1
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Sun R, Liu Z, Lv Y, Yang Y, Yang Y, Xiang Y, Jiang Q, Zhao C, Lv M, Zhang J, Zhang J, Ding C, Zhou D. FOCAD/miR-491-5p, downregulated by EGR1, function as tumor suppressor by inhibiting the proliferation and migration of gastric cancer cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 176:25-37. [PMID: 35788362 DOI: 10.1016/j.pbiomolbio.2022.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Gastric cancer is a common malignant tumor in China; however, its carcinogenesis remains unknown. Focadhesin (FOCAD) is a tumor suppressor gene in gliomas, its expression, role, and mechanism in gastric cancer have not been defined. The aim of the present study was to explore the expression pattern of FOCAD in human normal tissues and cancer tissues and elucidate the role and regulatory mechanism of Early Growth Response 1 (EGR1) in FOCAD and its intron, miR-491-5p, in gastric cancer. Immuno histochemical staining revealed that FOCAD is widely and highly expressed in normal gastric mucosa, but is absent in gastric cancer tissue. Based on an association analysis FOCAD expression was found to be negatively associated with lymph node metastasis (P = 0.004); higher FOCAD levels were associated with longer survival in patients with gastric cancer (P = 0.001). MTT, colony, Transwell chamber, and flow cytometry assays revealed that siFOCAD promoted cell proliferation, growth, and migration, and inhibited apoptosis. Furthermore, bioinformatic analysis, Fluorescence reporter gene and chromatin immunoprecipitation analyses confirmed that EGR1 binds to the promoter and negatively regulates FOCAD and miR-491-5p at the transcriptional level. The overexpression of EGR1 was also found to promote cell proliferation, growth, and migration, and inhibit apoptosis. Overall, FOCAD is specifically overexpressed in the gastric mucosa and is significantly downregulated in gastric cancer. To our knowledge, this is the first study to demonstrate that FOCAD is a tumor suppressor, higher FOCAD levels might be a better prognostic marker of gastric cancer, and FOCAD/miR-491-5p may be negatively regulated by EGR1.
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Affiliation(s)
- Ruifang Sun
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University 76 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Zhigang Liu
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, PR China.
| | - Yun Lv
- Pharmacy Intravenous Admixture Services, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Yanqi Yang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University 76 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, 1 Century Avenue, Xianyang, Shaanxi, PR China
| | - Yu Xiang
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, PR China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Chang'an Zhao
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University 76 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Moqi Lv
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University 76 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Jian Zhang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University 76 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Juan Zhang
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Caixia Ding
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, PR China
| | - Dangxia Zhou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University 76 Yanta West Road, Xi'an, Shaanxi, PR China.
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2
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Sadri F, Hosseini SF, Aghayei A, Fereidouni M, Rezaei Z. The Tumor Suppressor Roles and Mechanisms of MiR-491 in Human Cancers. DNA Cell Biol 2022; 41:810-823. [PMID: 35914029 DOI: 10.1089/dna.2022.0274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that bind to the 3' untranslated region (3'' UTR) of target mRNAs to control gene expression post-transcriptionally. Recent indications have highlighted their important roles in a variety of pathophysiological conditions as well as human malignancies. Dysregulated miRNAs act as tumor suppressor genes or oncogenes in a variety of cancers. MiR-491 has been shown to have a major effect on tumorigenesis in multiple malignancies through binding to specific genes and signaling cascades, thereby preventing cancer progression. This review provides an overview of miR-491 expression in regulatory mechanisms and biological procedures of tumor cells, as well as the prospective possible treatment effects of various types of human cancers.
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Affiliation(s)
- Farzad Sadri
- Student Research Committee, Department of Molecular Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Seyede Fatemeh Hosseini
- Department of Nursing, Tabas School of Nursing, Birjand University of Medical Sciences, Birjand, Iran
| | - Atena Aghayei
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Mohammad Fereidouni
- Department of Medical Immunology, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran.,Cellular and Molecular Research Center, Department of Immunology, Birjand University of Medical Sciences, Birjand, Iran
| | - Zohreh Rezaei
- Cellular and Molecular Research Center, Department of Immunology, Birjand University of Medical Sciences, Birjand, Iran.,Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran
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3
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Moreno Traspas R, Teoh TS, Wong PM, Maier M, Chia CY, Lay K, Ali NA, Larson A, Al Mutairi F, Al-Sannaa NA, Faqeih EA, Alfadhel M, Cheema HA, Dupont J, Bézieau S, Isidor B, Low DY, Wang Y, Tan G, Lai PS, Piloquet H, Joubert M, Kayserili H, Kripps KA, Nahas SA, Wartchow EP, Warren M, Bhavani GS, Dasouki M, Sandoval R, Carvalho E, Ramos L, Porta G, Wu B, Lashkari HP, AlSaleem B, BaAbbad RM, Abreu Ferrão AN, Karageorgou V, Ordonez-Herrera N, Khan S, Bauer P, Cogne B, Bertoli-Avella AM, Vincent M, Girisha KM, Reversade B. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis. Nat Genet 2022; 54:1214-1226. [PMID: 35864190 PMCID: PMC7615854 DOI: 10.1038/s41588-022-01120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Cirrhosis is usually a late-onset and life-threatening disease characterized by fibrotic scarring and inflammation that disrupts liver architecture and function. While it is typically the result of alcoholism or hepatitis viral infection in adults, its etiology in infants is much less understood. In this study, we report 14 children from ten unrelated families presenting with a syndromic form of pediatric liver cirrhosis. By genome/exome sequencing, we found recessive variants in FOCAD segregating with the disease. Zebrafish lacking focad phenocopied the human disease, revealing a signature of altered messenger RNA (mRNA) degradation processes in the liver. Using patient's primary cells and CRISPR-Cas9-mediated inactivation in human hepatic cell lines, we found that FOCAD deficiency compromises the SKI mRNA surveillance pathway by reducing the levels of the RNA helicase SKIC2 and its cofactor SKIC3. FOCAD knockout hepatocytes exhibited lowered albumin expression and signs of persistent injury accompanied by CCL2 overproduction. Our results reveal the importance of FOCAD in maintaining liver homeostasis and disclose a possible therapeutic intervention point via inhibition of the CCL2/CCR2 signaling axis.
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Affiliation(s)
- Ricardo Moreno Traspas
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze Shin Teoh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pui-Mun Wong
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Michael Maier
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Crystal Y Chia
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kenneth Lay
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Nur Ain Ali
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Austin Larson
- Section of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Fuad Al Mutairi
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Medical Genomic Research, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Huma Arshad Cheema
- Division of Pediatric Gastroenterology-Hepatology and Nutrition, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Juliette Dupont
- Department of Pediatrics, Genetic Services, Lisbon North University Hospital Center, Lisbon, Portugal
| | - Stéphane Bézieau
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Bertrand Isidor
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Dorrain Yanwen Low
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Grace Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hugues Piloquet
- Gastropediatrics Department, Nantes University Hospital Center, Nantes, France
| | - Madeleine Joubert
- Anatomopathology Department, Nantes University Hospital Center, Nantes, France
| | - Hulya Kayserili
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey
| | - Kimberly A Kripps
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric P Wartchow
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Majed Dasouki
- Department of Pediatric Genetics, AdventHealth Medical Group, Orlando, FL, USA
| | - Renata Sandoval
- Department of Oncogenetics, Hospital Sírio-Libanês, Brasília, Brazil
| | - Elisa Carvalho
- Department of Pediatric Gastroenterology and Hepatology, Hospital da Criança de Brasília José Alencar, UniCEUB, Brasília, Brazil
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo, Brazil
| | - Gilda Porta
- Department of Pediatric Hepatology, Transplant Unit, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College, Mangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Badr AlSaleem
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Raeda M BaAbbad
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | | | | | | | - Benjamin Cogne
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | | | - Marie Vincent
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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4
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FOCAD Indel in a Family With Juvenile Polyposis Syndrome. J Pediatr Gastroenterol Nutr 2022; 75:56-58. [PMID: 35622075 DOI: 10.1097/mpg.0000000000003470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Juvenile polyposis syndrome (JPS) is a childhood polyposis syndrome with up to a 50% lifetime risk of gastrointestinal cancer. Germline pathogenic variants in BMPR1A and SMAD4 are responsible for around 40% of cases of JPS, but for the majority of individuals, the underlying genetic cause is unknown. We identified a family for which polyposis spanned four generations, and the proband had a clinical diagnosis of JPS. Next-generation sequencing was conducted, followed by Sanger sequencing confirmation. We identified an internal deletion of the FOCAD gene in all family members tested that altered the reading frame and is predicted to be pathogenic. We conclude that inactivation of the FOCAD gene is likely to cause JPS in this family.
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5
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Jensen MR, Stoltze U, Hansen TVO, Bak M, Sehested A, Rechnitzer C, Mathiasen R, Scheie D, Larsen KB, Olsen TE, Muhic A, Skjøth-Rasmussen J, Rossing M, Schmiegelow K, Wadt K. 9p21.3 microdeletion involving CDKN2A/2B in a young patient with multiple primary cancers and review of the literature. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006164. [PMID: 35422439 PMCID: PMC9235845 DOI: 10.1101/mcs.a006164] [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: 12/07/2021] [Accepted: 04/01/2022] [Indexed: 11/29/2022] Open
Abstract
Germline pathogenic variants in CDKN2A predispose to various cancers, including melanoma, pancreatic cancer, and neural system tumors, whereas CDKN2B variants are associated with renal cell carcinoma. A few case reports have described heterozygous germline deletions spanning both CDKN2A and CDKN2B associated with a cancer predisposition syndrome (CPS) that constitutes a risk of cancer beyond those associated with haploinsufficiency of each gene individually, indicating an additive effect or a contiguous gene deletion syndrome. We report a young woman with a de novo germline 9p21 microdeletion involving the CDKN2A/CDKN2B genes, who developed six primary cancers since childhood, including a very rare extraskeletal osteosarcoma (eOS) at the age of 8. To our knowledge this is the first report of eOS in a patient with CDKN2A/CDKN2B deletion.
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Affiliation(s)
- Marlene Richter Jensen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Stoltze
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas Van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Catherine Rechnitzer
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Karen Bonde Larsen
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Tina Elisabeth Olsen
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Aida Muhic
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jane Skjøth-Rasmussen
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark, Institute of Clinical Medicine, Faculty of Medicine, University of Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark;
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6
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Lin SY, Su YP, Trauger ER, Song BP, Thompson EGC, Hoffman MC, Chang TT, Lin YJ, Kao YL, Cui Y, Hann HW, Park G, Shieh FS, Song W, Su YH. Detection of Hepatitis B Virus-Host Junction Sequences in Urine of Infected Patients. Hepatol Commun 2021; 5:1649-1659. [PMID: 34558837 PMCID: PMC8485884 DOI: 10.1002/hep4.1783] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/24/2021] [Accepted: 06/20/2021] [Indexed: 01/25/2023] Open
Abstract
Integrated hepatitis B virus (HBV) DNA, found in more than 85% of HBV-associated hepatocellular carcinomas (HBV-HCCs), can play a significant role in HBV-related liver disease progression. HBV-host junction sequences (HBV-JSs), created through integration events, have been used to determine HBV-HCC clonality. Here, we investigate the feasibility of analyzing HBV integration in a noninvasive urine liquid biopsy. Using an HBV-targeted next-generation sequencing (NGS) assay, we first identified HBV-JSs in eight HBV-HCC tissues and designed short-amplicon junction-specific polymerase chain reaction assays to detect HBV-JSs in matched urine. We detected and validated tissue-derived junctions in five of eight matched urine samples. Next, we screened 32 urine samples collected from 25 patients infected with HBV (5 with hepatitis, 10 with cirrhosis, 4 with HCC, and 6 post-HCC). Encouragingly, all 32 urine samples contained HBV-JSs detectable by HBV-targeted NGS. Of the 712 total HBV-JSs detected in urine, 351 were in gene-coding regions, 11 of which, including TERT (telomerase reverse transcriptase), had previously been reported as recurrent integration sites in HCC tissue and were found only in the urine patients with cirrhosis or HCC. The integration breakpoints of HBV DNA detected in urine were found predominantly (~70%) at a previously identified integration hotspot, HBV DR1-2 (down-regulator of transcription 1-2). Conclusion: HBV viral-host junction DNA can be detected in urine of patients infected with HBV. This study demonstrates the potential for a noninvasive urine liquid biopsy of integrated HBV DNA to monitor patients infected with HBV for HBV-associated liver diseases and the efficacy of antiviral therapy.
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Affiliation(s)
| | - Yih-Ping Su
- The Baruch S. Blumberg Research InstituteDoylestownPAUSA
| | | | | | | | | | - Ting-Tsung Chang
- Department of Internal MedicineNational Cheng Kung University Hospital, College of MedicineTainanTaiwan, Republic of China
| | - Yih-Jyh Lin
- Department of SurgeryNational Cheng Kung University Hospital, College of MedicineTainanTaiwan, Republic of China
| | - Yu-Lan Kao
- The Baruch S. Blumberg Research InstituteDoylestownPAUSA
| | - Yixiao Cui
- The Baruch S. Blumberg Research InstituteDoylestownPAUSA
| | - Hie-Won Hann
- Liver Disease Prevention CenterDivision of Gastroenterology and HepatologyThomas Jefferson University HospitalPhiladelphiaPAUSA
| | - Grace Park
- Liver Disease Prevention CenterDivision of Gastroenterology and HepatologyThomas Jefferson University HospitalPhiladelphiaPAUSA
| | | | - Wei Song
- JBS Science, Inc.DoylestownPAUSA
| | - Ying-Hsiu Su
- The Baruch S. Blumberg Research InstituteDoylestownPAUSA
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7
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Liu D, Ban HJ, El Sergani AM, Lee MK, Hecht JT, Wehby GL, Moreno LM, Feingold E, Marazita ML, Cha S, Szabo-Rogers HL, Weinberg SM, Shaffer JR. PRICKLE1 × FOCAD Interaction Revealed by Genome-Wide vQTL Analysis of Human Facial Traits. Front Genet 2021; 12:674642. [PMID: 34434215 PMCID: PMC8381734 DOI: 10.3389/fgene.2021.674642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The human face is a highly complex and variable structure resulting from the intricate coordination of numerous genetic and non-genetic factors. Hundreds of genomic loci impacting quantitative facial features have been identified. While these associations have been shown to influence morphology by altering the mean size and shape of facial measures, their effect on trait variance remains unclear. We conducted a genome-wide association analysis for the variance of 20 quantitative facial measurements in 2,447 European individuals and identified several suggestive variance quantitative trait loci (vQTLs). These vQTLs guided us to conduct an efficient search for gene-by-gene (G × G) interactions, which uncovered an interaction between PRICKLE1 and FOCAD affecting cranial base width. We replicated this G × G interaction signal at the locus level in an additional 5,128 Korean individuals. We used the hypomorphic Prickle1 Beetlejuice (Prickle1 Bj ) mouse line to directly test the function of Prickle1 on the cranial base and observed wider cranial bases in Prickle1 Bj/Bj . Importantly, we observed that the Prickle1 and Focadhesin proteins co-localize in murine cranial base chondrocytes, and this co-localization is abnormal in the Prickle1 Bj/Bj mutants. Taken together, our findings uncovered a novel G × G interaction effect in humans with strong support from both epidemiological and molecular studies. These results highlight the potential of studying measures of phenotypic variability in gene mapping studies of facial morphology.
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Affiliation(s)
- Dongjing Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Hyo-Jeong Ban
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Ahmed M. El Sergani
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical Center, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - George L. Wehby
- Department of Health Management and Policy, The University of Iowa, Iowa City, IA, United States
| | - Lina M. Moreno
- Department of Orthodontics, The University of Iowa, Iowa City, IA, United States
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Psychiatry, Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seongwon Cha
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Heather L. Szabo-Rogers
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Regenerative Medicine at the McGowan Institute, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Craniofacial Regeneration, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
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8
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Belhadj S, Terradas M, Munoz-Torres PM, Aiza G, Navarro M, Capellá G, Valle L. Candidate genes for hereditary colorectal cancer: Mutational screening and systematic review. Hum Mutat 2020; 41:1563-1576. [PMID: 32449991 DOI: 10.1002/humu.24057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/30/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022]
Abstract
Genome-wide approaches applied for the identification of new hereditary colorectal cancer (CRC) genes, identified several potential causal genes, including RPS20, IL12RB1, LIMK2, POLE2, MRE11, POT1, FAN1, WIF1, HNRNPA0, SEMA4A, FOCAD, PTPN12, LRP6, POLQ, BLM, MCM9, and the epigenetic inactivation of PTPRJ. Here we attempted to validate the association between variants in these genes and nonpolyposis CRC by performing a mutational screening of the genes and PTPRJ promoter methylation analysis in 473 familial/early-onset CRC cases, a systematic review of the published cases, and assessment of allele frequencies in control population. In the studied cohort, 24 (5%) carriers of (predicted) deleterious variants in the studied genes and no constitutional PTPRJ epimutations were identified. Assessment of allele frequencies in controls compared with familial/early-onset patients with CRC showed association with increased nonpolyposis CRC risk of disruptive variants in RPS20, IL12RB1, POLE2, MRE11 and POT1, and of FAN1 c.149T>G (p.Met50Arg). Lack of association was demonstrated for LIMK2, PTPN12, LRP6, PTPRJ, POLQ, BLM, MCM9 and FOCAD variants. Additional studies are required to provide conclusive evidence for SEMA4A, WIF1, HNRNPA0 c.-110G>C, and FOCAD large deletions.
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Affiliation(s)
- Sami Belhadj
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Pau M Munoz-Torres
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
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9
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Terradas M, Capellá G, Valle L. Dominantly Inherited Hereditary Nonpolyposis Colorectal Cancer Not Caused by MMR Genes. J Clin Med 2020; 9:jcm9061954. [PMID: 32585810 PMCID: PMC7355797 DOI: 10.3390/jcm9061954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/30/2022] Open
Abstract
In the past two decades, multiple studies have been undertaken to elucidate the genetic cause of the predisposition to mismatch repair (MMR)-proficient nonpolyposis colorectal cancer (CRC). Here, we present the proposed candidate genes according to their involvement in specific pathways considered relevant in hereditary CRC and/or colorectal carcinogenesis. To date, only pathogenic variants in RPS20 may be convincedly linked to hereditary CRC. Nevertheless, accumulated evidence supports the involvement in the CRC predisposition of other genes, including MRE11, BARD1, POT1, BUB1B, POLE2, BRF1, IL12RB1, PTPN12, or the epigenetic alteration of PTPRJ. The contribution of the identified candidate genes to familial/early onset MMR-proficient nonpolyposis CRC, if any, is extremely small, suggesting that other factors, such as the accumulation of low risk CRC alleles, shared environmental exposures, and/or gene-environmental interactions, may explain the missing heritability in CRC.
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Affiliation(s)
- Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain; (M.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain; (M.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain; (M.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, 08908 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-93-260-7145
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10
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Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M. Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation. Mol Cell 2020; 77:1222-1236.e13. [PMID: 32048998 PMCID: PMC7083229 DOI: 10.1016/j.molcel.2020.01.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
RNA decay is crucial for mRNA turnover and surveillance and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized versus redundant roles. Cytoplasmic pathways and links to translation are particularly enigmatic. By directly profiling decay factor targets and normal versus aberrant translation in mouse embryonic stem cells (mESCs), we uncovered extensive decay pathway specialization and crosstalk with translation. XRN1 (5'-3') mediates cytoplasmic bulk mRNA turnover whereas SKIV2L (3'-5') is universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance revealed AVEN and FOCAD as SKIV2L interactors. AVEN prevents ribosome stalls at structured regions, which otherwise require SKIV2L for clearance. This pathway is crucial for histone translation, upstream open reading frame (uORF) regulation, and counteracting ribosome arrest on small ORFs. In summary, we uncovered key targets, components, and functions of mammalian RNA decay pathways and extensive coupling to translation.
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Affiliation(s)
- Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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11
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Brand F, Förster A, Christians A, Bucher M, Thomé CM, Raab MS, Westphal M, Pietsch T, von Deimling A, Reifenberger G, Claus P, Hentschel B, Weller M, Weber RG. FOCAD loss impacts microtubule assembly, G2/M progression and patient survival in astrocytic gliomas. Acta Neuropathol 2020; 139:175-192. [PMID: 31473790 DOI: 10.1007/s00401-019-02067-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/12/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022]
Abstract
In search of novel genes associated with glioma pathogenesis, we have previously shown frequent deletions of the KIAA1797/FOCAD gene in malignant gliomas, and a tumor suppressor function of the encoded focadhesin impacting proliferation and migration of glioma cells in vitro and in vivo. Here, we examined an association of reduced FOCAD gene copy number with overall survival of patients with astrocytic gliomas, and addressed the molecular mechanisms that govern the suppressive effect of focadhesin on glioma growth. FOCAD loss was associated with inferior outcome in patients with isocitrate dehydrogenase 1 or 2 (IDH)-mutant astrocytic gliomas of WHO grades II-IV. Multivariate analysis considering age at diagnosis as well as IDH mutation, MGMT promoter methylation, and CDKN2A/B homozygous deletion status confirmed reduced FOCAD gene copy number as a prognostic factor for overall survival. Using a yeast two-hybrid screen and pull-down assays, tubulin beta-6 and other tubulin family members were identified as novel focadhesin-interacting partners. Tubulins and focadhesin co-localized to centrosomes where focadhesin was enriched in proximity to centrioles. Focadhesin was recruited to microtubules via its interaction partner SLAIN motif family member 2 and reduced microtubule assembly rates, possibly explaining the focadhesin-dependent decrease in cell migration. During the cell cycle, focadhesin levels peaked in G2/M phase and influenced time-dependent G2/M progression potentially via polo like kinase 1 phosphorylation, providing a possible explanation for focadhesin-dependent cell growth reduction. We conclude that FOCAD loss may promote biological aggressiveness and worsen clinical outcome of diffuse astrocytic gliomas by enhancing microtubule assembly and accelerating G2/M phase progression.
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Affiliation(s)
- Frank Brand
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Alisa Förster
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Anne Christians
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Martin Bucher
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Carina M Thomé
- Neurology Clinic and National Center for Tumor Diseases, Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical School, Bonn, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Claus
- Department of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ruthild G Weber
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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12
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Lorca V, Garre P. Current status of the genetic susceptibility in attenuated adenomatous polyposis. World J Gastrointest Oncol 2019; 11:1101-1114. [PMID: 31908716 PMCID: PMC6937445 DOI: 10.4251/wjgo.v11.i12.1101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Adenomatous polyposis (AP) is classified according to cumulative adenoma number in classical AP (CAP) and attenuated AP (AAP). Genetic susceptibility is the major risk factor in CAP due to mutations in the known high predisposition genes APC and MUTYH. However, the contribution of genetic susceptibility to AAP is lower and less understood. New predisposition genes have been recently proposed, and some of them have been validated, but their scarcity hinders accurate risk estimations and prevalence calculations. AAP is a heterogeneous condition in terms of severity, clinical features and heritability. Therefore, clinicians do not have strong discriminating criteria for the recommendation of the genetic study of known predisposition genes, and the detection rate is low. Elucidation and knowledge of new AAP high predisposition genes are of great importance to offer accurate genetic counseling to the patient and family members. This review aims to update the genetic knowledge of AAP, and to expound the difficulties involved in the genetic analysis of a highly heterogeneous condition such as AAP.
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Affiliation(s)
- Víctor Lorca
- Laboratorio de Oncología Molecular, Grupo de Investigación Clínica y Traslacional en Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Servicio de Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
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13
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Hsa_circ_0001361 promotes bladder cancer invasion and metastasis through miR-491-5p/MMP9 axis. Oncogene 2019; 39:1696-1709. [PMID: 31705065 DOI: 10.1038/s41388-019-1092-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
Abstract
Circular RNAs (circRNAs) have been increasingly indicated to be important participants in the development and progression of various malignant tumors. Our previous studies found that hundreds of circRNAs were aberrantly expressed in bladder cancer (BC) by high-throughput sequencing and we have confirmed that the downregulated circRNAs circHIPK3, circRNA BCRC-3, and circNR3C1 played inhibitory roles in BC progression. In this study, we focused on the upregulated circRNAs and identified a novel circular RNA, hsa_circ_0001361 (circ0001361), was expressed at high levels in BC tissues and cell lines based on RNA-Seq data and qRT-PCR analysis, and it was positively corelated with pathologic grade and muscle invasion. Moreover, Kaplan-Meier survival analysis implied that BC patients with high circ0001361 expression level had a poor overall survival. Functionally, circ0001361 promoted BC cell invasion and metastasis both in vitro and in vivo, but had no effect on cell cycle and proliferation. Mechanistically, RNA sequencing analysis indicated that MMP9 was upregulated in circ0001361-overexpressed BC cells, and MMP9 was verified to mediate circ0001361-induced cell migration and invasion. Furthermore, we demonstrated that circ0001361 could directly interact with miR-491-5p to upregulate MMP9 expression. Collectively, our findings indicate that circ0001361 plays oncogenic role in BC invasion and metastasis through targeting the miR-491-5p/MMP9 axis, and it might be a potential novel target for BC therapy.
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14
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Terradas M, Munoz-Torres PM, Belhadj S, Aiza G, Navarro M, Brunet J, Capellá G, Valle L. Contribution to colonic polyposis of recently proposed predisposing genes and assessment of the prevalence of NTHL1- and MSH3-associated polyposes. Hum Mutat 2019; 40:1910-1923. [PMID: 31243857 DOI: 10.1002/humu.23853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/12/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022]
Abstract
Technological advances have allowed the identification of new adenomatous and serrated polyposis genes, and of several candidate genes that require additional supporting evidence of causality. Through an exhaustive literature review and mutational screening of 177 unrelated polyposis patients, we assessed the involvement of MCM9, FOCAD, POLQ, and RNF43 in the predisposition to (nonserrated) colonic polyposis, as well as the prevalence of NTHL1 and MSH3 mutations among genetically unexplained polyposis patients. Our results, together with previously reported data and mutation frequency in controls, indicate that: MCM9 and POLQ mutations are not associated with polyposis; germline RNF43 mutations, with a prevalence of 1.5-2.5% among serrated polyposis patients, do not cause nonserrated polyposis; MSH3 biallelic mutations are highly infrequent among European polyposis patients, and the prevalence of NTHL1 biallelic mutations among unexplained polyposes is ~2%. Although nonsignificant, FOCAD predicted deleterious variants are overrepresented in polyposis patients compared to controls, warranting larger studies to provide definite evidence in favor or against their causal association with polyposis predisposition.
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Affiliation(s)
- Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Pau M Munoz-Torres
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Sami Belhadj
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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15
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Haaland ØA, Romanowska J, Gjerdevik M, Lie RT, Gjessing HK, Jugessur A. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000Res 2019; 8:960. [PMID: 31372216 PMCID: PMC6662680 DOI: 10.12688/f1000research.19571.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and now apply them to data from a genome-wide association study (GWAS) of families with children born with isolated CL/P. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. Our new methodology detects if PoO effects are different across environmental strata and is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects.
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Affiliation(s)
- Øystein Ariansen Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
| | - Rolv Terje Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Håkon Kristian Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
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16
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Haaland ØA, Romanowska J, Gjerdevik M, Lie RT, Gjessing HK, Jugessur A. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000Res 2019; 8:960. [PMID: 31372216 PMCID: PMC6662680 DOI: 10.12688/f1000research.19571.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and applied them to families with children born with isolated cleft palate only. Here, we used the same genome-wide association study (GWAS) dataset and methodology to screen for PoOxE effects in the larger sample of CL/P triads. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. The methodology applied in the analyses is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects.
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Affiliation(s)
- Øystein Ariansen Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
| | - Rolv Terje Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Håkon Kristian Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
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17
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Valle L, de Voer RM, Goldberg Y, Sjursen W, Försti A, Ruiz-Ponte C, Caldés T, Garré P, Olsen MF, Nordling M, Castellvi-Bel S, Hemminki K. Update on genetic predisposition to colorectal cancer and polyposis. Mol Aspects Med 2019; 69:10-26. [PMID: 30862463 DOI: 10.1016/j.mam.2019.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023]
Abstract
The present article summarizes recent developments in the characterization of genetic predisposition to colorectal cancer (CRC). The main themes covered include new hereditary CRC and polyposis syndromes, non-CRC hereditary cancer genes found mutated in CRC patients, strategies used to identify novel causal genes, and review of candidate genes that have been proposed to predispose to CRC and/or colonic polyposis. We provide an overview of newly described genes and syndromes associated with predisposition to CRC and polyposis, including: polymerase proofreading-associated polyposis, NTHL1-associated polyposis, mismatch repair gene biallelic inactivation-related adenomatous polyposis (including MSH3- and MLH3-associated polyposes), GREM1-associated mixed polyposis, RNF43-associated serrated polyposis, and RPS20 mutations as a rare cause of hereditary nonpolyposis CRC. The implementation of next generation sequencing approaches for genetic testing has exposed the presence of pathogenic germline variants in genes associated with hereditary cancer syndromes not traditionally linked to CRC, which may have an impact on genetic testing, counseling and surveillance. The identification of new hereditary CRC and polyposis genes has not deemed an easy endeavor, even though known CRC-related genes explain a small proportion of the estimated familial risk. Whole-genome sequencing may offer a technology for increasing this proportion, particularly if applied on pedigree data allowing linkage type of analysis. The final section critically surveys the large number of candidate genes that have been recently proposed for CRC predisposition.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Hospitalet de Llobregat, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain.
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yael Goldberg
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Spain
| | - Trinidad Caldés
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; Oncology Molecular Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Pilar Garré
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; Oncology Molecular Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Maren F Olsen
- Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Margareta Nordling
- Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sergi Castellvi-Bel
- Genetic Predisposition to Gastrointestinal Cancer Group, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.
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18
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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19
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Franch-Expósito S, Esteban-Jurado C, Garre P, Quintanilla I, Duran-Sanchon S, Díaz-Gay M, Bonjoch L, Cuatrecasas M, Samper E, Muñoz J, Ocaña T, Carballal S, López-Cerón M, Castells A, Vila-Casadesús M, Derdak S, Laurie S, Beltran S, Carvajal J, Bujanda L, Ruiz-Ponte C, Camps J, Gironella M, Lozano JJ, Balaguer F, Cubiella J, Caldés T, Castellví-Bel S. Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis. J Genet Genomics 2017; 45:41-45. [PMID: 29396139 DOI: 10.1016/j.jgg.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Clara Esteban-Jurado
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Isabel Quintanilla
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Saray Duran-Sanchon
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clinic de Barcelona, Barcelona 08036, Spain
| | - Esther Samper
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Sabela Carballal
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - María López-Cerón
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | | | - Maria Vila-Casadesús
- Bioinformatics Platform, CIBER of Hepatic and Digestive Diseases, Barcelona 08036, Spain
| | - Sophia Derdak
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Steven Laurie
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Sergi Beltran
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Jaime Carvajal
- Andalusian Developmental Biology Institute, CSIC-Pablo de Olavide University-Andalusian Regional Government, Sevilla 41013, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Biodonostia Institute, CIBER of Hepatic and Digestive Diseases, University of the Basque Country (UPV/EHU), San Sebastián 20080, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), CIBER of Rare Diseases, Genomics Medicine Group, Hospital Clínico Universitario, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
| | - Jordi Camps
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Meritxell Gironella
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Juan José Lozano
- Bioinformatics Platform, CIBER of Hepatic and Digestive Diseases, Barcelona 08036, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Ourense Biomedical Research Institute, Ourense 32005, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain.
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20
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Zhang D, Li Z, Xu X, Zhou D, Tang S, Yin X, Xu F, Li H, Zhou Y, Zhu T, Deng H, Zhang S, Huang Q, Wang J, Yin W, Zhu Y, Lai M. Deletions at SLC18A1 increased the risk of CRC and lower SLC18A1 expression associated with poor CRC outcome. Carcinogenesis 2017; 38:1057-1062. [PMID: 28968818 DOI: 10.1093/carcin/bgx088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/24/2017] [Indexed: 12/26/2022] Open
Abstract
Copy number variations (CNVs) contribute to the development of colorectal cancer (CRC). We conducted a two-stage association study to identify CNV risk loci for CRC. We performed a gene-based rare CNV study on 694 sporadic CRC and 1641 controls using Illumina Human-OmniExpress-12v1.0 BeadChips, and further replicated in 934 CRC cases and 2680 controls for risk CNVs by using TaqMan Copy Number Assay. Tumor buddings, cancer cells in the center of primary tumor and normal intestinal epithelial cells were captured using laser capture microdissection (LCM) and were assayed using AffymetrixGeneChip® Human Genome U133 Plus 2.0 Array. In addition, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data were assessed for the effects of risk CNVs. We found that germline deletions affecting the last six exons of SLC18A1 significantly associated with CRC with a combined P value of 6.4 × 10-5 by a two-stage analysis. Both in TCGA CRC RNA seq dataset and GDS4382, SLC18A1 was significantly down regulated in CRC tissues than in paired normal tissues (N = 32 and 17 pairs, P = 0.004 and 0.009, respectively). In LCM samples, similar observations were obtained that the expression levels of SLC18A1 in the tumor buddings, cancer cells in the center of primary tumor, and stroma of both tumor budding and cancer cells were lower than normal intestinal epithelial and stromal cells (fold change = 0.17-0.62, 0.12-0.57 and 0.37-0.68, respectively). In summary, the germline deletions at SLC18A1 contributed to the development of CRC. The role of SLC18A1 required further exploration.
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Affiliation(s)
- Dandan Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Zhenli Li
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Xiaohong Xu
- Clinical laboratory, The Affiliated Zhejiang Cancer Hospital of Zhejiang Chinese Medical University, Hangzhou 310022, China
| | - Dan Zhou
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Shunli Tang
- The Second Department of Clinical Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoyang Yin
- The Second Department of Clinical Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fangying Xu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Hui Li
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Yuan Zhou
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Tao Zhu
- Departments of Pathology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Hong Deng
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Shuai Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Qiong Huang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Jing Wang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
| | - Wei Yin
- The Core Facilities, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yimin Zhu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou 310058, China
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou 310058, China
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21
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Kumaran M, Cass CE, Graham K, Mackey JR, Hubaux R, Lam W, Yasui Y, Damaraju S. Germline copy number variations are associated with breast cancer risk and prognosis. Sci Rep 2017; 7:14621. [PMID: 29116104 PMCID: PMC5677082 DOI: 10.1038/s41598-017-14799-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array. Principal component analysis for population stratification revealed 84 outliers leaving 366 cases and 320 controls of Caucasian ancestry for association analysis; CNVs with frequency > 10% and overlapping with protein coding genes were considered for breast cancer risk and prognostic relevance. Coding genes within the CNVs identified were interrogated for gene- dosage effects by correlating copy number status with gene expression profiles in breast tumor tissue. We identified 200 CNVs associated with breast cancer (q-value < 0.05). Of these, 21 CNV regions (overlapping with 22 genes) also showed association with prognosis. We validated representative CNVs overlapping with APOBEC3B and GSTM1 genes using the TaqMan assay. Germline CNVs conferred dosage effects on gene expression in breast tissue. The candidate CNVs identified in this study warrant independent replication.
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Affiliation(s)
- Mahalakshmi Kumaran
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Carol E Cass
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Roland Hubaux
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Wan Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada. .,Cross Cancer Institute, Alberta Health Services, Edmonton, AB, Canada.
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22
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Roncucci L, Pedroni M, Mariani F. Attenuated adenomatous polyposis of the large bowel: Present and future. World J Gastroenterol 2017; 23:4135-4139. [PMID: 28694653 PMCID: PMC5483487 DOI: 10.3748/wjg.v23.i23.4135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/03/2017] [Accepted: 05/09/2017] [Indexed: 02/06/2023] Open
Abstract
Attenuated adenomatous polyposis (AAP) is a poorly understood syndrome, that can be defined as the presence of 10-99 synchronous adenomas in the large bowel, and it is considered a phenotypic variant of familial adenomatous polyposis (FAP). This definition has the advantage of simplicity, but it may include sporadic multiple adenomas of the large bowel at an extreme, or FAP cases on the other side. AAP shows a milder phenotype than FAP, with an older age of onset of adenomas and cancer, and less frequent extracolonic manifestations. AAP may be diagnosed as a single case in a family or, less frequently, it may be present in other family members, and it shows distinct pattern of inheritance. In less than 50% of cases, it may be caused by adenomatous polyposis coli (APC) or MUTYH mutations, referred to as APC-associated polyposis, inherited as an autosomal dominant trait, or MUTYH-associated polyposis, which shows an autosomal recessive mechanism of inheritance, respectively. Surveillance should rely on colonoscopy at regular intervals, with removal of adenomas and careful histological examination. When removal of polyps is not possible or advanced lesions are observed, the surgical approach is mandatory, being subtotal colectomy with ileo-rectal anastomosis the treatment of choice. Studies on this syndrome are lacking, and controversies are still present on many issues, thus, other clinical and genetic studies are requested.
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23
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Recent Discoveries in the Genetics of Familial Colorectal Cancer and Polyposis. Clin Gastroenterol Hepatol 2017; 15:809-819. [PMID: 27712984 DOI: 10.1016/j.cgh.2016.09.148] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023]
Abstract
The development of genome-wide massively parallel sequencing, ie, whole-genome and whole-exome sequencing, and copy number approaches has raised high expectations for the identification of novel hereditary colorectal cancer genes. Although relatively successful for genes causing adenomatous polyposis syndromes, both autosomal dominant and recessive, the identification of genes associated with hereditary non-polyposis colorectal cancer has proven extremely challenging, mainly because of the absence of major high-penetrance genes and the difficulty in demonstrating the functional impact of the identified variants and their causal association with tumor development. Indeed, most, if not all, novel candidate non-polyposis colorectal cancer genes identified so far lack corroborative data in independent studies. Here we review the novel hereditary colorectal cancer genes and syndromes identified and the candidate genes proposed in recent years as well as discuss the challenges we face.
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24
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Sun R, Liu Z, Tong D, Yang Y, Guo B, Wang X, Zhao L, Huang C. miR-491-5p, mediated by Foxi1, functions as a tumor suppressor by targeting Wnt3a/β-catenin signaling in the development of gastric cancer. Cell Death Dis 2017; 8:e2714. [PMID: 28358374 PMCID: PMC5386537 DOI: 10.1038/cddis.2017.134] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/23/2017] [Accepted: 02/28/2017] [Indexed: 02/07/2023]
Abstract
Accumulated evidence has suggested that microRNAs (miRNAs) have an important role in tumor development and progression by regulating diverse signaling pathways. However, the precise role of miRNAs in gastric cancer (GC) has not been elucidated. In this study, we describe the function and regulation network of miR-491-5p in GC. miR-491-5p is frequently downregulated in GC tissues compared with adjacent non-cancerous tissues. Forced expression of miR-491-5p significantly inhibits proliferation and colony formation, and promotes apoptosis in GC cells. Through bioinformatic analysis and luciferase assays, we confirm that miR-491-5p targets Wnt3a. Silencing Wnt3a inhibits cell proliferation and induces apoptosis. Similarly, restoration of Wnt3a counteracts the effects of miR-491-5p expression. Moreover, bioinformatic and luciferase assays indicate that the expression of miR-491-5p is regulated by Foxi1, which binds to its promoter and activates miR-491-5p expression. In conclusion, to the best of our knowledge, our findings are the first to demonstrate that Foxi1 is a key player in the transcriptional control of miR-491-5p and that miR-491-5p acts as an anti-oncogene by targeting Wnt3a/β-catenin signaling in GC. Our study reveals that Foxi1/miR-491-5p/Wnt3a/β-catenin signaling is critical in the progression of GC. Targeting the pathway described in this study may open up new prospects to restrict the progression of GC.
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Affiliation(s)
- Ruifang Sun
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Zhigang Liu
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Dongdong Tong
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Yang Yang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- School of Public Health, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Bo Guo
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Xiaofei Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Lingyu Zhao
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
| | - Chen Huang
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi 710061, P.R. China
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Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, Tu Z, Zhu J. Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication. Genome Med 2016; 8:15. [PMID: 26856537 PMCID: PMC4746932 DOI: 10.1186/s13073-016-0268-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/21/2016] [Indexed: 12/30/2022] Open
Abstract
Background Inter-tissue molecular interactions are critical to the function and behavior of biological systems in multicellular organisms, but systematic studies of interactions between tissues are lacking. Also, existing studies of inter-tissue interactions are based on direct gene expression correlations, which can’t distinguish correlations due to common genetic architectures versus biochemical or molecular signal exchange between tissues. Methods We developed a novel strategy to study inter-tissue interaction by removing effects of genetic regulation of gene expression (genetic decorrelation). We applied our method to the comprehensive atlas of gene expression across nine human tissues in the Genotype-Tissue Expression (GTEx) project to generate novel genetically decorrelated inter-tissue networks. From this we derived modules of genes important in inter-tissue interactions that are likely driven by biological signal exchange instead of their common genetic basis. Importantly we highlighted communication between tissues and elucidated gene activities in one tissue inducing gene expression changes in others. Results We reveal global unidirectional inter-tissue coordination of specific biological pathways such as protein synthesis. Using our data, we highlighted a clinically relevant example whereby heart expression of DPP4 was coordinated with a gene expression signature characteristic for whole blood proliferation, potentially impacting peripheral stem cell mobilization. We also showed that expression of the poorly characterized FOCAD in heart correlated with protein biosynthetic processes in the lung. Conclusions In summary, this is the first resource of human multi-tissue networks enabling the investigation of molecular inter-tissue interactions. With the networks in hand, we may systematically design combination therapies that simultaneously target multiple tissues or pinpoint potential side effects of a drug in other tissues. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0268-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quan Long
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tao Huang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Siwu Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yong Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhidong Tu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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