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Ma H, Song B, Guo S, Li G, Jin G. Identification of germline and somatic mutations in pancreatic adenosquamous carcinoma using whole exome sequencing. Cancer Biomark 2020; 27:389-397. [PMID: 31958074 DOI: 10.3233/cbm-190236] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Pancreatic cancer is one of the most lethal malignancies worldwide. Pancreatic adenosquamous carcinoma (PASC) is a rare histological type of pancreatic carcinoma with a poor prognosis. The median survival time after diagnosis is less than one year. It is believed that the pathogenesis of PASC is different from pancreatic adenocarcinoma. In this study, we tried to reveal the intrinsic gene mutations associated with PASC through whole exome sequencing. METHODS Both cancerous and paracancerous tissues were collected from 12 pathologically diagnosed PASC patients. Their clinical characteristics were collected, and patient survival information was obtained through follow-up. The correlations between the mutations and clinical characteristics were analysed. RESULTS Germline mutations were identified in MAP3K1 (9 cases), PDE4DIP (7), BCR (7), ALK (6), USP6 (5), AR (4), HLA-A (4), SPEN (4), KMT2D (3), NUTM2B (3), ZFHX3 (3), and MN1 (3), while somatic mutations were found in TP53 (5), KRAS (3), HRNR (3), and OBSCN (3). Peripheral tissue invasion was associated with somatic mutations in KRAS (P= 0.0339). Additionally, there were significant correlations between lymphatic metastasis and germline mutations in USP6 (P= 0.0228) and somatic mutations in OBSCN and HRNR (P= 0.0339). CONCLUSION In conclusion, susceptibility genes including MAP3K1, PDE4DIP, and BCR are frequently found to be mutated in the germlines of PASC patients. Somatic mutations in KRAS, OBSCN, and HRNR and germline mutations in USP6 are related to tumour invasion and metastasis, reinforcing the necessity of translating these potential biomarkers into clinical practice.
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Affiliation(s)
- Hongyun Ma
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bin Song
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Shiwei Guo
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gang Li
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gang Jin
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute for Advanced Communication and Data Science, Shanghai University, Shanghai, China
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2
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Gusev A, Lawrenson K, Lin X, Lyra PC, Kar S, Vavra KC, Segato F, Fonseca MA, Lee JM, Pejovic T, Liu G, Karlan BY, Freedman ML, Noushmehr H, Monteiro AN, Pharoah PD, Pasaniuc B, Gayther SA. A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants. Nat Genet 2019; 51:815-823. [PMID: 31043753 PMCID: PMC6548545 DOI: 10.1038/s41588-019-0395-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/15/2019] [Indexed: 12/31/2022]
Abstract
We sought to identify susceptibility genes for high-grade serous ovarian cancer (HGSOC) by performing a transcriptome-wide association study of gene expression and splice junction usage in HGSOC-relevant tissue types (N = 2,169) and the largest genome-wide association study available for HGSOC (N = 13,037 cases and 40,941 controls). We identified 25 transcriptome-wide association study significant genes, 7 at the junction level only, including LRRC46 at 19q21.32, (P = 1 × 10-9), CHMP4C at 8q21 (P = 2 × 10-11) and a PRC1 junction at 15q26 (P = 7 × 10-9). In vitro assays for CHMP4C showed that the associated variant induces allele-specific exon inclusion (P = 0.0024). Functional screens in HGSOC cell lines found evidence of essentiality for three of the new genes we identified: HAUS6, KANSL1 and PRC1, with the latter comparable to MYC. Our study implicates at least one target gene for 6 out of 13 distinct genome-wide association study regions, identifying 23 new candidate susceptibility genes for HGSOC.
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Affiliation(s)
- Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kate Lawrenson
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Paulo C. Lyra
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Siddhartha Kar
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Kevin C. Vavra
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Felipe Segato
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Brazil
| | - Marcos A.S. Fonseca
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Janet M Lee
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tanya Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Gang Liu
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | | | - Beth Y. Karlan
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Houtan Noushmehr
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Alvaro N. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Paul D.P. Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Bogdan Pasaniuc
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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3
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Detection of novel fusion-transcripts by RNA-Seq in T-cell lymphoblastic lymphoma. Sci Rep 2019; 9:5179. [PMID: 30914738 PMCID: PMC6435891 DOI: 10.1038/s41598-019-41675-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/14/2019] [Indexed: 02/08/2023] Open
Abstract
Fusions transcripts have been proven to be strong drivers for neoplasia-associated mutations, although their incidence in T-cell lymphoblastic lymphoma needs to be determined yet. Using RNA-Seq we have selected 55 fusion transcripts identified by at least two of three detection methods in the same tumour. We confirmed the existence of 24 predicted novel fusions that had not been described in cancer or normal tissues yet, indicating the accuracy of the prediction. Of note, one of them involves the proto oncogene TAL1. Other confirmed fusions could explain the overexpression of driver genes such as COMMD3-BMI1, LMO1 or JAK3. Five fusions found exclusively in tumour samples could be considered pathogenic (NFYG-TAL1, RIC3-TCRBC2, SLC35A3-HIAT1, PICALM MLLT10 and MLLT10-PICALM). However, other fusions detected simultaneously in normal and tumour samples (JAK3-INSL3, KANSL1-ARL17A/B and TFG-ADGRG7) could be germ-line fusions genes involved in tumour-maintaining tasks. Notably, some fusions were confirmed in more tumour samples than predicted, indicating that the detection methods underestimated the real number of existing fusions. Our results highlight the potential of RNA-Seq to identify new cryptic fusions, which could be drivers or tumour-maintaining passenger genes. Such novel findings shed light on the searching for new T-LBL biomarkers in these haematological disorders.
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Abstract
Several challenges present themselves when discussing current approaches to the prevention or treatment of pancreatic cancer. Up to 45% of the risk of pancreatic cancer is attributed to unknown causes, making effective prevention programs difficult to design. The most common type of pancreatic cancer, pancreatic ductal adenocarcinoma (PDAC), is generally diagnosed at a late stage, leading to a poor prognosis and 5-year survival estimate. PDAC tumors are heterogeneous, leading to many identified cell subtypes within one patient’s primary tumor. This explains why there is a high frequency of tumors that are resistant to standard treatments, leading to high relapse rates. This review will discuss how epigenetic technologies and epigenome-wide association studies have been used to address some of these challenges and the future promises these approaches hold.
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Affiliation(s)
- Rahul R Singh
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA; (R.R.S.); (K.M.R.)
| | - Katie M Reindl
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA; (R.R.S.); (K.M.R.)
| | - Rick J Jansen
- Department of Public Health, North Dakota State University, Fargo, ND 58102, USA
- Biostatistics Core Facility, North Dakota State University, Fargo, ND 58102, USA
- Center for Immunization Research and Education, North Dakota State University, Fargo, ND 58102, USA
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58102, USA
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Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome Biol 2017; 18:141. [PMID: 28750683 PMCID: PMC5530464 DOI: 10.1186/s13059-017-1266-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/27/2017] [Indexed: 11/22/2022] Open
Abstract
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. Integration of multi-omics data from 521 prostate tumor samples indicated a stronger regulatory impact of structural variants, as they affect more transcription factor hubs in the tissue-specific network. Moreover, crosstalk between transcription factor hub expression modulated by structural variants and methylation levels likely leads to the differential expression of target genes. We report known prostate tumor regulatory drivers and nominate novel transcription factors (ERF, CREB3L1, and POU2F2), which are supported by functional validation.
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Affiliation(s)
- Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Alexander Martinez-Fundichely
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Adeline Berger
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
- Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - Andre Neil Forbes
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Eric Minwei Liu
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Deli Liu
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Department of Urology, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Andrea Sboner
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA
| | - Pablo Tamayo
- Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - David S Rickman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA.
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Ekta Khurana
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA.
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Wytko C, Soto B, Ficklin SP. blend4php: a PHP API for galaxy. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:baw154. [PMID: 28077564 PMCID: PMC5225400 DOI: 10.1093/database/baw154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023]
Abstract
Galaxy is a popular framework for execution of complex analytical pipelines typically for large data sets, and is a commonly used for (but not limited to) genomic, genetic and related biological analysis. It provides a web front-end and integrates with high performance computing resources. Here we report the development of the blend4php library that wraps Galaxy’s RESTful API into a PHP-based library. PHP-based web applications can use blend4php to automate execution, monitoring and management of a remote Galaxy server, including its users, workflows, jobs and more. The blend4php library was specifically developed for the integration of Galaxy with Tripal, the open-source toolkit for the creation of online genomic and genetic web sites. However, it was designed as an independent library for use by any application, and is freely available under version 3 of the GNU Lesser General Public License (LPGL v3.0) at https://github.com/galaxyproject/blend4php. Database URL:https://github.com/galaxyproject/blend4php
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Affiliation(s)
- Connor Wytko
- Department of Horticulture and.,School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - Brian Soto
- Department of Horticulture and.,School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
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Al-Hebshi NN, Li S, Nasher AT, El-Setouhy M, Alsanosi R, Blancato J, Loffredo C. Exome sequencing of oral squamous cell carcinoma in users of Arabian snuff reveals novel candidates for driver genes. Int J Cancer 2016; 139:363-72. [PMID: 26934577 DOI: 10.1002/ijc.30068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/16/2016] [Indexed: 02/06/2023]
Abstract
The study sought to identify genetic aberrations driving oral squamous cell carcinoma (OSCC) development among users of shammah, an Arabian preparation of smokeless tobacco. Twenty archival OSCC samples, 15 of which with a history of shammah exposure, were whole-exome sequenced at an average depth of 127×. Somatic mutations were identified using a novel, matched controls-independent filtration algorithm. CODEX and Exomedepth coupled with a novel, Database of Genomic Variant-based filter were employed to call somatic gene-copy number variations. Significantly mutated genes were identified with Oncodrive FM and the Youn and Simon's method. Candidate driver genes were nominated based on Gene Set Enrichment Analysis. The observed mutational spectrum was similar to that reported by the TCGA project. In addition to confirming known genes of OSCC (TP53, CDKNA2, CASP8, PIK3CA, HRAS, FAT1, TP63, CCND1 and FADD) the analysis identified several candidate novel driver events including mutations of NOTCH3, CSMD3, CRB1, CLTCL1, OSMR and TRPM2, amplification of the proto-oncogenes FOSL1, RELA, TRAF6, MDM2, FRS2 and BAG1, and deletion of the recently described tumor suppressor SMARCC1. Analysis also revealed significantly altered pathways not previously implicated in OSCC including Oncostatin-M signalling pathway, AP-1 and C-MYB transcription networks and endocytosis. There was a trend for higher number of mutations, amplifications and driver events in samples with history of shammah exposure particularly those that tested EBV positive, suggesting an interaction between tobacco exposure and EBV. The work provides further evidence for the genetic heterogeneity of oral cancer and suggests shammah-associated OSCC is characterized by extensive amplification of oncogenes.
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Affiliation(s)
- Nezar Noor Al-Hebshi
- Department of Preventive Dentistry, College of Dentistry, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Shiyong Li
- Department of Oncology and Pharmacogenomics, Beijing Genome Institute (BGI), Shenzhen, Republic of China
| | - Akram Thabet Nasher
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Sana'a University, Yemen
| | - Maged El-Setouhy
- Substance Abuse Research Center (SARC), Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Rashad Alsanosi
- Substance Abuse Research Center (SARC), Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Jan Blancato
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Christopher Loffredo
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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