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Sudan R, Fernandes S, Srivastava N, Pedicone C, Meyer ST, Chisholm JD, Engelman RW, Kerr WG. LRBA Deficiency Can Lead to Lethal Colitis That Is Diminished by SHIP1 Agonism. Front Immunol 2022; 13:830961. [PMID: 35603158 PMCID: PMC9116273 DOI: 10.3389/fimmu.2022.830961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Humans homozygous for inactivating LRBA (lipopolysaccharide (LPS)-responsive beige-like anchor) mutations or with compound heterozygous mutations exhibit a spectrum of immune-related pathologies including inflammatory bowel disease (IBD). The cause of this pathology remains undefined. Here we show that disruption of the colon epithelial barrier in LRBA-deficient mice by dextran sulfate sodium (DSS) consumption leads to severe and uniformly lethal colitis. Analysis of bone marrow (BM) chimeras showed that susceptibility to lethal colitis is primarily due to LRBA deficiency in the immune compartment and not the gut epithelium. Further dissection of the immune defect in LRBA-deficient hosts showed that LRBA is essential for the expression of CTLA4 by Treg cells and IL22 and IL17 expression by ILC3 cells in the large intestine when the gut epithelium is compromised by DSS. We further show that SHIP1 agonism partially abrogates the severity and lethality of DSS-mediated colitis. Our findings indicate that enteropathy induced by LRBA deficiency has multiple causes and that SHIP1 agonism can partially abrogate the inflammatory milieu in the gut of LRBA-deficient hosts.
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Affiliation(s)
- Raki Sudan
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Sandra Fernandes
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Neetu Srivastava
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Chiara Pedicone
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Shea T Meyer
- Department of Chemistry, Syracuse University, Syracuse, NY, United States
| | - John D Chisholm
- Department of Chemistry, Syracuse University, Syracuse, NY, United States
| | - Robert W Engelman
- Department of Pathology and Cell Biology, University of South Florida, Tampa, FL, United States.,Department of Pediatrics, University of South Florida, Tampa, FL, United States.,H. Lee Moffitt Comprehensive Cancer Center & Research Institute, University of South Florida, Tampa, FL, United States
| | - William G Kerr
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, United States.,Department of Chemistry, Syracuse University, Syracuse, NY, United States
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Nekkanti A, Chakraborty P, Ghosh A, Iquebal MA, Jaiswal S, Baranwal VK. Transcriptomic Changes of Bemisia tabaci Asia II 1 Induced by Chilli Leaf Curl Virus Trigger Infection and Circulation in Its Vector. Front Microbiol 2022; 13:890807. [PMID: 35572639 PMCID: PMC9096263 DOI: 10.3389/fmicb.2022.890807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 03/25/2022] [Indexed: 11/24/2022] Open
Abstract
Bemisia tabaci (Hemiptera: Aleyrodidae) is a highly efficient vector in the spread of chilli leaf curl virus (ChiLCV, Begomovirus) which is a major constraint in the production of chilli in South Asia. Transcriptome analysis of B. tabaci post-6 h acquisition of ChiLCV showed differential expression of 80 (29 upregulated and 51 downregulated) genes. The maximum number of DEGs are categorized under the biological processes category followed by cellular components and molecular functions. KEGG analysis of DEGs showed that the genes are involved in the functions like metabolism, signaling pathways, cellular processes, and organismal systems. The expression of highly expressed 20 genes post-ChiLCV acquisition was validated in RT-qPCR. DEGs such as cytosolic carboxypeptidase 3, dual-specificity protein phosphatase 10, 15, dynein axonemal heavy chain 17, fasciclin 2, inhibin beta chain, replication factor A protein 1, and Tob1 were found enriched and favored the virus infection and circulation in B. tabaci. The present study provides an improved understanding of the networks of molecular interactions between B. tabaci and ChiLCV. The candidate genes of B. tabaci involved in ChiLCV transmission would be novel targets for the management of the B. tabaci-begomovirus complex.
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Affiliation(s)
- Aarthi Nekkanti
- Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, India.,Division of Entomology, Indian Agricultural Research Institute, New Delhi, India
| | - Prosenjit Chakraborty
- Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, India
| | - Amalendu Ghosh
- Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, India
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Li T, Cao H, Wu S, Zhong P, Ding J, Wang J, Wang F, He Z, Huang GL. Phosphorylated ATF1 at Thr184 promotes metastasis and regulates MMP2 expression in gastric cancer. J Transl Med 2022; 20:169. [PMID: 35397606 PMCID: PMC8994398 DOI: 10.1186/s12967-022-03361-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background Studies have revealed an important role of activating transcription factor 1 (ATF1) and phosphorylated ATF1 at Ser63 in tumors. Our previous study identified Thr184 as a novel phosphorylation site of ATF1. However, the role of phosphorylated ATF1 at Thr184 (p-ATF1-T184) in tumor is unclear. This study figured out the role of p-ATF1-T184 in the metastasis of gastric cancer (GC) and in the regulation of Matrix metallopeptidase 2 (MMP2). Methods Immunohistochemical analysis (IHC) was performed to analyze the level of p-ATF1-T184 and its relationship with clinicopathological characteristics. Wound scratch test, Transwell assay were used to observe the role of p-ATF1-T184 in the invasion and metastasis of GC. The regulation of MMP2 by p-ATF1-T184 was investigated by a series of experiments including quantitative RT-PCR, western blot, gelatin zymography assay, Chromatin immunoprecipitation (ChIP), luciferase reporter assay and cycloheximide experiment. The Cancer Genome Atlas (TCGA) data were used to analyze the expression and prognostic role of ATF1 and MMP2 in GC. Mass spectrometry (MS) following co-immunoprecipitation (co-IP) assay was performed to identify potential upstream kinases that would phosphorylate ATF1 at Thr184. Results High expression level of p-ATF1-T184 was found and significantly associated with lymph node metastasis and poor survival in a GC cohort of 126 patients. P-ATF1-T184 promoted migration and invasion of gastric cancer cells. Phosphorylation of ATF1-T184 could regulate the mRNA, protein expression and extracellular activity of MMP2. P-ATF1-T184 further increased the DNA binding ability, transcription activity, and stabilized the protein expression of ATF1. Moreover, TCGA data and IHC results suggested that the mRNA level of ATF1 and MMP2, and protein level of p-ATF1-T184 and MMP2 could be prognosis markers of GC. Two protein kinase related genes, LRBA and S100A8, were identified to be correlated with the expression ATF1 in GC. Conclusion Our results indicated that p-ATF1-T184 promoted metastasis of GC by regulating MMP2. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03361-3.
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Epigenetic aging of the demographically non-aging naked mole-rat. Nat Commun 2022; 13:355. [PMID: 35039495 PMCID: PMC8763950 DOI: 10.1038/s41467-022-27959-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 12/23/2021] [Indexed: 12/26/2022] Open
Abstract
The naked mole-rat (NMR) is an exceptionally long-lived rodent that shows no increase of mortality with age, defining it as a demographically non-aging mammal. Here, we perform bisulfite sequencing of the blood of > 100 NMRs, assessing > 3 million common CpG sites. Unsupervised clustering based on sites whose methylation correlates with age reveals an age-related methylome remodeling, and we also observe a methylome information loss, suggesting that NMRs age. We develop an epigenetic aging clock that accurately predicts the NMR age. We show that these animals age much slower than mice and much faster than humans, consistent with their known maximum lifespans. Interestingly, patterns of age-related changes of clock sites in Tert and Prpf19 differ between NMRs and mice, but there are also sites conserved between the two species. Together, the data indicate that NMRs, like other mammals, epigenetically age even in the absence of demographic aging of this species. The exceptionally long-lived naked mole-rat is characterized by the lack of increased mortality with aging. Here the authors perform epigenetic studies to show that naked mole-rats epigenetically age despite their non-increasing mortality rate.
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Rojas-Restrepo J, Caballero-Oteyza A, Huebscher K, Haberstroh H, Fliegauf M, Keller B, Kobbe R, Warnatz K, Ehl S, Proietti M, Grimbacher B. Establishing the Molecular Diagnoses in a Cohort of 291 Patients With Predominantly Antibody Deficiency by Targeted Next-Generation Sequencing: Experience From a Monocentric Study. Front Immunol 2021; 12:786516. [PMID: 34975878 PMCID: PMC8718408 DOI: 10.3389/fimmu.2021.786516] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Predominantly antibody deficiencies (PAD) are a heterogeneous group of disorders characterized by dysfunctional antibody production, low immunoglobulin levels in serum and impaired vaccine responses. The clinical picture is variable, ranging from mild symptoms to severe complications, which may include autoimmunity, gastrointestinal disease, allergy, and malignancies. If left untreated, PAD patients are at risk of enduring disease progression, irreversible organ damage, and reduced life expectancy. A timely diagnosis has been shown to significantly improve disease prognosis. Here, we report on our experience using targeted gene panel sequencing by employing Agilent's HaloPlex or SureSelect and Illumina's MiSeq technologies in a cohort of 291 individuals who presented with low or absent immunoglobulin levels in combination with or without other clinical features. In total, we have detected over 57 novel or previously reported relevant mutations in ADA, ADA2, BTK, CTLA4, LRBA, NFKB1, NFKB2, PIK3CD, STAT3, and TNFRSF13B. Overall, a genetic diagnosis could be made in 24.7% of the investigated patients. The percentage of coverage for the targeted regions ranged from 90% to 98% in this study. Moreover, functional assays were performed on a defined group of the patients carrying candidate variants in CTLA4, LRBA, NFKB1 and BTK, which confirmed their deleterious effect on protein expression and/or function. This study reiterates that the immunological heterogeneity of predominantly antibody deficiencies may have a diverse genetic origin, although certain clinical features may hint towards a specific group of defects. Employing targeted sequencing panels proves to be a very time- and cost-efficient, yet reliable, method for the establishment of a genetic diagnosis in individuals with PAD. However, in case of negative panel results, or if functional testing reveals inconspicuous observations in patients with a clear indication for genetic testing, further work-up including whole exome or whole genome sequencing should be considered.
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Affiliation(s)
- Jessica Rojas-Restrepo
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Andrés Caballero-Oteyza
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Resolving Infection Susceptibility (RESIST) – Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Katrin Huebscher
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Hanna Haberstroh
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Manfred Fliegauf
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Baerbel Keller
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Warnatz
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Michele Proietti
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Immunology, Hannover Medical University, Hannover, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Resolving Infection Susceptibility (RESIST) – Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
- Center for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany
- German Center for Infection Research (DZIF), Satellite Center Freiburg, Freiburg, Germany
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Nguyen TN, Padman BS, Zellner S, Khuu G, Uoselis L, Lam WK, Skulsuppaisarn M, Lindblom RSJ, Watts EM, Behrends C, Lazarou M. ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system. Mol Cell 2021; 81:2013-2030.e9. [PMID: 33773106 DOI: 10.1016/j.molcel.2021.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/20/2020] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
The sequestration of damaged mitochondria within double-membrane structures termed autophagosomes is a key step of PINK1/Parkin mitophagy. The ATG4 family of proteases are thought to regulate autophagosome formation exclusively by processing the ubiquitin-like ATG8 family (LC3/GABARAPs). We discover that human ATG4s promote autophagosome formation independently of their protease activity and of ATG8 family processing. ATG4 proximity networks reveal a role for ATG4s and their proximity partners, including the immune-disease protein LRBA, in ATG9A vesicle trafficking to mitochondria. Artificial intelligence-directed 3D electron microscopy of phagophores shows that ATG4s promote phagophore-ER contacts during the lipid-transfer phase of autophagosome formation. We also show that ATG8 removal during autophagosome maturation does not depend on ATG4 activity. Instead, ATG4s can disassemble ATG8-protein conjugates, revealing a role for ATG4s as deubiquitinating-like enzymes. These findings establish non-canonical roles of the ATG4 family beyond the ATG8 lipidation axis and provide an AI-driven framework for rapid 3D electron microscopy.
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Affiliation(s)
- Thanh Ngoc Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| | - Benjamin Scott Padman
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Susanne Zellner
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Grace Khuu
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Louise Uoselis
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Wai Kit Lam
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Marvin Skulsuppaisarn
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Runa S J Lindblom
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Emily M Watts
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
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Yang H, Xu F, Chen Y, Tian Z. Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate. Talanta 2021; 232:122437. [PMID: 34074422 DOI: 10.1016/j.talanta.2021.122437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/10/2021] [Accepted: 04/17/2021] [Indexed: 12/01/2022]
Abstract
Breast cancer is one of the most malignant diseases among females. N-glycoproteomics studies have shown that N-glycosylation alteration of tumor cells is the key player of cancer progression, multidrug resistance (MDR) and high mortality. Cancer stem cells (CSCs) have the remarkable potential of self-renewing and differentiation which leads to drug resistance and metastasis. To investigate the differentially expressed N-glycosylation in adriamycin-resistant breast cancer stem cells MCF-7/ADR CSCs (relative to MCF-7 CSCs) and find the putative biomarkers, 1:1 paired ZIC-HILIC-enriched and stable isotopic diethyl labelled (SIDE) intact N-glycopeptides from MCF-7/ADR CSCs and MCF-7 CSCs were analyzed with C18-RPLC-ESI-MS/MS (HCD with stepped NCE); differentially expressed intact N-glycopeptides (DEGPs) were identified and quantified via search engine GPSeeker. With control of spectrum-level FDR≤1%, 5515 intact N-glycopeptides were identified (1737 N-glycosites, 1705 peptide backbones and 1516 intact N-glycoproteins; 181 putative N-glycan linkages and 68 monosaccharide compositions). Among 5515 intact N-glycopeptide IDs, 3864 were identified with glycoform score≥1, i.e., one or more structure-diagnostic fragment ions were observed to distinguish sequence isomers. With the three technical replicates and the criteria of fold change≥1.5 and p value<0.05, 380 DEGPs (corresponding to 153 intact N-glycoproteins) were found along with 293 down-regulated and 87 up-regulated. For these 153 intact N-glycoproteins, the molecular functions and biological processes of were comprehensively discussed, and side-to-side comparison of differential expression results with other method were also made.
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Affiliation(s)
- Hailun Yang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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Gámez-Díaz L, Seidel MG. Different Apples, Same Tree: Visualizing Current Biological and Clinical Insights into CTLA-4 Insufficiency and LRBA and DEF6 Deficiencies. Front Pediatr 2021; 9:662645. [PMID: 33996698 PMCID: PMC8113415 DOI: 10.3389/fped.2021.662645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Cytotoxic T lymphocyte antigen-4 (CTLA-4) is a crucial immune checkpoint that is constitutively expressed in regulatory T (Treg) cells. Following T-cell activation, CTLA-4 is rapidly mobilized from its intracellular vesicle pool to the cell surface to control the availability of co-stimulatory B7 molecules, thereby maintaining immune homeostasis. Heterozygous mutations in CTLA-4 lead to defects in (i) CTLA-4 ligand binding, (ii) homo-dimerization, (iii) B7-transendocytosis, and (iv) CTLA-4 vesicle trafficking, resulting in an inborn error of immunity with predominant autoimmunity. CTLA-4 vesicle trafficking impairment is also observed in patients with lipopolysaccharide-responsive beige-like anchor protein (LRBA) deficiency or the differentially expressed in FDCP6 homolog (DEF6) deficiency, caused by biallelic mutations in LRBA and DEF6, respectively. Therefore, patients with CTLA-4 insufficiency, LRBA deficiency, and-most recently reported-DEF6 deficiency present an overlapping clinical phenotype mainly attributed to a defective suppressive activity of Tregs, as all three diseases reduce overall surface expression of CTLA-4. In this paper, we describe the clinical phenotypes of these immune checkpoint defects, their patho-mechanisms, and visually compare them to other immune regulatory disorders (IPEX syndrome, CD27, and CD70 deficiencies) by using the immune deficiency and dysregulation (IDDA version 2.1) "kaleidoscope" score. This illustrates the variability of the degrees and manifestations of immune deficiency and dysregulation. Patients characteristically present with an increased risk of infections, autoimmune cytopenias, multi-organ autoimmunity, and inflammation, which are often severe and life-threatening. Furthermore, these patients suffer an increased risk of developing malignancies, especially Non-Hodgkin's lymphoma. Successful treatment options include regular administration of soluble CTLA-4-Ig fusion protein, Treg cell-sparing immune suppressants like sirolimus or mycophenolate mofetil, and hematopoietic stem cell transplantation. This mini-review highlights the most relevant biological and clinical features as well as treatment options for CTLA-4 insufficiency and LRBA and DEF6 deficiencies.
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Affiliation(s)
- Laura Gámez-Díaz
- Faculty of Medicine, Center for Chronic Immunodeficiency, Institute for Immunodeficiency, Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Markus G. Seidel
- Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
- Research Unit for Pediatric Hematology and Immunology, Medical University of Graz, Graz, Austria
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9
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Gámez-Díaz L, Grimbacher B. Immune checkpoint deficiencies and autoimmune lymphoproliferative syndromes. Biomed J 2021; 44:400-411. [PMID: 34384744 PMCID: PMC8514790 DOI: 10.1016/j.bj.2021.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/15/2021] [Indexed: 12/30/2022] Open
Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is an inherited non-malignant and non-infectious lymphoproliferative syndrome caused by mutations in genes affecting the extrinsic apoptotic pathway (FAS, FASL, CASP10). The resulting FAS-mediated apoptosis defect accounts for the expansion and accumulation of autoreactive (double-negative) T cells leading to cytopenias, splenomegaly, lymphadenopathy, autoimmune disorders, and risk of lymphoma. However, there are other monogenetic disorders known as ALPS-like syndromes that can be clinically similar to ALPS but are genetically and biologically different, such as observed in patients with immune checkpoint deficiencies, particularly cytotoxic T-lymphocyte antigen 4 (CTLA-4) insufficiency and lipopolysaccharide-responsive beige-like anchor protein LRBA deficiency. CTLA-4 insufficiency is caused by heterozygous mutations in CTLA-4, an essential negative immune regulator that is constitutively expressed on regulatory T (Treg) cells. Mutations in CTLA-4 affect CTLA-4 binding to CD80-CD86 costimulatory molecules, CTLA-4 homodimerization, or CTLA-4 intracellular vesicle trafficking upon cell activation. Abnormal CTLA-4 trafficking is also observed in patients with LRBA deficiency, a syndrome caused by biallelic mutations in LRBA that abolishes the LRBA protein expression. Both immune checkpoint deficiencies are biologically characterized by low levels of CTLA-4 protein on the cell surface of Tregs, accounting for the autoimmune manifestations observed in CTLA4-insufficient and LRBA-deficient patients. In addition, both immune checkpoint deficiencies present with an overlapping but heterogeneous clinical picture despite the difference in inheritance and penetrance. In this review, we describe the most prominent clinical features of ALPS, CTLA-4 insufficiency and LRBA deficiency, emphasizing their corresponding biological mechanisms. We also provide some clinical and laboratory approaches to diagnose these three rare immune disorders, together with therapeutic strategies that have worked best at improving prognosis and quality life of patients.
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Affiliation(s)
- Laura Gámez-Díaz
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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10
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Maggiore R, Grossi A, Fioredda F, Palmisani E, Terranova P, Cappelli E, Lanza T, Pierri F, Guardo D, Calvillo M, Micalizzi C, Beccaria A, Coccia MC, Arrigo S, Dufour C, Ceccherini I, Miano M. Unusual Late-onset Enteropathy in a Patient With Lipopolysaccharide-responsive Beige-like Anchor Protein Deficiency. J Pediatr Hematol Oncol 2020; 42:e768-e771. [PMID: 31876783 DOI: 10.1097/mph.0000000000001708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In recent years, monogenic causes of immune dysregulation syndromes, with variable phenotypes, have been documented. Mutations in the lipopolysaccharide-responsive beige-like anchor (LRBA) protein are associated with common variable immunodeficiency, autoimmunity, chronic enteropathy, and immune dysregulation disorders. The LRBA protein prevents degradation of cytotoxic T-lymphocyte antigen 4 (CTLA4) protein, thus inhibiting immune responses. Both LRBA and CTLA4 deficiencies usually present with immune dysregulation, mostly characterized by autoimmunity and lymphoproliferation. In this report, we describe a patient with an atypical clinical onset of LRBA deficiency and the patient's response to abatacept, a fusion protein-drug that mimics the action of CTLA4.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Serena Arrigo
- Gastroenterology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Oldham RAA, Faber ML, Keppel TR, Buchberger AR, Waas M, Hari P, Gundry RL, Medin JA. Discovery and validation of surface N-glycoproteins in MM cell lines and patient samples uncovers immunotherapy targets. J Immunother Cancer 2020; 8:e000915. [PMID: 32771993 PMCID: PMC7418848 DOI: 10.1136/jitc-2020-000915] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) is characterized by clonal expansion of malignant plasma cells in the bone marrow. While recent advances in treatment for MM have improved patient outcomes, the 5-year survival rate remains ~50%. A better understanding of the MM cell surface proteome could facilitate development of new directed therapies and assist in stratification and monitoring of patient outcomes. METHODS In this study, we first used a mass spectrometry (MS)-based discovery-driven cell surface capture (CSC) approach to map the cell surface N-glycoproteome of MM cell lines. Next, we developed targeted MS assays, and applied these to cell lines and primary patient samples to refine the list of candidate tumor markers. Candidates of interest detected by MS on MM patient samples were further validated using flow cytometry (FCM). RESULTS We identified 696 MM cell surface N-glycoproteins by CSC, and developed 73 targeted MS detection assays. MS-based validation using primary specimens detected 30 proteins with significantly higher abundance in patient MM cells than controls. Nine of these proteins were identified as potential immunotherapeutic targets, including five that were validated by FCM, confirming their expression on the cell surface of primary MM patient cells. CONCLUSIONS This MM surface N-glycoproteome will be a valuable resource in the development of biomarkers and therapeutics. Further, we anticipate that our targeted MS assays will have clinical benefit for the diagnosis, stratification, and treatment of MM patients.
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Affiliation(s)
- Robyn A A Oldham
- Medical Biophysics, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mary L Faber
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Theodore R Keppel
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Amanda R Buchberger
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Matthew Waas
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Parameswaran Hari
- Division of Hematology Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebekah L Gundry
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jeffrey A Medin
- Medical Biophysics, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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12
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Moreno-Corona NC, Lopez-Ortega O, Flores Hermenegildo JM, Berron-Ruiz L, Rodriguez-Alba JC, Santos-Argumedo L, Lopez-Herrera G. Lipopolysaccharide-responsive beige-like anchor acts as a cAMP-dependent protein kinase anchoring protein in B cells. Scand J Immunol 2020; 92:e12922. [PMID: 32592188 DOI: 10.1111/sji.12922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/15/2020] [Accepted: 06/21/2020] [Indexed: 01/04/2023]
Abstract
Lipopolysaccharide (LPS)-responsive beige-like anchor (LRBA) protein was initially described as a monogenetic cause for common variable immune deficiency, a syndrome characterized by low levels of B cells, defects in memory B cell differentiation and hypogammaglobulinaemia. LRBA was identified as an LPS up-regulated gene in B cells, macrophages and T cells. LRBA weighs 320 kDa and has 2863 amino acids. Its sequence contains multiple domains, suggesting that LRBA can act as a scaffolding protein. It contains two putative binding sites for cAMP-dependent kinase (PKA) regulatory subunits, suggesting this protein can act as A-kinase anchor protein (AKAP); however, physical interactions involving LRBA and PKA have not been demonstrated to date, and functional roles for such interactions are unexplored. In this work, we investigated physical interactions involving LRBA with regulatory subunits of PKA in human B cell lines and primary human B cells. PKA is a holoenzyme composed of two regulatory subunits, which can be RIα, RIβ, RIIα or RIIβ, and two catalytic subunits, Cα or Cβ. We co-immunoprecipitated LRBA using Ramos B cell lymphoma cells and observed that LRBA interacts with RIIβ. Interestingly, St-Ht31, an inhibitory peptide that disrupts AKAP interactions with regulatory subunits, reduced the amount of interacting protein. Furthermore, in primary human B cells, LRBA was induced after CD40L and IL-4 stimulation, and under such activation, we found that LRBA interacts with RIIα and RIIβ, suggesting that LRBA acts as an AKAP and binds RII subunits. Interestingly, we also identified that LRBA interacts with activation-induced cytidine deaminase in primary B cells, suggesting that it is involved in B cell function.
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Affiliation(s)
- Nidia Carolina Moreno-Corona
- Biomedicina Molecular, Centro de Investigacion y de Estudios Avanzados, Mexico City, Mexico.,Unidad de Investigacion en Inmunodeficiencias, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Orestes Lopez-Ortega
- Biomedicina Molecular, Centro de Investigacion y de Estudios Avanzados, Mexico City, Mexico
| | - Jose Mizael Flores Hermenegildo
- Biomedicina Molecular, Centro de Investigacion y de Estudios Avanzados, Mexico City, Mexico.,Unidad de Investigacion en Inmunodeficiencias, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Laura Berron-Ruiz
- Unidad de Investigacion en Inmunodeficiencias, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Juan Carlos Rodriguez-Alba
- Unidad de Citometria de Flujo, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | | | - Gabriela Lopez-Herrera
- Unidad de Investigacion en Inmunodeficiencias, Instituto Nacional de Pediatria, Mexico City, Mexico
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13
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Chen J, Yang H, Teo ASM, Amer LB, Sherbaf FG, Tan CQ, Alvarez JJS, Lu B, Lim JQ, Takano A, Nahar R, Lee YY, Phua CZJ, Chua KP, Suteja L, Chen PJ, Chang MM, Koh TPT, Ong BH, Anantham D, Hsu AAL, Gogna A, Too CW, Aung ZW, Lee YF, Wang L, Lim TKH, Wilm A, Choi PS, Ng PY, Toh CK, Lim WT, Ma S, Lim B, Liu J, Tam WL, Skanderup AJ, Yeong JPS, Tan EH, Creasy CL, Tan DSW, Hillmer AM, Zhai W. Genomic landscape of lung adenocarcinoma in East Asians. Nat Genet 2020; 52:177-186. [PMID: 32015526 DOI: 10.1038/s41588-019-0569-6] [Citation(s) in RCA: 253] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 12/12/2019] [Indexed: 12/24/2022]
Abstract
Lung cancer is the world's leading cause of cancer death and shows strong ancestry disparities. By sequencing and assembling a large genomic and transcriptomic dataset of lung adenocarcinoma (LUAD) in individuals of East Asian ancestry (EAS; n = 305), we found that East Asian LUADs had more stable genomes characterized by fewer mutations and fewer copy number alterations than LUADs from individuals of European ancestry. This difference is much stronger in smokers as compared to nonsmokers. Transcriptomic clustering identified a new EAS-specific LUAD subgroup with a less complex genomic profile and upregulated immune-related genes, allowing the possibility of immunotherapy-based approaches. Integrative analysis across clinical and molecular features showed the importance of molecular phenotypes in patient prognostic stratification. EAS LUADs had better prediction accuracy than those of European ancestry, potentially due to their less complex genomic architecture. This study elucidated a comprehensive genomic landscape of EAS LUADs and highlighted important ancestry differences between the two cohorts.
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Affiliation(s)
- Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hechuan Yang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Audrey Su Min Teo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lidyana Bte Amer
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Faranak Ghazi Sherbaf
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chu Quan Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Bingxin Lu
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jia Qi Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Angela Takano
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Rahul Nahar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yin Yeng Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Khi Pin Chua
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lisda Suteja
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Pauline Jieqi Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei Mei Chang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Boon-Hean Ong
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, Singapore
| | - Devanand Anantham
- Department of Respiratory & Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Anne Ann Ling Hsu
- Department of Respiratory & Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Apoorva Gogna
- Department of Vascular & Interventional Radiology, Singapore General Hospital, Singapore, Singapore
| | - Chow Wei Too
- Department of Vascular & Interventional Radiology, Singapore General Hospital, Singapore, Singapore
| | - Zaw Win Aung
- Division of Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Yi Fei Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lanying Wang
- Division of Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Andreas Wilm
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Poh Sum Choi
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Poh Yong Ng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chee Keong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Bing Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Joe Poh Sheng Yeong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Eng-Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Division of Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Daniel Shao Weng Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore. .,Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.
| | - Axel M Hillmer
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| | - Weiwei Zhai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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14
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Martinez-Jaramillo C, Trujillo-Vargas CM. Dissecting the localization of lipopolysaccharide-responsive and beige-like anchor protein (LRBA) in the endomembrane system. Allergol Immunopathol (Madr) 2020; 48:8-17. [PMID: 31883622 DOI: 10.1016/j.aller.2019.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/26/2019] [Indexed: 12/13/2022]
Abstract
INTRODUCTION AND OBJECTIVES LRBA deficiency is caused by loss of LRBA protein expression, due to either homozygous or compounds heterozygous mutations in LRBA. LRBA deficiency has been shown to affect vesicular trafficking and autophagy. To date, LRBA has been observed in the cytosol, Golgi apparatus and some lysosomes in LPS-stimulated murine macrophages. The objectives of the present study were to study the LRBA localization in organelles involved in vesicular traffic, phagocytosis, and autophagy in mononuclear phagocytes (MP). MATERIALS AND METHODS We analyzed LRBA colocalization with different endosomes markets using confocal microscopy in MP. We used the autophagy inhibitors to determine the role of LRBA in formation, maturation or degradation of the autophagosome. RESULTS LRBA intracellular trafficking depends on the activity of the GTPase ADP ribosylation factor-1 (ARF) in MP. LRBA was identified in early, late endosomes but did not colocalize strongly with lysosomal markers. Although LRBA appears not to be recruited during the phagocytic cargo uptake, it greatly colocalized with the microtubule-associated protein 1A/1B-light chain 3 (LC3) under a steady state and this decreased after the induction of autophagy flux. Although the use of inhibitors of lysosome fusion did not restore the LRBA/LC3 colocalization, inhibitors of either early to late endosomes trafficking or PI3K pathway did. CONCLUSIONS Taken together, our results show that LRBA is located in endomembrane system vesicles, mainly in the early and late endosomes. Although LRBA appears not to be involved in the phagocytic uptake, it is recruited in the early steps of the autophagy flux.
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15
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Chinello M, Mauro M, Cantalupo G, Talenti G, Mariotto S, Balter R, De Bortoli M, Vitale V, Zaccaron A, Bonetti E, Di Carlo D, Barzaghi F, Cesaro S. Acute Cervical Longitudinally Extensive Transverse Myelitis in a Child With Lipopolysaccharide-Responsive-Beige-Like-Anchor-Protein (LRBA) Deficiency: A New Complication of a Rare Disease. Front Pediatr 2020; 8:580963. [PMID: 33178652 PMCID: PMC7596261 DOI: 10.3389/fped.2020.580963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/10/2020] [Indexed: 11/16/2022] Open
Abstract
Lipopolysaccharide responsive beige-like anchor protein (LRBA) deficiency is a primary immunodeficiency disorder (PID) that can cause a common variable immunodeficiency (CVID)-like disease. The typical features of the disease are autoimmunity, chronic diarrhea, and hypogammaglobulinemia. Neurological complications are also reported in patients affected by LRBA deficiency. We describe a 7-year old female with an acute cervical longitudinally extensive transverse myelitis (LETM) as a feature of LRBA deficiency. This is the first case of LETM associated with LRBA deficiency described in literature.
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Affiliation(s)
- Matteo Chinello
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Margherita Mauro
- Pediatric Department, Santa Maria Degli Angeli Hospital, Pordenone, Italy
| | | | - Giacomo Talenti
- Department of Diagnostics and Pathology, Neuroradiology Unit, Verona University Hospital, Verona, Italy
| | - Sara Mariotto
- Neurology Unit, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Rita Balter
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Virginia Vitale
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Ada Zaccaron
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Elisa Bonetti
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Federica Barzaghi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, San Raffaele Telethon Institute for Gene Therapy, Milan, Italy
| | - Simone Cesaro
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
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16
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Martínez-Jaramillo C, Gutierrez-Hincapie S, Arango JCO, Vásquez-Duque GM, Erazo-Garnica RM, Franco JL, Trujillo-Vargas CM. Clinical, immunological and genetic characteristic of patients with clinical phenotype associated to LRBA-deficiency in Colombia. Colomb Med (Cali) 2019; 50:176-191. [PMID: 32284663 PMCID: PMC7141146 DOI: 10.25100/cm.v50i3.3969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Background LPS-responsive beige -like anchor protein (LRBA) deficiency is a primary immunodeficiency disease caused by loss of LRBA protein expression, due to biallelic mutations in LRBA gene. LRBA deficiency patients exhibit a clinically heterogeneous syndrome. The main clinical complication of LRBA deficiency is immune dysregulation. Furthermore, hypogammaglobulinemia is found in more than half of patients with LRBA-deficiency. To date, no patients with this condition have been reported in Colombia. Objective To evaluate the expression of the LRBA protein in patients from Colombia with clinical phenotype associated to LRBA-deficiency. Methods In the present study the LRBA-expression in patients from Colombia with clinical phenotype associated to LRBA-deficiency was evaluated. After then, the clinical, the immunological characteristics and the possible genetic variants in LRBA or other genes associated with the immune system in patients that exhibit decrease protein expression was evaluated. Results In total, 112 patients with different clinical manifestations associated to the clinical LRBA phenotype were evaluated. The LRBA expression varies greatly between different healthy donors and patients. Despite the great variability in the LRBA expression, six patients with a decrease in LRBA protein expression were observed. However, no pathogenic or possible pathogenic biallelic variants in LRBA, or in genes related with the immune system were found. Conclusion LRBA expression varies greatly between different healthy donors and patients. Reduction LRBA-expression in 6 patients without homozygous mutations in LRBA or in associated genes with the immune system was observed. These results suggest the other genetic, epigenetic or environmental mechanisms, that might be regulated the LRBA-expression.
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Affiliation(s)
- Catalina Martínez-Jaramillo
- Universidad de Antioquia UdeA, Facultad de Medicina, Grupo de Inmunodeficiencias Primarias, Medellin, Colombia
| | | | | | | | | | - Jose Luis Franco
- Universidad de Antioquia UdeA, Facultad de Medicina, Grupo de Inmunodeficiencias Primarias, Medellin, Colombia
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17
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Dai X, Cheng H, Chen X, Li T, Zhang J, Jin G, Cai D, Huang Z. FOXA1 is Prognostic of Triple Negative Breast Cancers by Transcriptionally Suppressing SOD2 and IL6. Int J Biol Sci 2019; 15:1030-1041. [PMID: 31182923 PMCID: PMC6535797 DOI: 10.7150/ijbs.31009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/08/2019] [Indexed: 12/20/2022] Open
Abstract
Having markers feasible for breast cancer subtyping, especially for triple negative breast cancer identification is crucial for improving the treatment outcome of such cancers. Here we explore the role of FOXA1 in characterizing triple negative breast cancers and the driving mechanisms. Through in vitro examination of the expression pattern at both transcriptional and translational levels, patient relapse-free survival analysis, immunohistochemistry staining and prediction power assessment using clinical samples, as well as functional studies, we systematically compared the role of FOXA1 in identifying triple negative and luminal type of breast cancers and explored the mechanisms driving such functionalities. We report that FOXA1 under-expression can lead to increased malignancy and cancer stemness, and is a subtyping marker identifying triple negative breast cancers rather than the luminal subtype by transcriptionally suppressing the expression of SOD2 and IL6. We are the first to systematically address the significance of FOXA1 in triple negative breast cancer identification as a biomarker and elucidate the mechanism at the molecular level, through a sequential bioinformatics analysis and experimental validations both in vitro and in clinics. Our discoveries compliment the current biomarker modalities once verified using larger clinical cohorts and improve the precision on characterizing breast cancer heterogeneity.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Hongye Cheng
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao Chen
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Ting Li
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jia Zhang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Guoyin Jin
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Dongyan Cai
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Zhaohui Huang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
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18
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Mozdarani H, Kiaee F, Fekrvand S, Azizi G, Yazdani R, Zaki-Dizaji M, Mozdarani S, Mozdarani S, Nosrati H, Abolhassani H, Aghamohammadi A. G2-lymphocyte chromosomal radiosensitivity in patients with LPS responsive beige-like anchor protein (LRBA) deficiency. Int J Radiat Biol 2019; 95:680-690. [PMID: 30714845 DOI: 10.1080/09553002.2019.1577570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lipopolysaccharide-responsive, beige-like anchor protein (LRBA) deficiency is an autosomal recessive primary immunodeficiency disease characterized by a CVID-like phenotype, particularly severe autoimmunity and inflammatory bowel disease. This study was undertaken to evaluate radiation sensitivity in 11 LRBA-deficient patients. Therefore, stimulated lymphocytes of the studied subjects were exposed to a low dose γ-radiation (100 cGy) in the G2 phase of the cell cycle and chromosomal aberrations were scored. Lymphocytes of age-sex matched healthy individuals used in the same way as controls. Based on the G2-assay, six (54.5%) of the patients had higher radiosensitivity score comparing to the healthy control group, forming the radiosensitive LRBA-deficient patients. This chromosomal radiosensitivity showed that these patients are predisposed to autoimmunity and/or malignancy, and should be protected from unnecessary diagnostic and therapeutic procedures using ionizing radiation and exposure to other DNA damaging agents.
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Affiliation(s)
- Hossein Mozdarani
- a Faculty of Medical Sciences, Department of Medical Genetics , Tarbiat Modares University , Terhran , Iran
| | - Fatemeh Kiaee
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran.,c Department of Medical Immunology, School of Medicine , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Saba Fekrvand
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Gholamreza Azizi
- d Non-communicable Diseases Research Center , Alborz University of Medical Sciences , Karaj , Iran
| | - Reza Yazdani
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Majid Zaki-Dizaji
- a Faculty of Medical Sciences, Department of Medical Genetics , Tarbiat Modares University , Terhran , Iran
| | - Sahar Mozdarani
- e Cytogenome Medical Genetics laboratory , Chamran Medical Building , Tehran , Iran
| | - Sohail Mozdarani
- d Non-communicable Diseases Research Center , Alborz University of Medical Sciences , Karaj , Iran
| | - Hassan Nosrati
- f Radiotherapy Department , Cancer Institute, Imam Khomeini Hospital , Tehran , Iran
| | - Hassan Abolhassani
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran.,g Division of Clinical Immunology, Department of Laboratory Medicine , Karolinska Institutet at the Karolinska University Hospital Huddinge , Stockholm , Sweden
| | - Asghar Aghamohammadi
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
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19
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Martínez Jaramillo C, Trujillo-Vargas CM. LRBA in the endomembrane system. COLOMBIA MEDICA (CALI, COLOMBIA) 2018; 49:236-243. [PMID: 30410199 PMCID: PMC6220489 DOI: 10.25100/cm.v49i2.3802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Bi-allelic mutations in LRBA (from Lipopolysaccharide-responsive and beige-like anchor protein) result in a primary immunodeficiency with clinical features ranging from hypogammaglobulinemia and lymphoproliferative syndrome to inflammatory bowel disease and heterogeneous autoimmune manifestations. LRBA deficiency has been shown to affect vesicular trafficking, autophagy and apoptosis, which may lead to alterations of several molecules and processes that play key roles for immunity. In this review, we will discuss the relationship of LRBA with the endovesicular system in the context of receptor trafficking, autophagy and apoptosis. Since these mechanisms of homeostasis are inherent to all living cells and not only limited to the immune system and also, because they are involved in physiological as well as pathological processes such as embryogenesis or tumoral transformation, we envisage advancing in the identification of potential pharmacological agents to manipulate these processes.
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Affiliation(s)
- Catalina Martínez Jaramillo
- Grupo de Inmunodeficiencias primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Claudia M Trujillo-Vargas
- Grupo de Inmunodeficiencias primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
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20
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Gámez-Díaz L, Sigmund EC, Reiser V, Vach W, Jung S, Grimbacher B. Rapid Flow Cytometry-Based Test for the Diagnosis of Lipopolysaccharide Responsive Beige-Like Anchor (LRBA) Deficiency. Front Immunol 2018; 9:720. [PMID: 29740429 PMCID: PMC5925005 DOI: 10.3389/fimmu.2018.00720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/22/2018] [Indexed: 12/18/2022] Open
Abstract
The diagnosis of lipopolysaccharide-responsive beige-like-anchor-protein (LRBA) deficiency currently relies on gene sequencing approaches that do not support a timely diagnosis and clinical management. We developed a rapid and sensitive test for clinical implementation based on the detection of LRBA protein by flow cytometry in peripheral blood cells after stimulation. LRBA protein was assessed in a prospective cohort of 54 healthy donors and 57 patients suspected of LRBA deficiency. Receiver operating characteristics analysis suggested an LRBA:MFI ratio cutoff point of 2.6 to identify LRBA-deficient patients by FACS with 94% sensitivity and 80% specificity and to discriminate them from patients with a similar clinical picture but other disease-causing mutations. This easy flow cytometry-based assay allows a fast screening of patients with suspicion of LRBA deficiency reducing therefore the number of patients requiring LRBA sequencing and accelerating the treatment implementation. Detection of biallelic mutations in LRBA is however required for a definitive diagnosis.
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Affiliation(s)
- Laura Gámez-Díaz
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Elena C Sigmund
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Veronika Reiser
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Institute of Medical Biometry and Statistics, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Werner Vach
- Institute of Medical Biometry and Statistics, Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Sophie Jung
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Pôle de Médecine et de Chirurgie Bucco-Dentaires, University Hospital, Faculty of Dentistry, University of Strasbourg, Strasbourg, France
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, United Kingdom
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21
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Screening for susceptibility genes in hereditary non-polyposis colorectal cancer. Oncol Lett 2018; 15:9413-9419. [PMID: 29844832 DOI: 10.3892/ol.2018.8504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 09/22/2017] [Indexed: 01/29/2023] Open
Abstract
In the present study, hereditary non-polyposis colorectal cancer (HNPCC) susceptibility genes were screened for using whole exome sequencing in 3 HNPCC patients from 1 family and using single nucleotide polymorphism (SNP) genotyping assays in 96 other colorectal cancer and control samples. Peripheral blood was obtained from 3 HNPCC patients from 1 family; the proband and the proband's brother and cousin. High-throughput sequencing was performed using whole exome capture technology. Sequences were aligned against the HAPMAP, dbSNP130 and 1,000 Genome Project databases. Reported common variations and synonymous mutations were filtered out. Non-synonymous single nucleotide variants in the 3 HNPCC patients were integrated and the candidate genes were identified. Finally, SNP genotyping was performed for the genes in 96 peripheral blood samples. In total, 60.4 Gb of data was retrieved from the 3 HNPCC patients using whole exome capture technology. Subsequently, according to certain screening criteria, 15 candidate genes were identified. Among the 96 samples that had been SNP genotyped, 92 were successfully genotyped for 15 gene loci, while genotyping for HTRA1 failed in 4 sporadic colorectal cancer patient samples. In 12 control subjects and 81 sporadic colorectal cancer patients, genotypes at 13 loci were wild-type, namely DDX20, ZFYVE26, PIK3R3, SLC26A8, ZEB2, TP53INP1, SLC11A1, LRBA, CEBPZ, ETAA1, SEMA3G, IFRD2 and FAT1. The CEP290 genotype was mutant in 1 sporadic colorectal cancer patient and was wild-type in all other subjects. A total of 5 of the 12 control subjects and 30 of the 81 sporadic colorectal cancer patients had a mutant HTRA1 genotype. In all 3 HNPCC patients, the same mutant genotypes were identified at all 15 gene loci. Overall, 13 potential susceptibility genes for HNPCC were identified, namely DDX20, ZFYVE26, PIK3R3, SLC26A8, ZEB2, TP53INP1, SLC11A1, LRBA, CEBPZ, ETAA1, SEMA3G, IFRD2 and FAT1.
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22
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Kurtenbach S, Gießl A, Strömberg S, Kremers J, Atorf J, Rasche S, Neuhaus EM, Hervé D, Brandstätter JH, Asan E, Hatt H, Kilimann MW. The BEACH Protein LRBA Promotes the Localization of the Heterotrimeric G-protein G olf to Olfactory Cilia. Sci Rep 2017; 7:8409. [PMID: 28814779 PMCID: PMC5559528 DOI: 10.1038/s41598-017-08543-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
BEACH domain proteins are involved in membrane protein traffic and human diseases, but their molecular mechanisms are not understood. The BEACH protein LRBA has been implicated in immune response and cell proliferation, and human LRBA mutations cause severe immune deficiency. Here, we report a first functional and molecular phenotype outside the immune system of LRBA-knockout mice: compromised olfaction, manifesting in reduced electro-olfactogram response amplitude, impaired food-finding efficiency, and smaller olfactory bulbs. LRBA is prominently expressed in olfactory and vomeronasal chemosensory neurons of wild-type mice. Olfactory impairment in the LRBA-KO is explained by markedly reduced concentrations (20–40% of wild-type levels) of all three subunits αolf, β1 and γ13 of the olfactory heterotrimeric G-protein, Golf, in the sensory cilia of olfactory neurons. In contrast, cilia morphology and the concentrations of many other proteins of olfactory cilia are not or only slightly affected. LRBA is also highly expressed in photoreceptor cells, another cell type with a specialized sensory cilium and heterotrimeric G-protein-based signalling; however, visual function appeared unimpaired by the LRBA-KO. To our knowledge, this is the first observation that a BEACH protein is required for the efficient subcellular localization of a lipid-anchored protein, and of a ciliary protein.
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Affiliation(s)
- Stefan Kurtenbach
- Department of Cell Physiology, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Andreas Gießl
- Department of Biology, Animal Physiology, University of Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - Siv Strömberg
- Department of Neuroscience, Uppsala University, S-75124, Uppsala, Sweden
| | - Jan Kremers
- Department of Ophthalmology, University Hospital Erlangen, D-91054, Erlangen, Germany.,Department of Anatomy II, Friedrich-Alexander University Erlangen-Nürnberg, D-91054, Erlangen, Germany
| | - Jenny Atorf
- Department of Ophthalmology, University Hospital Erlangen, D-91054, Erlangen, Germany
| | - Sebastian Rasche
- Department of Cell Physiology, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Eva M Neuhaus
- Department of Pharmacology and Toxikology, University Hospital Jena, D-07747, Jena, Germany
| | - Denis Hervé
- Inserm UMR-S839, Institut du Fer a Moulin, Universite Pierre et Marie Curie, F-75005, Paris, France
| | | | - Esther Asan
- Institute of Anatomy and Cell Biology, University of Würzburg, D-97070, Würzburg, Germany
| | - Hanns Hatt
- Department of Cell Physiology, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Manfred W Kilimann
- Department of Neuroscience, Uppsala University, S-75124, Uppsala, Sweden. .,Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, D-37075, Göttingen, Germany.
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Gámez-Díaz L, Neumann J, Jäger F, Proietti M, Felber F, Soulas-Sprauel P, Perruzza L, Grassi F, Kögl T, Aichele P, Kilimann M, Grimbacher B, Jung S. Immunological phenotype of the murine Lrba knockout. Immunol Cell Biol 2017; 95:789-802. [PMID: 28652580 DOI: 10.1038/icb.2017.52] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 01/01/2023]
Abstract
Biallelic mutations in the human lipopolysaccharide responsive beige-like anchor (LRBA) gene lead to a primary immunodeficiency known as LRBA deficiency, characterized by a broad range of clinical manifestations including autoimmunity, organomegaly, hypogammaglobulinemia and recurrent infections. Considering the phenotypic heterogeneity in patients and the severity of the disease, our aim was to assess the role of LRBA in immune cells and to understand the underlying pathomechanisms through the study of a Lrba knockout (Lrba-/-) mouse model. LRBA-deficient mice did not show severe clinical or immunological signs of disease, either at steady state under specific-pathogen-free conditions, after vaccination with T-dependent and T-independent antigens, or in the context of acute infections with lymphocytic choriomeningitis virus (LCMV) or Salmonella Typhimurium. Although Lrba-/- mice were able to produce normal serum immunoglobulin M (IgM) and IgG and to mount a specific immune response after immunization, they showed elevated serum and secretory basal IgA levels. LRBA was dispensable for B- and T-cell development, as well as for in vitro B-cell proliferation, survival, isotype switching and plasmablast differentiation. Interestingly, Lrba-/- mice displayed decreased cytotoxic T-lymphocyte-associated protein-4 (CTLA-4) expression by regulatory T cells and activated conventional CD4+ and CD8+ T lymphocytes, reduced frequency of peritoneal B-1a cells along with diminished interleukin-10 production and increased percentages of T follicular helper cells in Peyer's patches, but without developing overt signs of autoimmunity. Our findings expand the role of LRBA in immune regulatory mechanisms previously reported in patients, and suggest a novel role in IgA production that is crucial for the protection of mucosal surfaces and gut-associated immune tolerance.
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Affiliation(s)
- Laura Gámez-Díaz
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Julika Neumann
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fiona Jäger
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michele Proietti
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Felicitas Felber
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pauline Soulas-Sprauel
- CNRS UPR 3572 'Immunopathology and Therapeutic Chemistry', Laboratory of Excellence Medalis, Institute of Molecular and Cellular Biology (IBMC), Strasbourg, France.,Department of Clinical Immunology and Internal Medicine, University Hospital, Strasbourg, France.,Faculty of Pharmacy, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Lisa Perruzza
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Fabio Grassi
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy.,Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Tamara Kögl
- Department of Immunology, Institute for Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany
| | - Peter Aichele
- Department of Immunology, Institute for Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany
| | - Manfred Kilimann
- Department of Molecular Neurobiology, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Sophie Jung
- Center for Chronic Immunodeficiency (CCI), Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Hôpitaux universitaires de Strasbourg, Pôle de Médecine et de Chirurgie Bucco-dentaires, Strasbourg, France.,Université de Strasbourg, Faculté de Chirurgie Dentaire, Strasbourg, France
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24
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Bratanič N, Kovač J, Pohar K, Trebušak Podkrajšek K, Ihan A, Battelino T, Avbelj Stefanija M. Multifocal gastric adenocarcinoma in a patient with LRBA deficiency. Orphanet J Rare Dis 2017; 12:131. [PMID: 28720148 PMCID: PMC5516372 DOI: 10.1186/s13023-017-0682-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023] Open
Abstract
Background Lipopolysaccharide-responsive, beige-like anchor protein (LRBA) deficiency is characterized by primary immunodeficiency and autoimmunity. Cancer may present another feature of LRBA deficiency. We describe a case history of a young adult with LRBA deficiency and two independent malignancies. Methods Family-trio whole exome sequencing with unbiased phenotype ontology approach was used for identification of causative mutations of a primary immune deficiency disorder. Additionally, we sought to identify germline mutations in genes known to be associated with two independent malignancies using a targeted approach. A cytotoxic T-lymphocyte associated protein 4 (CTLA4) expression in T lymphocytes was determined by flow cytometry. Results In the patient with clinical signs of LRBA deficiency multifocal gastric carcinoma and malignant melanoma were diagnosed and surgically treated at 19 and 27 years of age, respectively. Despite refusal of any adjuvant chemotherapy or radiotherapy, the patient demonstrated disease free survival for at least 13 years after the first cancer diagnosis. A homozygous frameshift deletion in LRBA gene (p.Glu946Ter) and two common variants in TYR gene were identified. Reduced CTLA4 expression in a subset of regulatory T lymphocytes was identified in the patient and his unaffected mother carrying a heterozygous LRBA mutation as compared to control in a dose-dependent manner. Conclusion This is the first description of gastric cancer and malignant melanoma in a young adult with LRBA deficiency. The role of LRBA gene knockout in cancer development and its prognosis remains to be elucidated. Electronic supplementary material The online version of this article (doi:10.1186/s13023-017-0682-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nina Bratanič
- Department of Pediatric Endocrinology, Diabetes and Metabolism, University Medical Centre, University Children's Hospital, Bohoriceva 20, 1000, Ljubljana, Slovenia
| | - Jernej Kovač
- University Medical Centre, University Children's Hospital, Unit for Special Laboratory Diagnostics, Vrazov trg 1, 1000, Ljubljana, Slovenia
| | - Katka Pohar
- University of Ljubljana, Faculty of Medicine, Institute for Microbiology and Immunology, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Katarina Trebušak Podkrajšek
- University Medical Centre, University Children's Hospital, Unit for Special Laboratory Diagnostics, Vrazov trg 1, 1000, Ljubljana, Slovenia.,University of Ljubljana, Faculty of Medicine, Vrazov trg 2, 1000, Ljubljana, Slovenia
| | - Alojz Ihan
- University of Ljubljana, Faculty of Medicine, Institute for Microbiology and Immunology, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolism, University Medical Centre, University Children's Hospital, Bohoriceva 20, 1000, Ljubljana, Slovenia.,University of Ljubljana, Faculty of Medicine, Vrazov trg 2, 1000, Ljubljana, Slovenia
| | - Magdalena Avbelj Stefanija
- Department of Pediatric Endocrinology, Diabetes and Metabolism, University Medical Centre, University Children's Hospital, Bohoriceva 20, 1000, Ljubljana, Slovenia.
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Le Morvan M, Zinovyev A, Vert JP. NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PLoS Comput Biol 2017; 13:e1005573. [PMID: 28650955 PMCID: PMC5507468 DOI: 10.1371/journal.pcbi.1005573] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 07/11/2017] [Accepted: 05/15/2017] [Indexed: 01/01/2023] Open
Abstract
Genome-wide somatic mutation profiles of tumours can now be assessed efficiently and promise to move precision medicine forward. Statistical analysis of mutation profiles is however challenging due to the low frequency of most mutations, the varying mutation rates across tumours, and the presence of a majority of passenger events that hide the contribution of driver events. Here we propose a method, NetNorM, to represent whole-exome somatic mutation data in a form that enhances cancer-relevant information using a gene network as background knowledge. We evaluate its relevance for two tasks: survival prediction and unsupervised patient stratification. Using data from 8 cancer types from The Cancer Genome Atlas (TCGA), we show that it improves over the raw binary mutation data and network diffusion for these two tasks. In doing so, we also provide a thorough assessment of somatic mutations prognostic power which has been overlooked by previous studies because of the sparse and binary nature of mutations.
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Affiliation(s)
- Marine Le Morvan
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France
- Institut Curie, 75248 Paris Cedex 5, France
- INSERM, U900, 75248 Paris Cedex 5, France
| | - Andrei Zinovyev
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France
- Institut Curie, 75248 Paris Cedex 5, France
- INSERM, U900, 75248 Paris Cedex 5, France
| | - Jean-Philippe Vert
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France
- Institut Curie, 75248 Paris Cedex 5, France
- INSERM, U900, 75248 Paris Cedex 5, France
- Department of Mathematics and Applications, Ecole normale supérieure, CNRS, PSL Research University, 75005 Paris, France
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26
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LRBA is Essential for Allogeneic Responses in Bone Marrow Transplantation. Sci Rep 2016; 6:36568. [PMID: 27824136 PMCID: PMC5099895 DOI: 10.1038/srep36568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/18/2016] [Indexed: 12/25/2022] Open
Abstract
The PH-BEACH-WD40 (PBW) protein family members play a role in coordinating receptor signaling and intracellular vesicle trafficking. LPS-Responsive-Beige-like Anchor (LRBA) is a PBW protein whose immune function remains elusive. Here we show that LRBA-null mice are viable, but exhibit compromised rejection of allogeneic, xenogeneic and missing self bone-marrow grafts. Further, we demonstrate that LRBA-null Natural Killer (NK) cells exhibit impaired signaling by the key NK activating receptors, NKp46 and NKG2D. However, induction of IFN-γ by cytokines remains intact, indicating LRBA selectively facilitates signals by receptors for ligands expressed on the surface of NK targets. Surprisingly, LRBA limits immunoregulatory cell numbers in tissues where GvHD is primed or initiated, and consistent with this LRBA-null mice also demonstrate resistance to lethal GvHD. These findings demonstrate that LRBA is redundant for host longevity while being essential for both host and donor-mediated immune responses and thus represents a unique and novel molecular target in transplant immunology.
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27
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Maffucci P, Filion CA, Boisson B, Itan Y, Shang L, Casanova JL, Cunningham-Rundles C. Genetic Diagnosis Using Whole Exome Sequencing in Common Variable Immunodeficiency. Front Immunol 2016; 7:220. [PMID: 27379089 PMCID: PMC4903998 DOI: 10.3389/fimmu.2016.00220] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 01/18/2023] Open
Abstract
Whole exome sequencing (WES) has proven an effective tool for the discovery of genetic defects in patients with primary immunodeficiencies (PIDs). However, success in dissecting the genetic etiology of common variable immunodeficiency (CVID) has been limited. We outline a practical framework for using WES to identify causative genetic defects in these subjects. WES was performed on 50 subjects diagnosed with CVID who had at least one of the following criteria: early onset, autoimmune/inflammatory manifestations, low B lymphocytes, and/or familial history of hypogammaglobulinemia. Following alignment and variant calling, exomes were screened for mutations in 269 PID-causing genes. Variants were filtered based on the mode of inheritance and reported frequency in the general population. Each variant was assessed by study of familial segregation and computational predictions of deleteriousness. Out of 433 variations in PID-associated genes, we identified 17 probable disease-causing mutations in 15 patients (30%). These variations were rare or private and included monoallelic mutations in NFKB1, STAT3, CTLA4, PIK3CD, and IKZF1, and biallelic mutations in LRBA and STXBP2. Forty-two other damaging variants were found but were not considered likely disease-causing based on the mode of inheritance and/or patient phenotype. WES combined with analysis of PID-associated genes is a cost-effective approach to identify disease-causing mutations in CVID patients with severe phenotypes and was successful in 30% of our cohort. As targeted therapeutics are becoming the mainstay of treatment for non-infectious manifestations in CVID, this approach will improve management of patients with more severe phenotypes.
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Affiliation(s)
- Patrick Maffucci
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles A Filion
- Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - Bertrand Boisson
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA; Necker Branch, Laboratory of Human Genetics of Infectious Diseases, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Imagine Institute, Paris Descartes University, Paris, France
| | - Yuval Itan
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University , New York, NY , USA
| | - Lei Shang
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University , New York, NY , USA
| | - Jean-Laurent Casanova
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA; Necker Branch, Laboratory of Human Genetics of Infectious Diseases, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Imagine Institute, Paris Descartes University, Paris, France; Howard Hughes Medical Institute, New York, NY, USA; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
| | - Charlotte Cunningham-Rundles
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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28
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Spectrum of Phenotypes Associated with Mutations in LRBA. J Clin Immunol 2015; 36:33-45. [DOI: 10.1007/s10875-015-0224-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/10/2015] [Indexed: 01/08/2023]
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29
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Wang B, Li K, Wang A, Reiser M, Saunders T, Lockey RF, Wang JW. Highly efficient CRISPR/HDR-mediated knock-in for mouse embryonic stem cells and zygotes. Biotechniques 2015; 59:201-2, 204, 206-8. [PMID: 26458548 DOI: 10.2144/000114339] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/27/2015] [Indexed: 11/23/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) gene editing technique, based on the non-homologous end-joining (NHEJ) repair pathway, has been used to generate gene knock-outs with variable sizes of small insertion/deletions with high efficiency. More precise genome editing, either the insertion or deletion of a desired fragment, can be done by combining the homology-directed-repair (HDR) pathway with CRISPR cleavage. However, HDR-mediated gene knock-in experiments are typically inefficient, and there have been no reports of successful gene knock-in with DNA fragments larger than 4 kb. Here, we describe the targeted insertion of large DNA fragments (7.4 and 5.8 kb) into the genomes of mouse embryonic stem (ES) cells and zygotes, respectively, using the CRISPR/HDR technique without NHEJ inhibitors. Our data show that CRISPR/HDR without NHEJ inhibitors can result in highly efficient gene knock-in, equivalent to CRISPR/HDR with NHEJ inhibitors. Although NHEJ is the dominant repair pathway associated with CRISPR-mediated double-strand breaks (DSBs), and biallelic gene knock-ins are common, NHEJ and biallelic gene knock-ins were not detected. Our results demonstrate that efficient targeted insertion of large DNA fragments without NHEJ inhibitors is possible, a result that should stimulate interest in understanding the mechanisms of high efficiency CRISPR targeting in general.
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Affiliation(s)
- Bangmei Wang
- Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Kunyu Li
- Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Amy Wang
- Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Michelle Reiser
- Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL
| | | | - Richard F Lockey
- Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL.,James A. Haley Veterans' Hospital, Tampa, FL
| | - Jia-Wang Wang
- Division of Allergy and Immunology, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, FL
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30
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Steffens A, Bräutigam A, Jakoby M, Hülskamp M. The BEACH Domain Protein SPIRRIG Is Essential for Arabidopsis Salt Stress Tolerance and Functions as a Regulator of Transcript Stabilization and Localization. PLoS Biol 2015; 13:e1002188. [PMID: 26133670 PMCID: PMC4489804 DOI: 10.1371/journal.pbio.1002188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
Abstract
Members of the highly conserved class of BEACH domain containing proteins (BDCPs) have been established as broad facilitators of protein-protein interactions and membrane dynamics in the context of human diseases like albinism, bleeding diathesis, impaired cellular immunity, cancer predisposition, and neurological dysfunctions. Also, the Arabidopsis thaliana BDCP SPIRRIG (SPI) is important for membrane integrity, as spi mutants exhibit split vacuoles. In this work, we report a novel molecular function of the BDCP SPI in ribonucleoprotein particle formation. We show that SPI interacts with the P-body core component DECAPPING PROTEIN 1 (DCP1), associates to mRNA processing bodies (P-bodies), and regulates their assembly upon salt stress. The finding that spi mutants exhibit salt hypersensitivity suggests that the local function of SPI at P-bodies is of biological relevance. Transcriptome-wide analysis revealed qualitative differences in the salt stress-regulated transcriptional response of Col-0 and spi. We show that SPI regulates the salt stress-dependent post-transcriptional stabilization, cytoplasmic agglomeration, and localization to P-bodies of a subset of salt stress-regulated mRNAs. Finally, we show that the PH-BEACH domains of SPI and its human homolog FAN (Factor Associated with Neutral sphingomyelinase activation) interact with DCP1 isoforms from plants, mammals, and yeast, suggesting the evolutionary conservation of an association of BDCPs and P-bodies.
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Affiliation(s)
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
- Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- * E-mail:
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Charbonnier LM, Janssen E, Chou J, Ohsumi TK, Keles S, Hsu JT, Massaad MJ, Garcia-Lloret M, Hanna-Wakim R, Dbaibo G, Alangari AA, Alsultan A, Al-Zahrani D, Geha RS, Chatila TA. Regulatory T-cell deficiency and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like disorder caused by loss-of-function mutations in LRBA. J Allergy Clin Immunol 2015; 135:217-27. [PMID: 25468195 PMCID: PMC4289093 DOI: 10.1016/j.jaci.2014.10.019] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 01/26/2023]
Abstract
BACKGROUND A number of heritable immune dysregulatory diseases result from defects affecting regulatory T (Treg) cell development, function, or both. They include immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome, which is caused by mutations in forkhead box P3 (FOXP3), and IPEX-like disorders caused by mutations in IL-2 receptor α (IL2RA), signal transducer and activator of transcription 5b (STAT5b), and signal transducer and activator of transcription 1 (STAT1). However, the genetic defects underlying many cases of IPEX-like disorders remain unknown. OBJECTIVE We sought to identify the genetic abnormalities in patients with idiopathic IPEX-like disorders. METHODS We performed whole-exome and targeted gene sequencing and phenotypic and functional analyses of Treg cells. RESULTS A child who presented with an IPEX-like syndrome and severe Treg cell deficiency was found to harbor a nonsense mutation in the gene encoding LPS-responsive beige-like anchor (LRBA), which was previously implicated as a cause of common variable immunodeficiency with autoimmunity. Analysis of subjects with LRBA deficiency revealed marked Treg cell depletion; profoundly decreased expression of canonical Treg cell markers, including FOXP3, CD25, Helios, and cytotoxic T lymphocyte-associated antigen 4; and impaired Treg cell-mediated suppression. There was skewing in favor of memory T cells and intense autoantibody production, with marked expansion of T follicular helper and contraction of T follicular regulatory cells. Whereas the frequency of recent thymic emigrants and the differentiation of induced Treg cells were normal, LRBA-deficient T cells exhibited increased apoptosis and reduced activities of the metabolic sensors mammalian target of rapamycin complexes 1 and 2. CONCLUSION LRBA deficiency is a novel cause of IPEX-like syndrome and Treg cell deficiency associated with metabolic dysfunction and increased apoptosis of Treg cells.
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Affiliation(s)
- Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Erin Janssen
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Toshiro K Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Mass
| | - Sevgi Keles
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Joyce T Hsu
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Michel J Massaad
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Maria Garcia-Lloret
- Division of Immunology, Department of Pediatrics, University of California at Los Angeles, Los Angeles, Calif
| | - Rima Hanna-Wakim
- Division of Pediatric Infectious Diseases, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- Division of Pediatric Infectious Diseases, American University of Beirut, Beirut, Lebanon
| | - Abdullah A Alangari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alsultan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Daifulah Al-Zahrani
- Immunology and Allergy, Pediatric Department, King Abdulaziz Medical City-WR, Jeddah, Saudi Arabia
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass.
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Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) denote a heterogeneous group of disorders associated with an imbalance of gut microbiome and the immune system. Importance of the immune system in the gut is endorsed by the presence of IBD-like symptoms in several primary immunodeficiencies. A fraction of early-onset IBDs presenting with more severe disease course and incomplete response to conventional treatment is assumed to be inherited in a Mendelian fashion, as exemplified by the recent discovery of interleukin (IL)-10 (receptor) deficiency. METHODS We analyzed a patient born to consanguineous parents suffering from severe intestinal manifestations since 6 months of age and later diagnosed as IBD. Eventually, she developed autoimmune manifestations including thyroiditis and type I diabetes at the age of 6 and 9 years, respectively. Combined single-nucleotide polymorphism array-based homozygosity mapping and exome sequencing was performed to identify the underlying genetic defect. Protein structural predictions were calculated using I-TASSER. Immunoblot was performed to assess protein expression. Flow cytometric analysis was applied to investigate B-cell subpopulations. RESULTS We identified a homozygous missense mutation (p.Ile2824Pro) in lipopolysaccharide-responsive and beige-like anchor (LRBA) affecting the C-terminal WD40 domain of the protein. In contrast to previously published LRBA-deficient patients, the mutant protein was expressed at similar levels to healthy controls. Immunophenotyping of the index patient revealed normal B-cell subpopulations except increased CD21 B cells. CONCLUSIONS We describe a patient with a novel missense mutation in LRBA who presented with IBD-like symptoms at early age, illustrating that LRBA deficiency should be considered in the differential diagnosis for IBD(-like) disease even in the absence of overt immunodeficiency.
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Seidel MG, Hirschmugl T, Gamez-Diaz L, Schwinger W, Serwas N, Deutschmann A, Gorkiewicz G, Zenz W, Windpassinger C, Grimbacher B, Urban C, Boztug K. Long-term remission after allogeneic hematopoietic stem cell transplantation in LPS-responsive beige-like anchor (LRBA) deficiency. J Allergy Clin Immunol 2014; 135:1384-90.e1-8. [PMID: 25539626 PMCID: PMC4429722 DOI: 10.1016/j.jaci.2014.10.048] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Markus G Seidel
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology-Oncology, Medical University Graz, Graz, Austria.
| | - Tatjana Hirschmugl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Laura Gamez-Diaz
- Center for Chronic Immunodeficiency, University Medical Center, Freiburg, Germany
| | - Wolfgang Schwinger
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology-Oncology, Medical University Graz, Graz, Austria
| | - Nina Serwas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Deutschmann
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University Graz, Graz, Austria
| | | | - Werner Zenz
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University Graz, Graz, Austria
| | | | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, University Medical Center, Freiburg, Germany
| | - Christian Urban
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology-Oncology, Medical University Graz, Graz, Austria
| | - Kaan Boztug
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria.
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Andres SA, Brock GN, Wittliff JL. Interrogating differences in expression of targeted gene sets to predict breast cancer outcome. BMC Cancer 2013; 13:326. [PMID: 23819905 PMCID: PMC3707751 DOI: 10.1186/1471-2407-13-326] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 06/26/2013] [Indexed: 11/13/2022] Open
Abstract
Background Genomics provides opportunities to develop precise tests for diagnostics, therapy selection and monitoring. From analyses of our studies and those of published results, 32 candidate genes were identified, whose expression appears related to clinical outcome of breast cancer. Expression of these genes was validated by qPCR and correlated with clinical follow-up to identify a gene subset for development of a prognostic test. Methods RNA was isolated from 225 frozen invasive ductal carcinomas,and qRT-PCR was performed. Univariate hazard ratios and 95% confidence intervals for breast cancer mortality and recurrence were calculated for each of the 32 candidate genes. A multivariable gene expression model for predicting each outcome was determined using the LASSO, with 1000 splits of the data into training and testing sets to determine predictive accuracy based on the C-index. Models with gene expression data were compared to models with standard clinical covariates and models with both gene expression and clinical covariates. Results Univariate analyses revealed over-expression of RABEP1, PGR, NAT1, PTP4A2, SLC39A6, ESR1, EVL, TBC1D9, FUT8, and SCUBE2 were all associated with reduced time to disease-related mortality (HR between 0.8 and 0.91, adjusted p < 0.05), while RABEP1, PGR, SLC39A6, and FUT8 were also associated with reduced recurrence times. Multivariable analyses using the LASSO revealed PGR, ESR1, NAT1, GABRP, TBC1D9, SLC39A6, and LRBA to be the most important predictors for both disease mortality and recurrence. Median C-indexes on test data sets for the gene expression, clinical, and combined models were 0.65, 0.63, and 0.65 for disease mortality and 0.64, 0.63, and 0.66 for disease recurrence, respectively. Conclusions Molecular signatures consisting of five genes (PGR, GABRP, TBC1D9, SLC39A6 and LRBA) for disease mortality and of six genes (PGR, ESR1, GABRP, TBC1D9, SLC39A6 and LRBA) for disease recurrence were identified. These signatures were as effective as standard clinical parameters in predicting recurrence/mortality, and when combined, offered some improvement relative to clinical information alone for disease recurrence (median difference in C-values of 0.03, 95% CI of -0.08 to 0.13). Collectively, results suggest that these genes form the basis for a clinical laboratory test to predict clinical outcome of breast cancer.
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Affiliation(s)
- Sarah A Andres
- Hormone Receptor Laboratory, Department of Biochemistry & Molecular Biology, Brown Cancer Center and the Institute for Molecular Diversity & Drug Design, University of Louisville, Louisville, KY 40292, USA
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Primary immunodeficiencies: a rapidly evolving story. J Allergy Clin Immunol 2013; 131:314-23. [PMID: 23374262 DOI: 10.1016/j.jaci.2012.11.051] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/06/2012] [Accepted: 11/29/2012] [Indexed: 12/28/2022]
Abstract
The characterization of primary immunodeficiencies (PIDs) in human subjects is crucial for a better understanding of the biology of the immune response. New achievements in this field have been possible in light of collaborative studies; attention paid to new phenotypes, infectious and otherwise; improved immunologic techniques; and use of exome sequencing technology. The International Union of Immunological Societies Expert Committee on PIDs recently reported on the updated classification of PIDs. However, new PIDs are being discovered at an ever-increasing rate. A series of 19 novel primary defects of immunity that have been discovered after release of the International Union of Immunological Societies report are discussed here. These new findings highlight the molecular pathways that are associated with clinical phenotypes and suggest potential therapies for affected patients.
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Cullinane AR, Schäffer AA, Huizing M. The BEACH is hot: a LYST of emerging roles for BEACH-domain containing proteins in human disease. Traffic 2013; 14:749-66. [PMID: 23521701 DOI: 10.1111/tra.12069] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 03/23/2013] [Indexed: 12/19/2022]
Abstract
BEACH (named after 'Beige and Chediak-Higashi') is a conserved ∼280 residue domain, present in nine human BEACH domain containing proteins (BDCPs). Most BDCPs are large, containing a PH-like domain for membrane association preceding their BEACH domain, and containing WD40 and other domains for ligand binding. Recent studies found that mutations in individual BDCPs cause several human diseases. BDCP alterations affect lysosome size (LYST and NSMAF), apoptosis (NSMAF), autophagy (LYST, WDFY3, LRBA), granule size (LYST, NBEAL2, NBEA) or synapse formation (NBEA). However, the roles of each BDCP in these membrane events remain controversial. After reviewing studies on individual BDCPs, we propose a unifying hypothesis that BDCPs act as scaffolding proteins that facilitate membrane events, including both fission and fusion, determined by their binding partners. BDCPs may also bind each other, enabling fusion or fission of vesicles that are not necessarily of the same type. Such mechanisms explain why different BDCPs may have roles in autophagy; each BDCP is specific for the cell type or the cargo, but not necessarily specific for attaching to the autophagosome. Further elucidation of these mechanisms, preferably carrying out the same experiment on multiple BDCPs, and possibly using patients' cells, may identify potential targets for therapy.
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Affiliation(s)
- Andrew R Cullinane
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
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Jiao X, Hooper SD, Djureinovic T, Larsson C, Wärnberg F, Tellgren-Roth C, Botling J, Sjöblom T. Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing. BMC Genomics 2013; 14:165. [PMID: 23496902 PMCID: PMC3600027 DOI: 10.1186/1471-2164-14-165] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 03/08/2013] [Indexed: 02/03/2023] Open
Abstract
Background Chromosomal rearrangements in the form of deletions, insertions, inversions and translocations are frequently observed in breast cancer genomes, and a subset of these rearrangements may play a crucial role in tumorigenesis. To identify novel somatic chromosomal rearrangements, we determined the genome structures of 15 hormone-receptor negative breast tumors by long-insert mate pair massively parallel sequencing. Results We identified and validated 40 somatic structural alterations, including the recurring fusion between genes DDX10 and SKA3 and translocations involving the EPHA5 gene. Other rearrangements were found to affect genes in pathways involved in epigenetic regulation, mitosis and signal transduction, underscoring their potential role in breast tumorigenesis. RNA interference-mediated suppression of five candidate genes (DDX10, SKA3, EPHA5, CLTC and TNIK) led to inhibition of breast cancer cell growth. Moreover, downregulation of DDX10 in breast cancer cells lead to an increased frequency of apoptotic nuclear morphology. Conclusions Using whole genome mate pair sequencing and RNA interference assays, we have discovered a number of novel gene rearrangements in breast cancer genomes and identified DDX10, SKA3, EPHA5, CLTC and TNIK as potential cancer genes with impact on the growth and proliferation of breast cancer cells.
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Affiliation(s)
- Xiang Jiao
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, SE 751 85, Sweden
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Drosophila rugose is a functional homolog of mammalian Neurobeachin and affects synaptic architecture, brain morphology, and associative learning. J Neurosci 2013; 32:15193-204. [PMID: 23100440 DOI: 10.1523/jneurosci.6424-11.2012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Neurobeachin (Nbea) is implicated in vesicle trafficking in the regulatory secretory pathway, but details on its molecular function are currently unknown. We have used Drosophila melanogaster mutants for rugose (rg), the Drosophila homolog of Nbea, to further elucidate the function of this multidomain protein. Rg is expressed in a granular pattern reminiscent of the Golgi network in neuronal cell bodies and colocalizes with transgenic Nbea, suggesting a function in secretory regulation. In contrast to Nbea(-/-) mice, rg null mutants are viable and fertile and exhibit aberrant associative odor learning, changes in gross brain morphology, and synaptic architecture as determined at the larval neuromuscular junction. At the same time, basal synaptic transmission is essentially unaffected, suggesting that structural and functional aspects are separable. Rg phenotypes can be rescued by a Drosophila rg+ transgene, whereas a mouse Nbea transgene rescues aversive odor learning and synaptic architecture; it fails to rescue brain morphology and appetitive odor learning. This dissociation between the functional redundancy of either the mouse or the fly transgene suggests that their complex composition of numerous functional and highly conserved domains support independent functions. We propose that the detailed compendium of phenotypes exhibited by the Drosophila rg null mutant provided here will serve as a test bed for dissecting the different functional domains of BEACH (for beige and human Chediak-Higashi syndrome) proteins, such as Rugose, mouse Nbea, or Nbea orthologs in other species, such as human.
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Alangari A, Alsultan A, Adly N, Massaad MJ, Kiani IS, Aljebreen A, Raddaoui E, Almomen AK, Al-Muhsen S, Geha RS, Alkuraya FS. LPS-responsive beige-like anchor (LRBA) gene mutation in a family with inflammatory bowel disease and combined immunodeficiency. J Allergy Clin Immunol 2012; 130:481-8.e2. [PMID: 22721650 PMCID: PMC3582381 DOI: 10.1016/j.jaci.2012.05.043] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 05/29/2012] [Accepted: 05/29/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Clinical immunology has traditionally relied on accurate phenotyping of the patient's immune dysfunction for the identification of a candidate gene or genes for sequencing and molecular confirmation. Although this is also true for other branches of medicine, the marked variability in immune-related phenotypes and the highly complex network of molecules that confer normal host immunity are challenges that clinical immunologists often face in their quest to establish a specific genetic diagnosis. OBJECTIVE We sought to identify the underlying genetic cause in a consanguineous family with chronic inflammatory bowel disease-like disorder and combined immunodeficiency. METHODS We performed exome sequencing followed by autozygome filtration. RESULTS A truncating mutation in LPS-responsive beige-like anchor (LRBA), which abolished protein expression, was identified as the most likely candidate variant in this family. CONCLUSION The combined exome sequencing and autozygosity mapping approach is a powerful tool in the study of atypical immune dysfunctions. We identify LRBA as a novel immunodeficiency candidate gene the precise role of which in the immune system requires future studies.
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Affiliation(s)
- Abdullah Alangari
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Abdulrahman Alsultan
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Nouran Adly
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh
| | - Michel J. Massaad
- Departments of Pathology, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Iram Shakir Kiani
- Departments of Internal Medicine, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Abdulrahman Aljebreen
- Departments of Internal Medicine, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Emad Raddaoui
- Departments of Pathology, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Abdul-Kareem Almomen
- Departments of Internal Medicine, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Saleh Al-Muhsen
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
| | - Raif S. Geha
- Department of the Division of Immunology, Children’s Hospital Boston and Harvard Medical School, Boston
| | - Fowzan S. Alkuraya
- Departments of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh
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Lopez-Herrera G, Tampella G, Pan-Hammarström Q, Herholz P, Trujillo-Vargas C, Phadwal K, Simon A, Moutschen M, Etzioni A, Mory A, Srugo I, Melamed D, Hultenby K, Liu C, Baronio M, Vitali M, Philippet P, Dideberg V, Aghamohammadi A, Rezaei N, Enright V, Du L, Salzer U, Eibel H, Pfeifer D, Veelken H, Stauss H, Lougaris V, Plebani A, Gertz E, Schäffer A, Hammarström L, Grimbacher B. Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity. Am J Hum Genet 2012; 90:986-1001. [PMID: 22608502 PMCID: PMC3370280 DOI: 10.1016/j.ajhg.2012.04.015] [Citation(s) in RCA: 345] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/07/2012] [Accepted: 04/11/2012] [Indexed: 12/14/2022] Open
Abstract
Most autosomal genetic causes of childhood-onset hypogammaglobulinemia are currently not well understood. Most affected individuals are simplex cases, but both autosomal-dominant and autosomal-recessive inheritance have been described. We performed genetic linkage analysis in consanguineous families affected by hypogammaglobulinemia. Four consanguineous families with childhood-onset humoral immune deficiency and features of autoimmunity shared genotype evidence for a linkage interval on chromosome 4q. Sequencing of positional candidate genes revealed that in each family, affected individuals had a distinct homozygous mutation in LRBA (lipopolysaccharide responsive beige-like anchor protein). All LRBA mutations segregated with the disease because homozygous individuals showed hypogammaglobulinemia and autoimmunity, whereas heterozygous individuals were healthy. These mutations were absent in healthy controls. Individuals with homozygous LRBA mutations had no LRBA, had disturbed B cell development, defective in vitro B cell activation, plasmablast formation, and immunoglobulin secretion, and had low proliferative responses. We conclude that mutations in LRBA cause an immune deficiency characterized by defects in B cell activation and autophagy and by susceptibility to apoptosis, all of which are associated with a clinical phenotype of hypogammaglobulinemia and autoimmunity.
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Affiliation(s)
- Gabriela Lopez-Herrera
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
- Immunodeficiency Research Unit, National Institute of Pediatrics, Mexico City 04530, Mexico
| | - Giacomo Tampella
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Qiang Pan-Hammarström
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Peer Herholz
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
| | - Claudia M. Trujillo-Vargas
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
- Group of Primary Immunodeficiencies, University of Antioquia, Medellin 1226, Colombia
| | - Kanchan Phadwal
- Biomedical Research Centre Translational Immunology Lab, National Institute for Health Research, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Anna Katharina Simon
- Biomedical Research Centre Translational Immunology Lab, National Institute for Health Research, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Medcial Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Michel Moutschen
- University of Liège Center of Immunology, Laboratory of Immunoendocrinology, Institute of Pathology, Liège-Sart Tilman 4000, Belgium
| | - Amos Etzioni
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Adi Mory
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Izhak Srugo
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Doron Melamed
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Kjell Hultenby
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Chonghai Liu
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
- Department of Pediatrics, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, China
| | - Manuela Baronio
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Massimiliano Vitali
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Pierre Philippet
- Department of Pediatrics, Centre Hospitalier Chrétien-Esperance, Montegnée 4420, Belgium
| | - Vinciane Dideberg
- University of Liège, Center for Human Genetics, Liège-Sart Tilman B-4000, Belgium
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences. Tehran 14194, Iran
| | - Nima Rezaei
- Molecular Immunology Research Center and Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 14194, Iran
| | - Victoria Enright
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
| | - Likun Du
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Ulrich Salzer
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
| | - Hermann Eibel
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Hematology and Oncology, Freiburg University Medical Center, Freiburg 79106, Germany
| | - Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Hans Stauss
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
| | - Vassilios Lougaris
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Alessandro Plebani
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - E. Michael Gertz
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894, USA
| | - Alejandro A. Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894, USA
| | - Lennart Hammarström
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Bodo Grimbacher
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
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Olszewski PK, Rozman J, Jacobsson JA, Rathkolb B, Strömberg S, Hans W, Klockars A, Alsiö J, Risérus U, Becker L, Hölter SM, Elvert R, Ehrhardt N, Gailus-Durner V, Fuchs H, Fredriksson R, Wolf E, Klopstock T, Wurst W, Levine AS, Marcus C, Hrabě de Angelis M, Klingenspor M, Schiöth HB, Kilimann MW. Neurobeachin, a regulator of synaptic protein targeting, is associated with body fat mass and feeding behavior in mice and body-mass index in humans. PLoS Genet 2012; 8:e1002568. [PMID: 22438821 PMCID: PMC3305408 DOI: 10.1371/journal.pgen.1002568] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 01/16/2012] [Indexed: 01/08/2023] Open
Abstract
Neurobeachin (Nbea) regulates neuronal membrane protein trafficking and is required for the development and functioning of central and neuromuscular synapses. In homozygous knockout (KO) mice, Nbea deficiency causes perinatal death. Here, we report that heterozygous KO mice haploinsufficient for Nbea have higher body weight due to increased adipose tissue mass. In several feeding paradigms, heterozygous KO mice consumed more food than wild-type (WT) controls, and this consumption was primarily driven by calories rather than palatability. Expression analysis of feeding-related genes in the hypothalamus and brainstem with real-time PCR showed differential expression of a subset of neuropeptide or neuropeptide receptor mRNAs between WT and Nbea+/− mice in the sated state and in response to food deprivation, but not to feeding reward. In humans, we identified two intronic NBEA single-nucleotide polymorphisms (SNPs) that are significantly associated with body-mass index (BMI) in adult and juvenile cohorts. Overall, data obtained in mice and humans suggest that variation of Nbea abundance or activity critically affects body weight, presumably by influencing the activity of feeding-related neural circuits. Our study emphasizes the importance of neural mechanisms in body weight control and points out NBEA as a potential risk gene in human obesity. Body weight and energy balance are under very complex neural, endocrine, and metabolic control. Correspondingly, recent research suggests that hundreds of genes contribute to human obesity and that only a small proportion of them have as yet been identified. Neurobeachin (Nbea) is a protein specifically expressed in nerve and endocrine cells and is important for neurotransmission, apparently by influencing the synaptic targeting of membrane proteins. Here, we show that heterozygous knockout mice, expressing Nbea at 50% of normal levels, display increased adipose tissue mass, abnormal feeding behavior, and modified expression of specific genes in the brainstem and hypothalamus known to be important for body weight control. Moreover, we find that NBEA gene polymorphisms are associated with body-mass index in adult and juvenile human cohorts. Our results demonstrate that variation of Nbea activity critically affects body weight, presumably by influencing the activity of feeding-related neural circuits. They emphasize the importance of neural mechanisms in body weight control, and they identify NBEA as a potential genetic risk factor in human obesity.
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Affiliation(s)
- Pawel K. Olszewski
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- Minnesota Obesity Center, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Molecular Nutritional Medicine, Else Kröner-Fresenius Center and ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Josefin A. Jacobsson
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Siv Strömberg
- Molecular Cell Biology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Wolfgang Hans
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Anica Klockars
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Johan Alsiö
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Ulf Risérus
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, München, Germany
| | - Sabine M. Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany
| | - Ralf Elvert
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nicole Ehrhardt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Robert Fredriksson
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, München, Germany
| | - Wolfgang Wurst
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany
- Max-Planck-Institute for Psychiatry, München, Germany
- Technical University München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik c/o Helmholtz Zentrum München, Neuherberg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Munich, Germany
| | - Allen S. Levine
- Minnesota Obesity Center, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Claude Marcus
- Department for Clinical Science, Intervention, and Technology, Karolinska Institutet, Division of Pediatrics, National Childhood Obesity Centre, Stockholm, Sweden
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
| | - Martin Klingenspor
- Molecular Nutritional Medicine, Else Kröner-Fresenius Center and ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Helgi B. Schiöth
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Manfred W. Kilimann
- Molecular Cell Biology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- * E-mail:
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Shi Z, Moult J. Structural and functional impact of cancer-related missense somatic mutations. J Mol Biol 2011; 413:495-512. [PMID: 21763698 DOI: 10.1016/j.jmb.2011.06.046] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 05/13/2011] [Accepted: 06/28/2011] [Indexed: 01/11/2023]
Abstract
A number of large-scale cancer somatic genome sequencing projects are now identifying genetic alterations in cancers. Evaluation of the effects of these mutations is essential for understanding their contribution to tumorigenesis. We have used SNPs3D, a software suite originally developed for analyzing nonsynonymous germ-line variants, to identify single-base mutations with a high impact on protein structure and function. Two machine learning methods are used: one identifying mutations that destabilize protein three-dimensional structure and the other utilizing sequence conservation and detecting all types of effects on in vivo protein function. Incorporation of detailed structure information into the analysis allows detailed interpretation of the functional effects of mutations in specific cases. Data from a set of breast and colorectal tumors were analyzed. In known cancer genes, mutations approaching 100% of mutations are found to impact protein function, supporting the view that these methods are appropriate for identifying driver mutations. Overall, 50-60% of all somatic missense mutations are predicted to have a high impact on structural stability or to more generally affect the function of the corresponding proteins. This value is similar to the fraction of all possible missense mutations that have a high impact and is much higher than the corresponding one for human population single-nucleotide polymorphisms, at about 30%. The majority of mutations in tumor suppressors destabilize protein structure, while mutations in oncogenes operate in more varied ways, including destabilization of less active conformational states. The set of high-impact mutations encompasses the possible drivers.
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Affiliation(s)
- Zhen Shi
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
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Cheng P, Zhou J, Gabrilovich D. Regulation of dendritic cell differentiation and function by Notch and Wnt pathways. Immunol Rev 2010; 234:105-19. [PMID: 20193015 DOI: 10.1111/j.0105-2896.2009.00871.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The process of dendritic cell differentiation is governed by a tightly controlled signaling network regulated by cytokines and direct interaction between progenitor cells and bone marrow stroma. Notch signaling represents one of the major pathways activated during direct interaction between hematopoietic progenitor cells and bone marrow stroma. Wnt pathway is activated by soluble proteins produced by bone marrow stroma. Until recently, the role of Notch and Wnt signaling in the development of myeloid cells and dendritic cells in particular remained unclear. In this review, we discuss recent exciting findings that shed light on the critical role of Notch and Wnt pathways, their interaction in differentiation and function of dendritic cells, and their impact on immune responses.
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Affiliation(s)
- Pingyan Cheng
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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Rocher-Ros V, Marco S, Mao JH, Gines S, Metzger D, Chambon P, Balmain A, Saura CA. Presenilin modulates EGFR signaling and cell transformation by regulating the ubiquitin ligase Fbw7. Oncogene 2010; 29:2950-61. [PMID: 20208556 DOI: 10.1038/onc.2010.57] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The epidermal growth factor receptor (EGFR) and Notch signaling pathways have antagonistic roles during epidermal differentiation and carcinogenesis. The molecular mechanisms regulating the crosstalk between EGFR and Notch during epidermal transformation are largely unknown. We found enhanced EGFR-dependent signaling, proliferation and oncogenic transformation caused by loss of presenilins (PS), the catalytic components of gamma-secretase that generates the Notch1 intracellular domain (NICD). The underlying mechanism for abnormal EGFR signaling in PS-deficient cells involves gamma-secretase-independent transcriptional upregulation of the E3 ubiquitin ligase Fbw7. Fbw7alpha, which targets NICD for degradation, regulates positively EGFR by affecting a proteasome-dependent ubiquitination step essential for constitutive degradation and stability of EGFR. To investigate the pathological relevance of this findings in vivo, we generated a novel epidermal conditional PS-deficient (ePS cDKO) mouse by deleting both PS in keratinocytes of the basal layer of the epidermis. The ePS cDKO mice develop epidermal hyperplasia associated with enhanced expression of both EGFR and Fbw7 and reduced NICD levels in keratinocytes. These findings establish a novel role for PS on epidermal growth and transformation by reciprocally regulating the EGFR and Notch signaling pathways through Fbw7.
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Affiliation(s)
- V Rocher-Ros
- Institut de Neurociències, Department de Bioquímica i Biologia Molecular, Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
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Medrihan L, Rohlmann A, Fairless R, Andrae J, Döring M, Missler M, Zhang W, Kilimann MW. Neurobeachin, a protein implicated in membrane protein traffic and autism, is required for the formation and functioning of central synapses. J Physiol 2009; 587:5095-106. [PMID: 19723784 DOI: 10.1113/jphysiol.2009.178236] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The development of neuronal networks in the brain requires the differentiation of functional synapses. Neurobeachin (Nbea) was identified as a putative regulator of membrane protein trafficking associated with tubulovesicular endomembranes and postsynaptic plasma membranes. Nbea is essential for evoked transmission at neuromuscular junctions, but its role in the central nervous system has not been characterized. Here, we have studied central synapses of a newly generated gene-trap knockout (KO) mouse line at embryonic day 18, because null-mutant mice are paralysed and die perinatally. Although the overall brain architecture was normal, we identified major abnormalities of synaptic function in mutant animals. In acute slices from the brainstem, both spontaneous excitatory and inhibitory postsynaptic currents were clearly reduced and failure rates of evoked inhibitory responses were markedly increased. In addition, the frequency of miniature excitatory and both the frequency and amplitudes of miniature inhibitory postsynaptic currents were severely diminished in KO mice, indicating a perturbation of both action potential-dependent and -independent transmitter release. Moreover, Nbea appears to be important for the formation and composition of central synapses because the area density of mature asymmetric contacts in the fetal brainstem was reduced to 30% of wild-type levels, and the expression levels of a subset of synaptic marker proteins were smaller than in littermate controls. Our data demonstrate for the first time a function of Nbea at central synapses that may be based on its presumed role in targeting membrane proteins to synaptic contacts, and are consistent with the 'excitatory-inhibitory imbalance' model of autism where Nbea gene rearrangements have been detected in some patients.
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Affiliation(s)
- Lucian Medrihan
- Center for Physiology, Georg-August University and DFG-Research Center of Molecular Physiology of the Brain, D-37073 Göttingen, Germany
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O'Neal J, Gao F, Hassan A, Monahan R, Barrios S, Kilimann MW, Lee I, Chng WJ, Vij R, Tomasson MH. Neurobeachin (NBEA) is a target of recurrent interstitial deletions at 13q13 in patients with MGUS and multiple myeloma. Exp Hematol 2009; 37:234-44. [PMID: 19135901 DOI: 10.1016/j.exphem.2008.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Revised: 09/17/2008] [Accepted: 10/15/2008] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Chromosome 13 deletions (del[13]), detected by metaphase cytogenetics, predict poor outcomes in multiple myeloma (MM), but the gene(s) responsible have not been conclusively identified. We sought to identify tumor-suppressor genes on chromosome 13 using a novel array comparative genomic hybridization (aCGH) strategy. MATERIALS AND METHODS We identified DNA copy number losses on chromosome 13 using genomic DNA isolated from CD138-enriched bone marrow cells (tumor) from 20 patients with MM, monoclonal gammopathy of undetermined significance, or amyloidosis. We used matched skin biopsy (germline) genomic DNA to control for copy number polymorphisms and a novel aCGH array dedicated to chromosome 13 to map somatic DNA gains and losses at ultra-high resolution (>385,000 probes; median probe spacing 60 bp). We analyzed microarray expression data from an additional 262 patient samples both with and without del[13]. RESULTS Two distinct minimally deleted regions at 13q14 and 13q13 were defined that affected the RB1 and NBEA genes, respectively. RB1 is a canonical tumor suppressor previously implicated in MM. NBEA is implicated in membrane trafficking in neurons, protein kinase A binding, and has no known role in cancer. Noncoding RNAs on chromosome 13 were not affected by interstitial deletions. Both the RB1 and NBEA genes were deleted in 40% of cases (8 of 20; 5 patients with del[13] detected by traditional methods and 3 patients with interstitial deletions detected by aCGH). Forty-one additional MM patient samples were used for complete exonic sequencing of RB1, but no somatic mutations were found. Along with RB1, NBEA gene expression was significantly reduced in cases with del[13]. CONCLUSIONS The NBEA gene at 13q13, and its expression are frequently disrupted in MM. Additional studies are warranted to evaluate the role of NBEA as a novel candidate tumor-suppressor gene.
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Affiliation(s)
- Julie O'Neal
- Department of Internal Medicine, Division of Oncology, Washington University, Siteman Cancer Center, St Louis, MO, USA
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Microarray and biochemical analysis of bufalin-induced apoptosis of HL-60 Cells. Biotechnol Lett 2008; 31:487-94. [PMID: 19039527 DOI: 10.1007/s10529-008-9888-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2008] [Revised: 11/10/2008] [Accepted: 11/11/2008] [Indexed: 01/08/2023]
Abstract
Bufalin is a natural toxin with anti-leukemic properties. It induces cell differentiation and apoptosis, as well as increasing the sensitivity of leukemia cells to other chemotherapeutic agents. We investigated the biological effects and molecular mechanisms of bufalin triggered apoptosis in HL-60 cells by gene expression profiling. The broad transcriptional response to bufalin was consistent with bufalin's action of regulating HL-60 cell proliferation and apoptosis, as well as its synergistic effect with other drugs. Further transcription factor ELISA experiments suggested that the transcription factors NFkappaB and AP-1 were activated to promote bufalin-induced HL-60 cell apoptosis. Our study provides new insights into the molecular mechanisms of bufalin, might prove to be beneficial in leukemia therapy.
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Abstract
Hematopoietic stem cells give rise to multiple lineages of cells. This process is governed by a tightly controlled signaling network regulated by cytokines and a direct cell-cell contact. Notch signaling represents one of the major pathways activated during direct interaction between hematopoietic progenitor cells and bone marrow stroma. A critical role of Notch signaling in differentiation of T- and B-lymphocytes has now been established. Until recently, the role of Notch signaling in the development of myeloid cells and particular dendritic cells remained unclear. In this review, we discuss recent exciting findings that shed light on the critical role of Notch in differentiation and the function of dendritic cells and its impact on immune responses.
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Affiliation(s)
- Pingyan Cheng
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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de Souza N, Vallier LG, Fares H, Greenwald I. SEL-2, theC. elegansneurobeachin/LRBA homolog, is a negative regulator oflin-12/Notchactivity and affects endosomal traffic in polarized epithelial cells. Development 2007; 134:691-702. [PMID: 17215302 DOI: 10.1242/dev.02767] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The vulval precursor cells (VPCs) of Caenorhabditis elegans are polarized epithelial cells that adopt a precise pattern of fates through regulated activity of basolateral LET-23/EGF receptor and apical LIN-12/Notch. During VPC patterning, there is reciprocal modulation of endocytosis and trafficking of both LET-23 and LIN-12. We identified sel-2 as a negative regulator of lin-12/Notch activity in the VPCs, and found that SEL-2 is the homolog of two closely related human proteins, neurobeachin(also known as BCL8B) and LPS-responsive, beige-like anchor protein (LRBA). SEL-2, neurobeachin and LRBA belong to a distinct subfamily of BEACH-WD40 domain-containing proteins. Loss of sel-2 activity leads to basolateral mislocalization and increased accumulation of LIN-12 in VPCs in which LET-23 is not active, and to impaired downregulation of basolateral LET-23 in VPCs in which LIN-12 is active. Downregulation of apical LIN-12 in the VPC in which LET-23 is active is not affected. In addition, in sel-2 mutants, the polarized cells of the intestinal epithelium display an aberrant accumulation of the lipophilic dye FM4-64 when the dye is presented to the basolateral surface. Our observations indicate that SEL-2/neurobeachin/LRBA is involved in endosomal traffic and may be involved in efficient delivery of cell surface proteins to the lysosome. Our results also suggest that sel-2 activity may contribute to the appropriate steady-state level of LIN-12 or to trafficking events that affect receptor activation.
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Affiliation(s)
- Natalie de Souza
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, 701 W. 168th Street, Hammer Health Sciences, New York, NY 10032, USA
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