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Wang J, Wan YW, Al-Ouran R, Huang M, Liu Z. CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model. Brief Bioinform 2023; 25:bbad380. [PMID: 38113079 PMCID: PMC10729864 DOI: 10.1093/bib/bbad380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/13/2023] [Indexed: 12/21/2023] Open
Abstract
Millions of RNA sequencing samples have been deposited into public databases, providing a rich resource for biological research. These datasets encompass tens of thousands of experiments and offer comprehensive insights into human cellular regulation. However, a major challenge is how to integrate these experiments that acquired at different conditions. We propose a new statistical tool based on beta-binomial distributions that can construct robust gene co-regulation network (CoRegNet) across tens of thousands of experiments. Our analysis of over 12 000 experiments involving human tissues and cells shows that CoRegNet significantly outperforms existing gene co-expression-based methods. Although the majority of the genes are linearly co-regulated, we did discover an interesting set of genes that are non-linearly co-regulated; half of the time they change in the same direction and the other half they change in the opposite direction. Additionally, we identified a set of gene pairs that follows the Simpson's paradox. By utilizing public domain data, CoRegNet offers a powerful approach for identifying functionally related gene pairs, thereby revealing new biological insights.
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Affiliation(s)
- Jiasheng Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX 77030, USA
| | | | - Meichen Huang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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2
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Xue T, Kong X, Ma L. Trends in the Epidemiology of Pneumocystis Pneumonia in Immunocompromised Patients without HIV Infection. J Fungi (Basel) 2023; 9:812. [PMID: 37623583 PMCID: PMC10455156 DOI: 10.3390/jof9080812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/19/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023] Open
Abstract
The increasing morbidity and mortality of life-threatening Pneumocystis pneumonia (PCP) in immunocompromised people poses a global concern, prompting the World Health Organization to list it as one of the 19 priority invasive fungal diseases, calling for increased research and public health action. In response to this initiative, we provide this review on the epidemiology of PCP in non-HIV patients with various immunodeficient conditions, including the use of immunosuppressive agents, cancer therapies, solid organ and stem cell transplantation, autoimmune and inflammatory diseases, inherited or primary immunodeficiencies, and COVID-19. Special attention is given to the molecular epidemiology of PCP outbreaks in solid organ transplant recipients; the risk of PCP associated with the increasing use of immunodepleting monoclonal antibodies and a wide range of genetic defects causing primary immunodeficiency; the trend of concurrent infection of PCP in COVID-19; the prevalence of colonization; and the rising evidence supporting de novo infection rather than reactivation of latent infection in the pathogenesis of PCP. Additionally, we provide a concise discussion of the varying effects of different immunodeficient conditions on distinct components of the immune system. The objective of this review is to increase awareness and knowledge of PCP in non-HIV patients, thereby improving the early identification and treatment of patients susceptible to PCP.
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Affiliation(s)
- Ting Xue
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province, Shanxi Province Key Laboratory of Respiratory, Department of Respiratory and Critical Care Medicine, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Xiaomei Kong
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province, Shanxi Province Key Laboratory of Respiratory, Department of Respiratory and Critical Care Medicine, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD 20892, USA
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3
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Camacho-Ordonez N, Ballestar E, Timmers HTM, Grimbacher B. What can clinical immunology learn from inborn errors of epigenetic regulators? J Allergy Clin Immunol 2021; 147:1602-1618. [PMID: 33609625 DOI: 10.1016/j.jaci.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022]
Abstract
The epigenome is at the interface between environmental factors and the genome, regulating gene transcription, DNA repair, and replication. Epigenetic modifications play a crucial role in establishing and maintaining cell identity and are especially crucial for neurology, musculoskeletal integrity, and the function of the immune system. Mutations in genes encoding for the components of the epigenetic machinery lead to the development of distinct disorders, especially involving the central nervous system and host defense. In this review, we focus on the role of epigenetic modifications for the function of the immune system. By studying the immune phenotype of patients with monogenic mutations in components of the epigenetic machinery (inborn errors of epigenetic regulators), we demonstrate the importance of DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and mRNA processing for immunity. Moreover, we give a short overview on therapeutic strategies targeting the epigenome.
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Affiliation(s)
- Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Urology, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, 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, Freiburg, Germany.
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4
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Unique Mutation in SP110 Resulting in Hepatic Veno-Occlusive Disease with Immunodeficiency. Case Rep Pediatr 2020; 2020:3460631. [PMID: 32395362 PMCID: PMC7199573 DOI: 10.1155/2020/3460631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/21/2019] [Accepted: 12/03/2019] [Indexed: 11/22/2022] Open
Abstract
Familial hepatic veno-occlusive disease with immunodeficiency (VODI, OMIM: 235550) is a rare form of combined immune deficiency (CID) that presents in the first few months of life with failure to thrive, recurrent infections, opportunistic infections along with liver impairment. Herein, we are describing a Pakistani patient with a homozygous novel variant in the SP110 gene, presenting with classical phenotypic manifestations of VODI. He presented at the age of 3 months with opportunistic infections and later developed liver failure. Conclusion. Hepatic veno-occlusive disease with immunodeficiency is a rare cause of immunodeficiency, and this is the first case report from the Middle East in a patient of Pakistani origin. It is important to have a high suspicion for this disease, in patients presenting early life with a picture of CID and deranged liver function, as the earlier the diagnosis and treatment, the better the prognosis.
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5
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The Speckled Protein (SP) Family: Immunity's Chromatin Readers. Trends Immunol 2020; 41:572-585. [PMID: 32386862 DOI: 10.1016/j.it.2020.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 01/25/2023]
Abstract
Chromatin 'readers' are central interpreters of the epigenome that facilitate cell-specific transcriptional programs and are therapeutic targets in cancer and inflammation. The Speckled Protein (SP) family of chromatin 'readers' in humans consists of SP100, SP110, SP140, and SP140L. SPs possess functional domains (SAND, PHD, bromodomain) that dock to DNA or post-translationally modified histones and a caspase activation and recruitment domain (CARD) to promote multimerization. Mutations within immune expressed SPs associate with numerous immunological diseases including Crohn's disease, multiple sclerosis, chronic lymphocytic leukemia, veno-occlusive disease with immunodeficiency, as well as Mycobacterium tuberculosis infection, underscoring their importance in immune regulation. In this review, we posit that SPs are central chromatin regulators of gene silencing that establish immune cell identity and function.
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6
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Delmonte OM, Baldin F, Ovchinsky N, Marquardsen F, Recher M, Notarangelo LD, Kosinski SM. Novel Missense Mutation inSP110Associated with Combined Immunodeficiency and Advanced Liver Disease Without VOD. J Clin Immunol 2019; 40:236-239. [PMID: 31721003 DOI: 10.1007/s10875-019-00715-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/30/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, USA.
| | - Fabian Baldin
- Immunodeficiency Clinic and Laboratory, Department Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Nadia Ovchinsky
- Division of Pediatric Gastroenterology, Albert Einstein College of Medicine, Children's Hospital at Montefiore, The Bronx, NY, USA
| | - Florian Marquardsen
- Immunodeficiency Clinic and Laboratory, Department Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Mike Recher
- Immunodeficiency Clinic and Laboratory, Department Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, USA
| | - Slawomir M Kosinski
- Division of Allergy and Immunology, St. Joseph's University Medical Center, Paterson, NJ, USA.
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7
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Understanding the Similarities and Differences between Hepatic and Pulmonary Veno-Occlusive Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1159-1175. [DOI: 10.1016/j.ajpath.2019.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 12/22/2022]
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8
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Preventive Effect of the Herbal Preparation, HemoHIM, on Cisplatin-Induced Immune Suppression. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:3494806. [PMID: 31015850 PMCID: PMC6446088 DOI: 10.1155/2019/3494806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/28/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
We determined the functional effect of the herbal preparation, HemoHIM, on the immune system, by examining the immunomodulatory activities of HemoHIM using immunocompromised mice. In this study, to examine the effect on the restoration of immune cells and balance in the immune system, we utilized a cisplatin-induced immunosuppression mouse model. Mice were injected intraperitoneally with cisplatin, an immunosuppressive anticancer, and then received oral doses of 100, 250, and 500 mg/kg of HemoHIM for 14 days. The HemoHIM prevented the cisplatin-induced loss of body and organ weight. In terms of innate immunity, natural killer (NK) cell activity and phagocytosis increased in the HemoHIM group compared to the cisplatin control group. The HemoHIM group also showed a significantly higher expression of Th1-mediated cytokines (interferon gamma (IFN-γ), interleukin-2 (IL-2), and tumor necrosis factor alpha (TNF-α)) and inhibited the production of Th2-mediated cytokine interleukin-4 (IL-4) compared to cisplatin control group. These findings indicate that HemoHIM enhances immune activity by modulating immune cell activity and cytokine secretion in immune-suppressed mice.
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9
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Abstract
Proper regulation of the immune system is required for protection against pathogens and preventing autoimmune disorders. Inborn errors of the immune system due to inherited or de novo germline mutations can lead to the loss of protective immunity, aberrant immune homeostasis, and the development of autoimmune disease, or combinations of these. Forward genetic screens involving clinical material from patients with primary immunodeficiencies (PIDs) can vary in severity from life-threatening disease affecting multiple cell types and organs to relatively mild disease with susceptibility to a limited range of pathogens or mild autoimmune conditions. As central mediators of innate and adaptive immune responses, T cells are critical orchestrators and effectors of the immune response. As such, several PIDs result from loss of or altered T cell function. PID-associated functional defects range from complete absence of T cell development to uncontrolled effector cell activation. Furthermore, the gene products of known PID causal genes are involved in diverse molecular pathways ranging from T cell receptor signaling to regulators of protein glycosylation. Identification of the molecular and biochemical cause of PIDs can not only guide the course of treatment for patients, but also inform our understanding of the basic biology behind T cell function. In this chapter, we review PIDs with known genetic causes that intrinsically affect T cell function with particular focus on perturbations of biochemical pathways.
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Affiliation(s)
- William A Comrie
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States; Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, United States
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States; Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, United States.
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10
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Sengupta I, Das D, Singh SP, Chakravarty R, Das C. Host transcription factor Speckled 110 kDa (Sp110), a nuclear body protein, is hijacked by hepatitis B virus protein X for viral persistence. J Biol Chem 2017; 292:20379-20393. [PMID: 29046350 DOI: 10.1074/jbc.m117.796839] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/13/2017] [Indexed: 12/20/2022] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML-NB) are sub-nuclear organelles that are the hub of numerous proteins. DNA/RNA viruses often hijack the cellular factors resident in PML-NBs to promote their proliferation in host cells. Hepatitis B virus (HBV), belonging to Hepadnaviridae family, remains undetected in early infection as it does not induce the innate immune response and is known to be the cause of several hepatic diseases leading to cirrhosis and hepatocellular carcinoma. The association of PML-NB proteins and HBV is being addressed in a number of recent studies. Here, we report that the PML-NB protein Speckled 110 kDa (Sp110) is SUMO1-modified and undergoes a deSUMOylation-driven release from the PML-NB in the presence of HBV. Intriguingly, Sp110 knockdown significantly reduced viral DNA load in the culture supernatant by activation of the type I interferon-response pathway. Furthermore, we found that Sp110 differentially regulates several direct target genes of hepatitis B virus protein X (HBx), a viral co-factor. Subsequently, we identified Sp110 as a novel interactor of HBx and found this association to be essential for the exit of Sp110 from the PML-NB during HBV infection and HBx recruitment on the promoter of these genes. HBx, in turn, modulates the recruitment of its associated transcription cofactors p300/HDAC1 to these co-regulated genes, thereby altering the host gene expression program in favor of viral persistence. Thus, we report a mechanism by which HBV can evade host immune response by hijacking the PML-NB protein Sp110, and therefore, we propose it to be a novel target for antiviral therapy.
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Affiliation(s)
- Isha Sengupta
- From the Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata-700064
| | - Dipanwita Das
- the Indian Council of Medical Research (ICMR) Virus Unit, Kolkata, Infectious Diseases and Beliaghata General Hospital Campus, Kolkata 700010, and
| | - Shivaram Prasad Singh
- the Kalinga Gastroenterology Foundation, Beam Diagnostics Premises, Cuttack-753001, India
| | - Runu Chakravarty
- the Indian Council of Medical Research (ICMR) Virus Unit, Kolkata, Infectious Diseases and Beliaghata General Hospital Campus, Kolkata 700010, and
| | - Chandrima Das
- From the Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata-700064,
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11
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Marquardsen FA, Baldin F, Wunderer F, Al-Herz W, Mikhael R, Lefranc G, Baz Z, Rezaee F, Hanna R, Kfir-Erenfeld S, Stepensky P, Meyer B, Jauch A, Bigler MB, Burgener AV, Higgins R, Navarini AA, Church JA, Chou J, Geha R, Notarangelo LD, Hess C, Berger CT, Bloch DB, Recher M. Detection of Sp110 by Flow Cytometry and Application to Screening Patients for Veno-occlusive Disease with Immunodeficiency. J Clin Immunol 2017; 37:707-714. [PMID: 28825155 DOI: 10.1007/s10875-017-0431-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/03/2017] [Indexed: 01/01/2023]
Abstract
Mutations in Sp110 are the underlying cause of veno-occlusive disease with immunodeficiency (VODI), a combined immunodeficiency that is difficult to treat and often fatal. Because early treatment is critically important for patients with VODI, broadly usable diagnostic tools are needed to detect Sp110 protein deficiency. Several factors make establishing the diagnosis of VODI challenging: (1) Current screening strategies to identify severe combined immunodeficiency are based on measuring T cell receptor excision circles (TREC). This approach will fail to identify VODI patients because the disease is not associated with severe T cell lymphopenia at birth; (2) the SP110 gene contains 17 exons, making it a challenge for Sanger sequencing. The recently developed next-generation sequencing (NGS) platforms that can rapidly determine the sequence of all 17 exons are available in only a few laboratories; (3) there is no standard functional assay to test for the effects of novel mutations in Sp110; and (4) it has been difficult to use flow cytometry to identify patients who lack Sp110 because of the low level of Sp110 protein in peripheral blood lymphocytes. We report here a novel flow cytometric assay that is easily performed in diagnostic laboratories and might thus become a standard assay for the evaluation of patients who may have VODI. In addition, the assay will facilitate investigations directed at understanding the function of Sp110.
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Affiliation(s)
- Florian A Marquardsen
- Immunodeficiency Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Fabian Baldin
- Immunodeficiency Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Florian Wunderer
- Anesthesia Center for Critical Care Research of the Department of Anesthesia, Critical Care, and Pain Medicine, Harvard Medical School and Massachusetts General Hospital, Massachusetts, MA, 02114, USA
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Raymond Mikhael
- Pediatrics Department, Hotel-Dieu Hospital, St Joseph University, Beirut, Lebanon
| | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, 34095, Montpellier Cedex 5, France
| | - Zeina Baz
- Saint George Hospital, University Medical Center, Beirut, Lebanon
| | - Fariba Rezaee
- Center for Pediatric Pulmonary Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Rabi Hanna
- Pediatric Hematology Oncology and Blood and Marrow Transplantation, Cleveland Clinic, Cleveland, OH, USA
| | | | - Polina Stepensky
- Bone Marrow Transplantation Department, Hadassah Hospital, Jerusalem, Israel
| | - Benedikt Meyer
- Immunodeficiency Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Annaise Jauch
- Immunodeficiency Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Marc B Bigler
- Immune Deficiency Genetics Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anne-Valérie Burgener
- Immunobiology Laboratory, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland
| | - Rebecca Higgins
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | | | - Joeseph A Church
- Division of Clinical Immunology and Allergy, Children's Hospital Los Angeles, Keck School of Medicine of University Southern California, Los Angeles, CA, USA
| | - Janet Chou
- Division of Immunology, Children's Hospital Boston, Boston, MA, USA
| | - Raif Geha
- Division of Immunology, Children's Hospital Boston, Boston, MA, USA
| | - Luigi D Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Hess
- Immunobiology Laboratory, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland
| | - Christoph T Berger
- Translational Immunology, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland
| | - Donald B Bloch
- Anesthesia Center for Critical Care Research of the Department of Anesthesia, Critical Care, and Pain Medicine, Harvard Medical School and Massachusetts General Hospital, Massachusetts, MA, 02114, USA.,Division of Rheumatology, Allergy and Immunology, Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Mike Recher
- Immunodeficiency Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland.
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Chen Q, Tong Q, Ge H, Li W, Liu J, Wang Y, Guo Z, Quan F, Zhang Y. Identification of SP110 in horse (Equus caballus): Isolation of novel splice variants and evidence of activation effects on macrophages. Tuberculosis (Edinb) 2016; 101:85-94. [PMID: 27865405 DOI: 10.1016/j.tube.2016.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 11/30/2022]
Abstract
SP110 has previously shown to be a genetic determinant of host resistance to the intracellular pathogen infection in mouse and human. However, its relevant biological information in large non-primate animals still remains unknown. Here we report the novel discovery and characterization of three transcript variants of horse SP110. The transcript variant 1 (Tv1) of horse SP110 with the longest open reading frame has four domains (Sp100, SAND, PHD and Bromo domain). Tv2 and Tv3 share the same N-terminal sequence as Tv1, which contains Sp100 and SAND. We show that Tv2 is generated from alternative splicing and deletion of Exon17-Exon18 segment, while Tv3 is generated by pre-mature transcriptional termination at Exon 16. Furthermore, we demonstrate that the heterologous expression of horse SP110 variants stimulate macrophages into an activation-like phenotype. The macrophages underwent a shift in enhancing the secretion of cytokines (interleukin-1 (IL-1) and TNF-α) and accelerating inducible nitric oxide synthase (iNOS) activity, and eventually went into apoptotic cell death. Intriguingly, horse SP110 Tv1 showed more capability to trigger the immune activities compared to Tv2 and Tv3. To our knowledge, the identification of SP110 transcript variants from horse is the first report on biological function of SP110 in perissodactyla animals.
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Affiliation(s)
- Qi Chen
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qi Tong
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hengtao Ge
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenzhong Li
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yongsheng Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zekun Guo
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China.
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13
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Thanmalagan RR, Naorem LD, Venkatesan A. Expression Data Analysis for the Identification of Potential Biomarker of Pregnancy Associated Breast Cancer. Pathol Oncol Res 2016; 23:537-544. [PMID: 27832451 DOI: 10.1007/s12253-016-0133-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022]
Abstract
Breast cancer affects every 1 of 3000 pregnant women or in the first post-partum year is referred as Pregnancy Associated Breast Cancer (PABC) in mid 30s. Even-though rare disease, classified under hormone receptor negative status which metastasis quickly to other parts by extra cellular matrix degradation. Hence it is important to find an optimal treatment option for a PABC patient. Also additional care should be taken to choose the drug; in order to avoid fetal malformation and post-partum stage side-effects. The adaptation of target based therapy in the clinical practice may help to substitute the mastectomy treatment. Recent studies suggested that certain altered Post Translational Modifications (PTMs) may be an indicative of breast cancer progression; an attempt is made to consider the over represented PTM as a parameter for gene selection. The public dataset of PABC from GEO were examined to select Differentially Expressed Genes (DEG). The corresponding PTMs for DEG were collected and association between them was found using data mining technique. Usually clustering algorithm has been applied for the study of gene expression with drawback of clustering of gene products based on specified features. But association rule mining method overcome this shortcoming and determines the useful and in depth relationships. From the association, genes were selected to study the interactions and pathways. These studies emphasis that the genes KLF12, FEN1 MUC1 and SP110, can be chosen as target, which control cancer development, without any harm to pregnancy as well as fetal developmental process.
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Affiliation(s)
| | | | - Amouda Venkatesan
- Centre for Bioinformatics, Pondicherry University, Puducherry, 605014, India.
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14
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Abstract
Sinusoidal obstruction syndrome (SOS) is characterized by damage to small hepatic vessels affecting particularly sinusoidal endothelium. Damaged sinusoids can be associated with a partial or complete occlusion of small hepatic veins, hence the previous denomination of hepatic veno-occlusive disease (VOD). Exposure to certain exogenous toxins appears to be specific to this condition and is frequently included in its definition. Typical histopathological features of SOS in a liver biopsy specimen are presented in the text. The purpose of this article is to provide an overview on the different entities corresponding to this general definition. Such entities include: (i) liver disease related to pyrrolizidine alcaloids; (ii) liver injury related to conditioning for hematopoietic stem cell transplantation; (iii) vascular liver disease occurring in patients treated with chemotherapy for liver metastasis of colorectal cancer; and (iv) other liver diseases related to toxic agents.
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Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy. Proc Natl Acad Sci U S A 2016; 113:E3091-100. [PMID: 27185954 DOI: 10.1073/pnas.1600084113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Canine degenerative myelopathy (DM) is a naturally occurring neurodegenerative disease with similarities to some forms of amyotrophic lateral sclerosis (ALS). Most dogs that develop DM are homozygous for a common superoxide dismutase 1 gene (SOD1) mutation. However, not all dogs homozygous for this mutation develop disease. We performed a genome-wide association analysis in the Pembroke Welsh Corgi (PWC) breed comparing DM-affected and -unaffected dogs homozygous for the SOD1 mutation. The analysis revealed a modifier locus on canine chromosome 25. A haplotype within the SP110 nuclear body protein (SP110) was present in 40% of affected compared with 4% of unaffected dogs (P = 1.5 × 10(-5)), and was associated with increased probability of developing DM (P = 4.8 × 10(-6)) and earlier onset of disease (P = 1.7 × 10(-5)). SP110 is a nuclear body protein involved in the regulation of gene transcription. Our findings suggest that variations in SP110-mediated gene transcription may underlie, at least in part, the variability in risk for developing DM among PWCs that are homozygous for the disease-related SOD1 mutation. Further studies are warranted to clarify the effect of this modifier across dog breeds.
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Bonilla FA, Khan DA, Ballas ZK, Chinen J, Frank MM, Hsu JT, Keller M, Kobrynski LJ, Komarow HD, Mazer B, Nelson RP, Orange JS, Routes JM, Shearer WT, Sorensen RU, Verbsky JW, Bernstein DI, Blessing-Moore J, Lang D, Nicklas RA, Oppenheimer J, Portnoy JM, Randolph CR, Schuller D, Spector SL, Tilles S, Wallace D. Practice parameter for the diagnosis and management of primary immunodeficiency. J Allergy Clin Immunol 2015; 136:1186-205.e1-78. [PMID: 26371839 DOI: 10.1016/j.jaci.2015.04.049] [Citation(s) in RCA: 400] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/18/2015] [Accepted: 04/23/2015] [Indexed: 02/07/2023]
Abstract
The American Academy of Allergy, Asthma & Immunology (AAAAI) and the American College of Allergy, Asthma & Immunology (ACAAI) have jointly accepted responsibility for establishing the "Practice parameter for the diagnosis and management of primary immunodeficiency." This is a complete and comprehensive document at the current time. The medical environment is a changing environment, and not all recommendations will be appropriate for all patients. Because this document incorporated the efforts of many participants, no single individual, including those who served on the Joint Task Force, is authorized to provide an official AAAAI or ACAAI interpretation of these practice parameters. Any request for information about or an interpretation of these practice parameters by the AAAAI or ACAAI should be directed to the Executive Offices of the AAAAI, the ACAAI, and the Joint Council of Allergy, Asthma & Immunology. These parameters are not designed for use by pharmaceutical companies in drug promotion.
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Edgar JA, Molyneux RJ, Colegate SM. Pyrrolizidine Alkaloids: Potential Role in the Etiology of Cancers, Pulmonary Hypertension, Congenital Anomalies, and Liver Disease. Chem Res Toxicol 2014; 28:4-20. [PMID: 25483859 DOI: 10.1021/tx500403t] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Large outbreaks of acute food-related poisoning, characterized by hepatic sinusoidal obstruction syndrome, hemorrhagic necrosis, and rapid liver failure, occur on a regular basis in some countries. They are caused by 1,2-dehydropyrrolizidine alkaloids contaminating locally grown grain. Similar acute poisoning can also result from deliberate or accidental consumption of 1,2-dehydropyrrolizidine alkaloid-containing herbal medicines, teas, and spices. In recent years, it has been confirmed that there is also significant, low-level dietary exposure to 1,2-dehydropyrrolizidine alkaloids in many countries due to consumption of common foods such as honey, milk, eggs, salads, and meat. The level of 1,2-dehydropyrrolizidine alkaloids in these foods is generally too low and too intermittent to cause acute toxicity. However, these alkaloids are genotoxic and can cause slowly developing chronic diseases such as pulmonary arterial hypertension, cancers, cirrhosis, and congenital anomalies, conditions unlikely to be easily linked with dietary exposure to 1,2-dehydropyrrolizidine alkaloids, especially if clinicians are unaware that such dietary exposure is occurring. This Perspective provides a comprehensive review of the acute and chronic toxicity of 1,2-dehydropyrrolizidine alkaloids and their potential to initiate certain chronic diseases, and suggests some associative considerations or indicators to assist in recognizing specific cases of diseases that may have resulted from dietary exposure to these hazardous natural substances. If it can be established that low-level dietary exposure to 1,2-dehydropyrrolizidine alkaloids is a significant cause of some of these costly and debilitating diseases, then this should lead to initiatives to reduce the level of these alkaloids in the food chain.
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Affiliation(s)
- John A Edgar
- CSIRO Food and Nutrition , 11 Julius Avenue, North Ryde, NSW 2113, Australia
| | - Russell J Molyneux
- Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo , 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | - Steven M Colegate
- Poisonous Plant Research Laboratory, ARS/USDA , 1150 East 1400 North, Logan, Utah 84341, United States
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Fan CQ, Crawford JM. Sinusoidal obstruction syndrome (hepatic veno-occlusive disease). J Clin Exp Hepatol 2014; 4:332-46. [PMID: 25755580 PMCID: PMC4298625 DOI: 10.1016/j.jceh.2014.10.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/20/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatic sinusoidal obstruction syndrome (SOS) is an obliterative venulitis of the terminal hepatic venules, which in its more severe forms imparts a high risk of mortality. SOS, also known as veno-occlusive disease (VOD), occurs as a result of cytoreductive therapy prior to hematopoietic stem cell transplantation (HSCT), following oxaliplatin-containing adjuvant or neoadjuvant chemotherapy for colorectal carcinoma metastatic to the liver and treated by partial hepatectomy, in patients taking pyrrolizidine alkaloid-containing herbal remedies, and in other particular settings such as the autosomal recessive condition of veno-occlusive disease with immunodeficiency (VODI). A central pathogenic event is toxic destruction of hepatic sinusoidal endothelial cells (SEC), with sloughing and downstream occlusion of terminal hepatic venules. Contributing factors are SEC glutathione depletion, nitric oxide depletion, increased intrahepatic expression of matrix metalloproteinases and vascular endothelial growth factor (VEGF), and activation of clotting factors. The clinical presentation of SOS includes jaundice, development of right upper-quadrant pain and tender hepatomegaly, ascites, and unexplained weight gain. Owing to the potentially critical condition of these patients, transjugular biopsy may be the preferred route for liver biopsy to exclude other potential causes of liver dysfunction and to establish a diagnosis of SOS. Treatment includes rigorous fluid management so as to avoid excessive fluid overload while avoiding too rapid diuresis or pericentesis, potential use of pharmaceutics such as defibrotide, coagulolytic agents, or methylprednisolone, and liver transplantation. Proposed strategies for prevention and prophylaxis include reduced-intensity conditioning radiation for HSCT, treatment with ursodeoxycholic acid, and inclusion of bevacizumab with oxaliplatin-based chemotherapeutic regimes. While significant progress has been made in understanding the pathogenesis of SOS and in mitigating against its adverse outcomes, this condition remains a serious complication of a selective group of medical treatments.
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Key Words
- AML, acute myeloid leukemia
- APRI, aspartate aminotransferase to platelet ratio
- AST, aspartate aminotransferase
- Bmab, bevacizumab
- Colorectal cancer
- DF, defibrotide
- FOLFOX, chemotherapy regimen containing Folinic acid, 5-Fluorouracil, and Oxaliplatin
- GO, gemtuzumab ozogamicin
- GSTM1, glutathione S-transferase M1
- GVHD, graft-versus-host disease
- HSCT, hematopoietic stem cell transplantation
- Hematopoietic stem cell transplantation
- Herbal remedies
- Liver
- MOF, multi-organ failure
- Oxaliplatin
- PML, promyelocytic leukemia protein
- RIC-HSCT, reduced-intensity conditioning hematopoietic stem cell transplantation
- RILD, radiation-induced liver disease
- RT, radiation therapy
- SEC, sinusoidal endothelial cells
- SOS, sinusoidal obstruction syndrome
- TBI, total body irradiation
- TIPS, transjugular intrahepatic porto-systemic shunt
- UPLC-MS, ultra-performance liquid chromatography-mass spectrometry
- V-PYRRO/NO, O(2)-vinyl 1-(pyrrolidin-1-yl)diazen-1-ium-1,2-diolate
- VEGF, vascular endothelial growth factor
- VEGFR, vascular endothelial growth factor receptor
- VOD, veno-occlusive disease
- VODI, veno-occlusive disease with immunodeficiency
- l-NAME, N(G)-nitro-l-arginine methyl ester
- s-ICAM-1, soluble intercellular adhesion molecular-1
- t-PA, tissue plasminogen activator
- v-WF, von Willebrand factor
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Affiliation(s)
| | - James M. Crawford
- Address for correspondence: James M. Crawford, North Shore-LIJ Laboratories, 10 Nevada Drive, Lake Success, NY 11042-1114, USA. Tel.: +1 516 719 1060; fax: +1 516 719 1062.
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Short AD, Boag A, Catchpole B, Kennedy LJ, Massey J, Rothwell S, Husebye E, Ollier B. A candidate gene analysis of canine hypoadrenocorticism in 3 dog breeds. J Hered 2013; 104:807-20. [PMID: 23997205 DOI: 10.1093/jhered/est051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Canine hypoadrenocorticism is believed to be an immune-related condition. It is rare in the overall dog population but shows a breed-related predisposition with Standard poodles and Portuguese water dogs having a greater prevalence of the condition. It shares many similarities with human primary adrenal insufficiency and is believed to be a naturally occurring, spontaneous model for the human condition. Short haplotype blocks and low levels of linkage disequilibrium in the human genome mean that the identification of genetic contributors to the condition requires large sample numbers. Pedigree dogs have high linkage disequilibrium and long haplotypes within a breed, increasing the potential of identifying novel genes that contribute to canine genetic disease. We investigated 222 SNPs from 42 genes that have been associated or may be implicated in human Addison's disease. We conducted case-control analyses in 3 pedigree dog breeds (Labrador retriever: affected n = 30, unaffected = 76; Cocker Spaniel: affected n = 19, unaffected = 53; Springer spaniel: affected n = 26, unaffected = 46) and identified 8 associated alleles in genes COL4A4, OSBPL9, CTLA4, PTPN22, and STXBP5 in 3 pedigree breeds. Association with immune response genes PTPN22 and CTLA4 in certain breeds suggests an underlying immunopathogenesis of the disease. These results suggest that canine hypoadrenocorticism could be a useful model for studying comparative genetics relevant to human Addison's disease.
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Affiliation(s)
- Andrea D Short
- the Centre for Integrated Genomic Medical Research, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
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