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Hsi RS, Zhang S, Triozzi JL, Hung AM, Xu Y, Bejan CA. Evaluation of Genetic Associations with Clinical Phenotypes of Kidney Stone Disease. EUR UROL SUPPL 2024; 67:38-44. [PMID: 39156495 PMCID: PMC11327546 DOI: 10.1016/j.euros.2024.07.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2024] [Indexed: 08/20/2024] Open
Abstract
Background and objective Previous studies have reported a strong genetic contribution to kidney stone risk. This study aims to identify genetic associations of kidney stone disease within a large-scale electronic health record system. Methods We performed genome-wide association studies (GWASs) for nephrolithiasis from genotyped samples of 5571 cases and 83 692 controls. This analysis included a primary GWAS focused on nephrolithiasis and subsequent subgroup GWASs stratified by stone composition types. For significant risk variants, we performed association analyses with stone composition and first-time 24-h urine parameters. To assess disease severity, we investigated the associations with age at first stone diagnosis, age at first stone-related procedure, and time between first and second stone-related procedures. Key findings and limitations The primary GWAS analysis identified ten significant loci, all located on chromosome 16 within coding regions of the UMOD gene. The strongest signal was rs28544423 (odds ratio 1.17, 95% confidence interval 1.11-1.23, p = 2.7 × 10-9). In subgroup GWASs stratified by six kidney stone composition subtypes, 19 significant loci were identified including two loci in coding regions (brushite; NXPH1, rs79970906 and rs4725104). The UMOD single nucleotide polymorphism rs28544423 was associated with differences in 24-h excretion of urinary analytes, and the minor allele was positively associated with calcium oxalate dihydrate stone composition (p < 0.05). No associations were found between UMOD variants and disease severity. Limitations include an omitted variable bias and a misclassification bias. Conclusions and clinical implications We replicated germline variants associated with kidney stone disease risk at UMOD and reported novel variants associated with stone composition. Genetic variants of UMOD are associated with differences in 24-h urine parameters and stone composition, but not disease severity. Patient summary We identify genetic variants linked to kidney stone disease within an electronic health record (EHR) system. These findings suggest a role for the EHR to enable a precision-medicine approach for stone disease.
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Affiliation(s)
- Ryan S. Hsi
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Siwei Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jefferson L. Triozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adriana M. Hung
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- VA Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical informatics, Vanderbilt University, Nashville, TN, USA
| | - Cosmin A. Bejan
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
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Hsi RS, Zhang S, Triozzi JL, Hung AM, Xu Y, Bejan CA. Evaluation of genetic associations with clinical phenotypes of kidney stone disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301501. [PMID: 38343797 PMCID: PMC10854345 DOI: 10.1101/2024.01.18.24301501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Introduction and Objective We sought to replicate and discover genetic associations of kidney stone disease within a large-scale electronic health record (EHR) system. Methods We performed genome-wide association studies (GWASs) for nephrolithiasis from genotyped samples of 5,571 cases and 83,692 controls. Among the significant risk variants, we performed association analyses of stone composition and first-time 24-hour urine parameters. To assess disease severity, we investigated the associations of risk variants with age at first stone diagnosis, age at first procedure, and time from first to second procedure. Results The main GWAS analysis identified 10 significant loci, each located on chromosome 16 within coding regions of the UMOD gene, which codes for uromodulin, a urine protein with inhibitory activity for calcium crystallization. The strongest signal was from SNP 16:20359633-C-T (odds ratio [OR] 1.17, 95% CI 1.11-1.23), with the remaining significant SNPs having similar effect sizes. In subgroup GWASs by stone composition, 19 significant loci were identified, of which two loci were located in coding regions (brushite; NXPH1 , rs79970906 and rs4725104). The UMOD SNP 16:20359633-C-T was associated with differences in 24-hour excretion of urinary calcium, uric acid, phosphorus, sulfate; and the minor allele was positively associated with calcium oxalate dihydrate stone composition (p<0.05). No associations were found between UMOD variants and disease severity. Conclusions We replicated germline variants associated with kidney stone disease risk at UMOD and reported novel variants associated with stone composition. Genetic variants of UMOD are associated with differences in 24-hour urine parameters and stone composition, but not disease severity.
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Increased Expression of NXPH4 Correlates with Immune Cell Infiltration and Unfavorable Prognosis in Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:5005747. [PMID: 36245978 PMCID: PMC9560829 DOI: 10.1155/2022/5005747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading malignant carcinomas. Despite the advancement in the treatment for HCC, such as precise hepatectomy, radiotherapy, transarterial therapies, chemotherapy, targeted treatments, and immunotherapy, the 5-year overall survival rate of HCC is extremely low. Hence, novel biomarkers are urgently needed for advancing the therapy and prognosis of HCC. Neurexophilin 4 (NXPH4) is a neuropeptide-like glycoprotein. The study is designed to investigate the function of NXPH4 in HCC through a comprehensive bioinformatics analysis. NXPH4 expression status and prognostic values were analyzed via multiple datasets, such as TCGA, GEO, and ICGC. The association between NXPH4 and immune cell infiltration was estimated by TIMER, TISIDB, and CIBERSORT. In vitro, we explored the biological function of NXPH4 in JHH7 and SNU182 cells through knocking down the expression of NXPH4 via siRNA. In general, NXPH4 was predominantly upregulated in HCC tumors, and increased NXPH4 expression predicted unfavorable prognosis. The gene enrichment analysis displayed that NXPH4 was related with metabolic pathways. NXPH4 expression was correlated with immune cell infiltration. NXPH4 knockdown significantly suppressed proliferation, migration, and invasion of JHH7 and SNU182 cells. This study suggested that the upregulation of NXPH4 is associated with adverse prognosis and immune cell infiltration in HCC. NXPH4 could be a novel biomarker of unfavorable prognosis and an underlying target for immunotherapy in HCC.
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Sun X, Xin S, Jin L, Zhang Y, Ye L. Neurexophilin 4 is a prognostic biomarker correlated with immune infiltration in bladder cancer. Bioengineered 2022; 13:13986-13999. [PMID: 35758021 PMCID: PMC9276049 DOI: 10.1080/21655979.2022.2085284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Recent studies have shown that NXPH family member 4 (NXPH4) plays an important role in the progression of cancer. However, the potential role of NXPH4 in bladder cancer (BCa) remains to be explored. The purpose of the present study was to identify whether NXPH4 could be used as a biomarker to predict the prognosis of BCa. We first examined the expression of NXPH4 in pan-cancer, and then focused on BCa. Univariate and multivariate Cox regression analysis were used to investigate whether NXPH4 could be used as an independent prognostic indicator. Gene set enrichment analysis (GSEA) was used for functional analysis of NXPH4-related genes. CIBERSORT algorithm was used to calculate immune cell infiltration levels with different NXPH4 expression. Finally, the expression of NXPH4 was validated in clinical tissue specimens and bladder cancer cell lines by immunohistochemistry and qRT-PCR. The tumor-promoting effects of NXPH4 were further investigated using counting kit-8 (CCK-8), colony formation, EdU assays, and tumor xenograft model. Our results showed that NXPH4 was highly expressed in BCa tissues. Patients in the high NXPH4 expression group had shorter overall survival (OS) and progression-free survival (PFS). We found that immune-related pathways were enriched in NXPH4-related genes. Immune cell infiltrations in BCa were also associated with different NXPH4 expression. NXPH4 was further found to be highly expressed in our validation specimens. The proliferative effect of NXPH4 was confirmed in BCa in vivo and in vitro. Overall, NXPH4 is a biomarker for predicting BCa prognosis and associated with immune infiltration.Abbreviations: NXPH4: Neurexophilin 4; BCa: Bladder cancer; TCGA-BLCA: The Cancer Genome Atlas Urothelial Bladder Carcinoma; shRNA: short hairpin RNA; NC: Negative control; OS: Overall survival; PFS: Progression-free survival; TME: Tumor microenvironment; IPS: immunophenoscore; ICIs: Immune checkpoint inhibitors; DEGs: Differential expression genes.
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Affiliation(s)
- Xianchao Sun
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liang Jin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ying Zhang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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Dashti H, Dehzangi I, Bayati M, Breen J, Beheshti A, Lovell N, Rabiee HR, Alinejad-Rokny H. Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. BMC Bioinformatics 2022; 23:138. [PMID: 35439935 PMCID: PMC9017053 DOI: 10.1186/s12859-022-04652-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/24/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Recent studies have observed causative mutations in susceptible genes related to colorectal cancer in 10 to 15% of the patients. This highlights the importance of identifying mutations for early detection of this cancer for more effective treatments among high risk individuals. Mutation is considered as the key point in cancer research. Many studies have performed cancer subtyping based on the type of frequently mutated genes, or the proportion of mutational processes. However, to the best of our knowledge, combination of these features has never been used together for this task. This highlights the potential to introduce better and more inclusive subtype classification approaches using wider range of related features to enable biomarker discovery and thus inform drug development for CRC. RESULTS In this study, we develop a new pipeline based on a novel concept called 'gene-motif', which merges mutated gene information with tri-nucleotide motif of mutated sites, for colorectal cancer subtype identification. We apply our pipeline to the International Cancer Genome Consortium (ICGC) CRC samples and identify, for the first time, 3131 gene-motif combinations that are significantly mutated in 536 ICGC colorectal cancer samples. Using these features, we identify seven CRC subtypes with distinguishable phenotypes and biomarkers, including unique cancer related signaling pathways, in which for most of them targeted treatment options are currently available. Interestingly, we also identify several genes that are mutated in multiple subtypes but with unique sequence contexts. CONCLUSION Our results highlight the importance of considering both the mutation type and mutated genes in identification of cancer subtypes and cancer biomarkers. The new CRC subtypes presented in this study demonstrates distinguished phenotypic properties which can be effectively used to develop new treatments. By knowing the genes and phenotypes associated with the subtypes, a personalized treatment plan can be developed that considers the specific phenotypes associated with their genomic lesion.
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Affiliation(s)
- Hamed Dashti
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, 11365, Tehran, Iran
| | - Iman Dehzangi
- Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, NJ, 08102, USA
| | - Masroor Bayati
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, 11365, Tehran, Iran
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, 5006, Australia.,Bioinformatics Hub, University of Adelaide, Adelaide, SA, 5006, Australia
| | - Amin Beheshti
- Department of Computing, Macquarie University, Sydney, NSW, 2109, Australia
| | - Nigel Lovell
- Tyree Institute of Health Engineering and The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Hamid R Rabiee
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, 11365, Tehran, Iran.
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia. .,UNSW Data Science Hub, The University of New South Wales, Sydney, NSW, 2052, Australia. .,Health Data Analytics Program, AI-Enabled Processes (AIP) Research Centre, Macquarie University, Sydney, 2109, Australia.
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Castro K, Ntranos A, Amatruda M, Petracca M, Kosa P, Chen EY, Morstein J, Trauner D, Watson CT, Kiebish MA, Bielekova B, Inglese M, Katz Sand I, Casaccia P. Body Mass Index in Multiple Sclerosis modulates ceramide-induced DNA methylation and disease course. EBioMedicine 2019; 43:392-410. [PMID: 30981648 PMCID: PMC6557766 DOI: 10.1016/j.ebiom.2019.03.087] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/24/2019] [Accepted: 03/29/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Multiple Sclerosis (MS) results from genetic predisposition and environmental variables, including elevated Body Mass Index (BMI) in early life. This study addresses the effect of BMI on the epigenome of monocytes and disease course in MS. METHODS Fifty-four therapy-naive Relapsing Remitting (RR) MS patients with high and normal BMI received clinical and MRI evaluation. Blood samples were immunophenotyped, and processed for unbiased plasma lipidomic profiling and genome-wide DNA methylation analysis of circulating monocytes. The main findings at baseline were validated in an independent cohort of 91 therapy-naïve RRMS patients. Disease course was evaluated by a two-year longitudinal follow up and mechanistic hypotheses tested in human cell cultures and in animal models of MS. FINDINGS Higher monocytic counts and plasma ceramides, and hypermethylation of genes involved in negative regulation of cell proliferation were detected in the high BMI group of MS patients compared to normal BMI. Ceramide treatment of monocytic cell cultures increased proliferation in a dose-dependent manner and was prevented by DNA methylation inhibitors. The high BMI group of MS patients showed a negative correlation between monocytic counts and brain volume. Those subjects at a two-year follow-up showed increased T1 lesion load, increased disease activity, and worsened clinical disability. Lastly, the relationship between body weight, monocytic infiltration, DNA methylation and disease course was validated in mouse models of MS. INTERPRETATION High BMI negatively impacts disease course in Multiple Sclerosis by modulating monocyte cell number through ceramide-induced DNA methylation of anti-proliferative genes. FUND: This work was supported by funds from the Friedman Brain Institute, NIH, and Multiple Sclerosis Society.
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Affiliation(s)
- Kamilah Castro
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NY, New York, United States of America
| | - Achilles Ntranos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, United States of America
| | - Mario Amatruda
- Advanced Science Research Center at The Graduate Center of The City University of New York and Inter-Institutional Center for Glial Biology at Icahn School of Medicine New York, New York, United States of America
| | - Maria Petracca
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, United States of America
| | - Peter Kosa
- Neuroimmunological Disease Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Emily Y Chen
- BERG, LLC. Framingham, MA, United States of America
| | - Johannes Morstein
- Department of Chemistry, New York University, NY, New York, United States of America
| | - Dirk Trauner
- Department of Chemistry, New York University, NY, New York, United States of America
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States of America
| | | | - Bibiana Bielekova
- Neuroimmunological Disease Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Matilde Inglese
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, United States of America
| | - Ilana Katz Sand
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, United States of America
| | - Patrizia Casaccia
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NY, New York, United States of America; Advanced Science Research Center at The Graduate Center of The City University of New York and Inter-Institutional Center for Glial Biology at Icahn School of Medicine New York, New York, United States of America.
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Duek P, Gateau A, Bairoch A, Lane L. Exploring the Uncharacterized Human Proteome Using neXtProt. J Proteome Res 2018; 17:4211-4226. [DOI: 10.1021/acs.jproteome.8b00537] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Staphylococcus aureus colonizes large segments of the human population and causes invasive infections due to its ability to escape phagocytic clearance. During infection, staphylococcal nuclease and adenosine synthase A convert neutrophil extracellular traps to deoxyadenosine (dAdo), which kills phagocytes. The mechanism whereby staphylococcal dAdo intoxicates phagocytes is not known. Here we used CRISPR-Cas9 mutagenesis to show that phagocyte intoxication involves uptake of dAdo via the human equilibrative nucleoside transporter 1, dAdo conversion to dAMP by deoxycytidine kinase and adenosine kinase, and signaling via subsequent dATP formation to activate caspase-3-induced cell death. Disruption of this signaling cascade confers resistance to dAdo-induced intoxication of phagocytes and may provide therapeutic opportunities for the treatment of infections caused by antibiotic-resistant S. aureus strains.
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Seielstad M, Page GP, Gaddis N, Lanteri M, Lee TH, Kakaiya R, Barcellos LF, Criswell LA, Triulzi D, Norris PJ, Busch MP. Genomewide association study of HLA alloimmunization in previously pregnant blood donors. Transfusion 2018; 58:402-412. [PMID: 29168253 PMCID: PMC5803399 DOI: 10.1111/trf.14402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/21/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Alloimmunization through blood transfusion, transplantation, or circulating fetal cells during pregnancy is a significant concern. Some exposed individuals make alloantibodies while others do not, implying variation in genetic risk factors. STUDY DESIGN AND METHODS We conducted a genomewide association study (GWAS) of 9,427,497 single-nucleotide polymorphisms (SNPs) to identify genetic variants for HLA alloimmunization in previously pregnant blood donors with (n = 752) and without (n = 753) HLA Class I or II alloantibodies. RESULTS A SNP in the neurexophilin 2 (NXPH2) gene surpassed genome-wide significance (p = 2.06 × 10-8 ), with multiple adjacent markers p < 10-6 , for women with anti-Class I alloantibodies only. Little is currently known about the function of NXPH2, although gene family members have been shown to impact immunity. SNPs in the E2F7 gene, a transcription factor related to cell cycle control and cellular proliferation, also approached genomewide significance (p = 2.5 × 10-7 ). CONCLUSION Further work to extend the GWAS approach and to characterize variants in NXPH2 and E2F7 in the context of alloantibody formation is warranted.
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Affiliation(s)
- Mark Seielstad
- Blood Systems Research Institute, San Francisco CA 94118
- Institute for Human Genetics, University of California San Francisco, San Francisco CA 94143
- Department of Laboratory Medicine, University of California San Francisco, San Francisco CA 94143
| | | | | | - Marion Lanteri
- Blood Systems Research Institute, San Francisco CA 94118
| | - Tzong-Hae Lee
- Blood Systems Research Institute, San Francisco CA 94118
| | | | - Lisa F. Barcellos
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Lindsey A. Criswell
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143
| | - Darrell Triulzi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213
| | - Philip J. Norris
- Blood Systems Research Institute, San Francisco CA 94118
- Department of Laboratory Medicine, University of California San Francisco, San Francisco CA 94143
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143
| | - Michael P. Busch
- Blood Systems Research Institute, San Francisco CA 94118
- Department of Laboratory Medicine, University of California San Francisco, San Francisco CA 94143
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Harkin LF, Lindsay SJ, Xu Y, Alzu'bi A, Ferrara A, Gullon EA, James OG, Clowry GJ. Neurexins 1-3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex. Cereb Cortex 2017; 27:216-232. [PMID: 28013231 PMCID: PMC5654756 DOI: 10.1093/cercor/bhw394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 12/02/2016] [Indexed: 12/17/2022] Open
Abstract
Neurexins (NRXNs) are presynaptic terminal proteins and candidate neurodevelopmental disorder susceptibility genes; mutations presumably upset synaptic stabilization and function. However, analysis of human cortical tissue samples by RNAseq and quantitative real-time PCR at 8-12 postconceptional weeks, prior to extensive synapse formation, showed expression of all three NRXNs as well as several potential binding partners. However, the levels of expression were not identical; NRXN1 increased with age and NRXN2 levels were consistently higher than for NRXN3. Immunohistochemistry for each NRXN also revealed different expression patterns at this stage of development. NRXN1 and NRXN3 immunoreactivity was generally strongest in the cortical plate and increased in the ventricular zone with age, but was weak in the synaptogenic presubplate (pSP) and marginal zone. On the other hand, NRXN2 colocalized with synaptophysin in neurites of the pSP, but especially with GAP43 and CASK in growing axons of the intermediate zone. Alternative splicing modifies the role of NRXNs and we found evidence by RNAseq for exon skipping at splice site 4 and concomitant expression of KHDBRS proteins which control this splicing. NRXN2 may play a part in early cortical synaptogenesis, but NRXNs could have diverse roles in development including axon guidance, and intercellular communication between proliferating cells and/or migrating neurons.
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Affiliation(s)
- Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: School of Healthcare Science, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: Wellcome Trust, Sanger Institute, Cambridge, CB10 1SA, UK
| | - Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Alexandra Ferrara
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Emily A Gullon
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Owen G James
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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Silverman-Gavrila RV, Silverman-Gavrila LB, Bilal KH, Bendeck MP. Spectrin alpha is important for rear polarization of the microtubule organizing center during migration and spindle pole assembly during division of neointimal smooth muscle cells. Cytoskeleton (Hoboken) 2015; 72:157-70. [DOI: 10.1002/cm.21222] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 01/31/2015] [Accepted: 04/07/2015] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Khawaja Hasan Bilal
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Canada
| | - Michelle P. Bendeck
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Canada
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12
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Wouters MM, Lambrechts D, Knapp M, Cleynen I, Whorwell P, Agréus L, Dlugosz A, Schmidt PT, Halfvarson J, Simrén M, Ohlsson B, Karling P, Van Wanrooy S, Mondelaers S, Vermeire S, Lindberg G, Spiller R, Dukes G, D'Amato M, Boeckxstaens G. Genetic variants in CDC42 and NXPH1 as susceptibility factors for constipation and diarrhoea predominant irritable bowel syndrome. Gut 2014; 63:1103-11. [PMID: 24041540 DOI: 10.1136/gutjnl-2013-304570] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The complex genetic aetiology underlying irritable bowel syndrome (IBS) needs to be assessed in large-scale genetic studies. Two independent IBS cohorts were genotyped to assess whether genetic variability in immune, neuronal and barrier integrity genes is associated with IBS. DESIGN 384 single nucleotide polymorphisms (SNPs) covering 270 genes were genotyped in an exploratory cohort (935 IBS patients, 639 controls). 33 SNPs with Puncorrected<0.05 were validated in an independent set of 497 patients and 887 controls. Genotype distributions of single SNPs were assessed using an additive genetic model in IBS and clinical subtypes, IBS-C and IBS-D, both in individual and combined cohorts. Trait anxiety (N=614 patients, 533 controls), lifetime depression (N=654 patients, 533 controls) and mRNA expression in rectal biopsies (N=22 patients, 29 controls) were correlated with SNP genotypes. RESULTS Two SNPs associated independently in the exploratory and validation cohort: rs17837965-CDC42 with IBS-C (ORexploratory=1.59 (1.05 to 1.76); ORvalidation=1.76 (1.03 to 3.01)) and rs2349775-NXPH1 with IBS-D (ORexploratory=1.28 (1.06 to 1.56); ORvalidation=1.42 (1.08 to 1.88)). When combining both cohorts, the association of rs2349775 withstood post hoc correction for multiple testing in the IBS-D subgroup. Additionally, three SNPs in immune-related genes (rs1464510-LPP, rs1881457-IL13, rs2104286-IL2RA), one SNP in a neuronal gene (rs2349775-NXPH1) and two SNPs in epithelial genes (rs245051-SLC26A2, rs17837965-CDC42) were weakly associated with total-IBS (Puncorrected<0.05). At the functional level, rs1881457 increased IL13 mRNA levels, whereas anxiety and depression scores did not correlate with rs2349775-NXPH1. CONCLUSIONS Rs2349775 (NXPH1) and rs17837965 (CDC42) were associated with IBS-D and IBS-C, respectively, in two independent cohorts. Further studies are warranted to validate our findings and to determine the mechanisms underlying IBS pathophysiology.
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Affiliation(s)
- Mira M Wouters
- Translational Research Center for Gastrointestinal Disorders, Leuven University, Leuven, Belgium
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven University, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, Leuven University, Leuven, Belgium
| | - Michael Knapp
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Isabelle Cleynen
- Translational Research Center for Gastrointestinal Disorders, Leuven University, Leuven, Belgium
| | - Peter Whorwell
- Department of Medicine, University of Manchester, Manchester, UK
| | - Lars Agréus
- Centre for Family Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aldona Dlugosz
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Jonas Halfvarson
- Department of Internal Medicine, Örebro University Hospital, Örebro, Sweden
| | - Magnus Simrén
- Department of Internal Medicine, Gothenburg University, Gothenburg, Sweden
| | - Bodil Ohlsson
- Department of Clinical Sciences, Skånes University Hospital, Malmoe, Sweden
| | | | - Sander Van Wanrooy
- Translational Research Center for Gastrointestinal Disorders, Leuven University, Leuven, Belgium
| | - Stéphanie Mondelaers
- Translational Research Center for Gastrointestinal Disorders, Leuven University, Leuven, Belgium
| | - Severine Vermeire
- Translational Research Center for Gastrointestinal Disorders, Leuven University, Leuven, Belgium
| | - Greger Lindberg
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - George Dukes
- Academic DPU, GlaxoSmithKline, Research Triangle Par, North Carolina, USA
| | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders, Leuven University, Leuven, Belgium
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Broxmeyer HE. Enhancing engraftment of cord blood cells via insight into the biology of stem/progenitor cell function. Ann N Y Acad Sci 2012; 1266:151-60. [PMID: 22901266 PMCID: PMC3428743 DOI: 10.1111/j.1749-6632.2012.06509.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cord blood (CB) transplantation has been used over the last 24 years to treat patients with malignant and nonmalignant disorders. CB has its advantages and disadvantages compared with other sources of hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) for transplantation. More knowledge of the cytokines and intracellular signaling molecules regulating HSCs and HPCs could be used to modulate these regulators for clinical benefit. This review provides information about the general field of CB transplantation and about studies from the author's laboratory that focus on regulation of HSCs and HPCs by CD26/DPPIV, SDF-1/CXCL12, the Rheb2-mTOR pathway, SIRT1, DEK, cyclin-dependent kinase inhibitors, and cytokines/growth factors. Cryopreservation of CB HSCs and HPCs is also briefly discussed.
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Affiliation(s)
- Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana
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Broxmeyer HE, Kappes F, Mor-Vaknin N, Legendre M, Kinzfogl J, Cooper S, Hangoc G, Markovitz DM. DEK regulates hematopoietic stem engraftment and progenitor cell proliferation. Stem Cells Dev 2012; 21:1449-54. [PMID: 21943234 PMCID: PMC3359622 DOI: 10.1089/scd.2011.0451] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 09/17/2011] [Indexed: 12/16/2022] Open
Abstract
DEK is a biochemically distinct protein that is generally found in the nucleus, where it is vital to global heterochromatin integrity. However, DEK is also secreted by cells (eg, macrophages) and influences other adjacent cells (eg, acts as a chemoattractant for certain mature blood cells). We hypothesized that DEK may modulate functions of hematopoietic stem (HSCs) and progenitor (HPCs) cells. C57Bl/6 mice were used to demonstrate that absolute numbers and cycling status of HPCs (colony forming unit-granulocyte macrophage [CFU-GM], burst forming unit-erythroid [BFU-E], and colony forming unit-granulocyte erythroid macrophage megakaryocyte [CFU-GEMM]) in bone marrow (BM) and spleen were significantly enhanced in DEK -/- as compared with wild-type (WT) control mice. Moreover, purified recombinant DEK protein inhibited colony formation in vitro by CFU-GM, BFU-E, and CFU-GEMM from WT BM cells and human cord blood (CB) cells in a dose-dependent fashion, demonstrating that DEK plays a negative role in HPC proliferation in vitro and in vivo. Suppression was direct acting as determined by inhibition of proliferation of single isolated CD34(+) CB cells in vitro. In contrast, DEK -/- BM cells significantly demonstrated reduced long term competitive and secondary mouse repopulating HSC capacity compared with WT BM cells, demonstrating that DEK positively regulates engrafting capability of self-renewing HSCs. This demonstrates that DEK has potent effects on HSCs, HPCs, and hematopoiesis, information of biological and potential clinical interest.
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Affiliation(s)
- Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5181, USA.
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Broxmeyer HE, Srour EF, Cooper S, Wallace CT, Hangoc G, Youn BS. Angiopoietin-like-2 and -3 act through their coiled-coil domains to enhance survival and replating capacity of human cord blood hematopoietic progenitors. Blood Cells Mol Dis 2011; 48:25-9. [PMID: 21983347 DOI: 10.1016/j.bcmd.2011.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 09/06/2011] [Indexed: 02/06/2023]
Abstract
Several angiopoietin-like (ANGPTL) molecules have been implicated in enhancement of ex-vivo expansion of murine and human (hu) hematopoietic stem cells, but there are no reports on hematopoietic progenitor cells (HPCs). We assessed purified recombinant endotoxin-free hu ANGPTL-2 Coiled-Coil (CC), -3, -3CC, -3 fibrinogen-like domain (FLD), -4, -4CC, -5CC, -6 and -7 for effects on proliferation and survival of HPCs from hu cord blood (CB). None of the ANGPTL molecules stimulated CB HPC proliferation, or enhanced or inhibited colony formation of CB HPC stimulated by various growth factors. However, ANGPTL-2CC, -3, and -3CC significantly enhanced survival of HPC (CFU-GM, BFU-E, CFU-GEMM) subjected to delayed addition of growth factors. Survival enhancing effects of ANGPTL-3 were neutralized by purified anti-ANGPTL-3, but not by anti-ANGPTL-4, -6, or -7. ANGPTL-2CC, -3, and -3CC, but not -4, -6, or -7 also enhanced replating capacity of single CB CFU-GEMM colonies, an estimate of the self-renewal capabilities of HPCs, by greater than 2 fold. Effects of at least ANGPTL-3CC may in part be mediated through phosphorylation of ERK. The ANGPTL molecules did not influence ex-vivo expansion of hu CB CD34(+) cells, alone, or in combination with SCF, TPO, Flt3-ligand, with or without IL-3. Thus, among ANGPTL family members, ANGPTL-2 and -3 had enhancing activities on human HPC survival and replating activity, effects requiring the CC domain of the ANGPTL molecules. This information is of relevance to hu HPC regulation.
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Affiliation(s)
- Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202-5181, USA.
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