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Hsu YL, Huang MS, Chang HY, Lee CH, Chen DP, Li YH, Chao TH, Liu YW, Liu PY. Application of genetic risk score for in-stent restenosis of second- and third-generation drug-eluting stents in geriatric patients. BMC Geriatr 2023; 23:443. [PMID: 37468836 DOI: 10.1186/s12877-023-04103-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 06/13/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The second-and third-generation drug-eluting stents (DESs) in-stent restenosis (ISR) genetic risk score (GRS) model has been previously validated. However, the model has not been validated in geriatric patients. Therefore, we conducted this study to test the feasibility of the DES-ISR GRS model in geriatric patients with coronary artery disease (CAD) in Taiwan. METHODS We conducted a retrospective, single-center cohort study and included geriatric patients (age ≥ 65 years) with CAD and second-or third-generation DES(s) deployment. Patients undergoing maintenance dialysis were excluded. ISR was defined as ≥ 50% luminal narrowing on the follow-up coronary arteriography. The DES-ISR GRS model included five selected exonic single-nucleotide polymorphisms (SNPs): CAMLG, GALNT2, C11orf84, THOC5, and SAMD11. The GRS was defined as the sum of the five selected SNPs for the risk allele. RESULTS We enrolled 298 geriatric patients from January 2010 and December 2019 in this study. After propensity score matching, there were 192 geriatric patients with CAD in the final analysis, of which 32 patients had ISR. Patients were divided into two groups based on their GRS values: low (0-2) and high (≥ 3) GRS. A high GRS was significantly associated with DES-ISR in geriatric patients. CONCLUSION Those geriatric patients with a high GRS had significantly higher second-or third-generation DES ISR rates. The five SNP-derived DES-ISR GRS model could provide genetic information for interventional cardiologists to treat geriatric patients with CAD. TRIAL REGISTRATION The primary study protocol was registered with clinicaltrials.org. with registration number: NCT03877614; on March 15, 2019. ( http://clinicaltrials.gov/ct2/show/NCT03877614 ).
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Affiliation(s)
- Yu-Ling Hsu
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Mu-Shiang Huang
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Hsien-Yuan Chang
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, 138 Sheng-Li Rd. North District, Tainan, 704, Taiwan
| | - Cheng-Han Lee
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Dao-Peng Chen
- KimForest Enterprise Co., Ltd, New Taipei City, 221, Taiwan
| | - Yi-Heng Li
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Ting-Hsin Chao
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Yen-Wen Liu
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan.
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, 138 Sheng-Li Rd. North District, Tainan, 704, Taiwan.
| | - Ping-Yen Liu
- Division of Cardiology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan.
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, 138 Sheng-Li Rd. North District, Tainan, 704, Taiwan.
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2
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Skerrett-Byrne DA, Nixon B, Bromfield EG, Breen J, Trigg NA, Stanger SJ, Bernstein IR, Anderson AL, Lord T, Aitken RJ, Roman SD, Robertson SA, Schjenken JE. Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide. BMC Genomics 2021; 22:728. [PMID: 34625024 PMCID: PMC8499523 DOI: 10.1186/s12864-021-07951-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The seminal vesicles synthesise bioactive factors that support gamete function, modulate the female reproductive tract to promote implantation, and influence developmental programming of offspring phenotype. Despite the significance of the seminal vesicles in reproduction, their biology remains poorly defined. Here, to advance understanding of seminal vesicle biology, we analyse the mouse seminal vesicle transcriptome under normal physiological conditions and in response to acute exposure to the reproductive toxicant acrylamide. Mice were administered acrylamide (25 mg/kg bw/day) or vehicle control daily for five consecutive days prior to collecting seminal vesicle tissue 72 h following the final injection. RESULTS A total of 15,304 genes were identified in the seminal vesicles with those encoding secreted proteins amongst the most abundant. In addition to reproductive hormone pathways, functional annotation of the seminal vesicle transcriptome identified cell proliferation, protein synthesis, and cellular death and survival pathways as prominent biological processes. Administration of acrylamide elicited 70 differentially regulated (fold-change ≥1.5 or ≤ 0.67) genes, several of which were orthogonally validated using quantitative PCR. Pathways that initiate gene and protein synthesis to promote cellular survival were prominent amongst the dysregulated pathways. Inflammation was also a key transcriptomic response to acrylamide, with the cytokine, Colony stimulating factor 2 (Csf2) identified as a top-ranked upstream driver and inflammatory mediator associated with recovery of homeostasis. Early growth response (Egr1), C-C motif chemokine ligand 8 (Ccl8), and Collagen, type V, alpha 1 (Col5a1) were also identified amongst the dysregulated genes. Additionally, acrylamide treatment led to subtle changes in the expression of genes that encode proteins secreted by the seminal vesicle, including the complement regulator, Complement factor b (Cfb). CONCLUSIONS These data add to emerging evidence demonstrating that the seminal vesicles, like other male reproductive tract tissues, are sensitive to environmental insults, and respond in a manner with potential to exert impact on fetal development and later offspring health.
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Affiliation(s)
- David A Skerrett-Byrne
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Elizabeth G Bromfield
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia.,Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - James Breen
- The Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Genomics Centre (SAGC), South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Computational & Systems Biology Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Adelaide Medical School, Faculty of Health & Medical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Natalie A Trigg
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Simone J Stanger
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Ilana R Bernstein
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Amanda L Anderson
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Tessa Lord
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - R John Aitken
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Shaun D Roman
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia
| | - Sarah A Robertson
- The Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Adelaide Medical School, Faculty of Health & Medical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - John E Schjenken
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia. .,Hunter Medical Research Institute, Pregnancy and Reproduction Program, New Lambton Heights, NSW, 2305, Australia.
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3
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Genetic risk model for in-stent restenosis of second-and third-generation drug-eluting stents. iScience 2021; 24:103082. [PMID: 34585120 PMCID: PMC8455661 DOI: 10.1016/j.isci.2021.103082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/20/2021] [Accepted: 08/31/2021] [Indexed: 12/02/2022] Open
Abstract
The new generation, i.e., second- and third-generation, drug-eluting stents (DESs) remain a risk of in-stent restenosis (ISR). We evaluated the power of a genetic risk score (GRS) model to identify high-risk populations for new generation DES ISR. We enrolled patients with coronary artery disease (CAD) treated with new generations DESs by a single-center cohort study in Taiwan and evaluated their genetic profile. After propensity score matching, there were 343 patients and 153 patients in the derivation and validation cohorts, respectively. Five selected single-nucleotide polymorphisms (SNPs), i.e., SNPs in CAMLG, GALNT2, C11orf84, THOC5, and SAMD11, were included to calculate the GRS for new generation DES ISR. In the derivation and the validation cohorts, patients with a GRS greater than or equal to 3 had significantly higher new generation DES ISR rates. We provide biological information for interventional cardiologists prior to percutaneous coronary intervention by specific five SNP-derived GRS. A validated GRS model identified high-risk population for new generation DES ISR This GRS includes 5 SNPs in exons: CAMLG, GALNT2, C11orf84, THOC5, and SAMD11 The patients with high GRSs (≥3) had higher rates of new generation DES ISR The GRS provides crucial information in shared decision-making process clinically
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4
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Azli B, Ravi S, Hair-Bejo M, Omar AR, Ideris A, Mat Isa N. Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection. BMC Genomics 2021; 22:461. [PMID: 34147086 PMCID: PMC8214787 DOI: 10.1186/s12864-021-07690-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation's food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. We had looked at identified novel genes that could elucidate the pathogenicity of the virus following infection and at possible disease resistance genes present in chickens. RESULTS A set of sequences retrieved from IBD virus-infected chickens that did not map to the chicken reference genome were de novo assembled, clustered and analysed. From six inbred chicken lines, we managed to assemble 10,828 uni-transcripts and screened 618 uni-transcripts which were the most significant sequences to known genes, as determined by BLASTX searches. Based on the differentially expressed genes (DEGs) analysis, 12 commonly upregulated and 18 downregulated uni-genes present in all six inbred lines were identified with false discovery rate of q-value < 0.05. Yet, only 9 upregulated and 13 downregulated uni-genes had BLAST hits against the Non-redundant and Swiss-Prot databases. The genome ontology enrichment keywords of these DEGs were associated with immune response, cell signalling and apoptosis. Consequently, the Weighted Gene Correlation Network Analysis R tool was used to predict the functional annotation of the remaining unknown uni-genes with no significant BLAST hits. Interestingly, the functions of the three upregulated uni-genes were predicted to be related to innate immune response, while the five downregulated uni-genes were predicted to be related to cell surface functions. These results further elucidated and supported the current molecular knowledge regarding the pathophysiology of chicken's bursal infected with IBDV. CONCLUSION Our data revealed the commonly up- and downregulated novel uni-genes identified to be immune- and extracellular binding-related, respectively. Besides, these novel findings are valuable contributions in improving the current existing integrative chicken transcriptomics annotation and may pave a path towards the control of viral particles especially towards the suppression of IBD and other infectious diseases in chickens.
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Affiliation(s)
- Bahiyah Azli
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Sharanya Ravi
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Mohd Hair-Bejo
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Abdul Rahman Omar
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Aini Ideris
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Nurulfiza Mat Isa
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
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5
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Huang B, Jin G, Qu C, Ma H, Ding C, Zhang Y, Liu W, Li W. Elevated Expression of NOTCH1 Associates with Lymph Node Metastasis of Gastric Cancer and Knock-Down of NOTCH1 Attenuates Tumor Cell Progression. Med Sci Monit 2019; 25:9939-9948. [PMID: 31874951 PMCID: PMC6944039 DOI: 10.12659/msm.918703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Gastric cancer is the third leading cause of cancer-related death, while its molecular mechanism has not been fully clarified. This study aims to explore the role of Notch signaling in the pathogenesis of gastric cancer. MATERIAL AND METHODS A total of 64 patients with gastric cancer were enrolled. The expressions of NOTCH1 in tumor tissues and adjacent non-tumor tissues were detected by immunohistochemistry staining. The correlation between NOTCH1 expression and clinicopathological features of patients was analyzed. NOTCH1 was knocked down in gastric cancer cells. The effects of NOTCH1 blockade on cell proliferation, migration and cell cycle distribution were analyzed. The expressions of ERK1/2 and phospho-ERK1/2 (p-ERK1/2) were detected using western blotting. RESULTS Gastric cancer tissues expressed higher level of NOTCH1 than adjacent non-tumor tissues (P<0.05). The high level of NOTCH1 was found to be correlated with gender (male) and lymph node metastasis. However, the expression level of NOTCH1 did not affect the overall survival of patients with gastric cancer. NOTCH1 knock-down repressed the migration and proliferation of gastric cancer cells. Moreover, the cell cycle was arrested at G0/G1 phase by NOTCH1 blockade. The expressions of ERK1/2 and p-ERK1/2 decreased with NOTCH1 knock-down. Further inhibition of ERK1/2 signaling by a MEK1/2 inhibitor U0126 reduced the proliferation of AGS cells, which aggravated the inhibition effect of NOTCH1 knock-down on cell proliferation. CONCLUSIONS NOTCH1 may play an oncogenic role in gastric cancer. Inhibition of NOTCH1 can efficiently attenuate gastric cancer cell progression, probably in part through cross-talking with ERK1/2 signaling pathway.
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Affiliation(s)
- Bo Huang
- Department of General Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
| | - Guorong Jin
- Central Laboratory, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
| | - Chongxiao Qu
- Department of Pathology, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
| | - Haining Ma
- Department of General Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
| | - Caiyun Ding
- Central Laboratory, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
| | - Yali Zhang
- Department of Pathology, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
| | - Weiwei Liu
- Department of Blood Transfusion, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Weibing Li
- Department of General Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China (mainland)
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6
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Chapman NH, Bernier RA, Webb SJ, Munson J, Blue EM, Chen DH, Heigham E, Raskind WH, Wijsman EM. Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. Hum Genet 2018; 137:807-815. [PMID: 30276537 PMCID: PMC6309233 DOI: 10.1007/s00439-018-1939-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/22/2018] [Indexed: 01/15/2023]
Abstract
Hundreds of genes have been implicated in autism spectrum disorders (ASDs). In genetically heterogeneous conditions, large families with multiple affected individuals provide strong evidence implicating a rare variant, and replication of the same variant in multiple families is unusual. We previously published linkage analyses and follow-up exome sequencing in seven large families with ASDs, implicating 14 rare exome variants. These included rs200195897, which was transmitted to four affected individuals in one family. We attempted replication of those variants in the MSSNG database. MSSNG is a unique resource for replication of ASD risk loci, containing whole genome sequence (WGS) on thousands of individuals diagnosed with ASDs and family members. For each exome variant, we obtained all carriers and their relatives in MSSNG, using a TDT test to quantify evidence for transmission and association. We replicated the transmission of rs200195897 to four affected individuals in three additional families. rs200195897 was also present in three singleton affected individuals, and no unaffected individuals other than transmitting parents. We identified two additional rare variants (rs566472488 and rs185038034) transmitted with rs200195897 on 1p36.33. Sanger sequencing confirmed the presence of these variants in the original family segregating rs200195897. To our knowledge, this is the first example of a rare haplotype being transmitted with ASD in multiple families. The candidate risk variants include a missense mutation in SAMD11, an intronic variant in NOC2L, and a regulatory region variant close to both genes. NOC2L is a transcription repressor, and several genes involved in transcription regulation have been previously associated with ASDs.
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Affiliation(s)
- N H Chapman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - R A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - S J Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - J Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - E M Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - D-H Chen
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - E Heigham
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - W H Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
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7
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Corton M, Avila-Fernández A, Campello L, Sánchez M, Benavides B, López-Molina MI, Fernández-Sánchez L, Sánchez-Alcudia R, da Silva LRJ, Reyes N, Martín-Garrido E, Zurita O, Fernández-San José P, Pérez-Carro R, García-García F, Dopazo J, García-Sandoval B, Cuenca N, Ayuso C. Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa. Sci Rep 2016; 6:35370. [PMID: 27734943 PMCID: PMC5062157 DOI: 10.1038/srep35370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/28/2016] [Indexed: 01/09/2023] Open
Abstract
Retinitis pigmentosa (RP), the most frequent form of inherited retinal dystrophy is characterized by progressive photoreceptor degeneration. Many genes have been implicated in RP development, but several others remain to be identified. Using a combination of homozygosity mapping, whole-exome and targeted next-generation sequencing, we found a novel homozygous nonsense mutation in SAMD11 in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families. SAMD11 is ortholog to the mouse major retinal SAM domain (mr-s) protein that is implicated in CRX-mediated transcriptional regulation in the retina. Accordingly, protein-protein network analysis revealed a significant interaction of SAMD11 with CRX. Immunoblotting analysis confirmed strong expression of SAMD11 in human retina. Immunolocalization studies revealed SAMD11 was detected in the three nuclear layers of the human retina and interestingly differential expression between cone and rod photoreceptors was observed. Our study strongly implicates SAMD11 as novel cause of RP playing an important role in the pathogenesis of human degeneration of photoreceptors.
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Affiliation(s)
- M Corton
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - A Avila-Fernández
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - L Campello
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - M Sánchez
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - B Benavides
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - M I López-Molina
- Department of Ophthalmology, Health Research Institute- Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain
| | - L Fernández-Sánchez
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - R Sánchez-Alcudia
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - L R J da Silva
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Universidade de Mogi das Cruzes, São Paulo, Brazil
| | - N Reyes
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - E Martín-Garrido
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - O Zurita
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - P Fernández-San José
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - R Pérez-Carro
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - F García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Bioinformatics in Rare Diseases (BIER), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - J Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Bioinformatics in Rare Diseases (BIER), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain.,Functional Genomics Node (INB), Valencia, Spain
| | - B García-Sandoval
- Department of Ophthalmology, Health Research Institute- Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain
| | - N Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - C Ayuso
- Department of Genetics &Genomics, Health Research Institute-Jiménez Díaz Foundation University Hospital (IIS-FJD), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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Chapman NH, Nato AQ, Bernier R, Ankenman K, Sohi H, Munson J, Patowary A, Archer M, Blue EM, Webb SJ, Coon H, Raskind WH, Brkanac Z, Wijsman EM. Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. Hum Genet 2015; 134:1055-68. [PMID: 26204995 PMCID: PMC4578871 DOI: 10.1007/s00439-015-1585-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/11/2015] [Indexed: 12/26/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders, characterized by impairment in communication and social interactions, and by repetitive behaviors. ASDs are highly heritable, and estimates of the number of risk loci range from hundreds to >1000. We considered 7 extended families (size 12-47 individuals), each with ≥3 individuals affected by ASD. All individuals were genotyped with dense SNP panels. A small subset of each family was typed with whole exome sequence (WES). We used a 3-step approach for variant identification. First, we used family-specific parametric linkage analysis of the SNP data to identify regions of interest. Second, we filtered variants in these regions based on frequency and function, obtaining exactly 200 candidates. Third, we compared two approaches to narrowing this list further. We used information from the SNP data to impute exome variant dosages into those without WES. We regressed affected status on variant allele dosage, using pedigree-based kinship matrices to account for relationships. The p value for the test of the null hypothesis that variant allele dosage is unrelated to phenotype was used to indicate strength of evidence supporting the variant. A cutoff of p = 0.05 gave 28 variants. As an alternative third filter, we required Mendelian inheritance in those with WES, resulting in 70 variants. The imputation- and association-based approach was effective. We identified four strong candidate genes for ASD (SEZ6L, HISPPD1, FEZF1, SAMD11), all of which have been previously implicated in other studies, or have a strong biological argument for their relevance.
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Affiliation(s)
- Nicola H Chapman
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Alejandro Q Nato
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Katy Ankenman
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Harkirat Sohi
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Center on Child Development and Disability, University of Washington, Seattle, WA, USA
| | - Ashok Patowary
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Marilyn Archer
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Elizabeth M Blue
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Sara Jane Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Center on Child Development and Disability, University of Washington, Seattle, WA, USA
| | - Hilary Coon
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Psychiatry, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Wendy H Raskind
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- University of Washington, University of Washington Tower, T15, 4333 Brooklyn Ave, NE, BOX 359460, Seattle, WA, 98195-9460, USA.
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