expression could be used as an independent indicator of poor prognosis in glioma patients. Conclusion Our study suggests that MXRA5 expression is associated with the clinicopathologic features and poor prognosis of gliomas. MXRA5 may play an important role in the immunosuppressive microenvironment of glioma. As a secreted glycoprotein, MXRA5 is a potential circulating biomarker for glioma, deserving further investigation.
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10
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Of mice and men - and guinea pigs? Ann Anat 2021; 238:151765. [PMID: 34000371 DOI: 10.1016/j.aanat.2021.151765] [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: 03/31/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/31/2022]
Abstract
This year marks the twentieth anniversary of the publication of the first draft of the human genome and its broad availability to the scientific community. In parallel, the annotation of the mouse genome led to the identification and analysis of countless genes by means of genetic manipulation. Today, when comparing both genomes, it might surprise that some genes are still seeking their respective homologs in either species. In this review, we aim at raising awareness for the remarkable differences between the researcher's favorite rodents, i.e., mice and rats, when it comes to the generation of rodent research models regarding genes with a particular delicate localization, namely the pseudoautosomal region on both sex chromosomes. Many of these genes are of utmost clinical relevance in humans and still miss a rodent disease model giving their absence in mice and rats or low sequence similarity compared to humans. The abundance of rodents within mammals prompted us to investigate different branches of rodents leading us to the re-discovery of the guinea pig as a mammalian research model for a distinct group of genes.
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11
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Yu C, Wong EM, Joo JE, Hodge AM, Makalic E, Schmidt D, Buchanan DD, Severi G, Hopper JL, English DR, Giles GG, Southey MC, Dugué PA. Epigenetic Drift Association with Cancer Risk and Survival, and Modification by Sex. Cancers (Basel) 2021; 13:cancers13081881. [PMID: 33919912 PMCID: PMC8070898 DOI: 10.3390/cancers13081881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary Ageing is the strongest cancer risk factor, and men and women exhibit different risk profiles in terms of incidence and survival. DNA methylation is known to strongly vary by age and sex. Epigenetic drift refers to age-related DNA methylation changes and the tendency for increasing discordance between epigenomes over time, but it remains unknown to what extent the epigenetic drift contributes to cancer risk and survival. The aims of this study were to identify age-associated, sex-associated and sexually dimorphic age-associated (age-by-sex-associated) DNA methylation markers and investigate whether age- and age-by-sex-associated markers are associated with cancer risk and survival. Our study, which used a total of 2754 matched case–control pairs with DNA methylation in pre-diagnostic blood, is the first large study to examine the association between sex-specific epigenetic drift and cancer development and progression. The results may be useful for cancer early diagnosis and prediction of prognosis. Abstract To investigate age- and sex-specific DNA methylation alterations related to cancer risk and survival, we used matched case–control studies of colorectal (n = 835), gastric (n = 170), kidney (n = 143), lung (n = 332), prostate (n = 869) and urothelial (n = 428) cancers, and mature B-cell lymphoma (n = 438). Linear mixed-effects models were conducted to identify age-, sex- and age-by-sex-associated methylation markers using a discovery (controls)-replication (cases) strategy. Replication was further examined using summary statistics from Generation Scotland (GS). Associations between replicated markers and risk of and survival from cancer were assessed using conditional logistic regression and Cox models (hazard ratios (HR)), respectively. We found 32,659, 23,141 and 48 CpGs with replicated associations for age, sex and age-by-sex, respectively. The replication rates for these CpGs using GS summary data were 94%, 86% and 91%, respectively. Significant associations for cancer risk and survival were identified at some individual age-related CpGs. Opposite to previous findings using epigenetic clocks, there was a strong negative trend in the association between epigenetic drift and risk of colorectal cancer. Methylation at two CpGs overlapping TMEM49 and ARX genes was associated with survival of overall (HR = 0.91, p = 7.7 × 10−4) and colorectal (HR = 1.52, p = 1.8 × 10−4) cancer, respectively, with significant age-by-sex interaction. Our results may provide markers for cancer early detection and prognosis prediction.
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Affiliation(s)
- Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; (C.Y.); (E.M.W.); (G.G.G.); (M.C.S.)
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; (C.Y.); (E.M.W.); (G.G.G.); (M.C.S.)
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jihoon Eric Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC 3010, Australia; (J.E.J.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Allison M. Hodge
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; (A.M.H.); (D.R.E.)
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
| | - Daniel Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC 3010, Australia; (J.E.J.); (D.D.B.)
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
| | - Gianluca Severi
- Centre de Recherche en Epidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Médecine Universités Paris-Saclay, UVSQ, Gustave Roussy, 94805 Villejuif, France;
- Department of Statistics, Computer Science and Applications “G. Parenti”, University of Florence, 50121 Firenze, Italy
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
| | - Dallas R. English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; (A.M.H.); (D.R.E.)
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
| | - Graham G. Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; (C.Y.); (E.M.W.); (G.G.G.); (M.C.S.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; (A.M.H.); (D.R.E.)
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; (C.Y.); (E.M.W.); (G.G.G.); (M.C.S.)
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; (A.M.H.); (D.R.E.)
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; (C.Y.); (E.M.W.); (G.G.G.); (M.C.S.)
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; (A.M.H.); (D.R.E.)
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; (E.M.); (D.S.); (J.L.H.)
- Correspondence:
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12
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Zheng S, Wang X, Fu Y, Li B, Xu J, Wang H, Huang Z, Xu H, Qiu Y, Shi Y, Li K. Targeted next-generation sequencing for cancer-associated gene mutation and copy number detection in 206 patients with non-small-cell lung cancer. Bioengineered 2021; 12:791-802. [PMID: 33629637 PMCID: PMC8291840 DOI: 10.1080/21655979.2021.1890382] [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] [Indexed: 12/25/2022] Open
Abstract
The knowledge of genetic variation in Chinese patients with non–small-cell lung cancer (NSCLC) is still limited. We aimed to profile this genetic variation in 206 Chinese patients with NSCLC using next-generation sequencing. Tumor tissues or whole-blood samples were collected and subjected to whole-exome targeted next-generation sequencing, which included 565 tumor-associated genes, for somatic gene mutation screening and copy number variation (CNV) detection. Potential functions of most commonly mutated genes and genes with CNV were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Atotal of 18,749 mutations were identified using targeted next-generation sequencing, and 85.3% of them were missense mutations. Among the mutation, conversions between pyrimidine and purine were predominant, and C> T/G > A was the most common substitution type. High frequencies of mutations were noted in TP53 (47.6%), EGFR (41.7%), CREBBP (23.1%), KMT2C (16.9%), MUC2 (16.6%), DNMT3A (15.5%), LRP1B (15.5%), MUC4 (15.5%), CDC27 (15.2%), and KRAS (12.8%). EGFR and KRAS mutations were mutually exclusive. The tumor mutation load showed differences depending on gender and tumor type. CNV analysis showed that BCORL1 and ARAF have the highest copy number amplification, whereas KDM6A and RBM10 showed the highest copy number deletion. GO and KEGG analyses indicated that high-frequency mutations and CNV genes were concentrated in tumor-related PI3K-Akt, FoxO, and Ras signaling pathway. Cumulatively, we studied somatic gene mutations involved in NSCLC and predicted their clinical significance in Chinese population. These findings may provide clues for etiology and drug target of NSCLC.
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Affiliation(s)
- Songbai Zheng
- Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China
| | - Xiaodan Wang
- Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China
| | - Ying Fu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Research and Development Institute, Sinotech Genomics, Shanghai, China
| | - Beibei Li
- Laboratory Medicine Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Laboratory Medicine Center, The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianhua Xu
- Laboratory Medicine Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haifang Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhen Huang
- Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China
| | - Hui Xu
- Technical Service Department, Guangzhou Huayin Medical Research Institute Co., Ltd., Guangzhou, China
| | - Yurong Qiu
- Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China
| | - Yaozhou Shi
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kui Li
- Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China.,Technical Service Department, Guangzhou Huayin Medical Research Institute Co., Ltd., Guangzhou, China
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13
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Vieira LA, Matás C, Torrecillas A, Saez F, Gadea J. Seminal plasma components from fertile stallions involved in the epididymal sperm freezability. Andrology 2020; 9:728-743. [PMID: 33185013 DOI: 10.1111/andr.12944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Seminal plasma (SP) plays a crucial role in sperm protection and functionality. However, the effect of SP on the sperm cryopreservation is dependent on the stallion and SP composition. The use of epididymal spermatozoa incubated in the presence of SP could help the identification of the components of SP that are able to confer protection upon the spermatozoa during freezing. OBJECTIVE The aims of this study were (i) to identify SP components involved in the potential protection of epididymal spermatozoa during the freeze-thawing process and (ii) to identify and evaluate the proteins likely related to sperm freezability, using two-dimensional difference gel electrophoresis (2D-DIGE). MATERIALS AND METHODS Epididymal spermatozoa from 4 stallions were incubated with SP (80%, v/v) or without SP (control) before freezing. Sperm parameters were evaluated after thawing (viability, chromatin condensation, acrosomal integrity, reactive oxygen species [ROS]) and SP composition: total antioxidant capacity (TAC), fatty acid composition, total protein concentration, and protein components by 2D-DIGE. RESULTS After thawing, the proportions of viable and acrosome-intact spermatozoa were higher than control when SP from two stallions was used (F and O). The SP of all stallions reduced ROS production in comparison with the control. After analyzing the SP components, it was found that total protein concentration, TAC, polyunsaturated fatty acids (PUFA), and eight specific proteins identified by 2D-DIGE were different between stallions. DISCUSSION These studies allow the identification of SP components that could be involved in sperm protection or cryotolerance. Use of this information could help in the selection of stallions according to their semen freezing capacity. CONCLUSION The composition of the SP probably contributes to semen cryotolerance capacity. Total protein, TAC, PUFA, and some proteins such as cysteine-rich secreted protein 3 could be used as biomarkers for the selection for sperm cryotolerance.
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Affiliation(s)
- Luis Alberto Vieira
- Department of Physiology, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia IMIB-Arrixaca, Murcia, Spain
| | - Carmen Matás
- Department of Physiology, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia IMIB-Arrixaca, Murcia, Spain
| | | | - Fara Saez
- Research Support Service, University of Murcia, Murcia, Spain
| | - Joaquín Gadea
- Department of Physiology, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia IMIB-Arrixaca, Murcia, Spain
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14
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Deep Sequencing Analysis Identified a Specific Subset of Mutations Distinctive of Biphasic Malignant Pleural Mesothelioma. Cancers (Basel) 2020; 12:cancers12092454. [PMID: 32872534 PMCID: PMC7563974 DOI: 10.3390/cancers12092454] [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] [Received: 07/28/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Malignant Pleural Mesothelioma (MPM) is a heterogeneous disease. Morphologically, three different phenotypes are distinguishable: epithelioid (e-), sarcomatoid (s-) and biphasic (biph-) MPM, the latest, being a mixture of e- and s-MPM cells. Being an intermediate entity, management of biph-MPM, remains debatable and controversial, with different guidelines recommending distinct approaches. Identification of biph-MPM associated genetic alterations, through deep sequencing analysis, may provide useful tools to understand these lesions. A retrospective cohort of 69 surgically resected MPMs, 39 biph-MPMs (56.5%) and 30 e-MPMs (43.5%) was selected. A separate set of 16 biph-MPM was used as validation set. Deep sequencing analysis on an MPM-specific custom panel (MPM_geneset) comprising 1041 amplicons spanning 34 genes was performed. A total of 588 variants and 5309 mutational events were detected. In total, 91.3% of MPMs showed at least one mutation and 76.8% showed co-occurrence of more than one alteration. Mutations in MXRA5 (p = 0.05) and NOD2 (p = 0.018) were significantly associated with biph-MPM both in the training and validation cohort and correlated with the extent of the sarcomatoid component. Mutations in NOD2 and XRCC6 correlated with patients’ survival. We demonstrated that biph-MPM are associated with a specific mutation set, and that genetic analysis at diagnosis may improve patients’ risk stratification.
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15
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Fully-Connected Neural Networks with Reduced Parameterization for Predicting Histological Types of Lung Cancer from Somatic Mutations. Biomolecules 2020; 10:biom10091249. [PMID: 32872133 PMCID: PMC7563438 DOI: 10.3390/biom10091249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/09/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022] Open
Abstract
Several challenges appear in the application of deep learning to genomic data. First, the dimensionality of input can be orders of magnitude greater than the number of samples, forcing the model to be prone to overfitting the training dataset. Second, each input variable’s contribution to the prediction is usually difficult to interpret, owing to multiple nonlinear operations. Third, genetic data features sometimes have no innate structure. To alleviate these problems, we propose a modification to Diet Networks by adding element-wise input scaling. The original Diet Networks concept can considerably reduce the number of parameters of the fully-connected layers by taking the transposed data matrix as an input to its auxiliary network. The efficacy of the proposed architecture was evaluated on a binary classification task for lung cancer histology, that is, adenocarcinoma or squamous cell carcinoma, from a somatic mutation profile. The dataset consisted of 950 cases, and 5-fold cross-validation was performed for evaluating the model performance. The model achieved a prediction accuracy of around 80% and showed that our modification markedly stabilized the learning process. Also, latent representations acquired inside the model allowed us to interpret the relationship between somatic mutation sites for the prediction.
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16
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Xiao H, Jiang Y, He W, Xu D, Chen P, Liu D, Liu J, Wang X, DiSanto ME, Zhang X. Identification and functional activity of matrix-remodeling associated 5 (MXRA5) in benign hyperplastic prostate. Aging (Albany NY) 2020; 12:8605-8621. [PMID: 32392178 PMCID: PMC7244086 DOI: 10.18632/aging.103175] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Objective: Benign prostatic hyperplasia (BPH) is a common condition in aging males. The current study aims to identify differentially expressed genes (DEGs) associated with BPH and to elucidate the role of matrix-remodeling associated 5 (MXRA5) protein and mitogen-activated protein kinase (MAPK) signaling pathways in BPH. Results: A total of 198 DEGs and a number of related pathways were identified with MXRA5 being one of the most significantly altered DEGs. MXRA5 was upregulated in BPH samples and localized mostly in stroma. Knockdown of MXRA5 induced stromal cell cycle arrest instead of inhibiting apoptosis. Consistently, MXRA5 overexpression enhanced epithelial cell proliferation. In addition, phosphorylated ERK1/2 and p38, key members of the MAPK family, were strongly decreased with knockdown but increased with overexpression. Conclusion: Our novel data demonstrates that upregulation of MXRA5 in the enlarged prostate could contribute to the development of BPH through increasing cell proliferation via the MAPK pathway. Thus, the MXRA5-MAPK system could be rediscovered as a new therapeutic target for treating BPH. Methods: Microarray analysis and integrated bioinformatics were conducted. The expression and biologic functions of MXRA5 was investigated via RT-PCR, western-blot, immunofluorescence, flow cytometry and MTT assay. Finally, genes involved in regulation of the MAPK pathway were investigated.
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Affiliation(s)
- He Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Current address: Urological Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Ye Jiang
- Department of Urology, People's Hospital of Qichun County, Huanggang, China
| | - Weixiang He
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Deqiang Xu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ping Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Daoquan Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianmin Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Michael E DiSanto
- Department of Surgery and Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Xinhua Zhang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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17
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Liu J, Ding G, Zou K, Jiang Z, Zhang J, Lu Y, Pignata A, Venner E, Liu P, Liu Z, Wangler MF, Sun Z. Genome sequencing analysis of a family with a child displaying severe abdominal distention and recurrent hypoglycemia. Mol Genet Genomic Med 2020; 8:e1130. [PMID: 31971667 PMCID: PMC7057095 DOI: 10.1002/mgg3.1130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/26/2019] [Accepted: 01/06/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Germline mutations in PTEN are associated with the PTEN hamartoma tumor syndrome (PHTS), an umbrella term used to describe a spectrum of autosomal-dominant disorders characterized by variable phenotypic manifestations associated with cell or tissue overgrowth. We report a boy who developed severe progressive abdominal distention due to a dramatic adipose mass from the age of 7 months and developed recurrent hypoinsulinemic hypoglycemia that led to seizures at the age of 4 years. METHODS Trio-based whole-genome sequencing was performed by using blood DNA from the child and his parents. The possible pathogenic variants were verified by Sanger sequencing. Functional characterization of the identified variant was completed by western blot. RESULTS The child inherited a single-nucleotide deletion NM_000314.6:c.849delA (p.Glu284Argfs) in the tumor suppressor gene PTEN from his father. The paternal family members have a history of cancer. It is conceivable that PTEN loss-of-function induced the adipose tumor growth and hypoglycemia, although the proband did not meet the usual diagnosis criteria of Cowden syndrome or Bannayan-Riley-Ruvalcaba syndrome that are characterized by germline mutations of PTEN. CONCLUSION This case underlines the variability of phenotypes associated with PTEN germline mutations and provides useful information for diagnosis and genetic counseling of PTEN-related diseases for pediatric patients.
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Affiliation(s)
- Jidong Liu
- Department of EndocrinologyQilu Hospital of Shandong UniversityJinanChina
- Department of Medicine‐EndocrinologyBaylor College of MedicineHoustonTXUSA
| | - Guolian Ding
- Department of Medicine‐EndocrinologyBaylor College of MedicineHoustonTXUSA
- The International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Embryo Original DiseasesShanghaiChina
| | - Kexin Zou
- The International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Embryo Original DiseasesShanghaiChina
| | - Ziru Jiang
- The International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Embryo Original DiseasesShanghaiChina
| | - Junyu Zhang
- The International Peace Maternity and Child Health HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Embryo Original DiseasesShanghaiChina
| | - Yunhua Lu
- Zhongxiang People's HospitalZhongxiangHubeiChina
| | - Antonella Pignata
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Eric Venner
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTXUSA
| | - Pengfei Liu
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's HospitalHoustonTXUSA
| | - Michael F. Wangler
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's HospitalHoustonTXUSA
- Department of PediatricsBaylor College of MedicineHoustonTXUSA
| | - Zheng Sun
- Department of Medicine‐EndocrinologyBaylor College of MedicineHoustonTXUSA
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
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18
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Gomez-Acevedo H, Dai Y, Strub G, Shawber C, Wu JK, Richter GT. Identification of putative biomarkers for Infantile Hemangiomas and Propranolol treatment via data integration. Sci Rep 2020; 10:3261. [PMID: 32094357 PMCID: PMC7039967 DOI: 10.1038/s41598-020-60025-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/20/2019] [Indexed: 12/29/2022] Open
Abstract
Infantile hemangiomas (IHs) are the most common benign tumors in early childhood. They show a distinctive mechanism of tumor growth in which a rapid proliferative phase is followed by a regression phase (involution). Propranolol is an approved treatment for IHs, but its mechanism of action remains unclear. We integrated and harmonized microRNA and mRNA transcriptome data from newly generated microarray data on IHs with publicly available data on toxicological transcriptomics from propranolol exposure, and with microRNA data from IHs and propranolol exposure. We identified subsets of putative biomarkers for proliferation and involution as well as a small set of putative biomarkers for propranolol's mechanism of action for IHs, namely EPAS1, LASP1, SLC25A23, MYO1B, and ALDH1A1. Based on our integrative data approach and confirmatory experiments, we concluded that hypoxia in IHs is regulated by EPAS1 (HIF-2α) instead of HIF-1α, and also that propranolol-induced apoptosis in endothelial cells may occur via mitochondrial stress.
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Affiliation(s)
- Horacio Gomez-Acevedo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| | - Yuemeng Dai
- Mesquite Rehabilitation Institute, Mesquite, Texas, USA
| | - Graham Strub
- Department of Otolaryngology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Carrie Shawber
- Department of Surgery, New York-Presbyterian/Morgan Stanley Children's Hospital, Columbia University, New York, New York, USA
| | - June K Wu
- Department of Reproductive Sciences in Obstetrics & Gynecology and Surgery, Columbia University, New York, New York, USA
| | - Gresham T Richter
- Department of Otolaryngology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Arkansas Children's Hospital, Little Rock, Arkansas, USA
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19
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Matsushima N, Takatsuka S, Miyashita H, Kretsinger RH. Leucine Rich Repeat Proteins: Sequences, Mutations, Structures and Diseases. Protein Pept Lett 2019; 26:108-131. [PMID: 30526451 DOI: 10.2174/0929866526666181208170027] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022]
Abstract
Mutations in the genes encoding Leucine Rich Repeat (LRR) containing proteins are associated with over sixty human diseases; these include high myopia, mitochondrial encephalomyopathy, and Crohn's disease. These mutations occur frequently within the LRR domains and within the regions that shield the hydrophobic core of the LRR domain. The amino acid sequences of fifty-five LRR proteins have been published. They include Nod-Like Receptors (NLRs) such as NLRP1, NLRP3, NLRP14, and Nod-2, Small Leucine Rich Repeat Proteoglycans (SLRPs) such as keratocan, lumican, fibromodulin, PRELP, biglycan, and nyctalopin, and F-box/LRR-repeat proteins such as FBXL2, FBXL4, and FBXL12. For example, 363 missense mutations have been identified. Replacement of arginine, proline, or cysteine by another amino acid, or the reverse, is frequently observed. The diverse effects of the mutations are discussed based on the known structures of LRR proteins. These mutations influence protein folding, aggregation, oligomerization, stability, protein-ligand interactions, disulfide bond formation, and glycosylation. Most of the mutations cause loss of function and a few, gain of function.
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Affiliation(s)
- Norio Matsushima
- Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan.,Institute of Tandem Repeats, Noboribetsu 059-0464, Japan
| | - Shintaro Takatsuka
- Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Hiroki Miyashita
- Institute of Tandem Repeats, Noboribetsu 059-0464, Japan.,Hokubu Rinsho Co., Ltd, Sapporo 060-0061, Japan
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
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20
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Hoshino I, Takahashi M, Akutsu Y, Murakami K, Matsumoto Y, Suito H, Sekino N, Komatsu A, Iida K, Suzuki T, Inoue I, Ishige F, Iwatate Y, Matsubara H. Genome-wide ChIP-seq data with a transcriptome analysis reveals the groups of genes regulated by histone demethylase LSD1 inhibition in esophageal squamous cell carcinoma cells. Oncol Lett 2019; 18:872-881. [PMID: 31289565 PMCID: PMC6539443 DOI: 10.3892/ol.2019.10350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
Expression of genes is controlled by histone modification, histone acetylation and methylation, but abnormalities of these modifications have been observed in carcinogenesis and cancer development. The effect of the lysine-specific histone demethylase 1 (LSD1) inhibitor, a demethylating enzyme of histones, is thought to be caused by controlling the expression of genes. The aim of the present study is to elucidate the efficacies of the LSD1 inhibitor on the gene expression of esophageal cancer cell lines using chromatin immunoprecipitation (ChIP)-Seq. A comprehensive analysis of gene expression changes in esophageal squamous cell carcinoma (ESCC) cell lines induced by the LSD1 inhibitor NCL1 was clarified via analysis using microarray. In addition, ChIP-seq analysis was conducted using a SimpleChIP plus Enzymatic Chromatin IP kit. NCL1 strongly suppressed the proliferation of T.Tn and TE2 cells, which are ESCC cell lines, and further induced apoptosis. According to the combinatory analysis of ChIP-seq and microarray, 17 genes were upregulated, and 16 genes were downregulated in both cell lines. The comprehensive gene expression study performed in the present study is considered to be useful for analyzing the mechanism of the antitumor effect of the LSD1 inhibitor in patients with ESCC.
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Affiliation(s)
- Isamu Hoshino
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan.,Division of Gastroenterological Surgery, Chiba Cancer Center, Chuo-ku, Chiba 260-8717, Japan
| | - Masahiko Takahashi
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Yasunori Akutsu
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Kentaro Murakami
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Yasunori Matsumoto
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Hiroshi Suito
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Nobufumi Sekino
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Aki Komatsu
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Keiko Iida
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kita-ku, Kyoto 403-8334, Japan
| | - Itsuro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Fumitaka Ishige
- Department of Hepatobiliary and Pancreatic Surgery, Chiba Cancer Center, Chuo-ku, Chiba 260-8717, Japan
| | - Yosuke Iwatate
- Department of Hepatobiliary and Pancreatic Surgery, Chiba Cancer Center, Chuo-ku, Chiba 260-8717, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670, Japan
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21
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Liu YT, Han XH, Xing PY, Hu XS, Hao XZ, Wang Y, Li JL, Zhang ZS, Yang ZH, Shi YK. Circular RNA profiling identified as a biomarker for predicting the efficacy of Gefitinib therapy for non-small cell lung cancer. J Thorac Dis 2019; 11:1779-1787. [PMID: 31285870 DOI: 10.21037/jtd.2019.05.22] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have become important treatment options for non-small cell lung cancer (NSCLC) patients with EGFR sensitive mutation. However, the detection of EGFR driver mutation is impeded by the lack of adequate tumor tissues, histopathological type, long detection period, and the heterogeneity of a tumor. Therefore, it is necessary to develop a more convenient method to guide the clinical use of EGFR-TKI. Circular RNAs (circRNAs) are characterized as a closed structure with covalently joined ends resistant to exonucleases may be a potential biomarker. In the present study, we aimed to screen circRNAs that may be associated with the efficacy of EGFR-TKI. Methods The expression of circRNAs sequenced by circular microarray in plasma samples between gefitinib effective and ineffective groups were compared. RT-qPCR further validated the results in an independent cohort. Kaplan-Meier curves were used to analyze the association between circRNA and progression-free survival (PFS) of NSCLC patients treated with gefitinib. Results In total, 52 NSCLC patients treated with gefitinib were included for analysis. 1,377 circRNAs were differentially expressed in gefitinib effective and ineffective groups, among which 989 circRNAs were up-regulated, and 388 circRNAs were down-regulated in the effective group. Furthermore, two differentially expressed circRNAs, hsa_circ_0109320 and hsa_circ_0134501, were validated by RT-qPCR in an independent cohort of 38 gefitinib-treated NSCLC patients. Elevated hsa_circ_0109320 was associated with longer PFS in gefitinib-treated NSCLC patients. Conclusions Taken together, hsa_circ_0109320 may be a potential biomarker for the efficacy of EGFR-TKI in NSCLC patients. This provides a new molecular typing method for individualized precision treatment.
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Affiliation(s)
- Yu-Tao Liu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Xiao-Hong Han
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Pu-Yuan Xing
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Xing-Sheng Hu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Xue-Zhi Hao
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Yan Wang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Jun-Ling Li
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Zhi-Shang Zhang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Zhi-Hao Yang
- Beijing CapitalBio Technology Company, Beijing 101111, China
| | - Yuan-Kai Shi
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
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22
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Ługowska A, Hetmańczyk-Sawicka K, Iwanicka-Nowicka R, Fogtman A, Cieśla J, Purzycka-Olewiecka JK, Sitarska D, Płoski R, Filocamo M, Lualdi S, Bednarska-Makaruk M, Koblowska M. Gene expression profile in patients with Gaucher disease indicates activation of inflammatory processes. Sci Rep 2019; 9:6060. [PMID: 30988500 PMCID: PMC6465595 DOI: 10.1038/s41598-019-42584-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/01/2019] [Indexed: 01/26/2023] Open
Abstract
Gaucher disease (GD) is a rare inherited metabolic disease caused by pathogenic variants in the GBA1 gene. So far, the pathomechanism of GD was investigated mainly in animal models. In order to delineate the molecular changes in GD cells we analysed gene expression profile in cultured skin fibroblasts from GD patients, control individuals and, additionally, patients with Niemann-Pick type C disease (NPC). We used expression microarrays with subsequent validation by qRT-PCR method. In the comparison GD patients vs. controls, the most pronounced relative fold change (rFC) in expression was observed for genes IL13RA2 and IFI6 (up-regulated) and ATOH8 and CRISPLD2 (down-regulated). Products of up-regulated and down-regulated genes were both enriched in genes associated with immune response. In addition, products of down-regulated genes were associated with cell-to-cell and cell-to-matrix interactions, matrix remodelling, PI3K-Akt signalling pathway and a neuronal survival pathway. Up-regulation of PLAU, IFIT1, TMEM158 and down-regulation of ATOH8 and ISLR distinguished GD patients from both NPC patients and healthy controls. Our results emphasize the inflammatory character of changes occurring in human GD cells indicating that further studies on novel therapeutics for GD should consider anti-inflammatory agents.
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Affiliation(s)
- Agnieszka Ługowska
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland.
| | | | - Roksana Iwanicka-Nowicka
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Fogtman
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Cieśla
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Dominika Sitarska
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, L.go G. Gaslini -16147, Genova, Italy
| | - Susanna Lualdi
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, L.go G. Gaslini -16147, Genova, Italy
| | | | - Marta Koblowska
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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23
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Zhou Z, Shen Y, Yin J, Xi F, Xu R, Lin D, Saijilafu, Chen J, Wang Y. Matrix remodeling associated 7 promotes differentiation of bone marrow mesenchymal stem cells toward osteoblasts. J Cell Physiol 2019; 234:18053-18064. [PMID: 30843215 DOI: 10.1002/jcp.28438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/10/2019] [Accepted: 02/14/2019] [Indexed: 01/15/2023]
Abstract
The matrix remodeling associated 7 (MXRA7) gene had been ill-studied and its biology remained to be discovered. Inspired by our previous findings and public datasets concerning MXRA7, we hypothesized that the MXRA7 gene might be involved in bone marrow mesenchymal stem cells (BMSCs) functions related to bone formation, which was checked by utilizing in vivo or in vitro methodologies. Micro-computed tomography of MXRA7-deficient mice demonstrated retarded osteogenesis, which was reflected by shorter femurs, lower bone mass in both trabecular and cortical bones compared with wild-type (WT) mice. Histology confirmed the osteopenia-like feature including thinner growth plates in MXRA7-deficient femurs. Immunofluorescence revealed less osteoblasts in MXRA7-deficient femurs. Polymerase chain reaction or western blot analysis showed that when WT BMSCs were induced to differentiate toward osteoblasts or adipocytes in culture, MXRA7 messenger RNA or protein levels were significantly increased alongside osteoblasts induction, but decreased upon adipocytes induction. Cultured MXRA7-deficient BMSCs showed decreased osteogenesis upon osteogenic differentiation induction as reflected by decreased calcium deposition or lower expression of genes responsible for osteogenesis. When recombinant MXRA7 proteins were supplemented in a culture of MXRA7-deficient BMSCs, osteogenesis or gene expression was fully restored. Upon osteoblast induction, the level of active β-catenin or phospho-extracellular signal-regulated kinase in MXRA7-deficient BMSCs was decreased compared with that in WT BMSCs, and these impairments could be rescued by recombinant MXRA7 proteins. In adipogenesis induction settings, the potency of MXRA7-deficient BMSCs to differentiate into adipocytes was increased over the WT ones. In conclusion, this study demonstrated that MXRA7 influences bone formation via regulating the balance between osteogenesis and adipogenesis in BMSCs.
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Affiliation(s)
- Zhishuai Zhou
- MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology-Thrombosis and Hemostasis Group, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Medical College, Soochow University, Suzhou, China
| | - Ying Shen
- MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology-Thrombosis and Hemostasis Group, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Medical College, Soochow University, Suzhou, China
| | - Juanjuan Yin
- MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology-Thrombosis and Hemostasis Group, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Medical College, Soochow University, Suzhou, China
| | - Feng Xi
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Renjie Xu
- Department of Orthopedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Dandan Lin
- MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology-Thrombosis and Hemostasis Group, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Medical College, Soochow University, Suzhou, China
| | - Saijilafu
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Jianquan Chen
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Yiqiang Wang
- MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology-Thrombosis and Hemostasis Group, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Medical College, Soochow University, Suzhou, China
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24
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Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network. PLoS Comput Biol 2018; 14:e1006436. [PMID: 30240439 PMCID: PMC6173447 DOI: 10.1371/journal.pcbi.1006436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/05/2018] [Accepted: 08/15/2018] [Indexed: 12/14/2022] Open
Abstract
Co-expression network analysis provides useful information for studying gene regulation in biological processes. Examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. One challenge in this type of analysis is that the sample sizes in each condition are usually small, making the statistical inference of co-expression patterns highly underpowered. A joint network construction that borrows information from related structures across conditions has the potential to improve the power of the analysis. One possible approach to constructing the co-expression network is to use the Gaussian graphical model. Though several methods are available for joint estimation of multiple graphical models, they do not fully account for the heterogeneity between samples and between co-expression patterns introduced by condition specificity. Here we develop the condition-adaptive fused graphical lasso (CFGL), a data-driven approach to incorporate condition specificity in the estimation of co-expression networks. We show that this method improves the accuracy with which networks are learned. The application of this method on a rat multi-tissue dataset and The Cancer Genome Atlas (TCGA) breast cancer dataset provides interesting biological insights. In both analyses, we identify numerous modules enriched for Gene Ontology functions and observe that the modules that are upregulated in a particular condition are often involved in condition-specific activities. Interestingly, we observe that the genes strongly associated with survival time in the TCGA dataset are less likely to be network hubs, suggesting that genes associated with cancer progression are likely to govern specific functions or execute final biological functions in pathways, rather than regulating a large number of biological processes. Additionally, we observed that the tumor-specific hub genes tend to have few shared edges with normal tissue, revealing tumor-specific regulatory mechanism. Gene co-expression networks provide insights into the mechanism of cellular activity and gene regulation. Condition-specific mechanisms may be identified by constructing and comparing co-expression networks of multiple conditions. We propose a novel statistical method to jointly construct co-expression networks for gene expression profiles from multiple conditions. By using a data-driven approach to capture condition-specific co-expression patterns, this method is effective in identifying both co-expression patterns that are specific to a condition and that are common across conditions. The application of this method to real datasets reveals interesting biological insights.
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25
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Ding L, Li S, Zhang Y, Gai J, Kou J. MXRA5 is decreased in preeclampsia and affects trophoblast cell invasion through the MAPK pathway. Mol Cell Endocrinol 2018; 461:248-255. [PMID: 28919298 DOI: 10.1016/j.mce.2017.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 01/07/2023]
Abstract
Preeclampsia causes gestational failure in a significant number of women annually. Insufficient trophoblast cell invasion plays an essential role in preeclampsia pathogenesis. Matrix-remodeling associated 5 (MXRA5) is a proteoglycan involved in adhesion and matrix remodeling. This study sought to explore the role of MXRA5 in trophoblast cell invasion. Preeclamptic villi were obtained for the delineation of MXRA5 expression. Specific MXRA5 siRNA and pcDNA3.1/MXRA5 were used to manipulate MXRA5 expression in HTR-8/SVneo. Cell viability was determined by MTT and apoptosis by flow cytometry. Cell invasion was evaluated using Matrigel invasion assay. MXRA5 expression was lower in preeclamptic villi and cytotrophoblasts. Silencing MXRA5 expression in HTR-8/SVneo decreased cell viability and invasion, which were augmented by MXRA5 overexpression. Furthermore, MXRA5 modulated N-cadherin, E-cadherin, MMP-2, and MMP-9 expression through p38 MAPK and ERK1/2 signaling transduction. In addition, the expression of MXRA5 was influenced by exogenous TNF-α but not by IFN-γ. Overexpression of MXRA5 attenuated HTR-8/SVneo apoptosis induced by TNF-α. MXRA5 is downregulated in preeclamptic cytotrophoblasts and can regulate trophoblast cell invasion via the MAPK pathway.
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Affiliation(s)
- Lan Ding
- The First Department of Obstetrics, Cangzhou Central Hospital, Cangzhou 061001, China
| | - Shaocong Li
- Department of Gynecology and Obstetrics, Liaocheng People's Hospital, Liaocheng 252000, China
| | - Yanshang Zhang
- Department of Obstetrics, Hebei General Hospital, Shijiazhuang 050051, China
| | - Junfeng Gai
- Department of Gynaecology, Binzhou City Center Hospital, Binzhou 251700, China
| | - Jianfang Kou
- Department of Gynaecology, The Affiliated Zhengzhou Hospital of Jinan University, Zhengzhou Second Hospital, Zhengzhou 450006, China.
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26
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Xiong D, Pan J, Yin Y, Jiang H, Szabo E, Lubet RA, Wang Y, You M. Novel mutational landscapes and expression signatures of lung squamous cell carcinoma. Oncotarget 2017; 9:7424-7441. [PMID: 29484121 PMCID: PMC5800913 DOI: 10.18632/oncotarget.23716] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/26/2017] [Indexed: 12/15/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a major subtype of Non-Small Cell Lung Cancer. To increase our understanding of the LUSC pathobiology, we performed exome sequencing and RNA-seq in 16 murine carcinogen-induced LUSC tumors and 8 normal murine lung tissue samples. Additionally, we conducted single-cell RNA-seq on two independent tumors from the same murine model. We identified a list of 59 cancer genes recurrently mutated in the mice LUSC tumors, 47 (80%) of which were also mutated in human LUSCs. At the single cell level, we detected unique clonal mutation patterns for each of the two LUSC tumors, being initiated from clones carrying the mutant Igfbp7 and Trp53 genes, respectively. We also identified an expression signature serving as an effective classifier for LUSC tumors and a strong predictor of survival outcomes of lung cancer patients. Lastly, we found that some of the mutant LUSC genes were associated with the significantly altered tumoral expression of inhibitory immune checkpoint genes such as PD-L1, VISTA, TIM3 and LAG3 in human LUSCs. The novel findings of clonal evolution, mutational landscapes and expression signatures of LUSC suggested new targets for the overall LUSC therapy and the immunotherapy of LUSC.
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Affiliation(s)
- Donghai Xiong
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jing Pan
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yuxin Yin
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hui Jiang
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Eva Szabo
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Ronald A Lubet
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Yian Wang
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ming You
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Khalilipour N, Baranova A, Jebelli A, Heravi-Moussavi A, Bruskin S, Abbaszadegan MR. Familial Esophageal Squamous Cell Carcinoma with damaging rare/germline mutations in KCNJ12/KCNJ18 and GPRIN2 genes. Cancer Genet 2017; 221:46-52. [PMID: 29405996 DOI: 10.1016/j.cancergen.2017.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 11/12/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
In Iran, esophageal cancer is the fourth common cancers in women and sixth common cancers in men. Here we evaluated the importance of familial risk factors and the role of genetic predisposition in Esophageal Squamous Cell Carcinoma (ESCC) using Whole-Exome Sequencing (WES). Germline damaging mutations were identified in WES data from 9 probands of 9 unrelated ESCC pedigrees. Mutations were confirmed with Sanger sequencing and evaluated amplification-refractory mutation system-Polymerase Chain Reaction (ARMS-PCR) in 50 non-related ethnically matched samples and in complete genomics database. Sixteen candidate variants were detected in ESCC 9 probands. Four of these 16 variants were rare damaging mutations including novel mutations in KCNJ12/KCNJ18, and GPRIN2 genes. This WES study in Iranian patients with ESCC, provides insight into the identification of novel germline mutations in familial ESCC. Our data suggest an association between specific mutations and increased risk of ESCC.
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Affiliation(s)
- Narjes Khalilipour
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ancha Baranova
- Research Center for Medical Genetics RAMS, Moscow, Russia
| | - Amir Jebelli
- Stem Cell and Regenerative Medicine Research Department, Iranian Academic Center for Education, Culture and Research (ACECR), Mashhad Branch, Mashhad, Iran
| | | | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun 2017; 8:1221. [PMID: 29089486 PMCID: PMC5663922 DOI: 10.1038/s41467-017-01355-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 09/12/2017] [Indexed: 11/23/2022] Open
Abstract
Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, we build a compendium of 2218 primary tumours across 12 human cancer types and systematically screen for homozygous deletions, aiming to identify rare tumour suppressors. Our analysis defines 96 genomic regions recurrently targeted by homozygous deletions. These recurrent homozygous deletions occur either over tumour suppressors or over fragile sites, regions of increased genomic instability. We construct a statistical model that separates fragile sites from regions showing signatures of positive selection for homozygous deletions and identify candidate tumour suppressors within those regions. We find 16 established tumour suppressors and propose 27 candidate tumour suppressors. Several of these genes (including MGMT, RAD17, and USP44) show prior evidence of a tumour suppressive function. Other candidate tumour suppressors, such as MAFTRR, KIAA1551, and IGF2BP2, are novel. Our study demonstrates how rare tumour suppressors can be identified through copy number meta-analysis. Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, the authors conduct pan-cancer analyses and apply statistical modelling to identify 27 candidate tumour suppressors, including MAFTRR, KIAA1551, and IGF2BP2.
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Robertson EP, Fletcher RJ, Austin JD. Microsatellite polymorphism in the endangered snail kite reveals a panmictic, low diversity population. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Li S, Choi YL, Gong Z, Liu X, Lira M, Kan Z, Oh E, Wang J, Ting JC, Ye X, Reinhart C, Liu X, Pei Y, Zhou W, Chen R, Fu S, Jin G, Jiang A, Fernandez J, Hardwick J, Kang MW, I H, Zheng H, Kim J, Mao M. Comprehensive Characterization of Oncogenic Drivers in Asian Lung Adenocarcinoma. J Thorac Oncol 2016; 11:2129-2140. [PMID: 27615396 DOI: 10.1016/j.jtho.2016.08.142] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/23/2016] [Accepted: 08/01/2016] [Indexed: 01/04/2023]
Abstract
INTRODUCTION The incidence rate of lung adenocarcinoma (LUAD), the predominant histological subtype of lung cancer, is elevated in Asians, particularly in female nonsmokers. The mutation patterns in LUAD in Asians might be distinct from those in LUAD in whites. METHODS We profiled 271 resected LUAD tumors (mainly stage I) to characterize the genomic landscape of LUAD in Asians with a focus on female nonsmokers. RESULTS Mutations in EGFR, KRAS, erb-b2 receptor tyrosine kinase 2 gene (ERBB2), and BRAF; gene fusions involving anaplastic lymphoma receptor tyrosine kinase gene (ALK), ROS1, and ret proto-oncogene (RET); and Met Proto-Oncogene Tyrosine Kinase (MET) exon 14 skipping were the major drivers in LUAD in Asians, exhibiting mutually exclusive and differing prevalence from those reported in studies of LUAD in non-Asians. In addition, we identified a novel mutational signature of XNX (the mutated base N in the middle flanked by two identical bases at the 5' and 3' positions) that was overrepresented in LUAD tumors in nonsmokers and negatively correlated with the overall mutational frequency. CONCLUSIONS In this cohort, approximately 85% of individuals have known driver mutations (EGFR 59.4%, KRAS 7.4%, ALK 7.4%, ERBB2 2.6%, ROS1 2.2%, RET 2.2%, MET 1.8%, BRAF 1.1%, and NRAS 0.4%). Seventy percent of smokers and 90% of nonsmokers had defined oncogenic drivers matching the U.S. Food and Drug Administration-approved targeted therapies.
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Affiliation(s)
- Shiyong Li
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Yoon-La Choi
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Zhuolin Gong
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | | | | | - Ensel Oh
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jian Wang
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | | | - Xiaoqiao Liu
- Merck Research Laboratories, Boston, Massachusetts
| | - Yunfei Pei
- Merck Research Laboratories, Boston, Massachusetts
| | - Wei Zhou
- Merck Research Laboratories, Boston, Massachusetts
| | - Ronghua Chen
- Merck Research Laboratories, Boston, Massachusetts
| | - Shijun Fu
- Shanghai Biochip Company, Shanghai, People's Republic of China
| | - Gang Jin
- Shanghai Biochip Company, Shanghai, People's Republic of China
| | - Awei Jiang
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | | | | | - Min Woong Kang
- Department of Thoracic and Cardiovascular Surgery, Chungnam National University School of Medicine, Daejun, Republic of Korea
| | - Hoseok I
- Department of Thoracic and Cardiovascular Surgery, Pusan National University School of Medicine, Pusan, Republic of Korea
| | | | - Jhingook Kim
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Mao Mao
- Pfizer Oncology, San Diego, California.
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Poveda J, Sanz AB, Fernandez-Fernandez B, Carrasco S, Ruiz-Ortega M, Cannata-Ortiz P, Ortiz A, Sanchez-Niño MD. MXRA5 is a TGF-β1-regulated human protein with anti-inflammatory and anti-fibrotic properties. J Cell Mol Med 2016; 21:154-164. [PMID: 27599751 PMCID: PMC5192817 DOI: 10.1111/jcmm.12953] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/12/2016] [Indexed: 01/15/2023] Open
Abstract
Current therapy for chronic kidney disease (CKD) is unsatisfactory because of an insufficient understanding of its pathogenesis. Matrix remodelling-associated protein 5 (MXRA5, adlican) is a human protein of unknown function with high kidney tissue expression, not present in rodents. Given the increased expression of MXRA5 in injured tissues, including the kidneys, we have suggested that MXRA5 may modulate kidney injury. MXRA5 immunoreactivity was observed in tubular cells in human renal biopsies and in urine from CKD patients. We then explored factors regulating MXRA5 expression and MXRA5 function in cultured human proximal tubular epithelial cells and explored MXRA5 expression in kidney cancer cells and kidney tissue. The fibrogenic cytokine transforming growth factor-β1 (TGFβ1) up-regulated MXRA5 mRNA and protein expression. TGFβ1-induced MXRA5 up-regulation was prevented by either interference with TGFβ1 activation of the TGFβ receptor 1 (TGFBR1, ALK5) or by the vitamin D receptor agonist paricalcitol. By contrast, the pro-inflammatory cytokine TWEAK did not modulate MXRA5 expression. MXRA5 siRNA-induced down-regulation of constitutive MXRA5 expression resulted in higher TWEAK-induced expression of chemokines. In addition, MXRA5 down-regulation resulted in a magnified expression of genes encoding extracellular matrix proteins in response to TGFβ1. Furthermore, in clear cell renal cancer, von Hippel-Lindau (VHL) regulated MXRA5 expression. In conclusion, MXRA5 is a TGFβ1- and VHL-regulated protein and, for the first time, we identify MXRA5 functions as an anti-inflammatory and anti-fibrotic molecule. This information may yield clues to design novel therapeutic strategies in diseases characterized by inflammation and fibrosis.
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Affiliation(s)
- Jonay Poveda
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | - Ana B Sanz
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | | | - Susana Carrasco
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | - Marta Ruiz-Ortega
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain.,School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | - Pablo Cannata-Ortiz
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | - Alberto Ortiz
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain.,School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain.,Fundacion Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain
| | - Maria D Sanchez-Niño
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
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Miyoshi T, Umemura S, Matsumura Y, Mimaki S, Tada S, Makinoshima H, Ishii G, Udagawa H, Matsumoto S, Yoh K, Niho S, Ohmatsu H, Aokage K, Hishida T, Yoshida J, Nagai K, Goto K, Tsuboi M, Tsuchihara K. Genomic Profiling of Large-Cell Neuroendocrine Carcinoma of the Lung. Clin Cancer Res 2016; 23:757-765. [PMID: 27507618 DOI: 10.1158/1078-0432.ccr-16-0355] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 07/20/2016] [Accepted: 07/29/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Although large-cell neuroendocrine carcinoma (LCNEC) of the lung shares many clinical characteristics with small-cell lung cancer (SCLC), little is known about its molecular features. We analyzed lung LCNECs to identify biologically relevant genomic alterations. EXPERIMENTAL DESIGN We performed targeted capture sequencing of all the coding exons of 244 cancer-related genes on 78 LCNEC samples [65 surgically resected cases, including 10 LCNECs combined with non-small cell lung cancer (NSCLC) types analyzed separately, and biopsies of 13 advanced cases]. Frequencies of genetic alterations were compared with those of 141 SCLCs (50 surgically resected cases and biopsies of 91 advanced cases). RESULTS We found a relatively high prevalence of inactivating mutations in TP53 (71%) and RB1 (26%), but the mutation frequency in RB1 was lower than that in SCLCs (40%, P = 0.039). In addition, genetic alterations in the PI3K/AKT/mTOR pathway were detected in 12 (15%) of the tumors: PIK3CA 3%, PTEN 4%, AKT2 4%, RICTOR 5%, and mTOR 1%. Other activating alterations were detected in KRAS (6%), FGFR1 (5%), KIT (4%), ERBB2 (4%), HRAS (1%), and EGFR (1%). Five of 10 cases of LCNECs combined with NSCLCs harbored previously reported driver gene alterations, all of which were shared between the two components. The median concordance rate of candidate somatic mutations between the two components was 71% (range, 60%-100%). CONCLUSIONS LCNECs have a similar genomic profile to SCLC, including promising therapeutic targets, such as the PI3K/AKT/mTOR pathway and other gene alterations. Sequencing-based molecular profiling is warranted in LCNEC for targeted therapies. Clin Cancer Res; 23(3); 757-65. ©2016 AACR.
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Affiliation(s)
- Tomohiro Miyoshi
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.,Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan.,Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Shigeki Umemura
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan. .,Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Yuki Matsumura
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Sachiyo Mimaki
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Satoshi Tada
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hideki Makinoshima
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Genichiro Ishii
- Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hibiki Udagawa
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.,Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Shingo Matsumoto
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.,Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Kiyotaka Yoh
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Seiji Niho
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Hironobu Ohmatsu
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Keiju Aokage
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Tomoyuki Hishida
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Junji Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Kanji Nagai
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Katsuya Tsuchihara
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
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Koringa PG, Jakhesara SJ, Rank DN, Joshi CG. Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing. 3 Biotech 2016; 6:38. [PMID: 28330108 PMCID: PMC4729760 DOI: 10.1007/s13205-015-0351-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/04/2015] [Indexed: 11/04/2022] Open
Abstract
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM. Data obtained were analysed using DNASTAR software package and case control analysis using SAS software. We found SNP present in BPIFA1 gene of B. indicus shows association with event of HC which reflects its potential to be a genetic marker. Bioinformatic analysis to detect structural and functional impact nsSNP of BPIFA1 added another layer of confirmation to our result. We successfully identified SNP associated with HC as well as demonstrated efficient approach for limited number of SNP discovery and validation in targeted genomics regions in large number of samples combining PCR amplification and Ion Torrent PGM sequencing which suits small-scale laboratories with limited budget.
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Fu S, Zhao J, Bai H, Duan J, Wang Z, An T, Wang J. High-fidelity of non-small cell lung cancer xenograft models derived from bronchoscopy-guided biopsies. Thorac Cancer 2015; 7:100-10. [PMID: 26813258 PMCID: PMC4718126 DOI: 10.1111/1759-7714.12291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 06/04/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND At present, there are two main types of lung cancer xenograft models: those derived from stable cell lines, and patient-derived xenograft models established by surgically resected tissues. However, these animal models may not reflect the biological and genetic characteristics of advanced non-small cell lung cancer (NSCLC). We utilized bronchoscopy-guided biopsy tissues of NSCLC patients to establish xenograft models and analyzed their histopathologic and genotypic fidelity with parental tumors. METHODS Tumor tissues of NSCLC patients taken via bronchoscope were subcutaneously implanted into mice with non-obese diabetic-severe combined immunodeficiency disease for model establishment and serial passage. The histopathology and genotype of the samples from bronchoscopy-guided biopsy-derived xenograft (BDX) models and their parental tumors were detected. RESULTS Thirty BDXs out of 114 NSCLC patients (26.32%) were successfully established. Smoking status significantly affected the success rate of NSCLC BDX establishment (P = 0.010). The BDX establishment success rate in squamous cell cancer was higher than in adenocarcinoma, with no significant difference (32.00% vs. 16.21%, P = 0.112). However, the growth rate of passage 1 BDX was slower than that of passages 2 and 3. Almost all NSCLC BDXs maintained similarity to their parental tumor tissues in regard to histologic characteristics, pathological markers, and driver-gene mutations. Only one BDX model lost the epidermal growth factor receptor mutation contained in tumor parental tissue, as a result of heterogeneity. CONCLUSIONS NSCLC BDXs maintained high fidelity of histopathology and genotype with their original tumors. NSCLC BDXs that possess the actual status of advanced lung carcinoma should be used in preclinical research.
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Affiliation(s)
- Shuai Fu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
| | - Jun Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
| | - Hua Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
| | - Jianchun Duan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
| | - Zhijie Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
| | - Tongtong An
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
| | - Jie Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Thoracic Medical Oncology Peking University School of Oncology Beijing Cancer Hospital & Institute Beijing China
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35
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Xiong D, Wang Y, Kupert E, Simpson C, Pinney S, Gaba C, Mandal D, Schwartz A, Yang P, de Andrade M, Pikielny C, Byun J, Li Y, Stambolian D, Spitz M, Liu Y, Amos C, Bailey-Wilson J, Anderson M, You M. A recurrent mutation in PARK2 is associated with familial lung cancer. Am J Hum Genet 2015; 96:301-8. [PMID: 25640678 DOI: 10.1016/j.ajhg.2014.12.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/16/2014] [Indexed: 11/27/2022] Open
Abstract
PARK2, a gene associated with Parkinson disease, is a tumor suppressor in human malignancies. Here, we show that c.823C>T (p.Arg275Trp), a germline mutation in PARK2, is present in a family with eight cases of lung cancer. The resulting amino acid change, p.Arg275Trp, is located in the highly conserved RING finger 1 domain of PARK2, which encodes an E3 ubiquitin ligase. Upon further analysis, the c.823C>T mutation was detected in three additional families affected by lung cancer. The effect size for PARK2 c.823C>T (odds ratio = 5.24) in white individuals was larger than those reported for variants from lung cancer genome-wide association studies. These data implicate this PARK2 germline mutation as a genetic susceptibility factor for lung cancer. Our results provide a rationale for further investigations of this specific mutation and gene for evaluation of the possibility of developing targeted therapies against lung cancer in individuals with PARK2 variants by compensating for the loss-of-function effect caused by the associated variation.
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Krishnan VG, Ebert PJ, Ting JC, Lim E, Wong SS, Teo ASM, Yue YG, Chua HH, Ma X, Loh GSL, Lin Y, Tan JHJ, Yu K, Zhang S, Reinhard C, Tan DSW, Peters BA, Lincoln SE, Ballinger DG, Laramie JM, Nilsen GB, Barber TD, Tan P, Hillmer AM, Ng PC. Whole-genome sequencing of asian lung cancers: second-hand smoke unlikely to be responsible for higher incidence of lung cancer among Asian never-smokers. Cancer Res 2014; 74:6071-81. [PMID: 25189529 DOI: 10.1158/0008-5472.can-13-3195] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Asian nonsmoking populations have a higher incidence of lung cancer compared with their European counterparts. There is a long-standing hypothesis that the increase of lung cancer in Asian never-smokers is due to environmental factors such as second-hand smoke. We analyzed whole-genome sequencing of 30 Asian lung cancers. Unsupervised clustering of mutational signatures separated the patients into two categories of either all the never-smokers or all the smokers or ex-smokers. In addition, nearly one third of the ex-smokers and smokers classified with the never-smoker-like cluster. The somatic variant profiles of Asian lung cancers were similar to that of European origin with G.C>T.A being predominant in smokers. We found EGFR and TP53 to be the most frequently mutated genes with mutations in 50% and 27% of individuals, respectively. Among the 16 never-smokers, 69% had an EGFR mutation compared with 29% of 14 smokers/ex-smokers. Asian never-smokers had lung cancer signatures distinct from the smoker signature and their mutation profiles were similar to European never-smokers. The profiles of Asian and European smokers are also similar. Taken together, these results suggested that the same mutational mechanisms underlie the etiology for both ethnic groups. Thus, the high incidence of lung cancer in Asian never-smokers seems unlikely to be due to second-hand smoke or other carcinogens that cause oxidative DNA damage, implying that routine EGFR testing is warranted in the Asian population regardless of smoking status.
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Affiliation(s)
- Vidhya G Krishnan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | | | | | - Elaine Lim
- Medical Oncology, Mount Elizabeth Medical Centre, Mount Elizabeth, Singapore. Medical Oncology, Tan Tock Seng Hospital, Singapore, Singapore; Medical Oncology, National University Hospital, Singapore, Singapore
| | | | - Audrey S M Teo
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Yong G Yue
- Lilly Corporate Center, Indianapolis, Indiana
| | - Hui-Hoon Chua
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Xiwen Ma
- Lilly Corporate Center, Indianapolis, Indiana
| | - Gary S L Loh
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Yuhao Lin
- Lilly Corporate Center, Indianapolis, Indiana
| | - Joanna H J Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore.
| | - Kun Yu
- Lilly Corporate Center, Indianapolis, Indiana
| | - Shenli Zhang
- Genomic Oncology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | | | - Daniel S W Tan
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | | | | | | | | | | | | | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore. Genomic Oncology, Duke-NUS Graduate Medical School, Singapore, Singapore. Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore
| | - Axel M Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore.
| | - Pauline C Ng
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore.
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Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients. Sci Rep 2014; 4:6036. [PMID: 25112956 PMCID: PMC5381403 DOI: 10.1038/srep06036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/24/2014] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the most common cause of cancer mortality worldwide, with an estimated 1.4 million deaths each year. Here we report whole-exome sequencing of nine tumor/normal tissue pairs from Chinese patients with non-small cell lung carcinoma (NSCLC). This allows us to identify a number of significantly mutated genes in NSCLC, which were highly enriched in DNA damage repair, NF-κB pathway, JAK/STAT signaling and chromatin modification. Notably, we identify a histone-lysine methyltransferase gene, namely, MLL2, as one of the most significantly mutated genes in our screen. In a following validation study, we identify deleterious mutations of MLL2 in 12 out of 105 (11.4%) NSCLC patients. Additionally, reduced or lost expression of MLL2 was commonly observed in tumor tissues as compared with paired adjacent non-tumor tissues regardless of mutation status. Together, our study defines the landscape of somatic mutations in Chinese NSCLC and supports the role of MLL2 mutation in the pathogenesis of the disease.
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38
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Warth A, Muley T, Dienemann H, Goeppert B, Stenzinger A, Schnabel PA, Schirmacher P, Penzel R, Weichert W. ROS1 expression and translocations in non-small-cell lung cancer: clinicopathological analysis of 1478 cases. Histopathology 2014; 65:187-94. [PMID: 24456475 DOI: 10.1111/his.12379] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/18/2014] [Indexed: 12/19/2022]
Abstract
AIMS Molecular characterization of non-small-cell lung cancer (NSCLC) has revealed multiple druggable mutations for targeted therapies. Recently, chromosomal rearrangements involving c-ros oncogene 1, receptor tyrosine kinase (ROS1) were identified, and patients seem to benefit from crizotinib treatment. The aim of this study was to identify the clinicopathological characteristics of NSCLC with ROS1 expression and translocation. METHODS AND RESULTS We screened 1478 NSCLCs with a ROS1-specific antibody, and tested positive cases with FISH. All positive cases were analysed for associated clinicopathological characteristics, including survival and molecular tumour composition. Sixty-eight cases (4.6%) showed ROS1 immunoreactivity, and ROS1 translocations were confirmed in nine cases (0.6%). ROS1 expression was predominantly found in female adenocarcinoma patients, in patients with low T stages, and in association with TTF1 and napsin expression, and certain histomorphological adenocarcinoma patterns (lepidic, acinar, and solid). ROS1 translocations occurred in conjunction with other driver mutations (EGFR, KRAS, and BRAF). ROS1 expression was found to be a stage-independent predictor of favourable survival. CONCLUSIONS ROS1 translocations are rare events in resected NSCLCs from Caucasian patients. Immunohistochemical screening for ROS1 expression and clinicopathological parameters, including female sex, early tumour stages, adenocarcinomas with TTF1 and/or napsin expression, and a distinct histomorphological growth pattern, strongly facilitate case enrichment. Molecularly driven multistep concepts might not be optimal for case selection.
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Affiliation(s)
- Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
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Bacolla A, Cooper DN, Vasquez KM. Mechanisms of base substitution mutagenesis in cancer genomes. Genes (Basel) 2014; 5:108-46. [PMID: 24705290 PMCID: PMC3978516 DOI: 10.3390/genes5010108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/24/2023] Open
Abstract
Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.
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Affiliation(s)
- Albino Bacolla
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
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Yu T, Lu Q, Ou X, Cao D, Yu Q. Association of sedentary behavior with the expression levels of biomarkers in colorectal cancer: clinical analysis of 228 patients. TOHOKU J EXP MED 2014; 232:167-76. [PMID: 24621823 DOI: 10.1620/tjem.232.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There is an association between sedentary behavior and the risk of colorectal cancer (CRC), but the underlying mechanism is unclear. CRC is characterized by the changes in the expression levels of biomarkers, including voltage-gated proton channel Hv1, matrix-remodeling associated 5 (MXRA5), DEK (inducing positive supercoils into circular DNA) and protein inhibitor of activated signal transducer and activators of transcription 3 (PIAS3). Thus, sedentary behavior may affect the expression levels of these biomarkers in the colorectal tissue. Here, we recruited 228 CRC patients (128 males, 57.8 ± 7.8 years; 100 females, 57.7 ± 7.5 years) and 80 healthy subjects (48 males, 57.5 ± 6.8 years; 32 females, 56.9 ± 6.5 years) from March 7th, 2010 to May 6th, 2012. All the subjects were unrelated Han Chinese with the similar cultural and economic background. All the subjects were interviewed concerning sedentary time (sitting time categories: less than 1, 1-3, 4-6, and more than 6 h/day). The daily sedentary time of most CRC patients was more than 4 h/day, while the sedentary time of most healthy subjects was less than 3 h/day. The expression levels of Hv1, MXRA5 and DEK mRNAs and proteins were higher in CRC tissues and the levels of PIAS3 mRNA and protein were lower when the daily sedentary time was longer in CRC patients (p < 0.05). The daily sedentary time was correlated with the protein levels of CRC biomarkers. Furthermore, the sedentary time was positively related with body mass index but not daily calorie intake.
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Affiliation(s)
- Ting Yu
- Department of Gastroenterology, Affiliated Zhongda Hospital of Southeast University
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41
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Ahn JW, Kim HS, Yoon JK, Jang H, Han SM, Eun S, Shim HS, Kim HJ, Kim DJ, Lee JG, Lee CY, Bae MK, Chung KY, Jung JY, Kim EY, Kim SK, Chang J, Kim HR, Kim JH, Lee MG, Cho BC, Lee JH, Bang D. Identification of somatic mutations in EGFR/KRAS/ALK-negative lung adenocarcinoma in never-smokers. Genome Med 2014; 6:18. [PMID: 24576404 PMCID: PMC3979047 DOI: 10.1186/gm535] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/18/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma is a highly heterogeneous disease with various etiologies, prognoses, and responses to therapy. Although genome-scale characterization of lung adenocarcinoma has been performed, a comprehensive somatic mutation analysis of EGFR/KRAS/ALK-negative lung adenocarcinoma in never-smokers has not been conducted. METHODS We analyzed whole exome sequencing data from 16 EGFR/KRAS/ALK-negative lung adenocarcinomas and additional 54 tumors in two expansion cohort sets. Candidate loci were validated by target capture and Sanger sequencing. Gene set analysis was performed using Ingenuity Pathway Analysis. RESULTS We identified 27 genes potentially implicated in the pathogenesis of lung adenocarcinoma. These included targetable genes involved in PI3K/mTOR signaling (TSC1, PIK3CA, AKT2) and receptor tyrosine kinase signaling (ERBB4) and genes not previously highlighted in lung adenocarcinomas, such as SETD2 and PBRM1 (chromatin remodeling), CHEK2 and CDC27 (cell cycle), CUL3 and SOD2 (oxidative stress), and CSMD3 and TFG (immune response). In the expansion cohort (N = 70), TP53 was the most frequently altered gene (11%), followed by SETD2 (6%), CSMD3 (6%), ERBB2 (6%), and CDH10 (4%). In pathway analysis, the majority of altered genes were involved in cell cycle/DNA repair (P <0.001) and cAMP-dependent protein kinase signaling (P <0.001). CONCLUSIONS The genomic makeup of EGFR/KRAS/ALK-negative lung adenocarcinomas in never-smokers is remarkably diverse. Genes involved in cell cycle regulation/DNA repair are implicated in tumorigenesis and represent potential therapeutic targets.
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Affiliation(s)
- Jin Woo Ahn
- Department of Chemistry, Yonsei University, Seoul 120-752, Korea
| | - Han Sang Kim
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea
- Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Jung-Ki Yoon
- College of Medicine, Seoul National University, Seoul 110-799, Korea
- Hwasung Public Health Center, Hwasung, Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 120-752, Korea
| | - Soo Min Han
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Sungho Eun
- Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Hyun-Jung Kim
- JE UK Institute for Cancer Research, Gumi City, Kyungbuk, Korea
| | - Dae Joon Kim
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Jin Gu Lee
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Young Lee
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Mi Kyung Bae
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung Young Chung
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Ye Jung
- Division of Pulmonology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Young Kim
- Division of Pulmonology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Kyu Kim
- Division of Pulmonology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Chang
- Division of Pulmonology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hye Ryun Kim
- Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Joo Hang Kim
- Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Min Goo Lee
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Byoung Chul Cho
- Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-752, Korea
- JE UK Institute for Cancer Research, Gumi City, Kyungbuk, Korea
| | - Ji Hyun Lee
- Department of Oral Biology, College of Dentistry, Yonsei University, Seoul, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 120-752, Korea
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The promise of whole-exome sequencing in medical genetics. J Hum Genet 2013; 59:5-15. [DOI: 10.1038/jhg.2013.114] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 09/29/2013] [Accepted: 10/11/2013] [Indexed: 12/14/2022]
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Hoang ML, Chen CH, Sidorenko VS, He J, Dickman KG, Yun BH, Moriya M, Niknafs N, Douville C, Karchin R, Turesky RJ, Pu YS, Vogelstein B, Papadopoulos N, Grollman AP, Kinzler KW, Rosenquist TA. Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing. Sci Transl Med 2013; 5:197ra102. [PMID: 23926200 PMCID: PMC3973132 DOI: 10.1126/scitranslmed.3006200] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In humans, exposure to aristolochic acid (AA) is associated with urothelial carcinoma of the upper urinary tract (UTUC). Exome sequencing of UTUCs from 19 individuals with documented exposure to AA revealed a remarkably large number of somatic mutations and an unusual mutational signature attributable to AA. Most of the mutations (72%) in these tumors were A:T-to-T:A transversions, located predominantly on the nontranscribed strand, with a strong preference for deoxyadenosine in a consensus sequence (T/CAG). This trinucleotide motif overlaps the canonical splice acceptor site, possibly accounting for the excess of splice site mutations observed in these tumors. The AA mutational fingerprint was found frequently in oncogenes and tumor suppressor genes in AA-associated UTUC. The AA mutational signature was observed in one patient's tumor from a UTUC cohort without previous indication of AA exposure. Together, these results directly link an established environmental mutagen to cancer through genome-wide sequencing and highlight its power to reveal individual exposure to carcinogens.
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Affiliation(s)
- Margaret L. Hoang
- Ludwig Center for Cancer Genetics and Therapeutics and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Chung-Hsin Chen
- Department of Urology, National Taiwan University Hospital and College of Medicine, Taipei 10002, Taiwan
| | - Viktoriya S. Sidorenko
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jian He
- Ludwig Center for Cancer Genetics and Therapeutics and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Kathleen G. Dickman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Byeong Hwa Yun
- Division of Environmental Health Sciences, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201, USA
| | - Masaaki Moriya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Noushin Niknafs
- Department of Biomedical Engineering, Institute for Computational Medicine, the Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christopher Douville
- Department of Biomedical Engineering, Institute for Computational Medicine, the Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Institute for Computational Medicine, the Johns Hopkins University, Baltimore, MD 21218, USA
| | - Robert J. Turesky
- Division of Environmental Health Sciences, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201, USA
| | - Yeong-Shiau Pu
- Department of Urology, National Taiwan University Hospital and College of Medicine, Taipei 10002, Taiwan
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Arthur P. Grollman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Thomas A. Rosenquist
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett 2012; 340:284-95. [PMID: 23174106 DOI: 10.1016/j.canlet.2012.11.025] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/13/2012] [Accepted: 11/13/2012] [Indexed: 02/06/2023]
Abstract
The advent of next generation sequencing (NGS) technologies has revolutionized the field of genomics, enabling fast and cost-effective generation of genome-scale sequence data with exquisite resolution and accuracy. Over the past years, rapid technological advances led by academic institutions and companies have continued to broaden NGS applications from research to the clinic. A recent crop of discoveries have highlighted the medical impact of NGS technologies on Mendelian and complex diseases, particularly cancer. However, the ever-increasing pace of NGS adoption presents enormous challenges in terms of data processing, storage, management and interpretation as well as sequencing quality control, which hinder the translation from sequence data into clinical practice. In this review, we first summarize the technical characteristics and performance of current NGS platforms. We further highlight advances in the applications of NGS technologies towards the development of clinical diagnostics and therapeutics. Common issues in NGS workflows are also discussed to guide the selection of NGS platforms and pipelines for specific research purposes.
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Affiliation(s)
- Jiekun Xuan
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China; National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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