1
|
Guardia T, Eason M, Kontrogianni-Konstantopoulos A. Obscurin: A multitasking giant in the fight against cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188567. [PMID: 34015411 PMCID: PMC8349851 DOI: 10.1016/j.bbcan.2021.188567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 12/19/2022]
Abstract
Giant obscurins (720-870 kDa), encoded by OBSCN, were originally discovered in striated muscles as cytoskeletal proteins with scaffolding and regulatory roles. Recently though, they have risen to the spotlight as key players in cancer development and progression. Herein, we provide a timely prudent synopsis of the expanse of OBSCN mutations across 16 cancer types. Given the extensive work on OBSCN's role in breast epithelium, we summarize functional studies implicating obscurins as potent tumor suppressors in breast cancer and delve into an in silico analysis of its mutational profile and epigenetic (de)regulation using different dataset platforms and sophisticated computational tools. Lastly, we formally describe the OBSCN-Antisense-RNA-1 gene, which belongs to the long non-coding RNA family and discuss its potential role in modulating OBSCN expression in breast cancer. Collectively, we highlight the escalating involvement of obscurins in cancer biology and outline novel potential mechanisms of OBSCN (de)regulation that warrant further investigation.
Collapse
Affiliation(s)
- Talia Guardia
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Matthew Eason
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Aikaterini Kontrogianni-Konstantopoulos
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, USA.
| |
Collapse
|
2
|
Grogan A, Kontrogianni-Konstantopoulos A. Unraveling obscurins in heart disease. Pflugers Arch 2018; 471:735-743. [PMID: 30099631 DOI: 10.1007/s00424-018-2191-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022]
Abstract
Obscurins, expressed from the single OBSCN gene, are a family of giant, modular, cytoskeletal proteins that play key structural and regulatory roles in striated muscles. They were first implicated in the development of heart disease in 2007 when two missense mutations were found in a patient diagnosed with hypertrophic cardiomyopathy (HCM). Since then, the discovery of over a dozen missense, frameshift, and splicing mutations that are linked to various forms of cardiomyopathy, including HCM, dilated cardiomyopathy (DCM), and left ventricular non-compaction (LVNC), has highlighted OBSCN as a potential disease-causing gene. At this time, the functional consequences of the identified mutations remain largely elusive, and much work has yet to be done to characterize the disease mechanisms of pathological OBSCN variants. Herein, we describe the OBSCN mutations known to date, discuss their potential impact on disease development, and provide future directions in order to better understand the involvement of obscurins in heart disease.
Collapse
Affiliation(s)
- Alyssa Grogan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD, 21201, USA
| | | |
Collapse
|
3
|
Rajendran BK, Deng CX. A comprehensive genomic meta-analysis identifies confirmatory role of OBSCN gene in breast tumorigenesis. Oncotarget 2017; 8:102263-102276. [PMID: 29254242 PMCID: PMC5731952 DOI: 10.18632/oncotarget.20404] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/26/2017] [Indexed: 12/15/2022] Open
Abstract
The giant multifunctional protein "OBSCURIN" is encoded by OBSCN gene and is mostly expressed in cardiac and other skeletal muscles responsible for myofibrils organization. Loss of OBSCURIN affects the entire downstream pathway proteins vital for various cellular functions including cell integration and cell adhesion. The OBSCN gene mutations are more frequently observed in various muscular diseases, and cancers. Nevertheless, the direct role of OBSCN in tumorigenesis remains elusive. Interestingly, in clinical breast cancer samples a significant number of function changing mutations have been identified in OBSCN gene. In this study, we identified a significant role of OBSCN by conducting an integrative analysis of copy number alterations, functional mutations, gene methylation and expression data from various BRCA cancer projects data available on cBioPortal and TCGA firebrowse portal. Finally, we carried out genetic network analysis, which revealed that OBSCN gene plays a significant role in GPCR, RAS, p75 or Wnt signaling pathways. Similarly, OBSCN gene interacts with many cancer-associated genes involved in breast tumorigenesis. The OBSCN gene probably regulates breast cancer progression and metastasis and the prognostic molecular signatures such as copy number alterations and gene expression of OBSCN may serve as a tool to identify breast tumorigenesis and metastasis.
Collapse
Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| |
Collapse
|
4
|
Larach DB, Engoren MC, Schmidt EM, Heung M. Genetic variants and acute kidney injury: A review of the literature. J Crit Care 2017; 44:203-211. [PMID: 29161666 DOI: 10.1016/j.jcrc.2017.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 11/11/2017] [Indexed: 12/25/2022]
Abstract
PURPOSE Limited data exists on potential genetic contributors to acute kidney injury. This review examines current knowledge of AKI genomics. MATERIALS AND METHODS 32 studies were selected from PubMed and GWAS Catalog queries for original data studies of human AKI genetics. Hand search of references identified 3 additional manuscripts. RESULTS 33 of 35 studies were hypothesis-driven investigations of candidate polymorphisms that either did not consistently replicate statistically significant findings, or obtained significant results only in few small-scale studies. Vote-counting meta-analysis of 9 variants examined in >1 candidate gene study showed ≥50% non-significant studies, with larger studies generally finding non-significant results. The remaining 2 studies were large-scale unbiased investigations: One examining 2,100 genes linked with cardiovascular, metabolic, and inflammatory syndromes identified BCL2, SERPINA4, and SIK3 variants, while a genome-wide association study (GWAS) identified variants in BBS9 and the GRM7|LMCD1-AS1 intergenic region. All studies had relatively small sample sizes (<2300 subjects). Study heterogeneity precluded candidate gene and GWA meta-analysis. CONCLUSIONS Most studies of AKI genetics involve hypothesis-driven (rather than hypothesis-generating) candidate gene investigations that have failed to identify contributory variants consistently. A limited number of unbiased, larger-scale studies have been carried out, but there remains a pressing need for additional GWA studies.
Collapse
Affiliation(s)
- Daniel B Larach
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Milo C Engoren
- Departments of Anesthesiology, Division of Critical Care Medicine, and Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ellen M Schmidt
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Heung
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
5
|
Wang Z, Sun Y, Fu X, Yu G, Wang C, Bao F, Yue Z, Li J, Sun L, Irwanto A, Yu Y, Chen M, Mi Z, Wang H, Huai P, Li Y, Du T, Yu W, Xia Y, Xiao H, You J, Li J, Yang Q, Wang N, Shang P, Niu G, Chi X, Wang X, Cao J, Cheng X, Liu H, Liu J, Zhang F. A large-scale genome-wide association and meta-analysis identified four novel susceptibility loci for leprosy. Nat Commun 2016; 7:13760. [PMID: 27976721 PMCID: PMC5172377 DOI: 10.1038/ncomms13760] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/31/2016] [Indexed: 11/18/2022] Open
Abstract
Leprosy, a chronic infectious disease, results from the uncultivable pathogen Mycobacterium leprae (M. leprae), and usually progresses to peripheral neuropathy and permanent progressive deformity if not treated. Previously published genetic studies have identified 18 gene/loci significantly associated with leprosy at the genome-wide significant level. However as a complex disease, only a small proportion of leprosy risk could be explained by those gene/loci. To further identify more susceptibility gene/loci, we hereby performed a three-stage GWAS comprising 8,156 leprosy patients and 15,610 controls of Chinese ancestry. Four novel loci were identified including rs6807915 on 3p25.2 (P=1.94 × 10−8, OR=0.89), rs4720118 on 7p14.3 (P=3.85 × 10−10, OR=1.16), rs55894533 on 8p23.1 (P=5.07 × 10−11, OR=1.15) and rs10100465 on 8q24.11 (P=2.85 × 10−11, OR=0.85). Altogether, these findings have provided new insight and significantly expanded our understanding of the genetic basis of leprosy.
Previous studies have shown genetic associations between leprosy and 18 different genes/loci. Here, Wang and colleagues perform genome-wide association study in Han Chinese leprosy patients and describe four novel loci to be associated to the disease.
Collapse
Affiliation(s)
- Zhenzhen Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Yonghu Sun
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Xi'an Fu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Gongqi Yu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250022, China
| | - Chuan Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Fangfang Bao
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Zhenhua Yue
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Jianke Li
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Lele Sun
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Astrid Irwanto
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yongxiang Yu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Mingfei Chen
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Zihao Mi
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Honglei Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Pengcheng Huai
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Yi Li
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Tiantian Du
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Wenjun Yu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Yang Xia
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Hailu Xiao
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Jiabao You
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Jinghui Li
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Qing Yang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Na Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Panpan Shang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Guiye Niu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China
| | - Xiaojun Chi
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Xiuhuan Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Jing Cao
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Xiujun Cheng
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China
| | - Hong Liu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Furen Zhang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.,Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong 250000, China.,School of Medicine, Shandong University, Jinan, Shandong 250000, China.,School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250022, China.,Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong 250000, China.,National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong 250000, China
| |
Collapse
|
6
|
Khan S, Muhammad N, Khan M, Kamal A, Rehman Z, Khan S. Genetics of human Bardet-Biedl syndrome, an updates. Clin Genet 2016; 90:3-15. [DOI: 10.1111/cge.12737] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 12/21/2015] [Accepted: 01/03/2016] [Indexed: 12/22/2022]
Affiliation(s)
- S.A. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - N. Muhammad
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - M.A. Khan
- Gomal Centre of Biochemistry and Biotechnology; Gomal University; Khyber Pakhtunkhwa Pakistan
- Genomic Core Facility; Interim Translational Research Institute; Doha Qatar
| | - A. Kamal
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - Z.U. Rehman
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
| | - S. Khan
- Department of Biotechnology and Genetic Engineering; Kohat University of Science and Technology; Khyber Pakhtunkhwa Pakistan
- Genomic Core Facility; Interim Translational Research Institute; Doha Qatar
| |
Collapse
|
7
|
Khan MA, Mohan S, Zubair M, Windpassinger C. Homozygosity mapping identified a novel protein truncating mutation (p.Ser100Leufs*24) of the BBS9 gene in a consanguineous Pakistani family with Bardet Biedl syndrome. BMC MEDICAL GENETICS 2016; 17:10. [PMID: 26846096 PMCID: PMC4743198 DOI: 10.1186/s12881-016-0271-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/19/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Bardet Biedl Syndrome (BBS) is a rare condition of multi-organ dysfunction with characteristic clinical features of retinal degeneration, truncal obesity, postaxial polydactyly, genital anomaly, intellectual disability and renal dysfunction. It is a hetero-genetic disorder and nineteen BBS genes have been discovered so far. METHODS Whole genome SNP genotyping was performed by using CytoScan® 750 K array (Affymetrix). Subsequently, the segregation of the disease locus in the whole family was carried out by genotyping STS markers within the homozygous interval. Finally, the mutation analysis was performed by Sanger DNA sequencing. RESULTS In the present molecular study a consanguineous Pakistani family, with autosomal recessive BBS, was analyzed. The clinical analysis of affected individuals presented with synpolydactyly, obesity, intellectual disability, renal abnormality and retinitis pigmentosa. The presented phenotype was consistent with the major features of BBS syndrome. Homozygosity mapping identified a common homozygous interval within the known BBS9 locus. Sequence analysis of BBS9/PTHB1 gene revealed a single base deletion of c.299delC (p.Ser100Leufs*24) in exon 4. This frame-shift mutation presumably leads to a 122 amino acid truncated protein with complete loss of its C-terminal PTHB1 domain in combination with a partial loss of the N-terminal PTHB1 domain as well. BBS9/PTHB1 gene mutations have been shown to be associated with BBS syndrome and to the best of our knowledge this study reports the first Pakistani family linked to the BBS9 gene. CONCLUSION Our molecular findings expand the mutational spectrum of BBS9 gene and also explain the genetic heterogeneity of Pakistan families with BBS syndrome. The growing number of mutations in BBS genes in combination with a detailed phenotypical description of patients will be helpful for genotype-phenotype correlation, targeted genetic diagnosis, prenatal screening and carrier testing of familial and non-familial BBS patients.
Collapse
Affiliation(s)
- Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University Dera Ismail Khan, Khyber-Pakhtoonkhwa, Khyber-Pakhtoonkhwa, 29050, Pakistan.
- Interim Translational Research Institute, Genomic Core Facility, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.
| | - Sumitra Mohan
- Institute of Human Genetics, Medical University of Graz, Graz, 8010, Austria.
| | - Muhammad Zubair
- Gomal Centre of Biochemistry and Biotechnology, Gomal University Dera Ismail Khan, Khyber-Pakhtoonkhwa, Khyber-Pakhtoonkhwa, 29050, Pakistan.
| | | |
Collapse
|
8
|
Stafford-Smith M, Li YJ, Mathew JP, Li YW, Ji Y, Phillips-Bute BG, Milano CA, Newman MF, Kraus WE, Kertai MD, Shah SH, Podgoreanu MV. Genome-wide association study of acute kidney injury after coronary bypass graft surgery identifies susceptibility loci. Kidney Int 2015; 88:823-32. [PMID: 26083657 PMCID: PMC4589439 DOI: 10.1038/ki.2015.161] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/18/2015] [Accepted: 04/09/2015] [Indexed: 12/25/2022]
Abstract
Acute kidney injury (AKI) is a common, serious complication of cardiac surgery. Since prior studies have supported a genetic basis for postoperative AKI, we conducted a genome-wide association study (GWAS) for AKI following coronary bypass graft (CABG) surgery. The discovery dataset consisted of 873 non-emergent CABG surgery patients with cardiopulmonary bypass (PEGASUS), while a replication dataset had 380 cardiac surgical patients (CATHGEN). Single nucleotide polymorphism (SNP) data were based on Illumina Human610-Quad (PEGASUS) and OMNI1-Quad (CATHGEN) BeadChips. We used linear regression with adjustment for a clinical AKI risk score to test SNP associations with the postoperative peak rise relative to preoperative serum creatinine concentration as a quantitative AKI trait. Nine SNPs meeting significance in the discovery set were detected. The rs13317787 in GRM7|LMCD1-AS1 intergenic region (3p21.6) and rs10262995 in BBS9 (7p14.3) were replicated with significance in the CATHGEN data set and exhibited significantly strong overall association following meta-analysis. Additional fine-mapping using imputed SNPs across these two regions and meta-analysis found genome wide significance at the GRM7|LMCD1-AS1 locus and a significantly strong association at BBS9. Thus, through an unbiased GWAS approach, we found two new loci associated with post-CABG AKI providing new insights into the pathogenesis of perioperative AKI.
Collapse
Affiliation(s)
- Mark Stafford-Smith
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA.,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Joseph P Mathew
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Yen-Wei Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Yunqi Ji
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Carmelo A Milano
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Mark F Newman
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Miklos D Kertai
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Svati H Shah
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Mihai V Podgoreanu
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | | |
Collapse
|
9
|
Lai LC, Tsai MH, Chen PC, Chen LH, Hsiao JH, Chen SK, Lu TP, Lee JM, Hsu CP, Hsiao CK, Chuang EY. SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women. J Biomed Sci 2014; 21:24. [PMID: 24650256 PMCID: PMC3994426 DOI: 10.1186/1423-0127-21-24] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous efforts have been made to elucidate the etiology and improve the treatment of lung cancer, but the overall five-year survival rate is still only 15%. Although cigarette smoking is the primary risk factor for lung cancer, only 7% of female lung cancer patients in Taiwan have a history of smoking. Since cancer results from progressive accumulation of genetic aberrations, genomic rearrangements may be early events in carcinogenesis. RESULTS In order to identify biomarkers of early-stage adenocarcinoma, the genome-wide DNA aberrations of 60 pairs of lung adenocarcinoma and adjacent normal lung tissue in non-smoking women were examined using Affymetrix Genome-Wide Human SNP 6.0 arrays. Common copy number variation (CNV) regions were identified by ≥30% of patients with copy number beyond 2 ± 0.5 of copy numbers for each single nucleotide polymorphism (SNP) and at least 100 continuous SNP variant loci. SNPs associated with lung adenocarcinoma were identified by McNemar's test. Loss of heterozygosity (LOH) SNPs were identified in ≥18% of patients with LOH in the locus. Aberration of SNP rs10248565 at HDAC9 in chromosome 7p21.1 was identified from concurrent analyses of CNVs, SNPs, and LOH. CONCLUSION The results elucidate the genetic etiology of lung adenocarcinoma by demonstrating that SNP rs10248565 may be a potential biomarker of cancer susceptibility.
Collapse
Affiliation(s)
- Liang-Chuan Lai
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Perry NA, Ackermann MA, Shriver M, Hu LYR, Kontrogianni-Konstantopoulos A. Obscurins: unassuming giants enter the spotlight. IUBMB Life 2013; 65:479-86. [PMID: 23512348 DOI: 10.1002/iub.1157] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/31/2013] [Indexed: 02/04/2023]
Abstract
Discovered about a decade ago, obscurin (~720 kDa) is a member of a family of giant proteins expressed in striated muscle that are essential for normal muscle function. Much of what we understand about obscurin stems from its functions in cardiac and skeletal muscle. However, recent evidence has indicated that variants of obscurin ("obscurins") are expressed in diverse cell types, where they contribute to distinct cellular processes. Dysfunction or abrogation of obscurins has also been implicated in the development of several pathological conditions, including cardiac hypertrophy and cancer. Herein, we present an overview of obscurins with an emphasis on novel findings that demonstrate their heretofore-unsuspected importance in cell signaling and disease progression.
Collapse
Affiliation(s)
- Nicole A Perry
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | | | | | | |
Collapse
|
11
|
Veleri S, Bishop K, Dalle Nogare DE, English MA, Foskett TJ, Chitnis A, Sood R, Liu P, Swaroop A. Knockdown of Bardet-Biedl syndrome gene BBS9/PTHB1 leads to cilia defects. PLoS One 2012; 7:e34389. [PMID: 22479622 PMCID: PMC3315532 DOI: 10.1371/journal.pone.0034389] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 03/01/2012] [Indexed: 01/23/2023] Open
Abstract
Bardet-Biedl Syndrome (BBS, MIM#209900) is a genetically heterogeneous disorder with pleiotropic phenotypes that include retinopathy, mental retardation, obesity and renal abnormalities. Of the 15 genes identified so far, seven encode core proteins that form a stable complex called BBSome, which is implicated in trafficking of proteins to cilia. Though BBS9 (also known as PTHB1) is reportedly a component of BBSome, its direct function has not yet been elucidated. Using zebrafish as a model, we show that knockdown of bbs9 with specific antisense morpholinos leads to developmental abnormalities in retina and brain including hydrocephaly that are consistent with the core phenotypes observed in syndromic ciliopathies. Knockdown of bbs9 also causes reduced number and length of cilia in Kupffer's vesicle. We also demonstrate that an orthologous human BBS9 mRNA, but not one carrying a missense mutation identified in BBS patients, can rescue the bbs9 morphant phenotype. Consistent with these findings, knockdown of Bbs9 in mouse IMCD3 cells results in the absence of cilia. Our studies suggest a key conserved role of BBS9 in biogenesis and/or function of cilia in zebrafish and mammals.
Collapse
Affiliation(s)
- Shobi Veleri
- Neurobiology-Neurodegeneration and Repair Laboratory (N-NRL), National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Bishop
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Damian E. Dalle Nogare
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Milton A. English
- Neurobiology-Neurodegeneration and Repair Laboratory (N-NRL), National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Trevor J. Foskett
- Neurobiology-Neurodegeneration and Repair Laboratory (N-NRL), National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ajay Chitnis
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Raman Sood
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paul Liu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory (N-NRL), National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
12
|
Abstract
Wilms' tumour (WT) is the most common malignant renal tumour of childhood. During the past two decades or so, molecular studies carried out on biopsy specimens and tumour-derived cell lines have identified a multitude of chromosomal and epigenetic alterations in WT. In addition, a significant amount of evidence has been gathered to identify the genes and signalling pathways that play a defining role in its genesis, growth, survival and treatment responsiveness. As such, these molecules and mechanisms constitute potential targets for novel therapeutic strategies for refractory WT. In this report we aim to review some of the many candidate genes and intersecting pathways that underlie the complexities of WT biology.
Collapse
|
13
|
Ohshima J, Haruta M, Arai Y, Kasai F, Fujiwara Y, Ariga T, Okita H, Fukuzawa M, Hata JI, Horie H, Kaneko Y. Two candidate tumor suppressor genes, MEOX2 and SOSTDC1, identified in a 7p21 homozygous deletion region in a Wilms tumor. Genes Chromosomes Cancer 2009; 48:1037-50. [PMID: 19760604 DOI: 10.1002/gcc.20705] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A SNP-based array analysis of 100 Wilms tumors (WT) from 97 patients identified 7p alterations (hemizygous and homozygous deletions and uniparental disomy) in nine tumors. The homozygous deletion (HD) region of 7p21 found in one tumor partially overlapped with another HD region reported previously, and was narrowed down to a 2.1-Mb region. Based on an expression analysis of 10 genes located in the HD region in 3 WT lines and previous studies on tumorigenic roles of MEOX2 and SOSTDC1, we further analyzed these two genes. Sequencing showed no mutation in MEOX2, but two missense mutations (L50F and Q129L) in SOSTDC1 in four tumors; L50F in two tumors was of germline origin. Expression levels (0, 1+ and 2+) of MEOX2 were lower in four tumors with 7p alterations than in 18 tumors with no 7p alterations (P = 0.017), and those of SOSTDC1 tended to be lower in five tumors with 7p alterations or SOSTDC1 mutation than in 17 tumors with no 7p alterations or SOSTDC1 mutation (P = 0.056). There were no significant differences in clinical characteristics between nine patients with 7p alterations and 88 patients with no 7p alterations; however, there was a difference in the status of IGF2 (uniparental disomy, loss of imprinting, or retention of imprinting) between the two patient groups (P = 0.028). Losses of MEOX2 and SOSTDC1 may accelerate angiogenesis and augment signals in the Wnt pathway, respectively. Both genes may be prime candidates for 7p tumor suppressor genes, which may have a role in the progression of Wilms tumorigenesis.
Collapse
Affiliation(s)
- Junjiro Ohshima
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Drake KM, Ruteshouser EC, Natrajan R, Harbor P, Wegert J, Gessler M, Pritchard-Jones K, Grundy P, Dome J, Huff V, Jones C, Aldred MA. Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562. Clin Cancer Res 2009; 15:5985-92. [PMID: 19789318 DOI: 10.1158/1078-0432.ccr-09-1065] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Wilms' tumor is a childhood cancer of the kidney with an incidence of approximately 1 in 10,000. Cooccurrence of Wilms' tumor with 2q37 deletion syndrome, an uncommon constitutional chromosome abnormality, has been reported previously in three children. Given these are independently rare clinical entities, we hypothesized that 2q37 harbors a tumor suppressor gene important in Wilms' tumor pathogenesis. EXPERIMENTAL DESIGN To test this, we performed loss of heterozygosity analysis in a panel of 226 sporadic Wilms' tumor samples and mutation analysis of candidate genes. RESULTS Loss of heterozygosity was present in at least 4% of cases. Two tumors harbored homozygous deletions at 2q37.1, supporting the presence of a tumor suppressor gene that follows a classic two-hit model. However, no other evidence of second mutations was found, suggesting that heterozygous deletion alone may be sufficient to promote tumorigenesis in concert with other genomic abnormalities. We show that miR-562, a microRNA within the candidate region, is expressed only in kidney and colon and regulates EYA1, a critical gene for renal development. miR-562 expression is reduced in Wilms' tumor and may contribute to tumorigenesis by deregulating EYA1. Two other candidate regions were localized at 2q37.3 and 2qter, but available data from patients with constitutional deletions suggest that these probably do not confer a high risk for Wilms' tumor. CONCLUSIONS Our data support the presence of a tumor suppressor gene at 2q37.1 and suggest that, in individuals with constitutional 2q37 deletions, any increased risk for developing Wilms' tumor likely correlates with deletions encompassing 2q37.1.
Collapse
Affiliation(s)
- Kylie M Drake
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Song PM, Zhang Y, He YF, Bao HM, Luo JH, Liu YK, Yang PY, Chen X. Bioinformatics analysis of metastasis-related proteins in hepatocellular carcinoma. World J Gastroenterol 2008; 14:5816-22. [PMID: 18855979 PMCID: PMC2751890 DOI: 10.3748/wjg.14.5816] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM: To analyze the metastasis-related proteins in hepatocellular carcinoma (HCC) and discover the biomarker candidates for diagnosis and therapeutic intervention of HCC metastasis with bioinformatics tools.
METHODS: Metastasis-related proteins were determined by stable isotope labeling and MS analysis and analyzed with bioinformatics resources, including Phobius, Kyoto encyclopedia of genes and genomes (KEGG), online mendelian inheritance in man (OMIM) and human protein reference database (HPRD).
RESULTS: All the metastasis-related proteins were linked to 83 pathways in KEGG, including MAPK and p53 signal pathways. Protein-protein interaction network showed that all the metastasis-related proteins were categorized into 19 function groups, including cell cycle, apoptosis and signal transduction. OMIM analysis linked these proteins to 186 OMIM entries.
CONCLUSION: Metastasis-related proteins provide HCC cells with biological advantages in cell proliferation, migration and angiogenesis, and facilitate metastasis of HCC cells. The bird’s eye view can reveal a global characteristic of metastasis-related proteins and many differentially expressed proteins can be identified as candidates for diagnosis and treatment of HCC.
Collapse
|
16
|
|
17
|
Perotti D, Gamba B, Sardella M, Spreafico F, Terenziani M, Collini P, Pession A, Nantron M, Fossati-Bellani F, Radice P. Functional inactivation of the WTX gene is not a frequent event in Wilms' tumors. Oncogene 2008; 27:4625-32. [PMID: 18391980 DOI: 10.1038/onc.2008.93] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
For many years the precise genetic etiology of the majority of Wilms' tumors has remained unexplained. Recently, the WTX gene, mapped to chromosome Xq11.1, has been reported to be lost or mutated in approximately one-third of Wilms' tumors. Moreover, in female cases, the somatically inactivated alleles were found to invariantly derive from the active chromosome X. Consequently, WTX has been proposed as a 'one-hit' tumor suppressor gene. To provide further insights on the contribution of WTX to the development of the disease, we have examined 102 Wilms' tumors, obtained from 43 male and 57 female patients. Quantitative PCR analyses detected WTX deletions in 5 of 45 (11%) tumors from males, whereas loss of heterozygosity at WTX-linked microsatellites was observed in 9 tumors from 50 informative females (19%). However, in the latter group, using a combination of HUMARA assay and bisulfite-modified DNA sequencing, we found that the deletion affected the active chromosome X only in two cases (4%). Sequence analyses detected an inactivating somatic mutation of WTX in a single tumor, in which a strongly reduced expression of the mutant allele respect to the wild-type allele was observed, a finding not consistent with its localization on the active chromosome X. Overall, a functional somatic nullizygosity of the WTX gene was ascertained only in seven of the Wilms' tumors included in the study (approximately 7%). Our findings indicate that previously reported estimates on the proportion of Wilms' tumors due to WTX alterations should be reconsidered.
Collapse
Affiliation(s)
- D Perotti
- Department of Experimental Oncology and Laboratories, Genetic Susceptibility to Cancer Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Mans DA, Voest EE, Giles RH. All along the watchtower: is the cilium a tumor suppressor organelle? Biochim Biophys Acta Rev Cancer 2008; 1786:114-25. [PMID: 18343234 DOI: 10.1016/j.bbcan.2008.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 02/10/2008] [Accepted: 02/14/2008] [Indexed: 01/09/2023]
Abstract
Cilia or flagella have been around since almost the beginning of life, and have now developed specialized cell-type specific functions from locomotion to acting as environmental sensors participating in cell signalling. Genetic defects affecting cilia result in a myriad of pathological instances, including infertility, obesity, blindness, deafness, skeletal malformations, and lung problems. However, the consistency in which the common kidney cyst is coupled with cilia dysfunction has raised interest in the possibility that ciliary dysfunction might contribute to other neoplasms as well. A suite of recent papers convincingly linking cilia to hedgehog signalling, platelet-derived growth factor signalling, Wnt signalling and the von Hippel-Lindau tumor suppressor protein has rapidly expanded the knowledge base connecting cilia to cancer. We propose that these data support the notion of the cilium as a cellular Watchtower, whose absence can be an initiating event in neoplastic growth. Furthermore, we predict that we are just now seeing the tip of the iceberg, and that the list of cancers associated with altered ciliary signalling will grow exponentially in the next few years.
Collapse
Affiliation(s)
- Dorus A Mans
- Department of Medical Oncology, University Medical Center Utrecht, The Netherlands
| | | | | |
Collapse
|
19
|
Unique diagnostic features and successful management of a patient with disseminated lymphangiomatosis and chylothorax. J Pediatr Hematol Oncol 2008; 30:66-9. [PMID: 18176185 DOI: 10.1097/mph.0b013e318159a55a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Disseminated lymphangiomatosis is a rare vascular tumor characterized by a proliferation of abnormal lymphatic channels that often involves multiple organ systems. One particularly morbid manifestation of this disorder is the presence of bony lytic lesions with associated chylothorax. Because of its unusual nature, this condition is often a diagnostic and therapeutic challenge. In this report, we present the diagnostic features, including a unique radiologic finding, and successful management of a 7-year-old girl with this condition using a combination of aggressive surgery and medical treatment with interferon and pamidronate.
Collapse
|
20
|
Balakrishnan A, Bleeker FE, Lamba S, Rodolfo M, Daniotti M, Scarpa A, van Tilborg AA, Leenstra S, Zanon C, Bardelli A. Novel somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res 2007; 67:3545-50. [PMID: 17440062 DOI: 10.1158/0008-5472.can-07-0065] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A recent systematic sequence analysis of well-annotated human protein coding genes or consensus coding sequences led to the identification of 189 genes displaying somatic mutations in breast and colorectal cancers. Based on their mutation prevalence, a subset of these genes was identified as cancer candidate (CAN) genes as they could be potentially involved in cancer. We evaluated the mutational profiles of 19 CAN genes in the highly aggressive tumors: glioblastoma, melanoma, and pancreatic carcinoma. Among other changes, we found novel somatic mutations in EPHA3, MLL3, TECTA, FBXW7, and OBSCN, affecting amino acids not previously found to be mutated in human cancers. Interestingly, we also found a germline nucleotide variant of OBSCN that was previously reported as a somatic mutation. Our results identify specific genetic lesions in glioblastoma, melanoma, and pancreatic cancers and indicate that CAN genes and their mutational profiles are tumor specific. Some of the mutated genes, such as the tyrosine kinase EPHA3, are clearly amenable to pharmacologic intervention and could represent novel therapeutic targets for these incurable cancers. We also speculate that similar to other oncogenes and tumor suppressor genes, mutations affecting OBSCN could be involved in cancer predisposition.
Collapse
Affiliation(s)
- Asha Balakrishnan
- Laboratory of Molecular Genetics, The Oncogenomics Center, Institute for Cancer Research and Treatment, University of Torino Medical School, Candiolo (TO) 10060, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Nishimura DY, Swiderski RE, Searby CC, Berg EM, Ferguson AL, Hennekam R, Merin S, Weleber RG, Biesecker LG, Stone EM, Sheffield VC. Comparative genomics and gene expression analysis identifies BBS9, a new Bardet-Biedl syndrome gene. Am J Hum Genet 2005; 77:1021-33. [PMID: 16380913 PMCID: PMC1285160 DOI: 10.1086/498323] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Accepted: 09/23/2005] [Indexed: 11/03/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive, genetically heterogeneous, pleiotropic human disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Eight BBS genes representing all known mapped loci have been identified. Mutation analysis of the known BBS genes in BBS patients indicate that additional BBS genes exist and/or that unidentified mutations exist in the known genes. To identify new BBS genes, we performed homozygosity mapping of small, consanguineous BBS pedigrees, using moderately dense SNP arrays. A bioinformatics approach combining comparative genomic analysis and gene expression studies of a BBS-knockout mouse model was used to prioritize BBS candidate genes within the newly identified loci for mutation screening. By use of this strategy, parathyroid hormone-responsive gene B1 (B1) was found to be a novel BBS gene (BBS9), supported by the identification of homozygous mutations in BBS patients. The identification of BBS9 illustrates the power of using a combination of comparative genomic analysis, gene expression studies, and homozygosity mapping with SNP arrays in small, consanguineous families for the identification of rare autosomal recessive disorders. We also demonstrate that small, consanguineous families are useful in identifying intragenic deletions. This type of mutation is likely to be underreported because of the difficulty of deletion detection in the heterozygous state by the mutation screening methods that are used in many studies.
Collapse
Affiliation(s)
- Darryl Y. Nishimura
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Ruth E. Swiderski
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Charles C. Searby
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Erik M. Berg
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Amanda L. Ferguson
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Raoul Hennekam
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Saul Merin
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Richard G. Weleber
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Leslie G. Biesecker
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Edwin M. Stone
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Val C. Sheffield
- Departments of Pediatrics and Ophthalmology and Howard Hughes Medical Institute, University of Iowa, Iowa City; Institute of Child Health, University College London, and Great Ormond Street Hospital for Children, National Health Service Trust, London; Department of Ophthalmology, Hadassah Medical Organization, Jerusalem; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland; and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
22
|
Mark HFL, Wyandt H, Pan A, Milunsky JM. Constitutional partial 1q trisomy mosaicism and Wilms tumor. ACTA ACUST UNITED AC 2005; 162:166-71. [PMID: 16213366 DOI: 10.1016/j.cancergencyto.2005.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 05/31/2005] [Accepted: 05/31/2005] [Indexed: 11/26/2022]
Abstract
We report on a female patient with severe-profound mental retardation, multiple congenital anomalies, as well as a history of mosaicism for partial 1q trisomy in the amniotic fluid and a previous Wilms tumor specimen. Peripheral blood and fibroblasts were studied and did not demonstrate the mosaicism initially detected for 1q. Array comparative genomic hybridization yielded negative results. Additional cytogenetic studies helped clarify the previous findings and revealed evidence of partial 1q trisomy mosaicism in normal kidney tissue and in a kidney lesion. GTG-banded results showing low-percentage mosaicism for the structural rearrangement der(1)t(1;1)(p36.1;q23) in both tissues were corroborated by fluorescence in situ hybridization studies. We hypothesize that the partial 1q trisomy predisposed the target tissue (in this case kidney) to neoplasia. This study provides further support for the hypothesis that certain constitutional chromosomal abnormalities can predispose to cancer. As detection of a low-percentage mosaicism may be hampered by the limits imposed by currently available technology and the constraint of a finite sample size, extra vigilance in monitoring other somatic tissues will be needed throughout the patient's lifetime. Anticipatory clinical guidance and prognostication are meaningful only if given accurate cytogenetic diagnoses. To the best of our knowledge, this is the first reported case of Wilms tumor associated with constitutional partial 1q trisomy, either in pure or mosaic form, with the particular 1q23 breakpoint in conjunction with a break on 1p36.1.
Collapse
Affiliation(s)
- Hon Fong L Mark
- Center for Human Genetics, Boston University School of Medicine, MA 02118, USA.
| | | | | | | |
Collapse
|
23
|
Perotti D, De Vecchi G, Testi MA, Lualdi E, Modena P, Mondini P, Ravagnani F, Collini P, Di Renzo F, Spreafico F, Terenziani M, Sozzi G, Fossati-Bellani F, Radice P. Germline mutations of the POU6F2 gene in Wilms tumors with loss of heterozygosity on chromosome 7p14. Hum Mutat 2005; 24:400-7. [PMID: 15459955 DOI: 10.1002/humu.20096] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Wilms tumor (WT) is a kidney malignancy of childhood characterized by highly heterogeneous genetic alterations. We previously reported the molecular and cytogenetic characterization of a WT (Case 30) carrying an interstitial deletion in chromosome 7p14 between markers D7S555 and D7S668. Loss of heterozygosity (LOH) analyses had revealed that this same region was lost in 8 out of 38 examined WTs, suggesting that the identified interval contains a putative tumor suppressor gene. To confirm this hypothesis, in this work, we analyzed an additional 35 WTs, four of which showed LOH in the region of interest. Furthermore, we were able to more accurately define the extension of the deletion in Case 30, mapping it within an interval not exceeding 390 kb, proximally to D7S555. To date, only a single expressed gene, POU6F2 (the POU domain, class 6, transcription factor 2; also known as RPF1), has been recognized in this interval. Sequencing of the gene in the 12 WTs showing LOH and in a corresponding numbers of WT cases without LOH, led to the identification of two germline nucleotide substitutions. The first occurred in the 5'-untranslated region, while the second caused an amino acid change in a glutamine repeat domain. These mutations, whose occurrence was not observed in more than 100 control subjects, were detected in two patients showing the loss of the constitutionally wild-type allele in tumor DNA. Together with the finding of the expression of the POU6F2 mouse homolog in both fetal and adult kidney, our observations suggest that the gene is a tumor suppressor and is involved in hereditary predisposition to WT.
Collapse
Affiliation(s)
- Daniela Perotti
- Department of Experimental Oncology and Laboratories, Istituto Nazionale Tumori, Milan, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Schlomm T, Gunawan B, Schulten HJ, Sander B, Thangavelu K, Graf N, Leuschner I, Ringert RH, Füzesi L. Effects of Chemotherapy on the Cytogenetic Constitution of Wilms' Tumor. Clin Cancer Res 2005; 11:4382-7. [PMID: 15958621 DOI: 10.1158/1078-0432.ccr-04-2123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The management of Wilms' tumors consists of a combination of surgery, chemotherapy, and possibly radiotherapy. To date, chemotherapy is being risk stratified according to histologic subtype and stage. Although the cytogenetic characteristics of Wilms' tumors are well established, the cytogenetic effects related to chemotherapy are widely unknown. We herein report on comparative genomic hybridization findings in 41 primary Wilms' tumors of blastemal type, of which 19 had received preoperative chemotherapy (PCT group) and 22 did not (non-PCT group). Overall, imbalances could be detected in 32 tumors, with +1q (17 cases), +7q (10 cases), +7p (6 cases), and -7p (6 cases) as the most common changes. Among these, +7q and -7p were both significantly associated with metastatic disease at the time of surgery (P = 0.002 and 0.007, respectively), and +7q was also associated with higher stage (stages III + IV; P = 0.003). There were significant differences in the cytogenetic constitution of tumors between the two treatment groups. As a trend, tumors in the preoperative-chemotherapy group had fewer changes (mean, 2.7) than those in the non-preoperative-chemotherapy group (mean, 3.8), and the frequencies of imbalances at 7p or +7q, respectively, were significantly lower compared with tumors in the non-preoperative-chemotherapy group (2 of 19 versus 10 of 22, P = 0.019; 1 of 19 versus 9 of 22, P = 0.011). In contrast, -1q was common in both the preop-CT group (10 of 19) and the non-preop-CT group (7 of 22). The results suggest that Wilms' tumor clones with +1q are not obliterated by preoperative chemotherapy, whereas cytogenetically more complex clones with +7q and/or imbalances at 7p seem more responsive and are more likely to be eliminated by chemotherapeutic treatment.
Collapse
Affiliation(s)
- Thorsten Schlomm
- Department of Urology, University of Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Ganly P, McDonald M, Spearing R, Morris CM. Constitutional t(5;7)(q11;p15) rearranged to acquire monosomy7q and trisomy 1q in a patient with myelodysplastic syndrome transforming to acute myelocytic leukemia. ACTA ACUST UNITED AC 2004; 149:125-30. [PMID: 15036888 DOI: 10.1016/j.cancergencyto.2003.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2003] [Accepted: 07/30/2003] [Indexed: 12/31/2022]
Abstract
We report the case of a 61-year-old woman who presented with a myelodysplastic syndrome (MDS) and a t(5;7)(q11.2;p15) in her bone marrow cells. Subsequent analysis of phytohemagglutinin-stimulated peripheral blood lymphocytes and cultured skin fibroblasts showed that the translocation was constitutional. Disruption of chromosome bands 5q11.2 and 7p15 has been described recurrently in MDS and acute myelocytic leukemia (AML) and, although the age of onset was not earlier than usual, it is nonetheless possible that genes interrupted by this translocation may been a predisposing factor for her condition. With progression to AML, a further rearrangement of the constitutional der(7)t(5;7) occurred, involving chromosome arm 1q. Fluorescence in situ hybridization (FISH) with whole-chromosome paints showed that the result of the second rearrangement, a t(1;7)(q32.1;q32), was observed, leading to trisomy of the segment 1q32.1 approximately qter and monosomy of the segment 7q32.1 approximately qter. The acquired imbalances, particularly loss of 7q, are commonly associated with MDS/AML and a poor prognosis; however, this patient remained in remission after treatment for more than two years before AML relapse, perhaps because the affected regions fall outside of the critical regions of imbalance.
Collapse
MESH Headings
- Bone Marrow Cells
- Cell Transformation, Neoplastic/genetics
- Chromosome Deletion
- Chromosome Painting
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 5
- Chromosomes, Human, Pair 7
- Female
- Humans
- Leukemia, Myeloid, Acute/genetics
- Middle Aged
- Myelodysplastic Syndromes/genetics
- Translocation, Genetic
- Trisomy
Collapse
Affiliation(s)
- Peter Ganly
- Cancer Genetics Research Group, Christchurch School of Medicine, PO Box 4345, Christchurch, New Zealand
| | | | | | | |
Collapse
|