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Belot A, Puy H, Hamza I, Bonkovsky HL. Update on heme biosynthesis, tissue-specific regulation, heme transport, relation to iron metabolism and cellular energy. Liver Int 2024. [PMID: 38888238 DOI: 10.1111/liv.15965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Heme is a primordial macrocycle upon which most aerobic life on Earth depends. It is essential to the survival and health of nearly all cells, functioning as a prosthetic group for oxygen-carrying proteins and enzymes involved in oxidation/reduction and electron transport reactions. Heme is essential for the function of numerous hemoproteins and has numerous other roles in the biochemistry of life. In mammals, heme is synthesised from glycine, succinyl-CoA, and ferrous iron in a series of eight steps. The first and normally rate-controlling step is catalysed by 5-aminolevulinate synthase (ALAS), which has two forms: ALAS1 is the housekeeping form with highly variable expression, depending upon the supply of the end-product heme, which acts to repress its activity; ALAS2 is the erythroid form, which is regulated chiefly by the adequacy of iron for erythroid haemoglobin synthesis. Abnormalities in the several enzymes of the heme synthetic pathway, most of which are inherited partial enzyme deficiencies, give rise to rare diseases called porphyrias. The existence and role of heme importers and exporters in mammals have been debated. Recent evidence established the presence of heme transporters. Such transporters are important for the transfer of heme from mitochondria, where the penultimate and ultimate steps of heme synthesis occur, and for the transfer of heme from cytoplasm to other cellular organelles. Several chaperones of heme and iron are known and important for cell health. Heme and iron, although promoters of oxidative stress and potentially toxic, are essential cofactors for cellular energy production and oxygenation.
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Affiliation(s)
- Audrey Belot
- Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Herve Puy
- Centre Français des Porphyries, Assistance Publique-Hôpitaux de Paris (APHP), Université de Paris Cité, INSERM U1149, Paris, France
| | - Iqbal Hamza
- Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, School of Medicine, University of Maryland, Baltimore, Maryland, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Herbert L Bonkovsky
- Section on Gastroenterology & Hepatology, Department of Medicine, Wake Forest University School of Medicine, Atrium Health Wake Forest Baptist, Winston-Salem, North Carolina, USA
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2
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Audiger C, Laâbi Y, Nie J, Gibson L, Wilson-Annan J, Brook-Carter P, Kueh A, Harris AW, Naik S, Nutt SL, Strasser A, Adams JM, Bouillet P, Chopin M. Mis-expression of GATA6 re-programs cell fate during early hematopoiesis. Cell Rep 2024; 43:114159. [PMID: 38676923 DOI: 10.1016/j.celrep.2024.114159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/06/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
The traditional view of hematopoiesis is that myeloid cells derive from a common myeloid progenitor (CMP), whereas all lymphoid cell populations, including B, T, and natural killer (NK) cells and possibly plasmacytoid dendritic cells (pDCs), arise from a common lymphoid progenitor (CLP). In Max41 transgenic mice, nearly all B cells seem to be diverted into the granulocyte lineage. Here, we show that these mice have an excess of myeloid progenitors, but their CLP compartment is ablated, and they have few pDCs. Nevertheless, T cell and NK cell development proceeds relatively normally. These hematopoietic abnormalities result from aberrant expression of Gata6 due to serendipitous insertion of the transgene enhancer (Eμ) in its proximity. Gata6 mis-expression in Max41 transgenic progenitors promoted the gene-regulatory networks that drive myelopoiesis through increasing expression of key transcription factors, including PU.1 and C/EBPa. Thus, mis-expression of a single key regulator like GATA6 can dramatically re-program multiple aspects of hematopoiesis.
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Affiliation(s)
- Cindy Audiger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Yacine Laâbi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Junli Nie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Leonie Gibson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Julie Wilson-Annan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Phillip Brook-Carter
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia; Federation University Australia, Ballarat, VIC 3350, Australia
| | - Andrew Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Alan W Harris
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Shalin Naik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia.
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia.
| | - Jerry M Adams
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Philippe Bouillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia
| | - Michaël Chopin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne; Melbourne, VIC 3052, Australia; Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
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3
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Choi K, Lee J, Kim G, Lim Y, Kang HJ. Recovery of synaptic loss and depressive-like behavior induced by GATA1 through blocking of the neuroinflammatory response. Front Cell Neurosci 2024; 18:1369951. [PMID: 38784708 PMCID: PMC11112091 DOI: 10.3389/fncel.2024.1369951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
GATA1, a member of the GATA transcription factor family, is a critical factor in hematopoietic system development. In a previous study, we demonstrated the increased expression of GATA1 in the dorsolateral prefrontal cortex (dlPFC) of patients suffering from depression and described its role as a transcriptional repressor of synapse-related genes. In this study, we investigated how GATA1 globally altered gene expression using multi-omics approaches. Through the combined analyses of ChIPseq, mRNAseq, and small RNAseq, we profiled genes that are potentially affected by GATA1 in cultured cortical neurons, and Gene Ontology (GO) analysis revealed that GATA1 might be associated with immune-related functions. We hypothesized that GATA1 induces immune activation, which has detrimental effects including synapse loss and depressive-like behavior. To test this hypothesis, we first performed a microglial morphometric analysis of a brain having overexpression of GATA1 because microglia are the resident immune cells of the central nervous system. Fractal analysis showed that the ramification and process length of microglia decreased in brains having GATA1 overexpression compared to the control, suggesting that GATA1 overexpression increases the activation of microglia. Through flow cytometry and immunohistochemical analysis, we found that activated microglia showed pro-inflammatory phenotypes characterized by the expression of CD86 and CD68. Finally, we demonstrated that the effects of GATA1 overexpression including synapse loss and depressive-like behavior could be blocked by inhibiting microglial activation using minocycline. These results will elucidate the regulatory mechanisms of GATA1 that affect pathophysiological conditions such as depression and provide a potential target for the treatment of depression.
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Affiliation(s)
| | | | | | | | - Hyo Jung Kang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
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4
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The role of GATA family transcriptional factors in haematological malignancies: A review: Retraction. Medicine (Baltimore) 2024; 103:e38232. [PMID: 38701322 PMCID: PMC11062697 DOI: 10.1097/md.0000000000038232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024] Open
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5
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Skok Gibbs C, Mahmood O, Bonneau R, Cho K. PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization. Genome Biol 2024; 25:88. [PMID: 38589899 PMCID: PMC11003171 DOI: 10.1186/s13059-024-03226-6] [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: 03/30/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
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Affiliation(s)
| | - Omar Mahmood
- Center for Data Science, New York University, New York, NY, 10011, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, 10011, USA
- Prescient Design, Genentech, New York, NY, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, 10011, USA.
- Prescient Design, Genentech, New York, NY, 10010, USA.
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Alamin M, Humaira Sultana M, Babarinde IA, Azad AKM, Moni MA, Xu H. Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs). Brief Bioinform 2024; 25:bbae230. [PMID: 38739758 PMCID: PMC11089419 DOI: 10.1093/bib/bbae230] [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: 12/22/2023] [Revised: 04/07/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
The complicated process of neuronal development is initiated early in life, with the genetic mechanisms governing this process yet to be fully elucidated. Single-cell RNA sequencing (scRNA-seq) is a potent instrument for pinpointing biomarkers that exhibit differential expression across various cell types and developmental stages. By employing scRNA-seq on human embryonic stem cells, we aim to identify differentially expressed genes (DEGs) crucial for early-stage neuronal development. Our focus extends beyond simply identifying DEGs. We strive to investigate the functional roles of these genes through enrichment analysis and construct gene regulatory networks to understand their interactions. Ultimately, this comprehensive approach aspires to illuminate the molecular mechanisms and transcriptional dynamics governing early human brain development. By uncovering potential links between these DEGs and intelligence, mental disorders, and neurodevelopmental disorders, we hope to shed light on human neurological health and disease. In this study, we have used scRNA-seq to identify DEGs involved in early-stage neuronal development in hESCs. The scRNA-seq data, collected on days 26 (D26) and 54 (D54), of the in vitro differentiation of hESCs to neurons were analyzed. Our analysis identified 539 DEGs between D26 and D54. Functional enrichment of those DEG biomarkers indicated that the up-regulated DEGs participated in neurogenesis, while the down-regulated DEGs were linked to synapse regulation. The Reactome pathway analysis revealed that down-regulated DEGs were involved in the interactions between proteins located in synapse pathways. We also discovered interactions between DEGs and miRNA, transcriptional factors (TFs) and DEGs, and between TF and miRNA. Our study identified 20 significant transcription factors, shedding light on early brain development genetics. The identified DEGs and gene regulatory networks are valuable resources for future research into human brain development and neurodevelopmental disorders.
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Affiliation(s)
- Md Alamin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | | | - Isaac Adeyemi Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - A K M Azad
- Department of Mathematics and Statistics, College of Science, Imam Muhammad Ibn Saud Islamic University, Riyadh 11432, Saudi Arabia
| | - Mohammad Ali Moni
- Artificial Intelligence and Cyber Futures Institute, Charles Sturt University, Bathurst, NSW 2795, Australia
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
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7
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Croucher PJP, Ridinger M, Becker PS, Lin TL, Silberman SL, Wang ES, Zeidan AM. Spliceosome mutations are associated with clinical response in a phase 1b/2 study of the PLK1 inhibitor onvansertib in combination with decitabine in relapsed or refractory acute myeloid leukemia. Ann Hematol 2023; 102:3049-3059. [PMID: 37702821 PMCID: PMC10567832 DOI: 10.1007/s00277-023-05442-9] [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: 08/10/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023]
Abstract
PLK1 is overexpressed in acute myeloid leukemia (AML). A phase 1b trial of the PLK1 inhibitor onvansertib (ONV) combined with decitabine (DAC) demonstrated initial safety and efficacy in patients with relapsed/refractory (R/R) AML. The current study aimed to identify molecular predictors of response to ONV + DAC in R/R AML patients. A total of 44 R/R AML patients were treated with ONV + DAC and considered evaluable for efficacy. Bone marrow (BM) samples were collected at baseline for genomic and transcriptomic analysis (n = 32). A 10-gene expression signature, predictive of response to ONV + DAC, was derived from the leading-edge genes of gene set enrichment analyses (GSEA). The gene signature was evaluated in independent datasets and used to identify associated mutated genes. Twenty percent of the patients achieved complete remission, with or without hematologic count recovery (CR/CRi), and 32% exhibited a ≥50% reduction in bone marrow blasts. Patients who responded to treatment had elevated mitochondrial function and OXPHOS. The gene signature was not associated with response to DAC alone in an independent dataset. By applying the signature to the BeatAML cohort (n = 399), we identified a positive association between predicted ONV + DAC response and mutations in splicing factors (SF). In the phase 1b/2 trial, patients with SF mutations (SRSF2, SF3B1) had a higher CR/CRi rate (50%) compared to those without SF mutations (9%). PLK1 inhibition with ONV in combination with DAC could be a potential therapy in R/R AML patients, particularly those with high OXPHOS gene expression and SF mutations.
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Affiliation(s)
- Peter J P Croucher
- Cardiff Oncology Inc., 11055 Flintkote Avenue, San Diego, CA, 92121, USA
| | - Maya Ridinger
- Cardiff Oncology Inc., 11055 Flintkote Avenue, San Diego, CA, 92121, USA
| | - Pamela S Becker
- Leukemia Division, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Tara L Lin
- Division of Hematologic Malignancies and Cellular Therapeutics, University of Kansas, Kansas City, KS, 66205, USA
| | | | - Eunice S Wang
- Leukemia Service, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Amer M Zeidan
- Yale University and Yale Cancer Center, New Haven, 333 Cedar Street, PO Box 208028, New Haven, CT, 06520-8028, USA.
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8
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Bourne JH, Campos J, Hopkin SJ, Whitworth K, Palis J, Senis YA, Rayes J, Iqbal AJ, Brill A. Megakaryocyte NLRP3 hyperactivation induces mild anemia and potentiates inflammatory response in mice. Front Immunol 2023; 14:1226196. [PMID: 37622117 PMCID: PMC10445124 DOI: 10.3389/fimmu.2023.1226196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/17/2023] [Indexed: 08/26/2023] Open
Abstract
Background The NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome has been described in both immune cells and platelets, but its role in the megakaryocyte (MK) lineage remains elusive. Objective The aim of this study was to explore the role of NLRP3 inflammasome in megakaryocytes and platelets. Methods We generated Nlrp3 A350V/+/Gp1ba-CreKI/+ mice carrying a mutation genetically similar to the one observed in human Muckle-Wells syndrome, which leads to hyperactivity of NLRP3 specifically in MK and platelets. Results Platelets from the mutant mice expressed elevated levels of both precursor and active form of caspase-1, suggesting hyperactivity of NLRP3 inflammasome. Nlrp3 A350V/+/Gp1ba-CreKI/+ mice developed normally and had normal platelet counts. Expression of major platelet receptors, platelet aggregation, platelet deposition on collagen under shear, and deep vein thrombosis were unchanged. Nlrp3 A350V/+/Gp1ba-CreKI/+ mice had mild anemia, reduced Ter119+ cells in the bone marrow, and splenomegaly. A mild increase in MK TGF-β1 might be involved in the anemic phenotype. Intraperitoneal injection of zymosan in Nlrp3 A350V/+/Gp1ba-CreKI/+ mice induced increased neutrophil egression and elevated levels of a set of proinflammatory cytokines, alongside IL-10 and G-CSF, in the peritoneal fluid as compared with control animals. Conclusion MK/platelet NLRP3 inflammasome promotes the acute inflammatory response and its hyperactivation in mice leads to mild anemia and increased extramedullary erythropoiesis.
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Affiliation(s)
- Joshua H. Bourne
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Inflammatory Diseases, Department of Medicine at Monash Health, School of Clinical Sciences, Monash Medical Centre, Monash University, Clayton, VIC, Australia
| | - Joana Campos
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sophie J. Hopkin
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Katharine Whitworth
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Yotis A. Senis
- Etablissement Français du Sang, Inserm Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)-S1255 Strasbourg, Université de Strasbourg, Strasbourg, France
| | - Julie Rayes
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Asif J. Iqbal
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alexander Brill
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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9
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Illingworth EJ, Maertens A, Sillé FCM. Transcriptomic Effects of Low-Dose Inorganic Arsenic Exposure on Murine Bone Marrow-Derived Macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550543. [PMID: 37546857 PMCID: PMC10402011 DOI: 10.1101/2023.07.26.550543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Both tissue-resident macrophages and monocytes recruited from the bone marrow that transform into tissue-resident cells play critical roles in mediating homeostasis as well as in the pathology of inflammatory diseases. Inorganic arsenic (iAs) is the most common drinking water contaminant worldwide and represents a major public health concern. Several diseases that macrophages have implicated involvement in are caused by iAs exposure, including cardiovascular disease, cancer, and increased risk of infectious disease. Therefore, understanding the effects of iAs exposure on macrophages can help us better grasp the full range of arsenic immunotoxicity and better design therapeutic targets for iAs-induced diseases particularly in exposed populations. In this study, we analyzed the transcriptome of low dose iAs-exposed male and female murine bone marrow-derived macrophages (BMDMs) with either M0, M1, or M2 stimulation. We identified differentially expressed genes by iAs in a sex- and stimulation-dependent manner and used bioinformatics tools to predict protein-protein interactions, transcriptional regulatory networks, and associated biological processes. Overall, our data suggest that M1-stimulated, especially female-derived, BMDMs are most susceptible to iAs exposure. Most notably, we observed significant downregulation of major proinflammatory transcription factors, like IRF8, and its downstream targets, as well as genes encoding proteins involved in pattern recognition and antigen presentation, such as TLR7, TLR8, and H2-D1, potentially providing causal insight regarding arsenic's role in perturbing immune responses to infectious diseases. We also observed significant downregulation of genes involved in processes crucial to coordinating a proinflammatory response including leukocyte migration, differentiation, and cytokine and chemokine production and response. Finally, we discovered that 24 X-linked genes were dysregulated in iAs-exposed female stimulation groups compared to only 3 across the iAs-exposed male stimulation groups. These findings elucidate the potential mechanisms underlying the sex-differential iAs-associated immune-related disease risk.
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10
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Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
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Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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11
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Premkumar T, Sajitha Lulu S. Molecular crosstalk between COVID-19 and Alzheimer's disease using microarray and RNA-seq datasets: A system biology approach. Front Med (Lausanne) 2023; 10:1151046. [PMID: 37359008 PMCID: PMC10286240 DOI: 10.3389/fmed.2023.1151046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/20/2023] [Indexed: 06/28/2023] Open
Abstract
Objective Coronavirus disease 2019 (COVID-19) is an infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The clinical and epidemiological analysis reported the association between SARS-CoV-2 and neurological diseases. Among neurological diseases, Alzheimer's disease (AD) has developed as a crucial comorbidity of SARS-CoV-2. This study aimed to understand the common transcriptional signatures between SARS-CoV-2 and AD. Materials and methods System biology approaches were used to compare the datasets of AD and COVID-19 to identify the genetic association. For this, we have integrated three human whole transcriptomic datasets for COVID-19 and five microarray datasets for AD. We have identified differentially expressed genes for all the datasets and constructed a protein-protein interaction (PPI) network. Hub genes were identified from the PPI network, and hub genes-associated regulatory molecules (transcription factors and miRNAs) were identified for further validation. Results A total of 9,500 differentially expressed genes (DEGs) were identified for AD and 7,000 DEGs for COVID-19. Gene ontology analysis resulted in 37 molecular functions, 79 cellular components, and 129 biological processes were found to be commonly enriched in AD and COVID-19. We identified 26 hub genes which includes AKT1, ALB, BDNF, CD4, CDH1, DLG4, EGF, EGFR, FN1, GAPDH, INS, ITGB1, ACTB, SRC, TP53, CDC42, RUNX2, HSPA8, PSMD2, GFAP, VAMP2, MAPK8, CAV1, GNB1, RBX1, and ITGA2B. Specific miRNA targets associated with Alzheimer's disease and COVID-19 were identified through miRNA target prediction. In addition, we found hub genes-transcription factor and hub genes-drugs interaction. We also performed pathway analysis for the hub genes and found that several cell signaling pathways are enriched, such as PI3K-AKT, Neurotrophin, Rap1, Ras, and JAK-STAT. Conclusion Our results suggest that the identified hub genes could be diagnostic biomarkers and potential therapeutic drug targets for COVID-19 patients with AD comorbidity.
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Salvatore M, Horlacher M, Marsico A, Winther O, Andersson R. Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility. NAR Genom Bioinform 2023; 5:lqad026. [PMID: 37007588 PMCID: PMC10052367 DOI: 10.1093/nargab/lqad026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
Dysfunction of regulatory elements through genetic variants is a central mechanism in the pathogenesis of disease. To better understand disease etiology, there is consequently a need to understand how DNA encodes regulatory activity. Deep learning methods show great promise for modeling of biomolecular data from DNA sequence but are limited to large input data for training. Here, we develop ChromTransfer, a transfer learning method that uses a pre-trained, cell-type agnostic model of open chromatin regions as a basis for fine-tuning on regulatory sequences. We demonstrate superior performances with ChromTransfer for learning cell-type specific chromatin accessibility from sequence compared to models not informed by a pre-trained model. Importantly, ChromTransfer enables fine-tuning on small input data with minimal decrease in accuracy. We show that ChromTransfer uses sequence features matching binding site sequences of key transcription factors for prediction. Together, these results demonstrate ChromTransfer as a promising tool for learning the regulatory code.
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Affiliation(s)
| | | | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Ole Winther
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
- Section for Cognitive Systems, DTU Compute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Department of Genomic medicine, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Robin Andersson
- To whom correspondence should be addressed. Tel: +45 35330245;
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13
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Subsets of Eosinophils in Asthma, a Challenge for Precise Treatment. Int J Mol Sci 2023; 24:ijms24065716. [PMID: 36982789 PMCID: PMC10052006 DOI: 10.3390/ijms24065716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
The existence of eosinophils was documented histopathologically in the first half of the 19th century. However, the term “eosinophils” was first used by Paul Ehrlich in 1878. Since their discovery and description, their existence has been associated with asthma, allergies, and antihelminthic immunity. Eosinophils may also be responsible for various possible tissue pathologies in many eosinophil-associated diseases. Since the beginning of the 21st century, the understanding of the nature of this cell population has undergone a fundamental reassessment, and in 2010, J. J. Lee proposed the concept of “LIAR” (Local Immunity And/or Remodeling/Repair), underlining the extensive immunoregulatory functions of eosinophils in the context of health and disease. It soon became apparent that mature eosinophils (in line with previous morphological studies) are not structurally, functionally, or immunologically homogeneous cell populations. On the contrary, these cells form subtypes characterized by their further development, immunophenotype, sensitivity to growth factors, localization, role and fate in tissues, and contribution to the pathogenesis of various diseases, including asthma. The eosinophil subsets were recently characterized as resident (rEos) and inflammatory (iEos) eosinophils. During the last 20 years, the biological therapy of eosinophil diseases, including asthma, has been significantly revolutionized. Treatment management has been improved through the enhancement of treatment effectiveness and a decrease in the adverse events associated with the formerly ultimately used systemic corticosteroids. However, as we observed from real-life data, the global treatment efficacy is still far from optimal. A fundamental condition, “sine qua non”, for correct treatment management is a thorough evaluation of the inflammatory phenotype of the disease. We believe that a better understanding of eosinophils would lead to more precise diagnostics and classification of asthma subtypes, which could further improve treatment outcomes. The currently validated asthma biomarkers (eosinophil count, production of NO in exhaled breath, and IgE synthesis) are insufficient to unveil super-responders among all severe asthma patients and thus give only a blurred picture of the adepts for treatment. We propose an emerging approach consisting of a more precise characterization of pathogenic eosinophils in terms of the definition of their functional status or subset affiliation by flow cytometry. We believe that the effort to find new eosinophil-associated biomarkers and their rational use in treatment algorithms may ameliorate the response rate to biological therapy in patients with severe asthma.
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14
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Menéndez-Gutiérrez MP, Porcuna J, Nayak R, Paredes A, Niu H, Núñez V, Paranjpe A, Gómez MJ, Bhattacharjee A, Schnell DJ, Sánchez-Cabo F, Welch JS, Salomonis N, Cancelas JA, Ricote M. Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. Blood 2023; 141:592-608. [PMID: 36347014 PMCID: PMC10082360 DOI: 10.1182/blood.2022016832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 11/10/2022] Open
Abstract
Hematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain hematopoietic fitness throughout life. In steady-state conditions, HSC exhaustion is prevented by the maintenance of most HSCs in a quiescent state, with cells entering the cell cycle only occasionally. HSC quiescence is regulated by retinoid and fatty-acid ligands of transcriptional factors of the nuclear retinoid X receptor (RXR) family. Herein, we show that dual deficiency for hematopoietic RXRα and RXRβ induces HSC exhaustion, myeloid cell/megakaryocyte differentiation, and myeloproliferative-like disease. RXRα and RXRβ maintain HSC quiescence, survival, and chromatin compaction; moreover, transcriptome changes in RXRα;RXRβ-deficient HSCs include premature acquisition of an aging-like HSC signature, MYC pathway upregulation, and RNA intron retention. Fitness loss and associated RNA transcriptome and splicing alterations in RXRα;RXRβ-deficient HSCs are prevented by Myc haploinsufficiency. Our study reveals the critical importance of RXRs for the maintenance of HSC fitness and their protection from premature aging.
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Affiliation(s)
| | - Jesús Porcuna
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Ramesh Nayak
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Hoxworth Blood Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Ana Paredes
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Haixia Niu
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Vanessa Núñez
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Manuel J. Gómez
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Anukana Bhattacharjee
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Daniel J. Schnell
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - John S. Welch
- Department of Internal Medicine, Washington University, St Louis, MO
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Internal Medicine, Washington University, St Louis, MO
| | - Jose A. Cancelas
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Hoxworth Blood Center, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Mercedes Ricote
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
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15
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Spurrell M, Oulhen N, Foster S, Perillo M, Wessel G. Gene regulatory divergence amongst echinoderms underlies appearance of pigment cells in sea urchin development. Dev Biol 2023; 494:13-25. [PMID: 36519720 PMCID: PMC9870932 DOI: 10.1016/j.ydbio.2022.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/14/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Larvae of the sea urchin, Strongylocentrotus purpuratus, have pigmented migratory cells implicated in immune defense and gut patterning. The transcription factor SpGcm activates the expression of many pigment cell-specific genes, including those involved in pigment biosynthesis (SpPks1 and SpFmo3) and immune related genes (e.g. SpMif5). Despite the importance of this cell type in sea urchins, pigmented cells are absent in larvae of the sea star, Patiria miniata. In this study, we tested the premises that sea stars lack genes to synthesize echinochrome pigment, that the genes are present but are not expressed in the larvae, or rather that the homologous gene expression does not contribute to echinochrome synthesis. Our results show that orthologs of sea urchin pigment cell-specific genes (PmPks1, PmFmo3-1 and PmMifL1-2) are present in the sea star genome and expressed in the larvae. Although no cell lineage homologous to migratory sea urchin pigment cells is present, dynamic gene activation accomplishes a similar spatial and temporal expression profile. The mechanisms regulating the expression of these genes, though, is highly divergent. In sea stars, PmGcm lacks the central role in pigment gene expression since it is not expressed in PmPks1 and PmFmo3-1-positive cells, and knockdown of Gcm does not abrogate pigment gene expression. Pigment genes are instead expressed in the coelomic mesoderm early in development before later being expressed in the ectoderm. These findings were supported by in situ RNA hybridization and comparative scRNA-seq analyses. We conclude that simply the coexpression of Pks1 and Fmo3 orthologs in cells of the sea star is not sufficient to underlie the emergence of the larval pigment cell in the sea urchin.
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Affiliation(s)
- Maxwell Spurrell
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Nathalie Oulhen
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Stephany Foster
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Margherita Perillo
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Gary Wessel
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA.
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16
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Stoltzfus AT, Campbell CJ, Worth MM, Hom K, Stemmler TL, Michel SLJ. Pb(II) coordination to the nonclassical zinc finger tristetraprolin: retained function with an altered fold. J Biol Inorg Chem 2023; 28:85-100. [PMID: 36478265 DOI: 10.1007/s00775-022-01980-1] [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: 06/06/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Tristetraprolin (TTP) is a nonclassical CCCH zinc finger (ZF) that plays a crucial role in regulating inflammation. TTP regulates cytokine mRNAs by specific binding of its two conserved ZF domains (CysX8CysX5CysX3His) to adenylate-uridylate-rich sequences (AREs) at the 3'-untranslated region, leading to degradation of the RNA. Dysregulation of TTP in animal models has demonstrated several cytokine-related syndromes, including chronic inflammation and autoimmune disorders. Exposure to Pb(II), a prevalent environmental toxin, is known to contribute to similar pathologies, in part by disruption of and/or competition with cysteine-rich metalloproteins. TTP's role during stress as a ubiquitous translational regulator of cell signaling (and dysfunction), which may underpin various phenotypes of Pb(II) toxicity, highlights the importance of understanding the interaction between TTP and Pb(II). The impact of Pb(II) binding on TTP's fold and RNA-binding function was analyzed via UV-Vis spectroscopy, circular dichroism, X-ray absorption spectroscopy, nuclear magnetic resonance spectroscopy, and fluorescence anisotropy. A construct containing the two ZF domains of TTP (TTP-2D) bound to Pb(II) with nanomolar affinity and exhibited a different geometry and fold in comparison to Zn2-TTP-2D. Despite the altered secondary structure, Pb(II)-substituted TTP-2D bound a canonical ARE sequence more selectively than Zn2-TTP-2D. Taken together, these data suggest that Pb(II) may interfere with proper TTP regulation and hinder the cell's ability to respond to inflammation.
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Affiliation(s)
- Andrew T Stoltzfus
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Courtney J Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Madison M Worth
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA.
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17
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Geng X, Wang C, Gao X, Chowdhury P, Weiss J, Villegas JA, Saed B, Perera T, Hu Y, Reneau J, Sverdlov M, Wolfe A, Brown N, Harms P, Bailey NG, Inamdar K, Hristov AC, Tejasvi T, Montes J, Barrionuevo C, Taxa L, Casavilca S, de Pádua Covas Lage JLA, Culler HF, Pereira J, Runge JS, Qin T, Tsoi LC, Hong HS, Zhang L, Lyssiotis CA, Ohe R, Toubai T, Zevallos-Morales A, Murga-Zamalloa C, Wilcox RA. GATA-3 is a proto-oncogene in T-cell lymphoproliferative neoplasms. Blood Cancer J 2022; 12:149. [PMID: 36329027 PMCID: PMC9633835 DOI: 10.1038/s41408-022-00745-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Neoplasms originating from thymic T-cell progenitors and post-thymic mature T-cell subsets account for a minority of lymphoproliferative neoplasms. These T-cell derived neoplasms, while molecularly and genetically heterogeneous, exploit transcription factors and signaling pathways that are critically important in normal T-cell biology, including those implicated in antigen-, costimulatory-, and cytokine-receptor signaling. The transcription factor GATA-3 regulates the growth and proliferation of both immature and mature T cells and has recently been implicated in T-cell neoplasms, including the most common mature T-cell lymphoma observed in much of the Western world. Here we show that GATA-3 is a proto-oncogene across the spectrum of T-cell neoplasms, including those derived from T-cell progenitors and their mature progeny, and further define the transcriptional programs that are GATA-3 dependent, which include therapeutically targetable gene products. The discovery that p300-dependent acetylation regulates GATA-3 mediated transcription by attenuating DNA binding has novel therapeutic implications. As most patients afflicted with GATA-3 driven T-cell neoplasms will succumb to their disease within a few years of diagnosis, these findings suggest opportunities to improve outcomes for these patients.
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Affiliation(s)
- Xiangrong Geng
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Chenguang Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Gao
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Pinki Chowdhury
- Department of Pediatrics, Dayton Children's Hospital, Wright State University Boonshoft School of Medicine, Dayton, OH, USA
| | - Jonathan Weiss
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - José A Villegas
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Ying Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - John Reneau
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Maria Sverdlov
- Department of Pathology, University of Illinois Chicago, Chicago, IL, USA
| | - Ashley Wolfe
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Noah Brown
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Paul Harms
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nathanael G Bailey
- Division of Hematopathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kedar Inamdar
- Department of Pathology, Henry Ford Hospital, Detroit, MI, USA
| | - Alexandra C Hristov
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Montes
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - Carlos Barrionuevo
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - Luis Taxa
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - Sandro Casavilca
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - J Luís Alberto de Pádua Covas Lage
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University, Laboratory of Medical Investigation 31 in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Sao Paulo, Brazil
| | - Hebert Fabrício Culler
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University, Laboratory of Medical Investigation 31 in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Sao Paulo, Brazil
| | - Juliana Pereira
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, Sao Paulo University, Non-Hodgkin's Lymphomas and Histiocytic Disorders, Sao Paulo, Brazil
| | - John S Runge
- Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Hanna S Hong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Rintaro Ohe
- Department of Pathology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Tomomi Toubai
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University of Medicine, Yamagata, Japan
| | | | | | - Ryan A Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA.
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18
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Zhang L, Wang Y, Cao C, Zhu Y, Huang W, Yang Y, Qiu H, Liu S, Wang D. Beneficial effect of Xuebijing against Pseudomonas aeruginosa infection in Caenorhabditis elegans. Front Pharmacol 2022; 13:949608. [PMID: 36120363 PMCID: PMC9470999 DOI: 10.3389/fphar.2022.949608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/01/2022] [Indexed: 12/14/2022] Open
Abstract
In the clinical intensive care units (ICU), the traditional Chinese medicine (TCM) formulation of Xuebijing has been frequently used for treating sepsis. Nevertheless, the underlying pharmacological mechanisms of Xuebijing remain largely unclear. Caenorhabditis elegans is an important experimental host for bacterial infections. Using C. elegans as an animal model, we here examined the potential of Xuebijing treatment against bacterial infection and the underlying mechanisms. Xuebijing treatment could inhibit the reduction tendency of lifespan caused by Pseudomonas aeruginosa infection. For the cellular mechanisms of this antibacterial infection property, we found that Xuebijing treatment rescued C. elegans lifespan to be against P. aeruginosa infection by inhibiting Pseudomonas colonization in the intestinal lumen. Meanwhile, the increase in the expression of antimicrobial genes induced by Pseudomonas infection was also suppressed by Xuebijing treatment. Moreover, the beneficial effect of Xuebijing against Pseudomonas infection depended on insulin, p38 MAPK, Wnt, DBL-1/TGF-β, ELT-2, and programmed cell death (PCD)-related signals. Although Xuebijing did not show obvious antibacterial activity, Xuebijing (100%) treatment could inhibit the Pseudomonas biofilm formation and decrease the expression of virulence genes (lasA, lasB, rhlA, rhlC, phzA, phzM, phzH, and phzS) and quorum sensing (QS)-related genes (lasI, lasR, rhlI, rhlR, pqsA, and pqsR). Our results support the potential role of Xuebijing treatment against bacterial infection in hosts.
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Affiliation(s)
- Le Zhang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Yuxing Wang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Chang Cao
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Yike Zhu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
- Department of Critical Care Medicine, Zhongda Hospital, Nanjing, China
| | - Wei Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
- Department of Critical Care Medicine, Zhongda Hospital, Nanjing, China
| | - Yi Yang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
- Department of Critical Care Medicine, Zhongda Hospital, Nanjing, China
| | - Haibo Qiu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
- Department of Critical Care Medicine, Zhongda Hospital, Nanjing, China
| | - Songqiao Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
- Department of Critical Care Medicine, Zhongda Hospital, Nanjing, China
- *Correspondence: Songqiao Liu, ; Dayong Wang,
| | - Dayong Wang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
- *Correspondence: Songqiao Liu, ; Dayong Wang,
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19
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Nicholas TJ, Al‐Sweel N, Farrell A, Mao R, Bayrak‐Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren M, Bonkowsky JL, Tristani‐Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir R, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med 2022; 10:e1888. [PMID: 35119225 PMCID: PMC9000945 DOI: 10.1002/mgg3.1888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Genetic disorders contribute to significant morbidity and mortality in critically ill newborns. Despite advances in genome sequencing technologies, a majority of neonatal cases remain unsolved. Complex structural variants (SVs) often elude conventional genome sequencing variant calling pipelines and will explain a portion of these unsolved cases. METHODS As part of the Utah NeoSeq project, we used a research-based, rapid whole-genome sequencing (WGS) protocol to investigate the genomic etiology for a newborn with a left-sided congenital diaphragmatic hernia (CDH) and cardiac malformations, whose mother also had a history of CDH and atrial septal defect. RESULTS Using both a novel, alignment-free and traditional alignment-based variant callers, we identified a maternally inherited complex SV on chromosome 8, consisting of an inversion flanked by deletions. This complex inversion, further confirmed using orthogonal molecular techniques, disrupts the ZFPM2 gene, which is associated with both CDH and various congenital heart defects. CONCLUSIONS Our results demonstrate that complex structural events, which often are unidentifiable or not reported by clinically validated testing procedures, can be discovered and accurately characterized with conventional, short-read sequencing and underscore the utility of WGS as a first-line diagnostic tool.
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Affiliation(s)
- Thomas J. Nicholas
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Najla Al‐Sweel
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Rong Mao
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Pinar Bayrak‐Toydemir
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | | | - Dawn Bentley
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Rachel Palmquist
- Division of Pediatric Neurology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
- Primary Children's Center for Personalized MedicineSalt Lake CityUSA
| | - Barry Moore
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Edgar J. Hernandez
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Michael J. Cormier
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | | | | | - Shawn Rynearson
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Carson Holt
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Mary Anne Karren
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Joshua L. Bonkowsky
- Division of Pediatric Neurology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
- Primary Children's Center for Personalized MedicineSalt Lake CityUSA
| | - Martin Tristani‐Firouzi
- Division of Pediatric Cardiology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Mark Yandell
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Aaron R. Quinlan
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUSA
| | - Luca Brunelli
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Reha M. Toydemir
- ARUP LaboratoriesSalt Lake CityUSA
- Department of PathologyUniversity of UtahSalt Lake CityUSA
| | - Brian J. Shayota
- Division of Medical Genetics, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - John C. Carey
- Division of Medical Genetics, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
| | - Steven E. Boyden
- Department of Human Genetics, Utah Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUSA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of PediatricsUniversity of Utah School of MedicineSalt Lake CityUSA
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20
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Conversion of a Non-Cancer-Selective Promoter into a Cancer-Selective Promoter. Cancers (Basel) 2022; 14:cancers14061497. [PMID: 35326649 PMCID: PMC8946048 DOI: 10.3390/cancers14061497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/11/2022] [Accepted: 03/03/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The rat progression elevated gene-3 (PEG-3) promoter displays cancer-selective expression, whereas the rat growth arrest and DNA damage inducible gene-34 (GADD34) promoter lacks cancer specificity. PEG-3 and GADD34 minimal promoters display strong sequence homology except for two single point mutations. Since mutations are prevalent in many gene promoters resulting in significant alterations in promoter specificity and activity, we have explored the relevance of these two nucleotide alterations in determining cancer-selective gene expression. We demonstrate that these two point mutations are required to transform a non-cancer-specific promoter (pGADD) into a cancer-selective promoter (pGAPE). Additionally, we found GATA2 transcription factor binding sites in the GAPE-Prom, which regulates pGAPE activity selectively in cancer cells. This newly created pGAPE has all the necessary elements making it an appropriate genetic tool to noninvasively deliver imaging agents to follow tumor growth and progression to metastasis and for generating conditionally replicating adenoviruses that can express and deliver their payload exclusively in cancer. Abstract Progression-elevated gene-3 (PEG-3) and rat growth arrest and DNA damage-inducible gene-34 (GADD34) display significant sequence homology with regulation predominantly transcriptional. The rat full-length (FL) and minimal (min) PEG-3 promoter display cancer-selective expression in rodent and human tumors, allowing for cancer-directed regulation of transgenes, viral replication and in vivo imaging of tumors and metastases in animals, whereas the FL- and min-GADD34-Prom lack cancer specificity. Min-PEG-Prom and min-GADD34-Prom have identical sequences except for two single-point mutation differences (at −260 bp and +159 bp). Engineering double mutations in the min-GADD34-Prom produce the GAPE-Prom. Changing one base pair (+159) or both point mutations in the min-GADD34-Prom, but not the FL-GADD34-Prom, results in cancer-selective transgene expression in diverse cancer cells (including prostate, breast, pancreatic and neuroblastoma) vs. normal counterparts. Additionally, we identified a GATA2 transcription factor binding site, promoting cancer specificity when both min-PEG-Prom mutations are present in the GAPE-Prom. Taken together, introducing specific point mutations in a rat min-GADD34-Prom converts this non-cancer-specific promoter into a cancer-selective promoter, and the addition of GATA2 with existing AP1 and PEA3 transcription factors enhances further cancer-selective activity of the GAPE-Prom. The GAPE-Prom provides a genetic tool to specifically regulate transgene expression in cancer cells.
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21
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Chu X, Qian M, Yang J, Wu D, Gao J, Cao L, Fang F, Pan J, Zhang H, Hu S. Effect of GATA3 rs3824662 gene polymorphism in Han Chinese children with pre-B-cell acute lymphoblastic leukemia with 10 years follow-up. Front Pediatr 2022; 10:1044866. [PMID: 36714653 PMCID: PMC9875006 DOI: 10.3389/fped.2022.1044866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
PURPOSE To evaluate the influence of GATA3 rs3824662 on pre-B-cell acute lymphoblastic leukemia (pre-B-cell ALL) susceptibility and long-term prognosis in Han Chinese children with pre-B-cell ALL treated with the CCLG-2008 protocol at the Children's Hospital of Soochow University. METHODS A total of 256 patients with childhood pre-B-cell ALL under the CCLG-2008 protocol were enrolled in this study, and 174 healthy children were used as case controls. GATA3 rs3824662 genotyping was performed using a polymerase chain reaction, followed by Sanger sequencing. The association of genotype with clinical characteristics, treatment response, adverse events, and outcomes were analyzed. RESULTS The A allele frequency of GATA3 rs3824662 in patients with pre-B cell ALL was significantly higher than that in healthy children (OR = 1.41, 95% CI = 1.042-1.908; P = 0.026). Among patients with pre-B-cell ALL, the GATA3 rs3824662 AA genotype was associated with poor prednisolone response and high blast cell burden on day 15 of the induction therapy (P = 0.011 and 0.007, respectively). Patients with the rs3824662 AA variant suffered more episodes of sepsis than those with the CC or CA variants (P = 0.021). The GATA3 rs3824662 AA genotype was significantly associated with sepsis [hazard ratio (HR) = 3.375; P = 0.01]. No significant differences were found in the cumulative incidence of relapse, overall survival, and event-free survival among all genotypes. CONCLUSION GATA3 rs3824662 was associated with susceptibility in Han Chinese children with pre-B-cell ALL and could be a possible risk factor for poor early treatment response and treatment-related sepsis.
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Affiliation(s)
- Xinran Chu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Maoxiang Qian
- Department of Hematology and Oncology, Institute of Biomedical Sciences, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Yang
- Department of Pediatrics, Subei People's Hospital of Jiangsu Province, Yangzhou, China
| | - Dong Wu
- Department of Pediatrics, Yiyuan People's Hospital, Zibo, China
| | - Jing Gao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Lu Cao
- Department of Emergency, Children's Hospital of Soochow University, Suzhou, China
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Hui Zhang
- Department of Hematology and Oncology, Fujian Branch of Shanghai Children's Medical Center, Fujian Children's Hospital, Fuzhou, China.,Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
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22
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Mahananda B, Vinay J, Palo A, Singh A, Sahu SK, Singh SP, Dixit M. SERPINB5 Genetic Variants rs2289519 and rs2289521 are Significantly Associated with Gallbladder Cancer Risk. DNA Cell Biol 2021; 40:706-712. [PMID: 33691472 DOI: 10.1089/dna.2021.0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Serine protease inhibitor b5 (SERPINB5) is a tumor suppressor gene that plays a critical role in various cellular processes. In gallbladder cancer (GBC), SERPINB5's aberrant expression is reported but its role in genetic predisposition is not known. We enrolled 270 cases and 296 controls and genotyped them for single nucleotide polymorphisms (SNPs) using direct DNA sequencing, followed by genotype-phenotype analysis in GBC and other cancer cell lines. Luciferase assay was done to determine the role of rs2289521 SNP on expression regulation. We found that two SERPINB5 variants rs2289519 and rs2289521 are significantly associated with GBC and contribute to genetic predisposition. The TT genotype of variant rs2289519 was found to be significantly associated (p = 0.008) with GBC in a recessive model. C allele of rs2289521 increased the risk for GBC significantly at genotypic (CT, p = 0.026) and allelic (p = 0.04) levels. In silico analysis and luciferase assay uncovered the probable regulatory role of the rs2289521 variant on expression. Genotype-phenotype correlation in GBC and breast cancer cell lines showed reduced expression of SERPINB5 in the presence of C allele that was consistent with the result of luciferase assay. Overall, our study reveals the genetic association of two SERPINB5 variants with GBC and rs2289521's possible role in the regulation of expression.
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Affiliation(s)
- Biswaheree Mahananda
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute, Mumbai, India
| | - J Vinay
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute, Mumbai, India
| | - Ananya Palo
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute, Mumbai, India
| | - Ayaskanta Singh
- Department of Gastroenterology and Hepato-Biliary Sciences, IMS & SUM Hospital, Sikshya O Anusandhan University, Bhubaneswar, India
| | - Saroj Kanta Sahu
- Department of Gastroenterology and Hepato-Biliary Sciences, IMS & SUM Hospital, Sikshya O Anusandhan University, Bhubaneswar, India
| | - Shivaram Prasad Singh
- Department of Gastroenterology, Sriram Chandra Bhanja Medical College and Hospital, Cuttack, India
| | - Manjusha Dixit
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute, Mumbai, India
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23
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Kelemu T, Erlandsson L, Seifu D, Abebe M, Teklu S, Storry JR, Hansson SR. Association of Maternal Regulatory Single Nucleotide Polymorphic CD99 Genotype with Preeclampsia in Pregnancies Carrying Male Fetuses in Ethiopian Women. Int J Mol Sci 2020; 21:ijms21165837. [PMID: 32823905 PMCID: PMC7461595 DOI: 10.3390/ijms21165837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/28/2022] Open
Abstract
Preeclampsia (PE) is a human specific syndrome with unknown etiology causing maternal and fetal morbidities and mortalities. In PE, maternal inflammatory responses are more exaggerated if the fetus is male than female. Other pregnancy complications such as spontaneous abortions are also more common if the fetus is male. Recent transcriptome findings showed an increased expression of CD99 in erythroid cells from male cord blood in PE. The single nucleotide polymorphism (SNP) rs311103, located in a GATA-binding site in a regulatory region on the X/Y chromosomes, governs a coordinated expression of the Xg blood group members CD99 and Xga in hematopoietic cells in a sex-dependent fashion. The rs311103C disrupts the GATA-binding site, resulting in decreased CD99 expression. We aimed to investigate the association between PE and the allele frequency of rs311103 in pregnancies in a fetal sex-dependent fashion. In a case-controlled study, we included 241 pregnant women, i.e., 105 PE cases and 136 normotensive controls. A SNP allelic discrimination analysis was performed on DNA from maternal venous blood and fetal cord blood by qPCR. A statistically significant association was observed between rs311103 allele frequency and PE in mothers carrying male fetuses. Therefore, the rs311103 genotype may play a role in the pathogenesis of PE in a fetal sex-specific manner.
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Affiliation(s)
- Tsehayneh Kelemu
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, P.O. Box 9086 Addis Ababa, Ethiopia; (T.K.); (D.S.)
| | - Lena Erlandsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden;
| | - Daniel Seifu
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, P.O. Box 9086 Addis Ababa, Ethiopia; (T.K.); (D.S.)
- Department of Biochemistry, Division of Biomedical Sciences, University of Global Health Equity, P.O. Box 6955 Kigali, Rwanda
| | - Markos Abebe
- Armauer Hanson Research Institute, P.O. Box 1005 Addis Ababa, Ethiopia;
| | - Sisay Teklu
- Department of Obstetrics and Gynecology, College of Health Sciences, Addis Ababa University, P.O. Box 9086 Addis Ababa, Ethiopia;
| | - Jill R. Storry
- Department of Hematology and Transfusion Medicine, Division of Laboratory Medicine, Lund University, 221 85 Lund, Sweden;
| | - Stefan R. Hansson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden;
- Correspondence: ; Tel.: +46-46-2223011
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24
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Feng S, Zeng D, Zheng J, Zhao D. New Insights of Human Parvovirus B19 in Modulating Erythroid Progenitor Cell Differentiation. Viral Immunol 2020; 33:539-549. [PMID: 32412895 DOI: 10.1089/vim.2020.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Human parvovirus B19 (B19), a human pathogen of the erythroparvovirus genus, is responsible for a variety of diseases. B19 cause less symptoms in healthy individuals, also cause acute and chronic anemia in immunodeficiency patients. Transient aplastic crisis and pure red cell aplasia are two kinds of anemic hemogram, respectively, in acute and chronic B19 infection phase, especially occurring in patients with a shortened red cell survival or with immunodeficiency. In addition, B19-infected pregnant women may cause hydrops fetalis or fetal loss. B19 possesses high affinity to bone marrow and fetal liver due to its extremely restricted cytotoxicity to erythroid progenitor cells (EPCs) mediated by viral proteins. The nonstructural protein NS1 is considered to be the major pathogenic factor, which has been shown to inhibit the differentiation and maturation of EPCs through inducing viral DNA damage responses and cell cycle arrest. The time phase property of NS1 activity during DNA replication and conformity to transient change of hemogram are suggestive of its role in regulating differentiation of hematopoietic cells, which is not completely understood. In this review, we summarized the bridge between B19 NS1 and Notch signaling pathway or transcriptional factors GATA, which play an important role in erythroid cell proliferation and differentiation, to provide a new insight of the potential mechanism of B19-induced differential inhibition of EPCs.
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Affiliation(s)
- Shuwen Feng
- Pediatrics Department, Children Digital and Health Data Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dongxin Zeng
- Pediatrics Department, Children Digital and Health Data Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junwen Zheng
- Pediatrics Department, Children Digital and Health Data Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dongchi Zhao
- Pediatrics Department, Children Digital and Health Data Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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25
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Creed TM, Baldeosingh R, Eberly CL, Schlee CS, Kim M, Cutler JA, Pandey A, Civin CI, Fossett NG, Kingsbury TJ. The PAX-SIX-EYA-DACH network modulates GATA-FOG function in fly hematopoiesis and human erythropoiesis. Development 2020; 147:dev.177022. [PMID: 31806659 DOI: 10.1242/dev.177022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
The GATA and PAX-SIX-EYA-DACH transcriptional networks (PSEDNs) are essential for proper development across taxa. Here, we demonstrate novel PSEDN roles in vivo in Drosophila hematopoiesis and in human erythropoiesis in vitro Using Drosophila genetics, we show that PSEDN members function with GATA to block lamellocyte differentiation and maintain the prohemocyte pool. Overexpression of human SIX1 stimulated erythroid differentiation of human erythroleukemia TF1 cells and primary hematopoietic stem-progenitor cells. Conversely, SIX1 knockout impaired erythropoiesis in both cell types. SIX1 stimulation of erythropoiesis required GATA1, as SIX1 overexpression failed to drive erythroid phenotypes and gene expression patterns in GATA1 knockout cells. SIX1 can associate with GATA1 and stimulate GATA1-mediated gene transcription, suggesting that SIX1-GATA1 physical interactions contribute to the observed functional interactions. In addition, both fly and human SIX proteins regulated GATA protein levels. Collectively, our findings demonstrate that SIX proteins enhance GATA function at multiple levels, and reveal evolutionarily conserved cooperation between the GATA and PSEDN networks that may regulate developmental processes beyond hematopoiesis.
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Affiliation(s)
- T Michael Creed
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rajkumar Baldeosingh
- Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Christian L Eberly
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Caroline S Schlee
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - MinJung Kim
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Curt I Civin
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nancy G Fossett
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tami J Kingsbury
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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26
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DePasquale EAK, Schnell D, Dexheimer P, Ferchen K, Hay S, Chetal K, Valiente-Alandí Í, Blaxall BC, Grimes H, Salomonis N. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Nucleic Acids Res 2019; 47:e138. [PMID: 31529053 PMCID: PMC6868361 DOI: 10.1093/nar/gkz789] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 02/03/2023] Open
Abstract
To understand the molecular pathogenesis of human disease, precision analyses to define alterations within and between disease-associated cell populations are desperately needed. Single-cell genomics represents an ideal platform to enable the identification and comparison of normal and diseased transcriptional cell populations. We created cellHarmony, an integrated solution for the unsupervised analysis, classification, and comparison of cell types from diverse single-cell RNA-Seq datasets. cellHarmony efficiently and accurately matches single-cell transcriptomes using a community-clustering and alignment strategy to compute differences in cell-type specific gene expression over potentially dozens of cell populations. Such transcriptional differences are used to automatically identify distinct and shared gene programs among cell-types and identify impacted pathways and transcriptional regulatory networks to understand the impact of perturbations at a systems level. cellHarmony is implemented as a python package and as an integrated workflow within the software AltAnalyze. We demonstrate that cellHarmony has improved or equivalent performance to alternative label projection methods, is able to identify the likely cellular origins of malignant states, stratify patients into clinical disease subtypes from identified gene programs, resolve discrete disease networks impacting specific cell-types, and illuminate therapeutic mechanisms. Thus, this approach holds tremendous promise in revealing the molecular and cellular origins of complex disease.
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Affiliation(s)
- Erica A K DePasquale
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Phillip Dexheimer
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stuart Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Íñigo Valiente-Alandí
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Burns C Blaxall
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - H Leighton Grimes
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
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27
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Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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28
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Riccio P, Sessa R, de Nicola S, Petruzziello F, Trombetti S, Menna G, Pepe G, Maddalena P, Izzo P, Grosso M. GATA-1 isoforms differently contribute to the production and compartmentation of reactive oxygen species in the myeloid leukemia cell line K562. J Cell Physiol 2019; 234:20829-20846. [PMID: 31049966 PMCID: PMC6767011 DOI: 10.1002/jcp.28688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022]
Abstract
Maintenance of a balanced expression of the two isoforms of the transcription factor GATA‐1, the full‐length protein (GATA‐1FL) and a shorter isoform (GATA‐1
S), contributes to control hematopoiesis, whereas their dysregulation can alter the differentiation/proliferation potential of hematopoietic precursors thereby eventually leading to a variety of hematopoietic disorders. Although it is well established that these isoforms play opposite roles in these remarkable processes, most of the molecular pathways involved remain unknown. Here, we demonstrate that GATA‐1FL and GATA‐1S are able to differently influence intracellular redox states and reactive oxygen species (ROS) compartmentation in the erythroleukemic K562 cell line, thus shedding novel mechanistic insights into the processes of cell proliferation and apoptosis resistance in myeloid precursors. Furthermore, given the role played by ROS signaling as a strategy to escape apoptosis and evade cell‐mediated immunity in myeloid cells, this study highlights a mechanism through which aberrant expression of GATA‐1 isoforms could play a role in the leukemogenic process.
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Affiliation(s)
- Patrizia Riccio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Raffaele Sessa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Sergio de Nicola
- CNR-SPIN, National Research Council, Institute for Superconductors, Innovative Materials and Devices, Naples, Italy
| | - Fara Petruzziello
- Pediatric Hematology Unit, Santobono-Pausilipon Hospital, Naples, Italy
| | - Silvia Trombetti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Giuseppe Menna
- Pediatric Hematology Unit, Santobono-Pausilipon Hospital, Naples, Italy
| | - Giampiero Pepe
- CNR-SPIN, National Research Council, Institute for Superconductors, Innovative Materials and Devices, Naples, Italy.,Department of Physics, University of Naples Federico II, Naples, Italy
| | | | - Paola Izzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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29
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Gallaway L, Jnah AJ. Transient Myeloproliferative Disorder: An Update for Neonatal Nurses. Neonatal Netw 2019; 38:144-150. [PMID: 31470381 DOI: 10.1891/0730-0832.38.3.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Down syndrome (DS) is a well-known genetic disorder that affects 700-1,000 infants per year. One particular comorbidity of DS is transient myeloproliferative disorder (TMD), a disease characterized by leukocytosis with elevated blast counts. Approximately 10 percent of DS infants develop TMD, which usually manifests during the first week of life and can lead to an extended hospitalization in a NICU. In addition to hallmark hematologic findings, other manifestations include jaundice, conjugated hyperbilirubinemia, hepatomegaly, and pericardial or pleural effusions. TMD generally resolves spontaneously in the first three months of life with the provision of timely medical management; however, survivors are at increased risk of developing acute myeloid leukemia (AML). Neonatal nurses need to have knowledge of this disorder to facilitate screening of DS infants and optimize family education and coordination of care.
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Jang W, Park J, Kwon A, Choi H, Kim J, Lee GD, Han E, Jekarl DW, Chae H, Han K, Yoon JH, Lee S, Chung NG, Cho B, Kim M, Kim Y. CDKN2B downregulation and other genetic characteristics in T-acute lymphoblastic leukemia. Exp Mol Med 2019; 51:1-15. [PMID: 30635552 PMCID: PMC6329696 DOI: 10.1038/s12276-018-0195-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/14/2023] Open
Abstract
We identified principal genetic alterations in 97.1% (99/102) of patients with T-acute lymphoblastic leukemia (T-ALL) using integrative genetic analyses, including massive parallel sequencing and multiplex ligation-dependent probe amplification (MLPA). A total of 133 mutations were identified in the following genes in descending order: NOTCH1 (66.7%), FBXW7 (19.6%), PHF6 (15.7%), RUNX1 (12.7%), NRAS (10.8%), and DNMT3A (9.8%). Copy number alterations were most frequently detected in CDKN2B, CDKN2A, and genes on 9p21.3 in T-ALL (45.1%). Gene expression data demonstrated the downregulation of CDKN2B in most cases of T-ALL, whereas CDKN2A downregulation was mainly restricted to deletions. Additional quantitative methylation analysis demonstrated that CDKN2B downregulation stemmed from deletion and hypermethylation. Analysis of 64 patients with CDKN2B hypermethylation indicated an association with an older age of onset and early T cell precursor ALL, which involved very early arrest of T cell differentiation. Genes associated with methylation and myeloid neoplasms, including DNMT3A and NRAS, were more commonly mutated in T-ALL with CDKN2B hypermethylation. In particular, a CDKN2B biallelic deletion or high methylation level (≥45%), the age of onset, and the GATA3 and SH2B3 mutations were factors associated with a poor prognosis. This study clarifies that one of the most important genetic events in T-ALL, namely, CDKN2B downregulation, occurs mechanistically via deletion and hypermethylation. Different susceptible genetic backgrounds exist based on the CDKN2B downregulation mechanism.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungja Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Ho Yoon
- Department of Hematology, Leukemia Research Institute, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seok Lee
- Department of Hematology, Leukemia Research Institute, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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Ohki K, Kiyokawa N, Saito Y, Hirabayashi S, Nakabayashi K, Ichikawa H, Momozawa Y, Okamura K, Yoshimi A, Ogata-Kawata H, Sakamoto H, Kato M, Fukushima K, Hasegawa D, Fukushima H, Imai M, Kajiwara R, Koike T, Komori I, Matsui A, Mori M, Moriwaki K, Noguchi Y, Park MJ, Ueda T, Yamamoto S, Matsuda K, Yoshida T, Matsumoto K, Hata K, Kubo M, Matsubara Y, Takahashi H, Fukushima T, Hayashi Y, Koh K, Manabe A, Ohara A. Clinical and molecular characteristics of MEF2D fusion-positive B-cell precursor acute lymphoblastic leukemia in childhood, including a novel translocation resulting in MEF2D-HNRNPH1 gene fusion. Haematologica 2019; 104:128-137. [PMID: 30171027 PMCID: PMC6312004 DOI: 10.3324/haematol.2017.186320] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Fusion genes involving MEF2D have recently been identified in precursor B-cell acute lymphoblastic leukemia, mutually exclusive of the common risk stratifying genetic abnormalities, although their true incidence and associated clinical characteristics remain unknown. We identified 16 cases of acute lymphoblastic leukemia and 1 of lymphoma harboring MEF2D fusions, including MEF2D-BCL9 (n=10), MEF2D-HNRNPUL1 (n=6), and one novel MEF2D-HNRNPH1 fusion. The incidence of MEF2D fusions overall was 2.4% among consecutive precursor B-cell acute lymphoblastic leukemia patients enrolled onto a single clinical trial. They frequently showed a cytoplasmic μ chain-positive pre-B immunophenotype, and often expressed an aberrant CD5 antigen. Besides up- and down-regulation of HDAC9 and MEF2C, elevated GATA3 expression was also a characteristic feature of MEF2D fusion-positive patients. Mutations of PHF6, recurrent in T-cell acute lymphoblastic leukemia, also showed an unexpectedly high frequency (50%) in these patients. MEF2D fusion-positive patients were older (median age 9 years) with elevated WBC counts (median: 27,300/ml) at presentation and, as a result, were mostly classified as NCI high risk. Although they responded well to steroid treatment, MEF2D fusion-positive patients showed a significantly worse outcome, with 53.3% relapse and subsequent death. Stem cell transplantation was ineffective as salvage therapy. Interestingly, relapse was frequently associated with the presence of CDKN2A/CDKN2B gene deletions. Our observations indicate that MEF2D fusions comprise a distinct subgroup of precursor B-cell acute lymphoblastic leukemia with a characteristic immunophenotype and gene expression signature, associated with distinct clinical features.
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Affiliation(s)
- Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Fuchu-shi
| | - Shinsuke Hirabayashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Hitoshi Ichikawa
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama-shi, Kanagawa
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Ai Yoshimi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito-shi
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Hiromi Sakamoto
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | | | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Hiroko Fukushima
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki
| | - Masako Imai
- Department of Pediatrics, Japanese Red Cross Musashino Hospital, Tokyo
| | - Ryosuke Kajiwara
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa
| | - Takashi Koike
- Department of Pediatrics, Tokai University School of Medicine, Kanagawa
| | - Isao Komori
- Department of Pediatrics, Matsudo City Hospital, Chiba
| | - Atsushi Matsui
- Department of Pediatrics, Japanese Red Cross Maebashi Hospital, Gunma
| | - Makiko Mori
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | - Koichi Moriwaki
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba
| | - Myoung-Ja Park
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa-shi
| | - Takahiro Ueda
- Department of Pediatrics, Nippon Medical School, Bunkyo-ku, Tokyo
| | - Shohei Yamamoto
- Department of Pediatrics, Showa University Fujigaoka Hospital, Yokohama-shi, Kanagawa
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama-shi, Kanagawa
| | - Yoichi Matsubara
- Director, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | | | - Takashi Fukushima
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki-shi, Gunma, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Akira Ohara
- Department of Pediatrics, Toho University Omori Medical Center, Tokyo
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Junkunlo K, Söderhäll K, Söderhäll I. Transglutaminase inhibition stimulates hematopoiesis and reduces aggressive behavior of crayfish, Pacifastacus leniusculus. J Biol Chem 2018; 294:708-715. [PMID: 30425101 DOI: 10.1074/jbc.ra118.005489] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/04/2018] [Indexed: 12/22/2022] Open
Abstract
Transglutaminase (TGase) is a Ca2+-dependent cross-linking enzyme, which has both enzymatic and nonenzymatic properties. TGase is involved in several cellular activities, including adhesion, migration, survival, apoptosis, and extracellular matrix (ECM) organization. In this study, we focused on the role of the TGase enzyme in controlling hematopoiesis in the crayfish, Pacifastacus leniusculus We hypothesized that a high TGase activity could mediate an interaction of progenitor cells with the ECM to maintain cells in an undifferentiated stage in the hematopoietic tissue (HPT). We found here that the reversible inhibitor cystamine decreases the enzymatic activity of TGase from crayfish HPT, as well as from guinea pig, in a concentration-dependent manner. Cystamine injection decreased TGase activity in HPT without affecting production of reactive oxygen species. Moreover, the decrease in TGase activity in the HPT increased the number of circulating hemocytes. Interestingly the cystamine-mediated TGase inhibition reduced aggressive behavior and movement in crayfish. In conclusion, we show that cystamine-mediated TGase inhibition directly releases HPT progenitor cells from the HPT into the peripheral circulation in the hemolymph and strongly reduces aggressive behavior in crayfish.
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Affiliation(s)
- Kingkamon Junkunlo
- From the Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, 752 36 Uppsala, Sweden and
| | - Kenneth Söderhäll
- the Science for Life Laboratory, Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, 752 36 Uppsala, Sweden
| | - Irene Söderhäll
- the Science for Life Laboratory, Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, 752 36 Uppsala, Sweden
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33
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Weidle UH, Rohwedder I, Birzele F, Weiss EH, Schiller C. LST1: A multifunctional gene encoded in the MHC class III region. Immunobiology 2018; 223:699-708. [PMID: 30055863 DOI: 10.1016/j.imbio.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/14/2018] [Indexed: 12/11/2022]
Abstract
The LST1 gene is located in the MHC class III cluster between the MHC class I and II regions. While most genes in this cluster have been sufficiently characterised, a definitive function and expression pattern for LST1 still remains elusive. In the present review we describe its promotor, gene organisation, splice variants and expression in human tissues, cell lines and cancer. We focus on LST1 expression in inflammation and discuss known correlations with autoimmune diseases and cancer. Current data on LST1 polymorphisms and their known associations with pathologies are also discussed in detail. We summarize the potential functions that have been described for the full-length LST1 protein including its function as a transmembrane adaptor protein with inhibitory signal transduction and its role as a membrane scaffold facilitating the formation of tunnelling nanotubes. We also discuss further potential functions by compiling all known LST1-interacting proteins. Furthermore, we address knowledge gaps and conflictive issues regarding disease association, non-hematopoietic expression and the discrepancy between RNA and protein expression data.
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Affiliation(s)
- Ulrich H Weidle
- Zentrum Seniorenstudium, Ludwig-Maximilians-Universität München, Hohenstaufenstrasse 1, 80801 München, Germany
| | - Ina Rohwedder
- Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Fabian Birzele
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Grenzacherstrasse 124, 4052 Basel, Switzerland
| | - Elisabeth H Weiss
- Zentrum Seniorenstudium, Ludwig-Maximilians-Universität München, Hohenstaufenstrasse 1, 80801 München, Germany; Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Christian Schiller
- Department of Biology II, Ludwig-Maximilians-Universität München, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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34
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Gozdecka M, Meduri E, Mazan M, Tzelepis K, Dudek M, Knights AJ, Pardo M, Yu L, Choudhary JS, Metzakopian E, Iyer V, Yun H, Park N, Varela I, Bautista R, Collord G, Dovey O, Garyfallos DA, De Braekeleer E, Kondo S, Cooper J, Göttgens B, Bullinger L, Northcott PA, Adams D, Vassiliou GS, Huntly BJP. UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs. Nat Genet 2018; 50:883-894. [PMID: 29736013 PMCID: PMC6029661 DOI: 10.1038/s41588-018-0114-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
Abstract
The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A (UTX) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss. By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML. Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.
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Affiliation(s)
- Malgorzata Gozdecka
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Milena Mazan
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | | | - Monika Dudek
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew J Knights
- Genomics of Gene Regulation, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Mercedes Pardo
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Lu Yu
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jyoti S Choudhary
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Vivek Iyer
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Haiyang Yun
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Naomi Park
- Sequencing Research Group, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ruben Bautista
- New Pipeline Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Grace Collord
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Oliver Dovey
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Saki Kondo
- Laboratory of Molecular Genetics, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jonathan Cooper
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Berthold Göttgens
- Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council, Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Lars Bullinger
- Department of Internal Medicine III, Ulm University Medical Centre, Ulm, Germany
- Medical Department, Division of Hematology, Oncology and Tumour Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
| | - Brian J P Huntly
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council, Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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Abstract
GATA2 is a transcription factor that binds to the promoter of hematopoietic genes. Mutations in one copy of the gene are associated with haploinsufficiency and reduced levels of protein. This results in reduced numbers of several cell types important for immune surveillance including dendritic cells, monocytes, CD4, and NK cells, as well as impaired NK cell function. Recently, GATA2 has been associated with several different presentations of severe Epstein–Barr virus (EBV) disease including primary infection requiring repeated hospitalizations, chronic active EBV disease, EBV-associated hydroa vacciniforme with hemophagocytosis, and EBV-positive smooth muscle tumors. EBV was found predominantly in B cells in each of the cases in which it was studied, unlike most cases of chronic active EBV disease in which the virus is usually present in T or NK cells. The variety of EBV-associated diseases seen in patients with GATA2 deficiency suggest that additional forms of severe EBV disease may be found in patients with GATA2 deficiency in the future.
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Affiliation(s)
- Jeffrey I Cohen
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Linder K, Iragavarapu C, Liu D. SETBP1 mutations as a biomarker for myelodysplasia /myeloproliferative neoplasm overlap syndrome. Biomark Res 2017; 5:33. [PMID: 29225884 PMCID: PMC5718013 DOI: 10.1186/s40364-017-0113-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022] Open
Abstract
Myelodysplasia (MDS) /myeloproliferative neoplasm (MPN) overlap syndrome has been described since the 2001 WHO classification as disorders that have both proliferative and dysplastic changes simultaneously. Specific disorders include chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia (JMML), BCR-ABL negative atypical chronic myeloid leukemia (aCML) and unclassifiable MDS/MPN (MPN/MDS-U). Recurrent gene mutations in these conditions have been described. Among them, SETBP1 mutations have been identified in up to 32% of aCML, 24% of JMML, 18% of CMML and 10% of MDS/MPN-U patients. The mutation hotspot lies in the amino acid residues 858–871 in the SETBP1 protein. SETBP1 mutations in MDS/MPN overlap syndrome is associated with accelerated transformation to leukemia and poor prognosis. In this review, we summarized the latest data on the role of SETBP1 mutations in the overlap syndrome. SETBP1 mutations may serve as a biomarker for the diagnosis and poor prognosis of the overlap syndrome.
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Affiliation(s)
- Katherine Linder
- Department of Medicine, New York Medical College and Westchester Medical Center, Valhalla, NY 10595 USA
| | - Chaitanya Iragavarapu
- Department of Medicine, New York Medical College and Westchester Medical Center, Valhalla, NY 10595 USA
| | - Delong Liu
- Department of Medicine, New York Medical College and Westchester Medical Center, Valhalla, NY 10595 USA
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37
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Nava T, Rivard GE, Bonnefoy A. Challenges on the diagnostic approach of inherited platelet function disorders: Is a paradigm change necessary? Platelets 2017; 29:148-155. [PMID: 29090587 DOI: 10.1080/09537104.2017.1356918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inherited platelet function disorders (IPFD) have been assessed for more than 50 years by aggregation- and secretion-based tests. Several decision trees are available intending to standardize the investigation of IPFD. A large variability of approaches is still in use among the laboratories across the world. In spite of costly and lengthy laboratory evaluation, the results have been found inconclusive or negative in a significant part of patients having bleeding manifestations. Molecular investigation of newly identified IPFD has recently contributed to a better understanding of the complexity of platelet function. Once considered "classic" IPFDs, Glanzmann thrombasthenia and Bernard-Soulier syndrome have each had their pathophysiology reassessed and their diagnosis made more precise and informative. Megakaryopoiesis, platelet formation, and function have been found tightly interlinked, with several genes being involved in both inherited thrombocytopenias and impaired platelet function. Moreover, genetic approaches have moved from being used as confirmatory diagnostic tests to being tools for identification of genetic variants associated with bleeding disorders, even in the absence of a clear phenotype in functional testing. In this study, we aim to address some limits of the conventional tests used for the diagnosis of IPFD, and to highlight the potential contribution of recent molecular tools and opportunities to rethink the way we should approach the investigation of IPFD.
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Affiliation(s)
- Tiago Nava
- a Centre Hospitalier Universitaire Sainte-Justine , Hematology and Oncology Division , Montréal , QC , Canada.,b Child and Adolescent Health, School of Medicine , Universidade Federal do Rio Grande do Sul (UFRGS) , Porto Alegre , Brazil
| | - Georges-Etienne Rivard
- a Centre Hospitalier Universitaire Sainte-Justine , Hematology and Oncology Division , Montréal , QC , Canada
| | - Arnaud Bonnefoy
- a Centre Hospitalier Universitaire Sainte-Justine , Hematology and Oncology Division , Montréal , QC , Canada
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38
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Beecham A, Dong C, Wright CB, Dueker N, Brickman AM, Wang L, DeCarli C, Blanton SH, Rundek T, Mayeux R, Sacco RL. Genome-wide scan in Hispanics highlights candidate loci for brain white matter hyperintensities. NEUROLOGY-GENETICS 2017; 3:e185. [PMID: 28975155 PMCID: PMC5619914 DOI: 10.1212/nxg.0000000000000185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/01/2017] [Indexed: 12/22/2022]
Abstract
Objective: To investigate genetic variants influencing white matter hyperintensities (WMHs) in the understudied Hispanic population. Methods: Using 6.8 million single nucleotide polymorphisms (SNPs), we conducted a genome-wide association study (GWAS) to identify SNPs associated with WMH volume (WMHV) in 922 Hispanics who underwent brain MRI as a cross-section of 2 community-based cohorts in the Northern Manhattan Study and the Washington Heights–Inwood Columbia Aging Project. Multiple linear modeling with PLINK was performed to examine the additive genetic effects on ln(WMHV) after controlling for age, sex, total intracranial volume, and principal components of ancestry. Gene-based tests of association were performed using VEGAS. Replication was performed in independent samples of Europeans, African Americans, and Asians. Results: From the SNP analysis, a total of 17 independent SNPs in 7 genes had suggestive evidence of association with WMHV in Hispanics (p < 1 × 10−5) and 5 genes from the gene-based analysis with p < 1 × 10−3. One SNP (rs9957475 in GATA6) and 1 gene (UBE2C) demonstrated evidence of association (p < 0.05) in the African American sample. Four SNPs with p < 1 × 10−5 were shown to affect binding of SPI1 using RegulomeDB. Conclusions: This GWAS of 2 community-based Hispanic cohorts revealed several novel WMH-associated genetic variants. Further replication is needed in independent Hispanic samples to validate these suggestive associations, and fine mapping is needed to pinpoint causal variants.
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Affiliation(s)
- Ashley Beecham
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Chuanhui Dong
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Clinton B Wright
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Nicole Dueker
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Adam M Brickman
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Liyong Wang
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Charles DeCarli
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Susan H Blanton
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Tatjana Rundek
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Richard Mayeux
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
| | - Ralph L Sacco
- John T. McDonald Department of Human Genetics (A.B., L.W., S.H.B., R.L.S.), John P Hussman Institute for Human Genomics (A.B., N.D., L.W., S.H.B.), Evelyn F. McKnight Brain Institute (C.D., C.B.W., T.R., R.L.S.), Department of Neurology (C.D., C.B.W., T.R., R.L.S.), and Department of Epidemiology and Public Health (C.B.W., T.R., R.L.S.), Miller School of Medicine, University of Miami, FL; Gertrude H. Sergievsky Center (A.M.B., R.M.), Taub Institute for Research on Alzheimer's Disease and the Aging Brain (A.M.B., R.M.), and Department of Neurology (A.M.B., R.M.), College of Physicians and Surgeons, Columbia University, New York; and Department of Neurology and Center for Neuroscience (C.D.), University of California at Davis, Sacramento
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Garn H, Renz H. GATA-3-specific DNAzyme - A novel approach for stratified asthma therapy. Eur J Immunol 2017; 47:22-30. [PMID: 27910098 DOI: 10.1002/eji.201646450] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/25/2016] [Accepted: 11/29/2016] [Indexed: 12/17/2022]
Abstract
It is now well established that type-2 immune mechanisms drive the inflammation in about 50% of asthma patients. The major cellular and molecular players regulating this important network have been identified. In terms of therapeutic intervention, cytokine and cytokine-receptor pathways have been given major attention, since these molecules are relatively easily accessible for a blockade through monoclonal antibodies, and a number of positive clinical results support this concept. However, targeting events controlling the type-2 immunity network upstream of selective cytokine pathways would be equally attractive. Type-2 immunity is regulated through a delicate interplay of several transcription factors (including GATA-3, STAT-6, NFAT, IRF4, c-maf), with GATA-3 as master regulator in this regard. Since transcription factors are intracellularly located they cannot be directly targeted by monoclonal antibodies. For intracellular targets, antisense technologies such as antisense DNA and siRNA have been shown to be a promising approach, and have recently made major advances toward clinical application. Here, we summarize the development of a GATA-3-specific DNAzyme-a molecule class that combines the superior specificity of antisense molecules with an inherent RNA-cleaving enzymatic activity-for the treatment of type-2-driven asthma from preclinical development toward a proof-of-concept clinical study.
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Affiliation(s)
- Holger Garn
- Institute of Laboratory Medicine and Pathobiochemistry, Philipps University Marburg, Medical Faculty, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Philipps University Marburg, Medical Faculty, Marburg, Germany
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40
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Kosuge N, Saio M, Matsumoto H, Aoyama H, Matsuzaki A, Yoshimi N. Nuclear features of infiltrating urothelial carcinoma are distinguished from low-grade noninvasive papillary urothelial carcinoma by image analysis. Oncol Lett 2017; 14:2715-2722. [PMID: 28928814 PMCID: PMC5588140 DOI: 10.3892/ol.2017.6474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 05/18/2017] [Indexed: 01/29/2023] Open
Abstract
Recent advances in computer technology have been made and image analysis (IA) has been introduced into pathological fields. The present study aimed to investigate the utility of IA for the evaluation of nuclear features and staining of immunohistochemistry (IHC) for Ki-67, p53 and GATA-binding protein 3 (GATA-3) in urothelial carcinoma tissue samples. A total of 49 cases of urothelial carcinoma tissue samples were obtained by transurethral resection of bladder tumors, which included 11 low-grade papillary urothelial carcinomas (LGPUCs), 1 non-invasive high-grade urothelial carcinoma and 37 infiltrating urothelial carcinomas (IUCs). Whole slide imaging (WSI) and IA were performed in Feulgen reaction and IHC-stained tissue samples. There was a significant difference in the average nuclear density, standard deviation (SD) of nuclear size and SD of nuclear minimum and maximum diameter between LGPUC and IUC, which is equivalent to the diagnostic features of IUC in nuclear variability, and hyperchromatic nuclei. In addition, the present study revealed that the SD of nuclear density was significantly different between the two groups. Regarding IA in IHC-stained tissue samples, Ki-67 was significantly overexpressed in IUC. Furthermore, the GATA-3 expression level in IUC samples with muscle invasion was significantly downregulated compared with that in non-muscle invasive tumors. The results of the present study suggest that IA in combination with WSI may be a beneficial tool for evaluating morphometric characteristics and performing semi-quantitative analysis of IHC.
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Affiliation(s)
- Noritake Kosuge
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa 903-0215, Japan
| | - Masanao Saio
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa 903-0215, Japan.,Department of Pathology, University of The Ryukyus Hospital, Nishihara, Nakagami, Okinawa 903-0215, Japan.,Department of Laboratory Sciences, Gunma University School of Health Sciences, Maebashi, Gunma 371-8514, Japan
| | - Hirofumi Matsumoto
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa 903-0215, Japan.,Department of Pathology, University of The Ryukyus Hospital, Nishihara, Nakagami, Okinawa 903-0215, Japan
| | - Hajime Aoyama
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa 903-0215, Japan
| | - Akiko Matsuzaki
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa 903-0215, Japan
| | - Naoki Yoshimi
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa 903-0215, Japan
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41
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Russo R, Andolfo I, Gambale A, De Rosa G, Manna F, Arillo A, Wandroo F, Bisconte MG, Iolascon A. GATA1 erythroid-specific regulation of SEC23B expression and its implication in the pathogenesis of congenital dyserythropoietic anemia type II. Haematologica 2017; 102:e371-e374. [PMID: 28550189 DOI: 10.3324/haematol.2016.162966] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy .,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Antonella Gambale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Gianluca De Rosa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Francesco Manna
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | | | - Farooq Wandroo
- Department of Haematology Sandwell and West Birmingham Hospital, NHS trust West Midlands UK
| | | | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
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42
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Yaguchi A, Ishibashi T, Terada K, Ueno-Yokohata H, Saito Y, Fujimura J, Shimizu T, Ohki K, Manabe A, Kiyokawa N. EP300-ZNF384 fusion gene product up-regulates GATA3 gene expression and induces hematopoietic stem cell gene expression signature in B-cell precursor acute lymphoblastic leukemia cells. Int J Hematol 2017; 106:269-281. [PMID: 28378055 DOI: 10.1007/s12185-017-2220-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 01/08/2023]
Abstract
ZNF384-related fusion genes are associated with a distinct subgroup of B-cell precursor acute lymphoblastic leukemias in childhood, with a frequency of approximately 3-4%. We previously identified a novel EP300-ZNF384 fusion gene. Patients with the ZNF384-related fusion gene exhibit a hematopoietic stem cell (HSC) gene expression signature and characteristic immunophenotype with negative or low expression of CD10 and aberrant expression of myeloid antigens, such as CD33 and CD13. However, the molecular basis of this pathogenesis remains completely unknown. In the present study, we examined the biological effects of EP300-ZNF384 expression induced by retrovirus-mediated gene transduction in an REH B-cell precursor acute lymphoblastic leukemia cell line, and observed the acquisition of the HSC gene expression signature and an up-regulation of GATA3 gene expression, as assessed by microarray analysis. In contrast, the gene expression profile induced by wild-type ZNF384 in REH cells was significantly different from that by EP300-ZNF384 expression. Together with the results of reporter assays, which revealed the enhancement of GATA3-promoter activity by EP300-ZNF384 expression, these findings suggest that EP300-ZNF384 mediates GATA3 gene expression and may be involved in the acquisition of the HSC gene expression signature and characteristic immunophenotype in B-cell precursor acute lymphoblastic leukemia cells.
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Affiliation(s)
- Akinori Yaguchi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takeshi Ishibashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kazuki Terada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Hitomi Ueno-Yokohata
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Junya Fujimura
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, 9-1 Akashi-cho, Chuo-ku, Tokyo, 104-8560, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
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43
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Wegman-Ostrosky T, Savage SA. The genomics of inherited bone marrow failure: from mechanism to the clinic. Br J Haematol 2017; 177:526-542. [PMID: 28211564 DOI: 10.1111/bjh.14535] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/19/2016] [Indexed: 12/31/2022]
Abstract
The inherited bone marrow failure syndromes (IBMFS) typically present with significant cytopenias in at least one haematopoietic cell lineage that may progress to pancytopenia, and are associated with increased risk of cancer. Although the clinical features of the IBMFS are often diagnostic, variable disease penetrance and expressivity may result in diagnostic dilemmas. The discovery of the genetic aetiology of the IBMFS has been greatly facilitated by next-generation sequencing methods. This has advanced understanding of the underlying biology of the IBMFS and been essential in improving clinical management and genetic counselling for affected patients. Herein we review the clinical features, underlying biology, and new genomic discoveries in the IBMFS, including Fanconi anaemia, dyskeratosis congenita, Diamond Blackfan anaemia, Shwachman Diamond syndrome and some disorders of the myeloid and megakaryocytic lineages.
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Affiliation(s)
- Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Research Division, Instituto Nacional de Cancerologia, Mexico City, Mexico
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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44
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Manghera M, Magnusson A, Douville RN. The sense behind retroviral anti-sense transcription. Virol J 2017; 14:9. [PMID: 28088235 PMCID: PMC5237517 DOI: 10.1186/s12985-016-0667-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 12/15/2022] Open
Abstract
Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.
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Affiliation(s)
- Mamneet Manghera
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Alycia Magnusson
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Renée N Douville
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada.
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45
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Cañete A, Carmona R, Ariza L, Sánchez MJ, Rojas A, Muñoz-Chápuli R. A population of hematopoietic stem cells derives from GATA4-expressing progenitors located in the placenta and lateral mesoderm of mice. Haematologica 2017; 102:647-655. [PMID: 28057738 PMCID: PMC5395105 DOI: 10.3324/haematol.2016.155812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/28/2016] [Indexed: 12/20/2022] Open
Abstract
GATA transcription factors are expressed in the mesoderm and endoderm during development. GATA1–3, but not GATA4, are critically involved in hematopoiesis. An enhancer (G2) of the mouse Gata4 gene directs its expression throughout the lateral mesoderm and the allantois, beginning at embryonic day 7.5, becoming restricted to the septum transversum by embryonic day 10.5, and disappearing by midgestation. We have studied the developmental fate of the G2-Gata4 cell lineage using a G2-Gata4Cre;R26REYFP mouse line. We found a substantial number of YFP+ hematopoietic cells of lymphoid, myeloid and erythroid lineages in embryos. Fetal CD41+/cKit+/CD34+ and Lin−/cKit+/CD31+ YFP+ hematopoietic progenitors were much more abundant in the placenta than in the aorta-gonad-mesonephros area. They were clonogenic in the MethoCult assay and fully reconstituted hematopoiesis in myeloablated mice. YFP+ cells represented about 20% of the hematopoietic system of adult mice. Adult YFP+ hematopoietic stem cells constituted a long-term repopulating, transplantable population. Thus, a lineage of adult hematopoietic stem cells is characterized by the expression of GATA4 in their embryonic progenitors and probably by its extraembryonic (placental) origin, although GATA4 appeared not to be required for hematopoietic stem cell differentiation. Both lineages basically showed similar physiological behavior in normal mice, but clinically relevant properties of this particular hematopoietic stem cell population should be checked in physiopathological conditions.
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Affiliation(s)
- Ana Cañete
- Department of Animal Biology, University of Málaga, Spain.,Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Málaga, Spain
| | - Rita Carmona
- Department of Animal Biology, University of Málaga, Spain.,Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Málaga, Spain
| | - Laura Ariza
- Department of Animal Biology, University of Málaga, Spain.,Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Málaga, Spain
| | - María José Sánchez
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide (UPO), Seville, Spain
| | - Anabel Rojas
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER) and Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas-CIBERDEM, Seville, Spain
| | - Ramón Muñoz-Chápuli
- Department of Animal Biology, University of Málaga, Spain .,Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Málaga, Spain
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Liu XF, Hummel M, Abecassis M. Epigenetic regulation of cellular and cytomegalovirus genes during myeloid cell development. ACTA ACUST UNITED AC 2017; 3. [PMID: 28707002 DOI: 10.18103/imr.v3i3.385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Myeloid cells are important cell types that carry human cytomegalovirus. Latent viral DNA is present in CD34+ progenitor cells and their derived monocytes. However, differentiation of latently infected monocytes to mature macrophages or dendritic cells causes reactivation of latent viruses. During hematopoietic development, pluripotent genes are repressed, and lineage specific genes are activated in a step-wise manner. This process is governed by cell-type specific chromatin states. Enhancers in the hematopoietic system are highly dynamic and established by pioneer (first tier) transcription factors (TFs), which set the stage for second and third tier TF binding. In this review, we examine the epigenetic mechanisms that regulate myeloid cell development, cell identity, and activation with a special focus on factors that regulate viral gene expression and the status of viral infection in myeloid cells.
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Affiliation(s)
- Xue-Feng Liu
- Comprehensive Transplant Center, Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Mary Hummel
- Comprehensive Transplant Center, Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
| | - Michael Abecassis
- Comprehensive Transplant Center, Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611
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Unexpected role for p19INK4d in posttranscriptional regulation of GATA1 and modulation of human terminal erythropoiesis. Blood 2016; 129:226-237. [PMID: 27879259 DOI: 10.1182/blood-2016-09-739268] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022] Open
Abstract
Terminal erythroid differentiation is tightly coordinated with cell-cycle exit, which is regulated by cyclins, cyclin-dependent kinases, and cyclin-dependent kinase inhibitors (CDKI), yet their roles in erythropoiesis remain to be fully defined. We show here that p19INK4d, a member of CDKI family, is abundantly expressed in erythroblasts and that p19INK4d knockdown delayed erythroid differentiation, inhibited cell growth, and led to increased apoptosis and generation of abnormally nucleated late-stage erythroblasts. Unexpectedly, p19INK4d knockdown did not affect cell cycle. Rather, it led to decreased expression of GATA1 protein. Importantly, the differentiation and nuclear defects were rescued by ectopic expression of GATA1. Because the GATA1 protein is protected by nuclear heat shock protein family (HSP) member HSP70, we examined the effects of p19INK4d knockdown on HSP70 and found that p19INK4d knockdown led to decreased expression of HSP70 and its nuclear localization. The reduced levels of HSP70 are the result of reduced extracellular signal-regulated kinase (ERK) activation. Further biochemical analysis revealed that p19INK4d directly binds to Raf kinase inhibitor PEBP1 and that p19INK4d knockdown increased the expression of PEBP1, which in turn led to reduced ERK activation. Thus we have identified an unexpected role for p19INK4d via a novel PEBP1-p-ERK-HSP70-GATA1 pathway. These findings are likely to have implications for improved understanding of disordered erythropoiesis.
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Mosaad YM, Elashery R, Darwish A, Sharaf Eldein OA, Barakat T, Marouf S, Abou El-Khier NT, Youssef LF, Fawzy IM. GATA3 rs3824662 gene polymorphism as possible risk factor in a cohort of Egyptian patients with pediatric acute lymphoblastic leukemia and its prognostic impact. Leuk Lymphoma 2016; 58:689-698. [PMID: 27684731 DOI: 10.1080/10428194.2016.1204656] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
To investigate the possible role of GATA3 rs3824662 polymorphism as risk factor for the development of acute lymphoblastic leukemia (ALL) in a cohort of Egyptian children and to evaluate its prognostic role. Typing of GATA3 rs3824662 polymorphism was done using real-time PCR for 116 patients with ALL and 273 healthy controls. The A allele and AA genotype were significantly higher in ALL patients (p = .015 and .016, respectively) especially B-ALL (p = .014 and .01, respectively). The AA genotype was associated with shorter disease free survival (DFS) in univariate (p = .017) and multivariate cox regression analysis (p = .028), increased incidence of relapse (p = .008) and poor prognosis (p = .028) in pediatric ALL. The GATA3 rs3824662 A allele and AA genotype may be risk factors for the development of pediatric ALL especially B-ALL in the studied cohort of Egyptian patients. The AA genotype is associated with shorter DSF, increased incidence of relapse and poor prognosis in pediatric ALL.
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Affiliation(s)
- Youssef M Mosaad
- a Clinical Immunology Unit, Clinical Pathology Department & Mansoura Research Center for Cord Stem Cells (MARC_CSC), Faculty of Medicine , Mansoura University , Mansoura , Egypt
| | - Rasha Elashery
- b Hematology/Oncology Unit , Mansoura University Children's Hospital , Mansoura , Egypt
| | - Ahmad Darwish
- b Hematology/Oncology Unit , Mansoura University Children's Hospital , Mansoura , Egypt
| | - Omar A Sharaf Eldein
- c Clinical Hematology Unit, Clinical Pathology Department, Faculty of Medicine , Mansoura University , Mansoura , Egypt
| | - Tarek Barakat
- d Pediatric Gastroenterology Unit , Mansoura University Children's Hospital , Mansoura , Egypt
| | - Samy Marouf
- c Clinical Hematology Unit, Clinical Pathology Department, Faculty of Medicine , Mansoura University , Mansoura , Egypt
| | - Noha T Abou El-Khier
- e Microbiology and Immunology Department , Mansoura Faculty of Medicine , Mansoura , Egypt
| | - Laila F Youssef
- f Department of Biochemistry, Faculty of Pharmacy , Mansoura University , Mansoura , Egypt
| | - Iman M Fawzy
- g Laboratory Medicine Department , Mansoura Fever Hospital, Ministry of Health , Mansoura , Egypt
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E2F and GATA switches turn off WD repeat domain 77 expression in differentiating cells. Biochem J 2016; 473:2331-43. [PMID: 27274086 DOI: 10.1042/bcj20160130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/06/2016] [Indexed: 02/01/2023]
Abstract
WDR77 (WD repeat domain 77) is expressed during earlier lung development when cells are rapidly proliferating, but is absent from adult lung. It is re-activated during lung tumorigenesis and is essential for lung cancer cell proliferation. Signalling pathways/molecules that control WDR77 gene expression are unknown. Promoter mapping, gel shift assay and ChIP revealed that the WDR77 promoter contains bona fide response elements for E2F and GATA transcriptional factors as demonstrated in prostate cancer, lung cancer and erythroid cells, as well as in mouse lung tissues. The WDR77 promoter is transactivated by E2F1, E2F3, GATA1 and GATA6, but suppressed by E2F6, GATA1 and GATA3 in prostate cancer PC3 cells. WDR77 expression is associated with E2F1, E2F3, GATA2 and GATA6 occupancy on the WDR77 gene, whereas, in contrast, E2F6, GATA1 and GATA3 occupancy is associated with the loss of WDR77 expression during erythroid maturation and lung development. More importantly, the loss of WDR77 expression that results from E2F and GATA switches is required for cellular differentiation of erythroid and lung epithelial cells. In contrast, lung cancer cells avoid post-mitotic differentiation by sustaining WDR77 expression. Altogether, the present study provides a novel molecular mechanism by which WDR77 is regulated during erythroid and lung development and lung tumorigenesis.
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SUMO5, a Novel Poly-SUMO Isoform, Regulates PML Nuclear Bodies. Sci Rep 2016; 6:26509. [PMID: 27211601 PMCID: PMC4876461 DOI: 10.1038/srep26509] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/04/2016] [Indexed: 12/23/2022] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML-NBs) are PML-based nuclear structures that regulate various cellular processes. SUMOylation, the process of covalently conjugating small ubiquitin-like modifiers (SUMOs), is required for both the formation and the disruption of PML-NBs. However, detailed mechanisms of how SUMOylation regulates these processes remain unknown. Here we report that SUMO5, a novel SUMO variant, mediates the growth and disruption of PML-NBs. PolySUMO5 conjugation of PML at lysine 160 facilitates recruitment of PML-NB components, which enlarges PML-NBs. SUMO5 also increases polySUMO2/3 conjugation of PML, resulting in RNF4-mediated disruption of PML-NBs. The acute promyelocytic leukemia oncoprotein PML-RARα blocks SUMO5 conjugation of PML, causing cytoplasmic displacement of PML and disruption of PML-NBs. Our work not only identifies a new member of the SUMO family but also reveals the mechanistic basis of the PML-NB life cycle in human cells.
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