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Lin X, Li X, Ma B, Hang L. Identification of novel immunomodulators in lung squamous cell carcinoma based on transcriptomic data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:1843-1860. [PMID: 35135231 DOI: 10.3934/mbe.2022086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cells in the tumor microenvironment are well known for their role in cancer development and prognosis. The processes of genetic changes and possible remodeling in the tumor microenvironment of lung squamous cell carcinoma, on the other hand, are mainly unclear. In this investigation, 1164 immunological differentially expressed genes (DEGs) were shown to have predictive significance. A prognostic model with high prediction accuracy was constructed using these genes and survival data. There were 1020 upregulated genes and 144 downregulated genes found, with 57 genes found to be important in the development of LUSC. We used least absolute shrinkage and selection operator (LASSO) regression analysis to determine the risk profiles of 9 genes based on the expression values of 57 prognosis-related genes. The AUCs of the developed prognostic model for predicting patient survival at 1, 3, and 5 years were 0.66, 0.61, and 0.63, respectively, based on the training data. For immune-correlation analysis in this survival model, we chose IGLC7, which was seen to predict patient survival with high accuracy. The effects on immune cells and synergistic effects with other immunomodulators were then investigated. We discovered that IGLC7 is involved in immune response and inflammatory activity using gene ontology analysis and genomic sequence variance analysis (GSVA), with a potential effect, especially on B cells and T cells. In conclusion, IGLC7 expression levels are related to the malignancy of LUSC based on the constructed prognostic model and can thus be a therapeutic target for patients with LUSC. Furthermore, IGLC7 may work in concert with other immune checkpoint members to regulate the immune microenvironment of LUSC. These discoveries might lead to a fresh understanding of the complicated interactions between cancer cells and the tumor microenvironment, particularly the population of immune cells, and a novel approach to future immunotherapeutic treatments for patients with LUSC.
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Affiliation(s)
- Xin Lin
- Department of Anesthesiology, Medical College of Soochow University, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215399, China
| | - Xingyuan Li
- Department of Anesthesiology, Kunshan Fourth People's Hospital, Kunshan 215399, China
| | - Binqiang Ma
- Department of Anesthesiology, Medical College of Soochow University, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215399, China
| | - Lihua Hang
- Department of Anesthesiology, Medical College of Soochow University, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215399, China
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Maloney S, Khan FA, Chenier TS, Diel de Amorim M, Anthony Hayes M, Scholtz EL. A comparison of the uterine proteome of mares in oestrus and dioestrus. Reprod Domest Anim 2018; 54:473-479. [DOI: 10.1111/rda.13375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Shawn‐Elizabeth Maloney
- Department of Population Medicine, Ontario Veterinary College University of Guelph Guelph Ontario Canada
| | - Firdous A. Khan
- Department of Population Medicine, Ontario Veterinary College University of Guelph Guelph Ontario Canada
- Department of Large Animal Medicine and Surgery, School of Veterinary Medicine St. George’s University True Blue Grenada
| | - Tracy S. Chenier
- Department of Population Medicine, Ontario Veterinary College University of Guelph Guelph Ontario Canada
| | - Mariana Diel de Amorim
- Department of Population Medicine, Ontario Veterinary College University of Guelph Guelph Ontario Canada
| | - Michael Anthony Hayes
- Department of Pathobiology, Ontario Veterinary College University of Guelph Guelph Ontario Canada
| | - Elizabeth L. Scholtz
- Department of Population Medicine, Ontario Veterinary College University of Guelph Guelph Ontario Canada
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Borga C, Park G, Foster C, Burroughs-Garcia J, Marchesin M, Shah R, Hasan A, Ahmed ST, Bresolin S, Batchelor L, Scordino T, Miles RR, Te Kronnie G, Regens JL, Frazer JK. Simultaneous B and T cell acute lymphoblastic leukemias in zebrafish driven by transgenic MYC: implications for oncogenesis and lymphopoiesis. Leukemia 2018; 33:333-347. [PMID: 30111845 PMCID: PMC6365377 DOI: 10.1038/s41375-018-0226-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/30/2018] [Accepted: 07/04/2018] [Indexed: 01/17/2023]
Abstract
Precursor-B cell acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer, but there are no useful zebrafish pre-B ALL models. We describe the first highly- penetrant zebrafish pre-B ALL, driven by human MYC. Leukemias express B lymphoblast-specific genes and are distinct from T cell ALL (T-ALL)—which these fish also develop. Zebrafish pre-B ALL shares in vivo features and expression profiles with human pre-B ALL, and these profiles differ from zebrafish T-ALL or normal B and T cells. These animals also exhibit aberrant lymphocyte development. As the only robust zebrafish pre-B ALL model and only example where T-ALL also develops, this model can reveal differences between MYC-driven pre-B vs. T-ALL and be exploited to discover novel pre-B ALL therapies.
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Affiliation(s)
- Chiara Borga
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Gilseung Park
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Clay Foster
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Jessica Burroughs-Garcia
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Matteo Marchesin
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Rikin Shah
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Ameera Hasan
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Syed T Ahmed
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Silvia Bresolin
- Department of Women's and Children's Health, University of Padua, Padua, 35128, Italy
| | - Lance Batchelor
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Teresa Scordino
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Rodney R Miles
- Department of Pathology, University of Utah and ARUP Institute for Clinical & Experimental Pathology, Salt Lake City, UT, 84108, USA
| | - Geertruy Te Kronnie
- Department of Women's and Children's Health, University of Padua, Padua, 35128, Italy
| | - James L Regens
- Center for Intelligence and National Security, University of Oklahoma, Norman, OK, 73019, USA
| | - J Kimble Frazer
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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Davoodi S, Cooke RF, Fernandes ACC, Cappellozza BI, Vasconcelos JLM, Cerri RLA. Expression of estrus modifies the gene expression profile in reproductive tissues on Day 19 of gestation in beef cows. Theriogenology 2015; 85:645-55. [PMID: 26525398 DOI: 10.1016/j.theriogenology.2015.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/22/2015] [Accepted: 10/01/2015] [Indexed: 11/16/2022]
Abstract
The aim of this study was to test the effect of expression of estrus at artificial insemination (AI) on endometrium, conceptus, and CL gene expression of beef cows. Thirty-six multiparous nonlactating Nelore cows were enrolled on an estradiol- and progesterone (P4)-based timed AI protocol (AI = Day 0) and then slaughtered for the endometrium, CL, and conceptus collection on Day 19. The animals were retrospectively grouped on the basis of cows that (1) showed signs of estrus near AI (n = 19; estrus) and (2) did not show any signs of estrus (n = 17; nonestrus). Body condition score, blood sampling, and ultrasound examination were performed on Days 0, 7, and 18 of the experiment followed by messenger RNA extraction and quantitative reverse transcription polymerase chain reaction analysis of 58 target genes. Data were checked for normality and analyzed by ANOVA for repeated measures using proc GLM, MIXED, and UNIVARIATE of SAS. Only pregnant cows were included in the analyses (n = 12; nonestrus, n = 11). Estrous expression had no correlation with parameters such as body condition score, preovulatory follicle and CL diameter, P4 concentration in plasma on Days 7 and 18 after AI, and interferon-tau concentration in the uterine flushing (P > 0.15); however, a significant increase was observed in conceptus size from cows that expressed estrus (P = 0.02; 38.3 ± 2.8 vs. 28.2 ± 2.9 mm). The majority of transcripts affected by estrous expression in the endometrium belong to the immune system and adhesion molecule family (MX1, MX2, MYL12A, MMP19, CXCL10, IGLL1, and SLPI; P ≤ 0.05), as well as those related with prostaglandin synthesis (OTR and COX-2; P ≤ 0.05). Genes related to apoptosis, P4 synthesis, and prostaglandin receptor were downregulated (CYP11A, BAX, and FPr; P < 0.05) in the CL tissue of cows that expressed estrus. In addition, four genes were identified as differentially expressed in the 19-day-old conceptus from cows that expressed estrus (ISG15, PLAU, BMP15, and EEF1A1; P < 0.05). There was also a significant effect of Day 7 concentration of P4 mainly affecting the immune system, adhesion molecules, and wnt signaling pathway of the endometrium (IGLL1, MX2, SLPI, TRD, APC, WNT2, GLYCAM1, and MYL12A; P < 0.05). A significant interaction between estrous expression and P4 concentration on Day 7 was more pronounced in immune system genes (MX1, MX2, TRD, SLPI, and IGLL1; P < 0.05). This study reported that estrous expression at the time of AI favorably altered the gene expression profile in reproductive tissues during the preimplantation phase toward a more receptive state to the elongating conceptus. These effects seem to be more evident in the endometrium during the time of dynamic remodeling for embryo implantation.
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Affiliation(s)
- S Davoodi
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - R F Cooke
- Eastern Oregon Agricultural Research Center, Oregon State University, Burns, Oregon, USA
| | - A C C Fernandes
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - B I Cappellozza
- Eastern Oregon Agricultural Research Center, Oregon State University, Burns, Oregon, USA
| | - J L M Vasconcelos
- Faculdade de Medicina Veterinária e Zootecnia, UNESP, Botucatu, São Paulo, Brazil
| | - R L A Cerri
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada.
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Array-based comparative genomic hybridization analysis reveals chromosomal copy number aberrations associated with clinical outcome in canine diffuse large B-cell lymphoma. PLoS One 2014; 9:e111817. [PMID: 25372838 PMCID: PMC4221131 DOI: 10.1371/journal.pone.0111817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/08/2014] [Indexed: 12/29/2022] Open
Abstract
Canine Diffuse Large B-cell Lymphoma (cDLBCL) is an aggressive cancer with variable clinical response. Despite recent attempts by gene expression profiling to identify the dog as a potential animal model for human DLBCL, this tumor remains biologically heterogeneous with no prognostic biomarkers to predict prognosis. The aim of this work was to identify copy number aberrations (CNAs) by high-resolution array comparative genomic hybridization (aCGH) in 12 dogs with newly diagnosed DLBCL. In a subset of these dogs, the genetic profiles at the end of therapy and at relapse were also assessed. In primary DLBCLs, 90 different genomic imbalances were counted, consisting of 46 gains and 44 losses. Two gains in chr13 were significantly correlated with clinical stage. In addition, specific regions of gains and losses were significantly associated to duration of remission. In primary DLBCLs, individual variability was found, however 14 recurrent CNAs (>30%) were identified. Losses involving IGK, IGL and IGH were always found, and gains along the length of chr13 and chr31 were often observed (>41%). In these segments, MYC, LDHB, HSF1, KIT and PDGFRα are annotated. At the end of therapy, dogs in remission showed four new CNAs, whereas three new CNAs were observed in dogs at relapse compared with the previous profiles. One ex novo CNA, involving TCR, was present in dogs in remission after therapy, possibly induced by the autologous vaccine. Overall, aCGH identified small CNAs associated with outcome, which, along with future expression studies, may reveal target genes relevant to cDLBCL.
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Jin Y, Sharma A, Bai S, Davis C, Liu H, Hopkins D, Barriga K, Rewers M, She JX. Risk of type 1 diabetes progression in islet autoantibody-positive children can be further stratified using expression patterns of multiple genes implicated in peripheral blood lymphocyte activation and function. Diabetes 2014; 63:2506-15. [PMID: 24595351 PMCID: PMC4066338 DOI: 10.2337/db13-1716] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is tremendous scientific and clinical value to further improving the predictive power of autoantibodies because autoantibody-positive (AbP) children have heterogeneous rates of progression to clinical diabetes. This study explored the potential of gene expression profiles as biomarkers for risk stratification among 104 AbP subjects from the Diabetes Autoimmunity Study in the Young (DAISY) using a discovery data set based on microarray and a validation data set based on real-time RT-PCR. The microarray data identified 454 candidate genes with expression levels associated with various type 1 diabetes (T1D) progression rates. RT-PCR analyses of the top-27 candidate genes confirmed 5 genes (BACH2, IGLL3, EIF3A, CDC20, and TXNDC5) associated with differential progression and implicated in lymphocyte activation and function. Multivariate analyses of these five genes in the discovery and validation data sets identified and confirmed four multigene models (BI, ICE, BICE, and BITE, with each letter representing a gene) that consistently stratify high- and low-risk subsets of AbP subjects with hazard ratios >6 (P < 0.01). The results suggest that these genes may be involved in T1D pathogenesis and potentially serve as excellent gene expression biomarkers to predict the risk of progression to clinical diabetes for AbP subjects.
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Affiliation(s)
- Yulan Jin
- Sino-American Institute of Translational Medicine, School of Pharmaceutical Sciences, Nanjing University of Technology, Nanjing, ChinaCenter for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GADepartment of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, GA
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GADepartment of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, GA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA
| | - Colleen Davis
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA
| | - Haitao Liu
- Sino-American Institute of Translational Medicine, School of Pharmaceutical Sciences, Nanjing University of Technology, Nanjing, ChinaCenter for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA
| | - Diane Hopkins
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA
| | - Kathy Barriga
- Barbara Davis Center for Childhood Diabetes, Aurora, CO
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, Aurora, CO
| | - Jin-Xiong She
- Sino-American Institute of Translational Medicine, School of Pharmaceutical Sciences, Nanjing University of Technology, Nanjing, ChinaCenter for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GADepartment of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, GA
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Abstract
BACKGROUND Intestinal allograft mucosa undergoes repopulation with host immunocytes. However, critical changes within key immunocyte subsets are not known. METHODS To explain acute cellular rejection after intestine transplantation (ITx) on the basis of altered mucosal immunocytes, rejecting and rejection-free ITx allografts (n=17) were compared with genome-wide expression arrays. Cells identified by cell/lineage-specific genes were evaluated by immunohistochemistry. The corresponding phenotype and donor-specific alloreactivity were characterized in peripheral blood. Time-dependent changes in candidate cell(s) were evaluated in biopsies from an independent cohort of 12 children with ITx. RESULTS Among 107 differentially expressed genes, three B-cell lineage-specific genes, CCR10, STAP1, and IGLL1, were down-regulated during ITx rejection and were selected for and achieved technical quantitative reverse transcription polymerase chain reaction replication. Down-regulation of the immunoglobulin (Ig)A+ plasma cell-specific CCR10 gene correlated with decreased mature mucosal CD138+ plasma cell numbers in corresponding biopsy specimens (r=0.761, P=0.006) and inversely correlated with enhanced alloreactivity of CD154+ T-cytotoxic memory cells (r=-0.56, P=0.031), which predict acute cellular rejection with high sensitivity. An independent cohort of serial biopsy specimens from 12 ITx recipients (1) confirmed relative CD138+ plasma cell depletion during rejection (P=0.042) and (2) showed increased IgG+-to-IgA+ cell ratios within 4 hr of reperfusion in rejection-prone allografts (P=0.037) and during ITx rejection (P=0.025), compared with rejection-free allografts. No differences existed late after ITx. Increased peripheral IgG+ CD27+ CD19+ memory B cells (P=0.004) were seen during ITx rejection in archived peripheral blood lymphocyte from test and replication cohorts. CONCLUSIONS Protracted depletion of the mucosal CD138+ plasma cell barrier and early mucosal infiltration with memory IgG+ cells characterize the rejection-prone intestine allograft. Mucosal IgA+ plasma cell barrier reconstitution may augur resolution of ITx rejection.
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Thomas R, Seiser EL, Motsinger-Reif A, Borst L, Valli VE, Kelley K, Suter SE, Argyle D, Burgess K, Bell J, Lindblad-Toh K, Modiano JF, Breen M. Refining tumor-associated aneuploidy through 'genomic recoding' of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas. Leuk Lymphoma 2011; 52:1321-35. [PMID: 21375435 PMCID: PMC4304668 DOI: 10.3109/10428194.2011.559802] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Identification of the genomic regions most intimately associated with non-Hodgkin lymphoma (NHL) pathogenesis is confounded by the genetic heterogeneity of human populations. We hypothesize that the restricted genetic variation of purebred dogs, combined with the contrasting architecture of the human and canine karyotypes, will increase the penetrance of fundamental NHL-associated chromosomal aberrations in both species. We surveyed non-random aneuploidy in 150 canine NHL cases, revealing limited genomic instability compared to their human counterparts and no evidence for CDKN2A/B deletion in canine B-cell NHL. 'Genomic recoding' of canine NHL data into a 'virtual human' chromosome format showed remarkably few regions of copy number aberration (CNA) shared between both species, restricted to regions of dog chromosomes 13 and 31, and human chromosomes 8 and 21. Our data suggest that gene discovery in NHL may be enhanced through comparative studies exploiting the less complex association between CNAs and tumor pathogenesis in canine patients.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
| | - Eric L. Seiser
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
| | - Alison Motsinger-Reif
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Department of Statistics, College of Agriculture and Life Sciences, North Carolina State University, Patterson Hall, 2501 Founders Drive, Raleigh, NC 27695, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Luke Borst
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Victor E. Valli
- VDx Veterinary Diagnostics, 2019 Anderson Rd Suite C, Davis CA 95616, USA
| | - Kathryn Kelley
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
| | - Steven E. Suter
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
| | - David Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh, Roslin, Midlothian, Scotland, UK
| | - Kristine Burgess
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, Grafton, MA 01536, USA
| | - Jerold Bell
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, Grafton, MA 01536, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jaime F. Modiano
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
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Combined microdeletions and CHD7 mutation causing severe CHARGE/DiGeorge syndrome: clinical presentation and molecular investigation by array-CGH. J Hum Genet 2010; 55:761-3. [PMID: 20686492 DOI: 10.1038/jhg.2010.95] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Phenotypic variation in CHARGE syndrome remains unexplained. A subcategory of CHARGE patients show overlapping phenotypic characteristics with DiGeorge syndrome (thymic hypo/aplasia, hypocalcemia, T-cell immunodeficiency). Very few have been tested or reported to carry a mutation of the CHD7 (chromodomain helicase DNA-binding domain) gene detected in two-thirds of CHARGE patients. In an attempt to explore the genetic background of a severe CHARGE/DiGeorge phenotype, we performed comparative genomic array hybridization in an infant carrier of a CHD7 mutation. The high-resolution comparative genomic array hybridization revealed interesting findings, including a deletion distal to the DiGeorge region and disruptions in other chromosomal regions of genes implicated in immunological and other functions possibly contributing to the patient's severe phenotype and early death.
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BLOMBERG BONNIEB, GLOZAK MICHELEA, DONOHOE MARYE. Regulation of Human λ Light Chain Gene Expressiona. Ann N Y Acad Sci 2008. [DOI: 10.1111/j.1749-6632.1995.tb55810.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA. Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum Mutat 2006; 27:545-52. [PMID: 16671097 DOI: 10.1002/humu.20335] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pseudogenes are remnants of gene duplication (nonprocessed pseudogenes) and retrotransposition (processed pseudogenes) events. This study describes methods for identifying gene conversion candidates from predicted pseudogenes. Pseudogenes may accumulate and harbor sequence variations over time that become disease-causing mutations when transferred to genes by gene conversion. A total of 14,476 pseudogenes were identified, including 3,426 nonprocessed pseudogenes. In addition, 1,945 nonprocessed pseudogenes that are localized near their progenitor gene were evaluated for their possible role in gene conversion and disease. All 11 known, human cases of gene conversion (with deleterious effects) involving pseudogenes were successfully identified by these methods. Among the pseudogenes identified is a retinitis pigmentosa 9 (RP9) pseudogene that carries a c.509A>G mutation which produces a p.Asp170Gly substitution that is associated with the RP9 form of autosomal dominant retinitis pigmentosa (adRP). The c.509A>G mutation in RP9 is a previously unrecognized example of gene conversion between the progenitor gene and its pseudogene. Notably, two processed pseudogenes also contain mutations associated with diseases. An inosine monophosphate dehydrogenase 1 (IMPDH1) pseudogene carries a c.676G>A mutation that produces a p.Asp226Asn substitution that causes the retinitis pigmentosa 10 (RP10) form of adRP; and a phosphoglycerate kinase 1 (PGK1) pseudogene (PGK1P1) carries a c.837T>C mutation that produces a p.Ile252Thr substitution that is associated with a phosphoglycerate kinase deficiency. Ranking of nonprocessed pseudogenes as candidates for gene conversion was also performed based on the sequence characteristics of published cases of pseudogene-mediated gene conversion. All results and tools produced by this study are available for download at: http://genome.uiowa.edu/pseudogenes.
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Affiliation(s)
- Jared M Bischof
- Coordinated Laboratory for Computational Genomics, The University of Iowa, Iowa City, Iowa 52240, USA
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Gisler R, Sigvardsson M. The human V-preB promoter is a target for coordinated activation by early B cell factor and E47. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 168:5130-8. [PMID: 11994467 DOI: 10.4049/jimmunol.168.10.5130] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of mature B lymphoid cells involves a highly orchestrated regulation of stage- and lineage-specific genes. In this study, we report an analysis of the human surrogate L chain VpreB promoter. The promoter has an overall homology of 56% to the mouse counterpart and displays a preB cell-restricted activity in transient transfections in cell lines. The promoter harbors three independent binding sites for early B cell factor (EBF) as defined by EMSA and supershift experiments. These sites were important for the full function of the promoter in a preB cell line, and chromatin immunoprecipitation experiments indicate that EBF interacts with the promoter in vivo. In addition to this, ectopic expression of EBF induces the activity of a reporter gene under control of the VpreB promoter in epithelioid HeLa cells, an effect augmented by coexpression of the basic-helix-loop helix transcription factor E47. The ability to interact directly with E47 was shared by the promoters controlling the human mb-1 and B29 genes. These data indicate that the human VpreB promoter is a direct target for activation by EBF and E47 and that functional collaboration between these proteins may be of great importance in human B cell development.
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Affiliation(s)
- Ramiro Gisler
- Laboratory for Cellular Differentiation, Department for Stem Cell Biology, BMC B12, 22184 Lund, Sweden.
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Donohoe ME, Beck-Engeser GB, Lonberg N, Karasuyama H, Riley RL, Jäck HM, Blomberg BB. Transgenic human lambda 5 rescues the murine lambda 5 nullizygous phenotype. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 164:5269-76. [PMID: 10799888 DOI: 10.4049/jimmunol.164.10.5269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The human lambda 5 (hu lambda 5) gene is the structural homologue of the murine lambda 5 (m lambda 5) gene and is transcriptionally active in pro-B and pre-B lymphocytes. The lambda 5 and VpreB polypeptides together with the Ig mu H chain and the signal-transducing subunits, Ig alpha and Ig beta, comprise the pre-B cell receptor. To further investigate the pro-B/pre-B-specific transcription regulation of hu lambda 5 in an in vivo model, we generated mouse lines that contain a 28-kb genomic fragment encompassing the entire hu lambda 5 gene. High levels of expression of the transgenic hu lambda 5 gene were detected in bone marrow pro-B and pre-B cells at the mRNA and protein levels, suggesting that the 28-kb transgene fragment contains all the transcriptional elements necessary for the stage-specific B progenitor expression of hu lambda 5. Flow cytometric and immunoprecipitation analyses of bone marrow cells and Abelson murine leukemia virus-transformed pre-B cell lines revealed the hu lambda 5 polypeptide on the cell surface and in association with mouse Ig mu and mouse VpreB. Finally, we found that the hu lambda 5 transgene is able to rescue the pre-B lymphocyte block when bred onto the m lambda 5-/- background. Therefore, we conclude that the hu lambda 5 polypeptide can biochemically and functionally substitute for m lambda 5 in vivo in pre-B lymphocyte differentiation and proliferation. These studies on the mouse and human pre-B cell receptor provide a model system to investigate some of the molecular requirements necessary for B cell development.
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MESH Headings
- Abelson murine leukemia virus/genetics
- Animals
- B-Lymphocyte Subsets/cytology
- B-Lymphocyte Subsets/immunology
- B-Lymphocyte Subsets/metabolism
- Binding Sites, Antibody/genetics
- Bone Marrow Cells/immunology
- Bone Marrow Cells/metabolism
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cell Lineage/genetics
- Cell Lineage/immunology
- Crosses, Genetic
- Female
- Gene Expression Regulation/immunology
- Humans
- Immunoglobulin Heavy Chains/metabolism
- Immunoglobulin Light Chains
- Immunoglobulin Light Chains, Surrogate
- Immunoglobulin lambda-Chains/biosynthesis
- Immunoglobulin lambda-Chains/genetics
- Immunoglobulin lambda-Chains/metabolism
- Immunoglobulin mu-Chains/metabolism
- Immunophenotyping
- Male
- Membrane Glycoproteins/biosynthesis
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Transgenic
- Receptors, Antigen, B-Cell/biosynthesis
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Stem Cells/cytology
- Stem Cells/immunology
- Stem Cells/metabolism
- Testis/immunology
- Testis/metabolism
- Thymus Gland/immunology
- Thymus Gland/metabolism
- Transgenes/immunology
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Affiliation(s)
- M E Donohoe
- Department of Microbiology, University of Miami School of Medicine, Miami, FL 33101, USA
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14
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Conley ME, Rapalus L, Boylin EC, Rohrer J, Minegishi Y. Gene conversion events contribute to the polymorphic variation of the surrogate light chain gene lambda 5/14.1. Clin Immunol 1999; 93:162-7. [PMID: 10527692 DOI: 10.1006/clim.1999.4785] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Normally occurring and experimentally induced models of immunodeficiency indicate that B cell development and antibody production are influenced by genetic factors. It is highly likely that polymorphic variants in genes that encode receptors for growth and differentiation factors, signal transduction molecules, and components of the B cell and pre-B-cell receptor complex contribute to this genetic control. We have identified a surprisingly large number of polymorphic variants in lambda5/14.1. Together with VpreB, lambda5/14.1 forms the surrogate light chain in the pre-B-cell receptor complex. Thirteen variant alleles of lambda5/14.1 were found in 134 unrelated individuals. Nine of these variants result in changes in the amino acid sequence of this small protein. The majority of the single base pair substitutions in lambda5/14.1 could be attributed to gene conversion events in which donor sequences from the lambda5 pseudogenes, 16.1, 16.2, and Glambda1, replace the wild-type sequence in the lambda5/14.1 functional gene. These findings indicate that gene conversion events play a major role in generating diversity that could affect stability or expression of the pre-B-cell receptor complex.
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Affiliation(s)
- M E Conley
- Department of Pediatrics, University of Tennessee College of Medicine, Memphis, Tennessee 38101, USA
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15
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Ghia P, ten Boekel E, Rolink AG, Melchers F. B-cell development: a comparison between mouse and man. IMMUNOLOGY TODAY 1998; 19:480-5. [PMID: 9785673 DOI: 10.1016/s0167-5699(98)01330-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A common variable immunodeficiency (CVID) patient, who carries mutations on both alleles of the gene encoding the surrogate light chain component lambda 5/14.1, shows a similar phenotype of B-cell deficiency as the lambda 5-deficient mutant mouse. As discussed here by Paolo Ghia and colleagues, this points to a remarkably similar developmental pathway of B cells in humans and mice.
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Affiliation(s)
- P Ghia
- Dana Farber Cancer Institute Boston, MA, USA
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16
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Minegishi Y, Coustan-Smith E, Wang YH, Cooper MD, Campana D, Conley ME. Mutations in the human lambda5/14.1 gene result in B cell deficiency and agammaglobulinemia. J Exp Med 1998; 187:71-7. [PMID: 9419212 PMCID: PMC2199185 DOI: 10.1084/jem.187.1.71] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/1997] [Revised: 10/27/1997] [Indexed: 02/05/2023] Open
Abstract
B cell precursors transiently express a pre-B cell receptor complex consisting of a rearranged mu heavy chain, a surrogate light chain composed of lambda5/14.1 and VpreB, and the immunoglobulin (Ig)-associated signal transducing chains, Igalpha and Igbeta. Mutations in the mu heavy chain are associated with a complete failure of B cell development in both humans and mice, whereas mutations in murine lambda5 result in a leaky phenotype with detectable humoral responses. In evaluating patients with agammaglobulinemia and markedly reduced numbers of B cells, we identified a boy with mutations on both alleles of the gene for lambda5/14.1. The maternal allele carried a premature stop codon in the first exon of lambda5/14.1 and the paternal allele demonstrated three basepair substitutions in a 33-basepair sequence in exon 3. The three substitutions correspond to the sequence in the lambda5/14. 1 pseudogene 16.1 and result in an amino acid substitution at an invariant proline. When expressed in COS cells, the allele carrying the pseudogene sequence resulted in defective folding and secretion of mutant lambda5/14.1. These findings indicate that expression of the functional lambda5/14.1 is critical for B cell development in the human.
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Affiliation(s)
- Y Minegishi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennesse 38105, USA
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17
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Collins JE, Mungall AJ, Badcock KL, Fay JM, Dunham I. The organization of the gamma-glutamyl transferase genes and other low copy repeats in human chromosome 22q11. Genome Res 1997; 7:522-31. [PMID: 9149947 DOI: 10.1101/gr.7.5.522] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A clone map consisting of YACs, cosmids, and fosmids has been constructed covering low copy repeat regions of human chromosome 22q11. A combination of clone restriction digest analysis, single-copy landmark content analysis, HindIII-Sau3AI fingerprinting, and sequencing of PCR products derived from clones was required to resolve the map in this region. Seven repeat-containing contigs were placed in 22q11, five containing gamma-glutamyl transferase (GGT) sequences described previously. In one case, a single interval at the resolution of the YAC map was shown to contain at least three GGT sequences after higher resolution mapping. The sequence information was used to design a rapid PCR/restriction digest technique that distinguishes the GGT loci placed in the YAC map. This approach has allowed us to resolve the previous cDNA and mapping information relating to GGT and link it to the physical map of 22q11.
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18
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McDermid HE, McTaggart KE, Riazi MA, Hudson TJ, Budarf ML, Emanuel BS, Bell CJ. Long-range mapping and construction of a YAC contig within the cat eye syndrome critical region. Genome Res 1996; 6:1149-59. [PMID: 8973909 DOI: 10.1101/gr.6.12.1149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cat eye syndrome (CES) is typically associated with a supernumerary bisatellited marker chromosome derived from human chromosome 22pter to 22q11.2. The region of 22q duplicated in the typical CES marker chromosome extends between the centromere and locus D22S36. We have constructed a long-range restriction map of this region using pulsed-field gel electrophoresis and probes to 10 loci (11 probes). The map covers -3.6 Mb. We have also used 15 loci to construct a yeast artificial chromosome contig, which encompasses about half of the region critical to the production of the CES phenotype (centromere to D22S57). Thus, the CES critical region has been mapped and a substantial portion of it cloned in preparation for the isolation of genes in this region.
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Affiliation(s)
- H E McDermid
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.
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19
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Schiff C, Milili M, Zucman-Rossi J, Djabali M, Fougereau M. Composite exon structure of an unusual Ig lambda-like gene located at human 22q11 position. Mamm Genome 1996; 7:598-602. [PMID: 8678981 DOI: 10.1007/s003359900177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The surrogate light chain, composed of the VpreB and the lambda-like proteins, plays a critical role in controlling the early stages of B lymphocyte development. The lambda-like locus, located on the q11. 2-q11.3 region of human Chromosome (Chr) 22, contains three genes (14.1 Flambda-1, and 16.1) among which only the 14.1 is functional. This gene contains three exons, whereas the others lack exon 1. We have isolated in fetal liver a transcript of the Flambda-1 gene that contains the exon 3 sequence and a long non-Ig related sequence upstream. We show that this sequence resulted from the splicing of three new exons located telomeric to the Flambda-1 gene, highly homologous to beta-glucuronidase exon 11 (Chr 7), to the ABR exon 8 (Chr 17), and to an Expressed Sequence Tag (EST), respectively. We also show that this chimeric transcript is expressed in cells or tissues from various origins. This composite gene structure appears to be a new example of human genome flexibility, which can be explained by mechanisms such as exon shuffling and which results in the emergence of new transcription units inserted in regions involved in translocations.
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Affiliation(s)
- C Schiff
- Centre d'Immunologie de Marseille Luminy (CIML), Case 906, 13288 Marseille Cedex 09 France
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20
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Asenbauer H, Klobeck HG. Tissue-specific deoxyribonuclease I-hypersensitive sites in the vicinity of the immunoglobulin C lambda cluster of man. Eur J Immunol 1996; 26:142-50. [PMID: 8566057 DOI: 10.1002/eji.1830260122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
During B cell development, the onset of DNA rearrangements, expression, and somatic hypermutation of Ig genes are regulated through the complex interaction of cis-acting elements with trans-acting factors. Our aim is to identify DNA elements required during activation of the human Ig lambda light chain genes. Determination of deoxyribonuclease (DNase) I-hypersensitive sites in complex regulated genes can lead to the identification of sequence elements which would have been overlooked by employing transient transfection protocols. We have therefore investigated the chromatin structure of human J-C lambda genes and identified three DNase I-hypersensitive sites (HSS-1, -2, and -3) within an 8-kb region downstream of the J-C lambda 7 gene. HSS-2 and HSS-3 are B cell specific. The DNase I-hypersensitive sites are also present in kappa-producing cell lines which have not rearranged the Ig lambda locus and produce germ-line J-C lambda transcripts. We conclude that in mature B cells, both kappa and lambda loci are in an active structure regardless of the type of light chain they produce. This suggests that the chromatin structure of both loci is opened early in B cell development and that the active structure persists in mature B cells. The observed temporal order (first kappa, then lambda) of activation can be explained by consecutive synthesis of the appropriate regulating factors and the tight regulation of the recombination machinery through the products of L chain gene rearrangements.
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Affiliation(s)
- H Asenbauer
- Adolf Butenandt Institut für Physiologische Chemie, Universität München, Germany
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