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Ylagan M, Xu Q, Kowalski J. TTSBBC: triplex target site biomarkers and barcodes in cancer. Nucleic Acids Res 2024; 52:W547-W555. [PMID: 38661214 PMCID: PMC11223863 DOI: 10.1093/nar/gkae312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.
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Affiliation(s)
- Maya Ylagan
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX78712, USA
| | - Qi Xu
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX78712, USA
| | - Jeanne Kowalski
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX78712, USA
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Rudà R, Horbinski C, van den Bent M, Preusser M, Soffietti R. IDH inhibition in gliomas: from preclinical models to clinical trials. Nat Rev Neurol 2024; 20:395-407. [PMID: 38760442 DOI: 10.1038/s41582-024-00967-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Gliomas are the most common malignant primary brain tumours in adults and cannot usually be cured with standard cancer treatments. Gliomas show intratumoural and intertumoural heterogeneity at the histological and molecular levels, and they frequently contain mutations in the isocitrate dehydrogenase 1 (IDH1) or IDH2 gene. IDH-mutant adult-type diffuse gliomas are subdivided into grade 2, 3 or 4 IDH-mutant astrocytomas and grade 2 or 3 IDH-mutant, 1p19q-codeleted oligodendrogliomas. The product of the mutated IDH genes, D-2-hydroxyglutarate (D-2-HG), induces global DNA hypermethylation and interferes with immunity, leading to stimulation of tumour growth. Selective inhibitors of mutant IDH, such as ivosidenib and vorasidenib, have been shown to reduce D-2-HG levels and induce cellular differentiation in preclinical models and to induce MRI-detectable responses in early clinical trials. The phase III INDIGO trial has demonstrated superiority of vorasidenib, a brain-penetrant pan-mutant IDH inhibitor, over placebo in people with non-enhancing grade 2 IDH-mutant gliomas following surgery. In this Review, we describe the pathway of development of IDH inhibitors in IDH-mutant low-grade gliomas from preclinical models to clinical trials. We discuss the practice-changing implications of the INDIGO trial and consider new avenues of investigation in the field of IDH-mutant gliomas.
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Affiliation(s)
- Roberta Rudà
- Division of Neuro-Oncology, Department of Neuroscience 'Rita Levi Montalcini', University of Turin, Turin, Italy.
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martin van den Bent
- Brain Tumour Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Riccardo Soffietti
- Division of Neuro-Oncology, Department of Neuroscience 'Rita Levi Montalcini', University of Turin, Turin, Italy
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3
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Tuminello S, Ashebir YA, Schroff C, Ramaswami S, Durmus N, Chen Y, Snuderl M, Shao Y, Reibman J, Arslan AA. Genome-wide DNA methylation profiles and breast cancer among World Trade Center survivors. Environ Epidemiol 2024; 8:e313. [PMID: 38841706 PMCID: PMC11152787 DOI: 10.1097/ee9.0000000000000313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
Background Increased incidence of cancer has been reported among World Trade Center (WTC)-exposed persons. Aberrant DNA methylation is a hallmark of cancer development. To date, only a few small studies have investigated the relationship between WTC exposure and DNA methylation. The main objective of this study was to assess the DNA methylation profiles of WTC-exposed community members who remained cancer free and those who developed breast cancer. Methods WTC-exposed women were selected from the WTC Environmental Health Center clinic, with peripheral blood collected during routine clinical monitoring visits. The reference group was selected from the NYU Women's Health Study, a prospective cohort study with blood samples collected before 9 November 2001. The Infinium MethylationEPIC array was used for global DNA methylation profiling, with adjustments for cell type composition and other confounders. Annotated probes were used for biological pathway and network analysis. Results A total of 64 WTC-exposed (32 cancer free and 32 with breast cancer) and 32 WTC-unexposed (16 cancer free and 16 with prediagnostic breast cancer) participants were included. Hypermethylated cytosine-phosphate-guanine probe sites (defined as β > 0.8) were more common among WTC-exposed versus unexposed participants (14.3% vs. 4.5%, respectively, among the top 5000 cytosine-phosphate-guanine sites). Cancer-related pathways (e.g., human papillomavirus infection, cGMP-PKG) were overrepresented in WTC-exposed groups (breast cancer patients and cancer-free subjects). Compared to the unexposed breast cancer patients, 47 epigenetically dysregulated genes were identified among WTC-exposed breast cancers. These genes formed a network, including Wnt/β-catenin signaling genes WNT4 and TCF7L2, and dysregulation of these genes contributes to cancer immune evasion. Conclusion WTC exposure likely impacts DNA methylation and may predispose exposed individuals toward cancer development, possibly through an immune-mediated mechanism.
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Affiliation(s)
- Stephanie Tuminello
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
| | - Yibeltal Arega Ashebir
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
| | - Chanel Schroff
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Sitharam Ramaswami
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Nedim Durmus
- Department of Medicine, NYU Grossman School of Medicine, New York City, New York
| | - Yu Chen
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
- NYU Perlmutter Comprehensive Cancer Center, New York City, New York
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Yongzhao Shao
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
- NYU Perlmutter Comprehensive Cancer Center, New York City, New York
| | - Joan Reibman
- Department of Medicine, NYU Grossman School of Medicine, New York City, New York
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York City, New York
| | - Alan A. Arslan
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
- NYU Perlmutter Comprehensive Cancer Center, New York City, New York
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York City, New York
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Sands B, Yun SR, Oshima J, Mendenhall AR. Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576748. [PMID: 38328214 PMCID: PMC10849558 DOI: 10.1101/2024.01.22.576748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undefined epigenetic programs act to probabilistically silence individual autosomal alleles, generating unique individuals, even from genetic clones. This sort of random monoallelic expression can explain variation in traits and diseases that differences in genes and environments cannot. Here, we developed the nematode Caenorhabditis elegans to study monoallelic expression in whole tissues, and defined a developmental genetic regulation pathway. We found maternal H3K9 histone methyltransferase (HMT) SET-25/SUV39/G9a works with HPL-2/HP1 and LIN-61/L3MBTL2 to randomly silence alleles in the intestinal progenitor E-cell of 8-cell embryos to cause monoallelic expression. SET-25 was antagonized by another maternal H3K9 HMT, MET-2/SETDB1, which works with LIN-65/ATF7ZIP and ARLE-14/ARL14EP to prevent monoallelic expression. The HMT-catalytic SET domains of both MET-2 and SET-25 were required for regulating monoallelic expression. Our data support a model wherein SET-25 and MET-2 regulate histones during development to generate patterns of somatic monoallelic expression that are persistent but not heritable.
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Lobanova YV, Zhenilo SV. Genomic Imprinting and Random Monoallelic Expression. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:84-96. [PMID: 38467547 DOI: 10.1134/s000629792401005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 03/13/2024]
Abstract
The review discusses the mechanisms of monoallelic expression, such as genomic imprinting, in which gene transcription depends on the parental origin of the allele, and random monoallelic transcription. Data on the regulation of gene activity in the imprinted regions are summarized with a particular focus on the areas controlling imprinting and factors influencing the variability of the imprintome. The prospects of studies of the monoallelic expression are discussed.
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Affiliation(s)
- Yaroslava V Lobanova
- Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Svetlana V Zhenilo
- Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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Tuminello S, Nguyen E, Durmus N, Alptekin R, Yilmaz M, Crisanti MC, Snuderl M, Chen Y, Shao Y, Reibman J, Taioli E, Arslan AA. World Trade Center Exposure, DNA Methylation Changes, and Cancer: A Review of Current Evidence. EPIGENOMES 2023; 7:31. [PMID: 38131903 PMCID: PMC10742700 DOI: 10.3390/epigenomes7040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction: Known carcinogens in the dust and fumes from the destruction of the World Trade Center (WTC) towers on 9 November 2001 included metals, asbestos, and organic pollutants, which have been shown to modify epigenetic status. Epigenome-wide association analyses (EWAS) using uniform (Illumina) methodology have identified novel epigenetic profiles of WTC exposure. Methods: We reviewed all published data, comparing differentially methylated gene profiles identified in the prior EWAS studies of WTC exposure. This included DNA methylation changes in blood-derived DNA from cases of cancer-free "Survivors" and those with breast cancer, as well as tissue-derived DNA from "Responders" with prostate cancer. Emerging molecular pathways related to the observed DNA methylation changes in WTC-exposed groups were explored and summarized. Results: WTC dust exposure appears to be associated with DNA methylation changes across the genome. Notably, WTC dust exposure appears to be associated with increased global DNA methylation; direct dysregulation of cancer genes and pathways, including inflammation and immune system dysregulation; and endocrine system disruption, as well as disruption of cholesterol homeostasis and lipid metabolism. Conclusion: WTC dust exposure appears to be associated with biologically meaningful DNA methylation changes, with implications for carcinogenesis and development of other chronic diseases.
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Affiliation(s)
- Stephanie Tuminello
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
| | - Emelie Nguyen
- Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, NY 10016, USA
| | - Nedim Durmus
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ramazan Alptekin
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Muhammed Yilmaz
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yu Chen
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Yongzhao Shao
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Joan Reibman
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Emanuela Taioli
- Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, NY 10016, USA
| | - Alan A. Arslan
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY 10016, USA
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Kravitz SN, Ferris E, Love MI, Thomas A, Quinlan AR, Gregg C. Random allelic expression in the adult human body. Cell Rep 2023; 42:111945. [PMID: 36640362 PMCID: PMC10484211 DOI: 10.1016/j.celrep.2022.111945] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/17/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Genes are typically assumed to express both parental alleles similarly, yet cell lines show random allelic expression (RAE) for many autosomal genes that could shape genetic effects. Thus, understanding RAE in human tissues could improve our understanding of phenotypic variation. Here, we develop a methodology to perform genome-wide profiling of RAE and biallelic expression in GTEx datasets for 832 people and 54 tissues. We report 2,762 autosomal genes with some RAE properties similar to randomly inactivated X-linked genes. We found that RAE is associated with rapidly evolving regions in the human genome, adaptive signaling processes, and genes linked to age-related diseases such as neurodegeneration and cancer. We define putative mechanistic subtypes of RAE distinguished by gene overlaps on sense and antisense DNA strands, aggregation in clusters near telomeres, and increased regulatory complexity and inputs compared with biallelic genes. We provide foundations to study RAE in human phenotypes, evolution, and disease.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Elliott Ferris
- Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alun Thomas
- Department of Internal Medicine, Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Christopher Gregg
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA.
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Colombo C, Pogliaghi G, Tosi D, Muzza M, Bulfamante G, Persani L, Fugazzola L, Cirello V. Thyroid cancer harboring PTEN and TP53 mutations: A peculiar molecular and clinical case report. Front Oncol 2022; 12:949098. [PMID: 36119511 PMCID: PMC9478947 DOI: 10.3389/fonc.2022.949098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
To date, the molecular mechanisms that underline aggressiveness and resistance to tyrosine kinase inhibitors in some thyroid carcinomas (TCs) are not known yet. We report the case of a young patient with a metastatic poorly differentiated (PDTC) and follicular thyroid carcinoma (FTC) refractory to conventional therapies and to Sorafenib. The patient, despite an initial partial response, died of progressive disease 21 months after diagnosis. The genetic analysis performed on the primary tumor and on lymph nodes and distant metastases allowed to identify a frameshift mutation (p.P248Tfs*5) in the PTEN gene, never described in TC. This mutation was present in the primary tumor and, with a lower allelic frequency, in metastases diagnosed after treatment with Sorafenib. Mutations in TP53 (p.C135Y and c.920-2A>G previously detected in anaplastic carcinomas and p.M133R never found in TC) were also detected in the primary tissue together with a mono-allelic expression of the p.C135Y mutant at RNA level. At metastatic sites level, we found only the TP53 splicing mutation c.920-2A>G. The presence of defects in mismatch repair (MMR) proteins and genomic instability was also evaluated. The primary tumor showed a partial expression of MMR proteins together with a strong genomic instability. In conclusion, we demonstrated that the rare combination of somatic PTEN and TP53 mutations in a patient with a metastatic FTC, together with the presence of tumor heterogeneity and genomic instability, might be associated with a high tumor aggressiveness and resistance to treatments.
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Affiliation(s)
- Carla Colombo
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Gabriele Pogliaghi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, Milan, Italy
| | - Delfina Tosi
- Unit of Human Pathology, Department of Health Sciences Santi Paolo e Carlo Medical School, University of Milan, Milan, Italy
| | - Marina Muzza
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, Milan, Italy
| | - Gaetano Bulfamante
- Unit of Human Pathology, Department of Health Sciences Santi Paolo e Carlo Medical School, University of Milan, Milan, Italy
| | - Luca Persani
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Laura Fugazzola
- Division of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Valentina Cirello
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, Milan, Italy
- *Correspondence: Valentina Cirello,
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Gupte R, Lin KY, Nandu T, Lea JS, Kraus WL. Combinatorial Treatment with PARP-1 Inhibitors and Cisplatin Attenuates Cervical Cancer Growth through Fos-Driven Changes in Gene Expression. Mol Cancer Res 2022; 20:1183-1192. [PMID: 35503086 PMCID: PMC9357060 DOI: 10.1158/1541-7786.mcr-22-0111] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/10/2022] [Accepted: 04/26/2022] [Indexed: 02/07/2023]
Abstract
Cervical cancer continues to be a significant cause of cancer-related deaths in women. The most common treatment for cervical cancer involves the use of the drug cisplatin in conjunction with other therapeutics. However, the development of cisplatin resistance in patients can hinder the efficacy of these treatments, so alternatives are needed. In this study, we found that PARP inhibitors (PARPi) could attenuate the growth of cells representing cervical adenocarcinoma and cervical squamous cell carcinoma. Moreover, a combination of PARPi with cisplatin increased cisplatin-mediated cytotoxicity in cervical cancer cells. This was accompanied by a dramatic alteration of the transcriptome. The FOS gene, which encodes the transcription factor Fos, was one of the most highly upregulated genes in the dual treatment condition, leading to increased Fos protein levels, greater Fos binding to chromatin, and the subsequent induction of Fos target genes. Increased expression of Fos was sufficient to hinder cervical cancer growth, as shown by ectopic expression of Fos in cervical cancer cells. Conversely, Fos knockdown enhanced cell growth. Collectively, these results indicate that by inducing FOS expression, PARPi treatment in combination with cisplatin leads to inhibition of cervical cancer proliferation, likely through a Fos-specific gene expression program. IMPLICATIONS Our observations, which link the gene regulatory effects of PARPi + cisplatin to the growth inhibitory effects of FOS expression in cervical cancer cells, strengthen the rationale for using PARPi with cisplatin as a therapy for cervical cancer.
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Affiliation(s)
- Rebecca Gupte
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ken Y. Lin
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9032
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi S. Lea
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9032
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Address for manuscript correspondence and publication: W. Lee Kraus, Ph.D., Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-8511, Phone: 214-648-2388, Fax: 214-648-0383,
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Tuminello S, Zhang Y, Yang L, Durmus N, Snuderl M, Heguy A, Zeleniuch-Jacquotte A, Chen Y, Shao Y, Reibman J, Arslan AA. Global DNA Methylation Profiles in Peripheral Blood of WTC-Exposed Community Members with Breast Cancer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095104. [PMID: 35564499 PMCID: PMC9105091 DOI: 10.3390/ijerph19095104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022]
Abstract
Breast cancer represents the most common cancer diagnosis among World Trade Center (WTC)-exposed community members, residents, and cleanup workers enrolled in the WTC Environmental Health Center (WTC EHC). The primary aims of this study were (1) to compare blood DNA methylation profiles of WTC-exposed community members with breast cancer and WTC-unexposed pre-diagnostic breast cancer blood samples, and (2) to compare the DNA methylation differences among the WTC EHC breast cancer cases and WTC-exposed cancer-free controls. Gene pathway enrichment analyses were further conducted. There were significant differences in DNA methylation between WTC-exposed breast cancer cases and unexposed prediagnostic breast cancer cases. The top differentially methylated genes were Intraflagellar Transport 74 (IFT74), WD repeat-containing protein 90 (WDR90), and Oncomodulin (OCM), which are commonly upregulated in tumors. Probes associated with established tumor suppressor genes (ATM, BRCA1, PALB2, and TP53) were hypermethylated among WTC-exposed breast cancer cases compared to the unexposed group. When comparing WTC EHC breast cancer cases vs. cancer-free controls, there appeared to be global hypomethylation among WTC-exposed breast cancer cases compared to exposed controls. Functional pathway analysis revealed enrichment of several gene pathways in WTC-exposed breast cancer cases including endocytosis, proteoglycans in cancer, regulation of actin cytoskeleton, axon guidance, focal adhesion, calcium signaling, cGMP-PKG signaling, mTOR, Hippo, and oxytocin signaling. The results suggest potential epigenetic links between WTC exposure and breast cancer in local community members enrolled in the WTC EHC program.
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Affiliation(s)
- Stephanie Tuminello
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (Y.Z.); (A.Z.-J.); (Y.C.); (Y.S.)
- Correspondence: (S.T.); (A.A.A.)
| | - Yian Zhang
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (Y.Z.); (A.Z.-J.); (Y.C.); (Y.S.)
| | - Lei Yang
- Foundation Medicine, Cambridge, MA 02141, USA;
| | - Nedim Durmus
- Department of Medicine, New York University Langone Health, New York, NY 10016, USA; (N.D.); (J.R.)
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA; (M.S.); (A.H.)
| | - Adriana Heguy
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA; (M.S.); (A.H.)
- NYU Langone’s Genome Technology Center, New York, NY 10016, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (Y.Z.); (A.Z.-J.); (Y.C.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Yu Chen
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (Y.Z.); (A.Z.-J.); (Y.C.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Yongzhao Shao
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (Y.Z.); (A.Z.-J.); (Y.C.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Joan Reibman
- Department of Medicine, New York University Langone Health, New York, NY 10016, USA; (N.D.); (J.R.)
| | - Alan A. Arslan
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (Y.Z.); (A.Z.-J.); (Y.C.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
- Department of Obstetrics and Gynecology, New York University Langone Health, New York, NY 10016, USA
- Correspondence: (S.T.); (A.A.A.)
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11
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RNA-seq for revealing the function of the transcriptome. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [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: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
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Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
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13
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Fu R, Qin P, Zou X, Hu Z, Hong N, Wang Y, Jin W. A Comprehensive Characterization of Monoallelic Expression During Hematopoiesis and Leukemogenesis via Single-Cell RNA-Sequencing. Front Cell Dev Biol 2021; 9:702897. [PMID: 34722498 PMCID: PMC8548578 DOI: 10.3389/fcell.2021.702897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is becoming a powerful tool to investigate monoallelic expression (MAE) in various developmental and pathological processes. However, our knowledge of MAE during hematopoiesis and leukemogenesis is limited. In this study, we conducted a systematic interrogation of MAEs in bone marrow mononuclear cells (BMMCs) at single-cell resolution to construct a MAE atlas of BMMCs. We identified 1,020 constitutive MAEs in BMMCs, which included imprinted genes such as MEG8, NAP1L5, and IRAIN. We classified the BMMCs into six cell types and identified 74 cell type specific MAEs including MTSS1, MOB1A, and TCF12. We further identified 114 random MAEs (rMAEs) at single-cell level, with 78.1% single-allele rMAE and 21.9% biallelic mosaic rMAE. Many MAEs identified in BMMCs have not been reported and are potentially hematopoietic specific, supporting MAEs are functional relevance. Comparison of BMMC samples from a leukemia patient with multiple clinical stages showed the fractions of constitutive MAE were correlated with fractions of leukemia cells in BMMCs. Further separation of the BMMCs into leukemia cells and normal cells showed that leukemia cells have much higher constitutive MAE and rMAEs than normal cells. We identified the leukemia cell-specific MAEs and relapsed leukemia cell-specific MAEs, which were enriched in immune-related functions. These results indicate MAE is prevalent and is an important gene regulation mechanism during hematopoiesis and leukemogenesis. As the first systematical interrogation of constitutive MAEs, cell type specific MAEs, and rMAEs during hematopoiesis and leukemogenesis, the study significantly increased our knowledge about the features and functions of MAEs.
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Affiliation(s)
- Ruiqing Fu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Pengfei Qin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xianghui Zou
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yun Wang
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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14
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Lee DD, Komosa M, Sudhaman S, Leão R, Zhang CH, Apolonio JD, Hermanns T, Wild PJ, Klocker H, Nassiri F, Zadeh G, Diplas BH, Yan H, Gallinger S, Pugh TJ, Ramaswamy V, Taylor MD, Castelo-Branco P, Nunes NM, Tabori U. Dual role of allele-specific DNA hypermethylation within the TERT promoter in cancer. J Clin Invest 2021; 131:146915. [PMID: 34720085 DOI: 10.1172/jci146915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Aberrant activation of telomerase in human cancer is achieved by various alterations within the TERT promoter, including cancer-specific DNA hypermethylation of the TERT hypermethylated oncological region (THOR). However, the impact of allele-specific DNA methylation within the TERT promoter on gene transcription remains incompletely understood. Using allele-specific next-generation sequencing, we screened a large cohort of normal and tumor tissues (n = 652) from 10 cancer types and identified that differential allelic methylation (DAM) of THOR is restricted to cancerous tissue and commonly observed in major cancer types. THOR-DAM was more common in adult cancers, which develop through multiple stages over time, than in childhood brain tumors. Furthermore, THOR-DAM was especially enriched in tumors harboring the activating TERT promoter mutations (TPMs). Functional studies revealed that allele-specific gene expression of TERT requires hypomethylation of the core promoter, both in TPM and TERT WT cancers. However, the expressing allele with hypomethylated core TERT promoter universally exhibits hypermethylation of THOR, while the nonexpressing alleles are either hypermethylated or hypomethylated throughout the promoter. Together, our findings suggest a dual role for allele-specific DNA methylation within the TERT promoter in the regulation of TERT expression in cancer.
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Affiliation(s)
- Donghyun D Lee
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Martin Komosa
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ricardo Leão
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Cindy H Zhang
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joana D Apolonio
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Hermanns
- Department of Urology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Germany.,Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
| | - Helmut Klocker
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Farshad Nassiri
- Division of Neurosurgery, University of Toronto, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Division of Neurosurgery, University of Toronto, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Bill H Diplas
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pedro Castelo-Branco
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Faro, Portugal.,Algarve Biomedical Center Research Institute, Faro, Portugal.,Centre for Biomedical Research, University of Algarve, Faro, Portugal.,Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Nuno Miguel Nunes
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Uri Tabori
- Program in Genetics and Genome Biology and.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
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15
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Du Q, Smith GC, Luu PL, Ferguson JM, Armstrong NJ, Caldon CE, Campbell EM, Nair SS, Zotenko E, Gould CM, Buckley M, Chia KM, Portman N, Lim E, Kaczorowski D, Chan CL, Barton K, Deveson IW, Smith MA, Powell JE, Skvortsova K, Stirzaker C, Achinger-Kawecka J, Clark SJ. DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity. Cell Rep 2021; 36:109722. [PMID: 34551299 DOI: 10.1016/j.celrep.2021.109722] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.
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Affiliation(s)
- Qian Du
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Grady C Smith
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Phuc Loi Luu
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - James M Ferguson
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, Murdoch, WA 6150, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | | | - Shalima S Nair
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Elena Zotenko
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Cathryn M Gould
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Michael Buckley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kee-Ming Chia
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Neil Portman
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Dominik Kaczorowski
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Kirston Barton
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Ira W Deveson
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Martin A Smith
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, UNSW Sydney, NSW 2010, Australia
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia.
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16
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Latif G, Alghazo J, Sibai FN, Iskandar DNFA, Khan AH. Recent Advancements in Fuzzy C-means Based Techniques for Brain MRI Segmentation. Curr Med Imaging 2021; 17:917-930. [PMID: 33397241 DOI: 10.2174/1573405616666210104111218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/08/2020] [Accepted: 11/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Variations of image segmentation techniques, particularly those used for Brain MRI segmentation, vary in complexity from basic standard Fuzzy C-means (FCM) to more complex and enhanced FCM techniques. OBJECTIVE In this paper, a comprehensive review is presented on all thirteen variations of FCM segmentation techniques. In the review process, the concentration is on the use of FCM segmentation techniques for brain tumors. Brain tumor segmentation is a vital step in the process of automatically diagnosing brain tumors. Unlike segmentation of other types of images, brain tumor segmentation is a very challenging task due to the variations in brain anatomy. The low contrast of brain images further complicates this process. Early diagnosis of brain tumors is indeed beneficial to patients, doctors, and medical providers. RESULTS FCM segmentation works on images obtained from magnetic resonance imaging (MRI) scanners, requiring minor modifications to hospital operations to early diagnose tumors as most, if not all, hospitals rely on MRI machines for brain imaging. CONCLUSION In this paper, we critically review and summarize FCM based techniques for brain MRI segmentation.
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Affiliation(s)
- Ghazanfar Latif
- College of Computer Engineering and Sciences, Prince Mohammad bin Fahd University, Khobar, Saudi Arabia
| | - Jaafar Alghazo
- College of Computer Engineering and Sciences, Prince Mohammad bin Fahd University, Khobar, Saudi Arabia
| | - Fadi N Sibai
- College of Computer Engineering and Sciences, Prince Mohammad bin Fahd University, Khobar, Saudi Arabia
| | - D N F Awang Iskandar
- Faculty of Computer Science and Information Technology, Universiti Malaysia, Sarawak, Malaysia
| | - Adil H Khan
- Department of Electrical Engineering, Prince Mohammad bin Fahd University, Khobar, Saudi Arabia
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17
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Robles-Espinoza CD, Mohammadi P, Bonilla X, Gutierrez-Arcelus M. Allele-specific expression: applications in cancer and technical considerations. Curr Opin Genet Dev 2021; 66:10-19. [PMID: 33383480 PMCID: PMC7985293 DOI: 10.1016/j.gde.2020.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 11/18/2022]
Abstract
Allele-specific gene expression can influence disease traits. Non-coding germline genetic variants that alter regulatory elements can cause allele-specific gene expression and contribute to cancer susceptibility. In tumors, both somatic copy number alterations and somatic single nucleotide variants have been shown to lead to allele-specific expression of genes, many of which are considered drivers of tumor growth. Here, we review recent studies revealing the pervasive presence of this phenomenon in cancer susceptibility and progression. Furthermore, we underscore the importance of careful experimental design and computational analysis for accurate allelic expression quantification and avoidance of false positives. Finally, we discuss additional methodological challenges encountered in cancer studies and in the burgeoning field of single-cell transcriptomics.
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Affiliation(s)
- Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Mexico; Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA, USA
| | - Ximena Bonilla
- Department of Computer Science, ETH Zurich, Universitätsstr. 6, 8092 Zürich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland; University Hospital Zurich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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18
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Lasocki A, Rosenthal MA, Roberts-Thomson SJ, Neal A, Drummond KJ. Neuro-Oncology and Radiogenomics: Time to Integrate? AJNR Am J Neuroradiol 2020; 41:1982-1988. [PMID: 32912874 DOI: 10.3174/ajnr.a6769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/27/2020] [Indexed: 12/17/2022]
Abstract
Radiogenomics aims to predict genetic markers based on imaging features. The critical importance of molecular markers in the diagnosis and management of intracranial gliomas has led to a rapid growth in radiogenomics research, with progressively increasing complexity. Despite the advances in the techniques being examined, there has been little translation into the clinical domain. This has resulted in a growing disconnect between cutting-edge research and assimilation into clinical practice, though the fundamental goal is for these techniques to improve patient care. The goal of this review, therefore, is to discuss possible clinical scenarios in which the addition of radiogenomics may aid patient management. This includes facilitating patient counseling, determining optimal patient management when complete molecular characterization is not possible, reclassifying tumors, and overcoming some of the limitations of histologic assessment. The review also discusses considerations for selecting relevant radiogenomic features based on the clinical setting.
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Affiliation(s)
- A Lasocki
- From the Department of Cancer Imaging (A.L.)
- Sir Peter MacCallum Department of Oncology (A.L.)
| | - M A Rosenthal
- Medical Oncology (M.A.R.), Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - A Neal
- Neurology (A.N.)
- Department of Neuroscience, Faculty of Medicine (A.N.), Nursing and Health Sciences, Central Clinical School, Monash University, Melbourne, Australia
| | - K J Drummond
- Department of Surgery (K.J.D.), The University of Melbourne, Parkville, Australia
- Neurosurgery (K.J.D.), The Royal Melbourne Hospital, Parkville, Australia
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19
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Arslan AA, Tuminello S, Yang L, Zhang Y, Durmus N, Snuderl M, Heguy A, Zeleniuch-Jacquotte A, Shao Y, Reibman J. Genome-Wide DNA Methylation Profiles in Community Members Exposed to the World Trade Center Disaster. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17155493. [PMID: 32751422 PMCID: PMC7432006 DOI: 10.3390/ijerph17155493] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022]
Abstract
The primary goal of this pilot study was to assess feasibility of studies among local community members to address the hypothesis that complex exposures to the World Trade Center (WTC) dust and fumes resulted in long-term epigenetic changes. We enrolled 18 WTC-exposed cancer-free women from the WTC Environmental Health Center (WTC EHC) who agreed to donate blood samples during their standard clinical visits. As a reference WTC unexposed group, we randomly selected 24 age-matched cancer-free women from an existing prospective cohort who donated blood samples before 11 September 2001. The global DNA methylation analyses were performed using Illumina Infinium MethylationEpic arrays. Statistical analyses were performed using R Bioconductor package. Functional genomic analyses were done by mapping the top 5000 differentially expressed CpG sites to the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database. Among cancer-free subjects, we observed substantial methylation differences between WTC-exposed and unexposed women. The top 15 differentially methylated gene probes included BCAS2, OSGIN1, BMI1, EEF1A2, SPTBN5, CHD8, CDCA7L, AIDA, DDN, SNORD45C, ZFAND6, ARHGEF7, UBXN8, USF1, and USP12. Several cancer-related pathways were enriched in the WTC-exposed subjects, including endocytosis, mitogen-activated protein kinase (MAPK), viral carcinogenesis, as well as Ras-associated protein-1 (Rap1) and mammalian target of rapamycin (mTOR) signaling. The study provides preliminary data on substantial differences in DNA methylation between WTC-exposed and unexposed populations that require validation in further studies.
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Affiliation(s)
- Alan A. Arslan
- Department of Obstetrics and Gynecology, New York University Langone Health, New York, NY 10016, USA
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (S.T.); (L.Y.); (Y.Z.); (A.Z.-J.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
- Correspondence:
| | - Stephanie Tuminello
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (S.T.); (L.Y.); (Y.Z.); (A.Z.-J.); (Y.S.)
| | - Lei Yang
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (S.T.); (L.Y.); (Y.Z.); (A.Z.-J.); (Y.S.)
| | - Yian Zhang
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (S.T.); (L.Y.); (Y.Z.); (A.Z.-J.); (Y.S.)
| | - Nedim Durmus
- Department of Medicine, New York University Langone Health, New York, NY 10016, USA; (N.D.); (J.R.)
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA; (M.S.); (A.H.)
| | - Adriana Heguy
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA; (M.S.); (A.H.)
- NYU Langone’s Genome Technology Center, New York, NY 10016, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (S.T.); (L.Y.); (Y.Z.); (A.Z.-J.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Yongzhao Shao
- Department of Population Health, New York University Langone Health, New York, NY 10016, USA; (S.T.); (L.Y.); (Y.Z.); (A.Z.-J.); (Y.S.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Joan Reibman
- Department of Medicine, New York University Langone Health, New York, NY 10016, USA; (N.D.); (J.R.)
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20
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Kaur P, Campo D, Porras TB, Ring A, Lu J, Chairez Y, Su Y, Kang I, Lang JE. A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer. Int J Mol Sci 2020; 21:ijms21144826. [PMID: 32650480 PMCID: PMC7402350 DOI: 10.3390/ijms21144826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). The variant allele fractions (VAFs) of somatic variants were remarkably similar between amplified and non-amplified cell line samples as technical replicates. In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases. The most frequently recurrent gene mutations in clinical samples were associated with an elevated C > T mutational signature. We found complex rearrangement patterns including intra- and inter-chromosomal rearrangements, singleton, and recurrent gene fusions, and tandem duplications. We observed high molecular discordance for somatic alterations between paired samples consistent with marked heterogeneity of the somatic landscape. The most prevalent copy number calls were focal deletion events in CTCs and metastases. Our results demonstrate the feasibility of an integrated workflow for the identification of a complete repertoire of somatic alterations and highlight the intrapatient genomic differences that occur between CTCs and metastases.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
| | - Daniel Campo
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Tania B. Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA;
| | - Alexander Ring
- Department of Oncology and Hematology, UniversitätsSpital Zürich, Rämistrasse 100, 8091 Zürich, Switzerland;
| | - Janice Lu
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Yvonne Chairez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Yunyun Su
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
| | - Irene Kang
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie E. Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Correspondence: ; Tel.: +1-(323)-442-8140
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21
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de Souza MM, Zerlotini A, Rocha MIP, Bruscadin JJ, Diniz WJDS, Cardoso TF, Cesar ASM, Afonso J, Andrade BGN, Mudadu MDA, Mokry FB, Tizioto PC, de Oliveira PSN, Niciura SCM, Coutinho LL, Regitano LCDA. Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. Sci Rep 2020; 10:10204. [PMID: 32576896 PMCID: PMC7311436 DOI: 10.1038/s41598-020-67089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/20/2020] [Indexed: 11/09/2022] Open
Abstract
Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.
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Affiliation(s)
- Marcela Maria de Souza
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, SP, Brazil
| | - Marina Ibelli Pereira Rocha
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jennifer Jessica Bruscadin
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Wellison Jarles da Silva Diniz
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Juliana Afonso
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Fabiana Barichello Mokry
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
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22
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Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives. Sci Rep 2020; 10:3939. [PMID: 32127560 PMCID: PMC7054319 DOI: 10.1038/s41598-020-60466-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Although human induced pluripotent stem cell (hiPSC) lines are karyotypically normal, they retain the potential for mutation in the genome. Accordingly, intensive and relevant quality controls for clinical-grade hiPSCs remain imperative. As a conceptual approach, we performed RNA-seq-based broad-range genetic quality tests on GMP-compliant human leucocyte antigen (HLA)-homozygous hiPSCs and their derivatives under postdistribution conditions to investigate whether sequencing data could provide a basis for future quality control. We found differences in the degree of single-nucleotide polymorphism (SNP) occurring in cells cultured at three collaborating institutes. However, the cells cultured at each centre showed similar trends, in which more SNPs occurred in late-passage hiPSCs than in early-passage hiPSCs after differentiation. In eSNP karyotyping analysis, none of the predicted copy number variations (CNVs) were identified, which confirmed the results of SNP chip-based CNV analysis. HLA genotyping analysis revealed that each cell line was homozygous for HLA-A, HLA-B, and DRB1 and heterozygous for HLA-DPB type. Gene expression profiling showed a similar differentiation ability of early- and late-passage hiPSCs into cardiomyocyte-like, hepatic-like, and neuronal cell types. However, time-course analysis identified five clusters showing different patterns of gene expression, which were mainly related to the immune response. In conclusion, RNA-seq analysis appears to offer an informative genetic quality testing approach for such cell types and allows the early screening of candidate hiPSC seed stocks for clinical use by facilitating safety and potential risk evaluation.
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23
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Jang H, Park S, Kim J, Kim JH, Kim SY, Cho S, Park SG, Park BC, Kim S, Kim JH. The Tumor Suppressor, p53, Negatively Regulates Non-Canonical NF-κB Signaling through miRNAInduced Silencing of NF-κB-Inducing Kinase. Mol Cells 2020; 43:23-33. [PMID: 31870133 PMCID: PMC6999715 DOI: 10.14348/molcells.2019.0239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 01/06/2023] Open
Abstract
NF-κB signaling through both canonical and non-canonical pathways plays a central role in immune responses and inflammation. NF-κB-inducing kinase (NIK) stabilization is a key step in activation of the non-canonical pathway and its dysregulation implicated in various hematologic malignancies. The tumor suppressor, p53, is an established cellular gatekeeper of proliferation. Abnormalities of the TP53 gene have been detected in more than half of all human cancers. While the non-canonical NF-κB and p53 pathways have been explored for several decades, no studies to date have documented potential cross-talk between these two cancer-related mechanisms. Here, we demonstrate that p53 negatively regulates NIK in an miRNA-dependent manner. Overexpression of p53 decreased the levels of NIK, leading to inhibition of the non-canonical NF-κB pathway. Conversely, its knockdown led to increased levels of NIK, IKKα phosphorylation, and p100 processing. Additionally, miR-34b induced by nutlin-3 directly targeted the coding sequences (CDS) of NIK. Treatment with anti-miR-34b-5p augmented NIK levels and subsequent non-canonical NF-κB signaling. Our collective findings support a novel cross-talk mechanism between non-canonical NF-κB and p53.
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Affiliation(s)
- Hanbit Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
| | - Seulki Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113,
Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Jong Hwan Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141,
Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141,
Korea
| | - Sayeon Cho
- College of Pharmacy, Chung-Ang University, Seoul 06974,
Korea
| | - Sung Goo Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113,
Korea
| | - Byoung Chul Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113,
Korea
| | - Sunhong Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113,
Korea
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113,
Korea
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24
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Abstract
BACKGROUND Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20% of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. METHODS To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer's guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. RESULTS MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. CONCLUSION The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.
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25
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Wang H, Lou D, Wang Z. Crosstalk of Genetic Variants, Allele-Specific DNA Methylation, and Environmental Factors for Complex Disease Risk. Front Genet 2019; 9:695. [PMID: 30687383 PMCID: PMC6334214 DOI: 10.3389/fgene.2018.00695] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 12/12/2018] [Indexed: 01/04/2023] Open
Abstract
Over the past decades, genome-wide association studies (GWAS) have identified thousands of phenotype-associated DNA sequence variants for potential explanations of inter-individual phenotypic differences and disease susceptibility. However, it remains a challenge for translating the associations into causative mechanisms for complex diseases, partially due to the involved variants in the noncoding regions and the inconvenience of functional studies in human population samples. So far, accumulating evidence has suggested a complex crosstalk among genetic variants, allele-specific binding of transcription factors (ABTF), and allele-specific DNA methylation patterns (ASM), as well as environmental factors for disease risk. This review aims to summarize the current studies regarding the interactions of the aforementioned factors with a focus on epigenetic insights. We present two scenarios of single nucleotide polymorphisms (SNPs) in coding regions and non-coding regions for disease risk, via potentially impacting epigenetic patterns. While a SNP in a coding region may confer disease risk via altering protein functions, a SNP in non-coding region may cause diseases, via SNP-altering ABTF, ASM, and allele-specific gene expression (ASE). The allelic increases or decreases of gene expression are key for disease risk during development. Such ASE can be achieved via either a "SNP-introduced ABTF to ASM" or a "SNP-introduced ASM to ABTF." Together with our additional in-depth review on insulator CTCF, we are convinced to propose a working model that the small effect of a SNP acts through altered ABTF and/or ASM, for ASE and eventual disease outcome (named as a "SNP intensifier" model). In summary, the significance of complex crosstalk among genetic factors, epigenetic patterns, and environmental factors requires further investigations for disease susceptibility.
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Affiliation(s)
- Huishan Wang
- Laboratory of Human Environmental Epigenome, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
- Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dan Lou
- Laboratory of Human Environmental Epigenome, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Zhibin Wang
- Laboratory of Human Environmental Epigenome, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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26
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Abstract
Allele-specific expression arises when transcriptional activity at the different alleles of a gene differs considerably. Although extensive research has been carried out to detect and characterize this phenomenon, the landscape of allele-specific expression in cancer is still poorly understood. In this chapter, we describe a fast and reliable analysis pipeline to study allele-specific expression in cancer using next-generation sequencing data. The pipeline provides a gene-level analysis approach that exploits paired germline DNA and tumor RNA sequencing data and benefits from parallel computation resources when available.
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Affiliation(s)
- Alessandro Romanel
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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27
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Liu Z, Dong X, Li Y. A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer. Front Genet 2018; 9:570. [PMID: 30538721 PMCID: PMC6277598 DOI: 10.3389/fgene.2018.00570] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/06/2018] [Indexed: 12/30/2022] Open
Abstract
Accumulating evidence from small-scale studies has suggested that allele-specific expression (ASE) plays an important role in tumor initiation and progression. However, little is known about genome-wide ASE in tumors. In this study, we conducted a comprehensive analysis of ASE in individuals with colorectal cancer (CRC) on a genome-wide scale. We identified 5.4 thousand genome-wide ASEs of single nucleotide variations (SNVs) from tumor and normal tissues of 59 individuals with CRC. We observed an increased ASE level in tumor samples and the ASEs enriched as hotspots on the genome. Around 63% of the genes located there were previously reported to contain complex regulatory elements, e.g., human leukocyte antigen (HLA), or were implicated in tumor progression. Focussing on the allelic expression of somatic mutations, we found that 37.5% of them exhibited ASE, and genes harboring such somatic mutations, were enriched in important pathways implicated in cancers. In addition, by comparing the expected and observed ASE events in tumor samples, we identified 50 tumor specific ASEs which possibly contributed to the somatic events in the regulatory regions of the genes and significantly enriched known cancer driver genes. By analyzing CRC ASEs from several perspectives, we provided a systematic understanding of how ASE is implicated in both tumor and normal tissues and will be of critical value in guiding ASE studies in cancer.
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Affiliation(s)
- Zhi Liu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
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28
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Defining essential genes for human pluripotent stem cells by CRISPR-Cas9 screening in haploid cells. Nat Cell Biol 2018; 20:610-619. [PMID: 29662178 DOI: 10.1038/s41556-018-0088-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/20/2018] [Indexed: 12/20/2022]
Abstract
The maintenance of pluripotency requires coordinated expression of a set of essential genes. Using our recently established haploid human pluripotent stem cells (hPSCs), we generated a genome-wide loss-of-function library targeting 18,166 protein-coding genes to define the essential genes in hPSCs. With this we could allude to an intrinsic bias of essentiality across cellular compartments, uncover two opposing roles for tumour suppressor genes and link autosomal-recessive disorders with growth-retardation phenotypes to early embryogenesis. hPSC-enriched essential genes mainly encode transcription factors and proteins related to cell-cycle and DNA-repair, revealing that a quarter of the nuclear factors are essential for normal growth. Our screen also led to the identification of growth-restricting genes whose loss of function provides a growth advantage to hPSCs, highlighting the role of the P53-mTOR pathway in this context. Overall, we have constructed an atlas of essential and growth-restricting genes in hPSCs, revealing key aspects of cellular essentiality and providing a reference for future studies on human pluripotency.
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29
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Tian L, Khan A, Ning Z, Yuan K, Zhang C, Lou H, Yuan Y, Xu S. Genome-wide comparison of allele-specific gene expression between African and European populations. Hum Mol Genet 2018; 27:1067-1077. [DOI: 10.1093/hmg/ddy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lei Tian
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Asifullah Khan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200 KP, Pakistan
| | - Zhilin Ning
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyi Lou
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Yuan Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
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30
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Chen M, Zhang J, Sampieri K, Clohessy JG, Mendez L, Gonzalez-Billalabeitia E, Liu XS, Lee YR, Fung J, Katon JM, Menon AV, Webster KA, Ng C, Palumbieri MD, Diolombi MS, Breitkopf SB, Teruya-Feldstein J, Signoretti S, Bronson RT, Asara JM, Castillo-Martin M, Cordon-Cardo C, Pandolfi PP. An aberrant SREBP-dependent lipogenic program promotes metastatic prostate cancer. Nat Genet 2018; 50:206-218. [PMID: 29335545 DOI: 10.1038/s41588-017-0027-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/01/2017] [Indexed: 12/15/2022]
Abstract
Lipids, either endogenously synthesized or exogenous, have been linked to human cancer. Here we found that PML is frequently co-deleted with PTEN in metastatic human prostate cancer (CaP). We demonstrated that conditional inactivation of Pml in the mouse prostate morphs indolent Pten-null tumors into lethal metastatic disease. We identified MAPK reactivation, subsequent hyperactivation of an aberrant SREBP prometastatic lipogenic program, and a distinctive lipidomic profile as key characteristic features of metastatic Pml and Pten double-null CaP. Furthermore, targeting SREBP in vivo by fatostatin blocked both tumor growth and distant metastasis. Importantly, a high-fat diet (HFD) induced lipid accumulation in prostate tumors and was sufficient to drive metastasis in a nonmetastatic Pten-null mouse model of CaP, and an SREBP signature was highly enriched in metastatic human CaP. Thus, our findings uncover a prometastatic lipogenic program and lend direct genetic and experimental support to the notion that a Western HFD can promote metastasis.
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Affiliation(s)
- Ming Chen
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jiangwen Zhang
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Katia Sampieri
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,GSK Vaccines, Antigen Identification and Molecular Biology, Siena, Italy
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Preclinical Murine Pharmacogenetics Facility and Mouse Hospital, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lourdes Mendez
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Enrique Gonzalez-Billalabeitia
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xue-Song Liu
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yu-Ru Lee
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jacqueline Fung
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jesse M Katon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Archita Venugopal Menon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kaitlyn A Webster
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Christopher Ng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Maria Dilia Palumbieri
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Moussa S Diolombi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Julie Teruya-Feldstein
- Department of Pathology, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mireia Castillo-Martin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Champalimaud Center for the Unknown, Lisbon, Portugal
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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31
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Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F. Inherited determinants of early recurrent somatic mutations in prostate cancer. Nat Commun 2017; 8:48. [PMID: 28663546 PMCID: PMC5491529 DOI: 10.1038/s41467-017-00046-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/13/2017] [Accepted: 04/28/2017] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer is a highly heritable molecularly and clinically heterogeneous disease. To discover germline events involved in prostate cancer predisposition, we develop a computational approach to nominate heritable facilitators of somatic genomic events in the context of the androgen receptor signaling. Here, we use a ranking score and benign prostate transcriptomes to identify a non-coding polymorphic regulatory element at 7p14.3 that associates with DNA repair and hormone-regulated transcript levels and with an early recurrent prostate cancer-specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene. The locus shows allele-specific activity that is concomitantly modulated by androgen receptor and by CCAAT/enhancer-binding protein (C/EBP) beta (CEBPB). Deletion of this locus via CRISPR-Cas9 leads to deregulation of the genes predicted to interact with the 7p14.3 locus by Hi-C chromosome conformation capture data. This study suggests that a polymorphism at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone-dependent DNA damage response. Prostate cancer is a heterogeneous disease, and many cases show somatic mutations of SPOP. Here, the authors show that a non-coding polymorphic regulatory element at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone dependent DNA damage response.
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Affiliation(s)
- Alessandro Romanel
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Sonia Garritano
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Blerta Stringa
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Mirjam Blattner
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Davide Dalfovo
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Dimple Chakravarty
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA
| | - David Soong
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kellie A Cotter
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA
| | - Gianluca Petris
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Paola Gasperini
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Anna Cereseto
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA
| | - Ekta Khurana
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Alberto Inga
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Mark A Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Francesca Demichelis
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, Italy. .,Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.
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Kim D, Jung YG, Roh S. Microarray analysis of embryo-derived bovine pluripotent cells: The vulnerable state of bovine embryonic stem cells. PLoS One 2017; 12:e0173278. [PMID: 28257460 PMCID: PMC5336296 DOI: 10.1371/journal.pone.0173278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/17/2017] [Indexed: 12/20/2022] Open
Abstract
Although there are many studies about pluripotent stem cells, little is known about pluripotent pathways and the difficulties of maintaining the pluripotency of bovine cells in vitro. Here, we investigated differently expressed genes (DEG) in bovine embryo-derived stem-like cells (eSLCs) from various origins to validate their distinct characteristics of pluripotency and differentiation. We identified core pluripotency markers and additional markers which were not determined as pluripotency markers yet in bovine eSLCs. Using the KEGG database, TGFβ, WNT, and LIF signaling were related to the maintenance of pluripotency. In contrast, some DEGs related to the LIF pathway were down-regulated, suggesting that reactivation of the pathway may be required for the establishment of true bovine embryonic stem cells (ESCs). Interestingly, oncogenes were co-down-regulated, while tumor suppressor genes were co-up-regulated in eSLCs, implying that this pattern may induce abnormal teratomas. These data analyses of signaling pathways provide essential information on authentic ESCs in addition to providing evidence for pluripotency in bovine eSLCs.
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Affiliation(s)
- Daehwan Kim
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, Seoul National University School of Dentistry, Seoul, Republic of Korea
| | | | - Sangho Roh
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, Seoul National University School of Dentistry, Seoul, Republic of Korea
- * E-mail:
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33
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Kim W, Ludlow AT, Min J, Robin JD, Stadler G, Mender I, Lai TP, Zhang N, Wright WE, Shay JW. Regulation of the Human Telomerase Gene TERT by Telomere Position Effect-Over Long Distances (TPE-OLD): Implications for Aging and Cancer. PLoS Biol 2016; 14:e2000016. [PMID: 27977688 PMCID: PMC5169358 DOI: 10.1371/journal.pbio.2000016] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/10/2016] [Indexed: 02/07/2023] Open
Abstract
Telomerase is expressed in early human development and then becomes silenced in most normal tissues. Because ~90% of primary human tumors express telomerase and generally maintain very short telomeres, telomerase is carefully regulated, particularly in large, long-lived mammals. In the current report, we provide substantial evidence for a new regulatory control mechanism of the rate limiting catalytic protein component of telomerase (hTERT) that is determined by the length of telomeres. We document that normal, young human cells with long telomeres have a repressed hTERT epigenetic status (chromatin and DNA methylation), but the epigenetic status is altered when telomeres become short. The change in epigenetic status correlates with altered expression of TERT and genes near to TERT, indicating a change in chromatin. Furthermore, we identified a chromosome 5p telomere loop to a region near TERT in human cells with long telomeres that is disengaged with increased cell divisions as telomeres progressively shorten. Finally, we provide support for a role of the TRF2 protein, and possibly TERRA, in the telomere looping maintenance mechanism through interactions with interstitial TTAGGG repeats. This provides new insights into how the changes in genome structure during replicative aging result in an increased susceptibility to age-related diseases and cancer prior to the initiation of a DNA damage signal.
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Affiliation(s)
- Wanil Kim
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Andrew T Ludlow
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jaewon Min
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jerome D Robin
- Faculté de Médecine, Tour Pasteur 8éme Étage, Nice, France
| | - Guido Stadler
- Berkeley Lights, Inc., Emeryville, California, United States of America
| | - Ilgen Mender
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tsung-Po Lai
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ning Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Akutsu H, Nasu M, Morinaga S, Motoyama T, Homma N, Machida M, Yamazaki-Inoue M, Okamura K, Nakabayashi K, Takada S, Nakamura N, Kanzaki S, Hata K, Umezawa A. In vivo maturation of human embryonic stem cell-derived teratoma over time. Regen Ther 2016; 5:31-39. [PMID: 31245498 PMCID: PMC6581884 DOI: 10.1016/j.reth.2016.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/19/2016] [Indexed: 12/31/2022] Open
Abstract
Transformation of human embryonic stem cells (hESC) is of interest to scientists who use them as a raw material for cell-processed therapeutic products. However, the WHO and ICH guidelines provide only study design advice and general principles for tumorigenicity tests. In this study, we performed in vivo tumorigenicity tests (teratoma formation) and genome-wide sequencing analysis of undifferentiated hESCs i.e. SEES-1, -2 and -3 cells. We followed up with teratoma formation histopathologically after subcutaneous injection of SEES cells into immunodeficient mice in a qualitative manner and investigated the transforming potential of the teratomas. Maturity of SEES-teratomas perceptibly increased after long-term implantation, while areas of each tissue component remained unchanged. We found neither atypical cells/structures nor cancer in the teratomas even after long-term implantation. The teratomas generated by SEES cells matured histologically over time and did not increase in size. We also analyzed genomic structures and sequences of SEES cells during cultivation by SNP bead arrays and next-generation sequencing, respectively. The nucleotide substitution rate was 3.1 × 10-9, 4.0 × 10-9, and 4.6 × 10-9 per each division in SEES-1, SEES-2, and SEES-3 cells, respectively. Heterozygous single-nucleotide variations were detected, but no significant homologous mutations were found. Taken together, these results imply that SEES-1, -2, and -3 cells do not exhibit in vivo transformation and in vitro genomic instability.
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Affiliation(s)
- Hidenori Akutsu
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Michiyo Nasu
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | | | - Teiichi Motoyama
- Department of Pathology, Yamagata University School of Medicine, Yamagata, Japan
| | - Natsumi Homma
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- School of BioMedical Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masakazu Machida
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mayu Yamazaki-Inoue
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Naoko Nakamura
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seiichi Kanzaki
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
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Takemoto K, Ii M, Nishizuka SS. Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160267. [PMID: 27703689 PMCID: PMC5043308 DOI: 10.1098/rsos.160267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/04/2016] [Indexed: 05/23/2023]
Abstract
Elucidation of tumour suppression mechanisms is a major challenge in cancer biology. Therefore, Peto's paradox, or low cancer incidence in large animals, has attracted focus. According to the gene-abundance hypothesis, which considers the increase/decrease in cancer-related genes with body size, researchers evaluated the associations between gene abundance and body size. However, previous studies only focused on a few specific gene functions and have ignored the alternative hypothesis (metabolic rate hypothesis): in this hypothesis, the cellular metabolic rate and subsequent oxidative stress decreases with increasing body size. In this study, we have elected to explore the gene-abundance hypothesis taking into account the metabolic rate hypothesis. Thus, we comprehensively investigated the correlation between the number of genes in various functional categories and body size while at the same time correcting for the mass-specific metabolic rate (Bc). A number of gene functions that correlated with body size were initially identified, but they were found to be artefactual due to the decrease in Bc with increasing body size. By contrast, immune system-related genes were found to increase with increasing body size when the correlation included this correction for Bc. These findings support the gene-abundance hypothesis and emphasize the importance of also taking into account the metabolic rate when evaluating gene abundance-body size relationships. This finding may be useful for understanding cancer evolution and tumour suppression mechanisms as well as for determining cancer-related genes and functions.
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Affiliation(s)
- Kazuhiro Takemoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Masato Ii
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Satoshi S. Nishizuka
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
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36
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Yeo S, Hodgkinson CA, Zhou Z, Jung J, Leung M, Yuan Q, Goldman D. The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits. BMC Genomics 2016; 17:620. [PMID: 27515598 PMCID: PMC4982227 DOI: 10.1186/s12864-016-2922-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/07/2016] [Indexed: 12/16/2022] Open
Abstract
Background Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL’s for complex phenotypes. Results We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Conclusions Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2922-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seungeun Yeo
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Colin A Hodgkinson
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Zhifeng Zhou
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Jeesun Jung
- Laboratory of Epidemiology and Biometry, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Ming Leung
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Qiaoping Yuan
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - David Goldman
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA.
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Darbro BW, Singh R, Zimmerman MB, Mahajan VB, Bassuk AG. Autism Linked to Increased Oncogene Mutations but Decreased Cancer Rate. PLoS One 2016; 11:e0149041. [PMID: 26934580 PMCID: PMC4774916 DOI: 10.1371/journal.pone.0149041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/25/2016] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is one phenotypic aspect of many monogenic, hereditary cancer syndromes. Pleiotropic effects of cancer genes on the autism phenotype could lead to repurposing of oncology medications to treat this increasingly prevalent neurodevelopmental condition for which there is currently no treatment. To explore this hypothesis we sought to discover whether autistic patients more often have rare coding, single-nucleotide variants within tumor suppressor and oncogenes and whether autistic patients are more often diagnosed with neoplasms. Exome-sequencing data from the ARRA Autism Sequencing Collaboration was compared to that of a control cohort from the Exome Variant Server database revealing that rare, coding variants within oncogenes were enriched for in the ARRA ASD cohort (p<1.0 x 10(-8)). In contrast, variants were not significantly enriched in tumor suppressor genes. Phenotypically, children and adults with ASD exhibited a protective effect against cancer, with a frequency of 1.3% vs. 3.9% (p<0.001), but the protective effect decreased with age. The odds ratio of neoplasm for those with ASD relative to controls was 0.06 (95% CI: 0.02, 0.19; p<0.0001) in the 0 to 14 age group; 0.35 (95% CI: 0.14, 0.87; p = 0.024) in the 15 to 29 age group; 0.41 (95% CI: 0.15, 1.17; p = 0.095) in the 30 to 54 age group; and 0.49 (95% CI: 0.14, 1.74; p = 0.267) in those 55 and older. Both males and females demonstrated the protective effect. These findings suggest that defects in cellular proliferation, and potentially senescence, might influence both autism and neoplasm, and already approved drugs targeting oncogenic pathways might also have therapeutic value for treating autism.
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Affiliation(s)
- Benjamin W. Darbro
- Department of Pediatrics, Division of Medical Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- The Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (BD); (AB)
| | - Rohini Singh
- Department of Pediatrics, Division of Medical Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Pediatrics, Division of Pediatric Hematology/Oncology/BMT, University of Iowa, Iowa City, Iowa, United States of America
| | - M. Bridget Zimmerman
- Department of Biostatistics, University of Iowa College of Public Health, Iowa City, Iowa, United States of America
| | - Vinit B. Mahajan
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexander G. Bassuk
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Pediatrics, Division of Neurology, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, Iowa, United States of America
- University of Iowa eHealth and eNovation Center, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (BD); (AB)
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Touat M, Dhermain F, André F, Sanson M. Adapting the drivers to the road: a new strategy for cancer evolution? Ann Oncol 2015; 26:827-829. [DOI: 10.1093/annonc/mdv137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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39
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Romanel A, Lago S, Prandi D, Sboner A, Demichelis F. ASEQ: fast allele-specific studies from next-generation sequencing data. BMC Med Genomics 2015; 8:9. [PMID: 25889339 PMCID: PMC4363342 DOI: 10.1186/s12920-015-0084-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/12/2015] [Indexed: 11/17/2022] Open
Abstract
Background Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. Such studies often present with computationally challenging burdens that hinder genome-wide investigations across large datasets that are now becoming available through the 1,000 Genomes Project and The Cancer Genome Atlas (TCGA) initiatives. Results We present ASEQ, a tool to perform gene-level allele-specific expression (ASE) analysis from paired genomic and transcriptomic NGS data without requiring paternal and maternal genome data. ASEQ offers an easy-to-use set of modes that transparently to the user takes full advantage of a built-in fast computational engine. We report its performances on a set of 20 individuals from the 1,000 Genomes Project and show its detection power on imprinted genes. Next we demonstrate high level of ASE calls concordance when comparing it to AlleleSeq and MBASED tools. Finally, using a prostate cancer dataset we report on a higher fraction of ASE genes with respect to healthy individuals and show allele-specific events nominated by ASEQ in genes that are implicated in the disease. Conclusions ASEQ can be used to rapidly and reliably screen large NGS datasets for the identification of allele specific features. It can be integrated in any NGS pipeline and runs on computer systems with multiple CPUs, CPUs with multiple cores or across clusters of machines. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0084-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessandro Romanel
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Sara Lago
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Davide Prandi
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, USA. .,Institute for Computational Biomedicine, Weill Cornell Medical College, New York, USA. .,Institute for Precision Medicine, Weill Cornell Medical College & New York Presbyterian Hospital, New York, USA.
| | - Francesca Demichelis
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy. .,Institute for Computational Biomedicine, Weill Cornell Medical College, New York, USA. .,Institute for Precision Medicine, Weill Cornell Medical College & New York Presbyterian Hospital, New York, USA.
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40
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Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD, Etchin J, Lawton L, Sallan SE, Silverman LB, Loh ML, Hunger SP, Sanda T, Young RA, Look AT. Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science 2014; 346:1373-7. [PMID: 25394790 PMCID: PMC4720521 DOI: 10.1126/science.1259037] [Citation(s) in RCA: 581] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In certain human cancers, the expression of critical oncogenes is driven from large regulatory elements, called super-enhancers, that recruit much of the cell's transcriptional apparatus and are defined by extensive acetylation of histone H3 lysine 27 (H3K27ac). In a subset of T-cell acute lymphoblastic leukemia (T-ALL) cases, we found that heterozygous somatic mutations are acquired that introduce binding motifs for the MYB transcription factor in a precise noncoding site, which creates a super-enhancer upstream of the TAL1 oncogene. MYB binds to this new site and recruits its H3K27 acetylase-binding partner CBP, as well as core components of a major leukemogenic transcriptional complex that contains RUNX1, GATA-3, and TAL1 itself. Additionally, most endogenous super-enhancers found in T-ALL cells are occupied by MYB and CBP, which suggests a general role for MYB in super-enhancer initiation. Thus, this study identifies a genetic mechanism responsible for the generation of oncogenic super-enhancers in malignant cells.
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Affiliation(s)
- Marc R Mansour
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Lars Anders
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Alla Berezovskaya
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alejandro Gutierrez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Division of Pediatric Hematology-Oncology, Boston Children's Hospital, MA 02115, USA
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Julia Etchin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Lee Lawton
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Division of Pediatric Hematology-Oncology, Boston Children's Hospital, MA 02115, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Division of Pediatric Hematology-Oncology, Boston Children's Hospital, MA 02115, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California San Francisco, CA 94143, USA
| | - Stephen P Hunger
- Pediatric Hematology/Oncology/BMT, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, and Department of Medicine, Yong Loo Lin School of Medicine, 117599, Singapore
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Division of Pediatric Hematology-Oncology, Boston Children's Hospital, MA 02115, USA.
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Wakimoto H, Tanaka S, Curry WT, Loebel F, Zhao D, Tateishi K, Chen J, Klofas LK, Lelic N, Kim JC, Dias-Santagata D, Ellisen LW, Borger DR, Fendt SM, Heiden MGV, Batchelor TT, Iafrate AJ, Cahill DP, Chi AS. Targetable signaling pathway mutations are associated with malignant phenotype in IDH-mutant gliomas. Clin Cancer Res 2014; 20:2898-909. [PMID: 24714777 PMCID: PMC4070445 DOI: 10.1158/1078-0432.ccr-13-3052] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE Isocitrate dehydrogenase (IDH) gene mutations occur in low-grade and high-grade gliomas. We sought to identify the genetic basis of malignant phenotype heterogeneity in IDH-mutant gliomas. METHODS We prospectively implanted tumor specimens from 20 consecutive IDH1-mutant glioma resections into mouse brains and genotyped all resection specimens using a CLIA-certified molecular panel. Gliomas with cancer driver mutations were tested for sensitivity to targeted inhibitors in vitro. Associations between genomic alterations and outcomes were analyzed in patients. RESULTS By 10 months, 8 of 20 IDH1-mutant gliomas developed intracerebral xenografts. All xenografts maintained mutant IDH1 and high levels of 2-hydroxyglutarate on serial transplantation. All xenograft-producing gliomas harbored "lineage-defining" mutations in CIC (oligodendroglioma) or TP53 (astrocytoma), and 6 of 8 additionally had activating mutations in PIK3CA or amplification of PDGFRA, MET, or N-MYC. Only IDH1 and CIC/TP53 mutations were detected in non-xenograft-forming gliomas (P = 0.0007). Targeted inhibition of the additional alterations decreased proliferation in vitro. Moreover, we detected alterations in known cancer driver genes in 13.4% of IDH-mutant glioma patients, including PIK3CA, KRAS, AKT, or PTEN mutation or PDGFRA, MET, or N-MYC amplification. IDH/CIC mutant tumors were associated with PIK3CA/KRAS mutations whereas IDH/TP53 tumors correlated with PDGFRA/MET amplification. Presence of driver alterations at progression was associated with shorter subsequent progression-free survival (median 9.0 vs. 36.1 months; P = 0.0011). CONCLUSION A subset of IDH-mutant gliomas with mutations in driver oncogenes has a more malignant phenotype in patients. Identification of these alterations may provide an opportunity for use of targeted therapies in these patients. Clin Cancer Res; 20(11); 2898-909. ©2014 AACR.
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Affiliation(s)
- Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Shota Tanaka
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Division of Hematology/Oncology, Department of Neurology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - William T. Curry
- Department of Neurosurgery, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Franziska Loebel
- Department of Neurosurgery, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Dan Zhao
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Division of Hematology/Oncology, Department of Neurology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Kensuke Tateishi
- Department of Neurosurgery, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Juxiang Chen
- Translational Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lindsay K. Klofas
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Division of Hematology/Oncology, Department of Neurology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Nina Lelic
- Department of Neurosurgery, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - James C. Kim
- Department of Pathology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Dora Dias-Santagata
- Translational Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Leif W. Ellisen
- Translational Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Darrell R. Borger
- Translational Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Sarah-Maria Fendt
- Vesalius Research Center, VIB, and Department of Oncology, KU Leuven, Leuven, Belgium
| | - Matthew G. Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tracy T. Batchelor
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Division of Hematology/Oncology, Department of Neurology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - A. John Iafrate
- Translational Research Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Andrew S. Chi
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Division of Hematology/Oncology, Department of Neurology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Translational Neuro-Oncology Laboratory, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
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42
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Non-invasive in vivo assessment of IDH1 mutational status in glioma. Nat Commun 2014; 4:2429. [PMID: 24019001 DOI: 10.1038/ncomms3429] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/12/2013] [Indexed: 12/19/2022] Open
Abstract
Gain-of-function mutations of the isocitrate dehydrogenase 1 (IDH1) gene are among the most prevalent in low-grade gliomas and secondary glioblastoma. They lead to intracellular accumulation of the oncometabolite 2-hydroxyglutarate, represent an early pathogenic event and are considered a therapeutic target. Here we show, in this proof-of-concept study, that [1-(13)C] α-ketoglutarate can serve as a metabolic imaging agent for non-invasive, real-time, in vivo monitoring of mutant IDH1 activity, and can inform on IDH1 status. Using (13)C magnetic resonance spectroscopy in combination with dissolution dynamic nuclear polarization, the metabolic fate of hyperpolarized [1-(13)C] α-ketoglutarate is studied in isogenic glioblastoma cells that differ only in their IDH1 status. In lysates and tumours that express wild-type IDH1, only hyperpolarized [1-(13)C] α-ketoglutarate can be detected. In contrast, in cells that express mutant IDH1, hyperpolarized [1-(13)C] 2-hydroxyglutarate is also observed, both in cell lysates and in vivo in orthotopic tumours.
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43
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Smith RM, Webb A, Papp AC, Newman LC, Handelman SK, Suhy A, Mascarenhas R, Oberdick J, Sadee W. Whole transcriptome RNA-Seq allelic expression in human brain. BMC Genomics 2013; 14:571. [PMID: 23968248 PMCID: PMC3765493 DOI: 10.1186/1471-2164-14-571] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/16/2013] [Indexed: 01/27/2023] Open
Abstract
Background Measuring allelic RNA expression ratios is a powerful approach for detecting cis-acting regulatory variants, RNA editing, loss of heterozygosity in cancer, copy number variation, and allele-specific epigenetic gene silencing. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying allelic expression imbalance (AEI), but numerous factors bias allelic RNA ratio measurements. Here, we compare RNA-Seq allelic ratios measured in nine different human brain regions with a highly sensitive and accurate SNaPshot measure of allelic RNA ratios, identifying factors affecting reliable allelic ratio measurement. Accounting for these factors, we subsequently surveyed the variability of RNA editing across brain regions and across individuals. Results We find that RNA-Seq allelic ratios from standard alignment methods correlate poorly with SNaPshot, but applying alternative alignment strategies and correcting for observed biases significantly improves correlations. Deploying these methods on a transcriptome-wide basis in nine brain regions from a single individual, we identified genes with AEI across all regions (SLC1A3, NHP2L1) and many others with region-specific AEI. In dorsolateral prefrontal cortex (DLPFC) tissues from 14 individuals, we found evidence for frequent regulatory variants affecting RNA expression in tens to hundreds of genes, depending on stringency for assigning AEI. Further, we find that the extent and variability of RNA editing is similar across brain regions and across individuals. Conclusions These results identify critical factors affecting allelic ratios measured by RNA-Seq and provide a foundation for using this technology to screen allelic RNA expression on a transcriptome-wide basis. Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain. With respect to RNA editing, the similarities within and between individuals leads us to conclude that this post-transcriptional process is under heavy regulatory influence to maintain an optimal degree of editing for normal biological function.
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Affiliation(s)
- Ryan M Smith
- Department of Pharmacology, Program in Pharmacogenomics; College of Medicine, The Ohio State University Wexner Medical Center, 5184A Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, USA.
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Horbinski C. What do we know about IDH1/2 mutations so far, and how do we use it? Acta Neuropathol 2013; 125:621-36. [PMID: 23512379 DOI: 10.1007/s00401-013-1106-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/09/2013] [Indexed: 12/16/2022]
Abstract
Whole genome analyses have facilitated the discovery of clinically relevant genetic alterations in a variety of diseases, most notably cancer. A prominent example of this was the discovery of mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) in a sizeable proportion of gliomas and some other neoplasms. Herein the normal functions of these enzymes, how the mutations alter their catalytic properties, the effects of their D-2-hydroxyglutarate metabolite, technical considerations in diagnostic neuropathology, implications about prognosis and therapeutic considerations, and practical applications and controversies regarding IDH1/2 mutation testing are discussed.
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Affiliation(s)
- Craig Horbinski
- Department of Pathology, University of Kentucky, 307 Combs Cancer Research Facility, 800 Rose Street, Lexington, KY 40536, USA.
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Germline allele-specific expression of DAPK1 in chronic lymphocytic leukemia. PLoS One 2013; 8:e55261. [PMID: 23383130 PMCID: PMC3557246 DOI: 10.1371/journal.pone.0055261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/20/2012] [Indexed: 01/10/2023] Open
Abstract
We previously reported a rare germline variant (c.1-6531) that resulted in allele–specific expression (ASE) of death-associated protein kinase 1 (DAPK1) and predisposition to chronic lymphocytic leukemia (CLL). We investigated a cohort of CLL patients lacking this mutation for the presence of ASE of DAPK1. We developed a novel strategy that combines single-nucleotide primer extension (SNuPE) with MALDI-TOF mass spectrometry, and detected germline DAPK1 ASE in 17 out of 120 (14.2%) CLL patients associated with a trend towards younger age at diagnosis. ASE was absent in 63 healthy controls. Germline cells of CLL patients with ASE showed increased levels of DNA methylation in the promoter region, however, neither genetic nor further epigenetic aberrations could be identified in the DAPK1 5′ upstream regulatory region, within distinct exons or in the 3′-UTR. We identified B-lymphoid malignancy related cell line models harboring allelic imbalance and found that allele-specific methylation in DAPK1 is associated with ASE. Our data indicate that ASE at the DAPK1 gene locus is a recurrent event, mediated by epigenetic mechanisms and potentially predisposing to CLL.
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46
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Flanagan S, Lee M, Li CCY, Suter CM, Buckland ME. Promoter Methylation Analysis of IDH Genes in Human Gliomas. Front Oncol 2012; 2:193. [PMID: 23267435 PMCID: PMC3525876 DOI: 10.3389/fonc.2012.00193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/29/2012] [Indexed: 01/22/2023] Open
Abstract
Mutations in isocitrate dehydrogenase (IDH)-1 or -2 are found in the majority of WHO grade II and III astrocytomas and oligodendrogliomas, and secondary glioblastomas. Almost all described mutations are heterozygous missense mutations affecting a conserved arginine residue in the substrate binding site of IDH1 (R132) or IDH2 (R172). But the exact mechanism of IDH mutations in neoplasia is not understood. It has been proposed that IDH mutations impart a “toxic gain-of-function” to the mutant protein, however a dominant-negative effect of mutant IDH has also been described, implying that IDH may function as a tumor suppressor gene. As most, if not all, tumor suppressor genes are inactivated by epigenetic silencing, in a wide variety of tumors, we asked if IDH1 or IDH2 carry the epigenetic signature of a tumor suppressor by assessing cytosine methylation at their promoters. Methylation was quantified in 68 human brain tumors, including both IDH-mutant and IDH wildtype, by bisulfite pyrosequencing. In all tumors examined, CpG methylation levels were less than 8%. Our data demonstrate that inactivation of IDH function through promoter hypermethylation is not common in human gliomas and other brain tumors. These findings do not support a tumor suppressor role for IDH genes in human gliomas.
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Affiliation(s)
- Simon Flanagan
- Discipline of Pathology, University of Sydney Sydney, NSW, Australia ; Department of Neuropathology, Royal Prince Alfred Hospital Sydney, NSW, Australia
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Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, Sinari S, Moses TM, Wong S, Dinh J, Christoforides A, Blum JL, Aitelli CL, Osborne CR, Izatt T, Kurdoglu A, Baker A, Koeman J, Barbacioru C, Sakarya O, De La Vega FM, Siddiqui A, Hoang L, Billings PR, Salhia B, Tolcher AW, Trent JM, Mousses S, Von Hoff D, Carpten JD. Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. Mol Cancer Ther 2012; 12:104-16. [PMID: 23171949 DOI: 10.1158/1535-7163.mct-12-0781] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancer (TNBC) is characterized by the absence of expression of estrogen receptor, progesterone receptor, and HER-2. Thirty percent of patients recur after first-line treatment, and metastatic TNBC (mTNBC) has a poor prognosis with median survival of one year. Here, we present initial analyses of whole genome and transcriptome sequencing data from 14 prospective mTNBC. We have cataloged the collection of somatic genomic alterations in these advanced tumors, particularly those that may inform targeted therapies. Genes mutated in multiple tumors included TP53, LRP1B, HERC1, CDH5, RB1, and NF1. Notable genes involved in focal structural events were CTNNA1, PTEN, FBXW7, BRCA2, WT1, FGFR1, KRAS, HRAS, ARAF, BRAF, and PGCP. Homozygous deletion of CTNNA1 was detected in 2 of 6 African Americans. RNA sequencing revealed consistent overexpression of the FOXM1 gene when tumor gene expression was compared with nonmalignant breast samples. Using an outlier analysis of gene expression comparing one cancer with all the others, we detected expression patterns unique to each patient's tumor. Integrative DNA/RNA analysis provided evidence for deregulation of mutated genes, including the monoallelic expression of TP53 mutations. Finally, molecular alterations in several cancers supported targeted therapeutic intervention on clinical trials with known inhibitors, particularly for alterations in the RAS/RAF/MEK/ERK and PI3K/AKT/mTOR pathways. In conclusion, whole genome and transcriptome profiling of mTNBC have provided insights into somatic events occurring in this difficult to treat cancer. These genomic data have guided patients to investigational treatment trials and provide hypotheses for future trials in this irremediable cancer.
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Affiliation(s)
- David W Craig
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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