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Martinez-Marin D, Helmer RA, Kaur G, Washburn RL, Martinez-Zaguilan R, Sennone SR, Dufour JM, Chilton BS. Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in lymphatic intravascular metastatic niches. PLoS One 2023; 18:e0291023. [PMID: 37682902 PMCID: PMC10490896 DOI: 10.1371/journal.pone.0291023] [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: 06/20/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Helicase-like transcription factor (HLTF) also known as SMARCA3, protects genome integrity. A tumor suppressor, HLTF is expressed in tumor cells but not in the tumor microenvironment (TME) in early-stage colorectal cancer (CRC). With disease progression, there is high concordance between epigenetic silencing of HLTF in CRC cells and negligible HLTF expression in the TME. We developed a cell line-derived xenograft (CDX) model and show for the first time that HLTF-deletion in cancer cells and the TME results in metabolic reprogramming that mitigates oxidative stress in lymphatic intravascular metastatic niches. The two metabolic pathways that derive energy from glucose-glycolysis and oxidative phosphorylation (OXPHOS)-are variously utilized by cancer cells depending upon the TME. HIF-1α, a master regulator of glycolysis, was eliminated from a role in reprogramming metabolism to satisfy CDX energetic requirements by RNAseq and spatial transcriptomics. Variability in the gut microbiome, with a putative role in altered metabolism, was also eliminated. HLTF-deleted cancer cells recovered from DNA damage at a transcriptomic level induction of DNA repair and OXPHOS genes linked to an amoeboid-associated phenotype at the tumor border (confocal microscopy). HLTF-deleted cancer and endothelial cells of lymphatic (PDPN) intravascular niches in the TME shared a site-specific protein S-glutathionylation signature (2D DIGE, MALDI-TOF/TOF mass spectrometry) for three glycolytic enzymes (PGK1 Cys379/380, PGAM1 Cys55, ENOA1 Cys119) that diverted glycolysis in support of continued glutathione biosynthesis. The collective absence of HLTF/Hltf from tumor and TME achieved redox homeostasis throughout the CDX and promoted metastasis.
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Affiliation(s)
- Dalia Martinez-Marin
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Immunology and Molecular Microbiology, Texas Tech University-Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Current address: Garrison Independent School District, Garrison, Texas, United States of America
| | - Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rachel L. Washburn
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Souad R. Sennone
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Texas Center for Comparative Cancer Research, Texas Tech University School of Veterinary Medicine, Amarillo, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Texas Center for Comparative Cancer Research, Texas Tech University School of Veterinary Medicine, Amarillo, Texas, United States of America
- School of Medicine Cancer Center, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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Kaur G, Helmer RA, Martinez-Marin D, Sennoune SR, Washburn RL, Martinez-Zaguilan R, Dufour JM, Chilton BS. Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality. PLoS One 2023; 18:e0286109. [PMID: 37624843 PMCID: PMC10456192 DOI: 10.1371/journal.pone.0286109] [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: 12/05/2022] [Accepted: 05/09/2023] [Indexed: 08/27/2023] Open
Abstract
Epigenetic mechanisms are integral to pancreatic β cell function. Promoter hypermethylation of the helicase like-transcription factor (HLTF) gene-a component of the cellular DNA damage response that contributes to genome stability-has been implicated in age-associated changes in β cells. To study HLTF, we generated global and β cell-specific (β) Hltf knockout (KO) immune competent (IC) and immune deficient (ID) Rag2-/IL2- mice. IC global and β Hltf KO mice were neonatal lethal whereas ID global and β Hltf KO newborn mice had normal survival. This focused our investigation on the effects of Rag2 interruption with common gamma chain interruption on β cell function/survival. Three-way transcriptomic (RNAseq) analyses of whole pancreata from IC and ID newborn β Hltf KO and wild type (Hltf +/+) controls combined with spatially resolved transcriptomic analysis of formalin fixed paraffin embedded tissue, immunohistochemistry and laser scanning confocal microscopy showed DNA damage caused by β Hltf KO in IC mice upregulated the Hmgb1-Rage axis and a gene signature for innate immune cells. Perforin-delivered granzyme A (GzmA) activation of DNase, Nme1, showed damaged nuclear single-stranded DNA (γH2AX immunostaining). This caspase-independent method of cell death was supported by transcriptional downregulation of Serpinc1 gene that encodes a serine protease inhibitor of GzmA. Increased transcriptional availability of complement receptors C3ar1 and C5ar1 likely invited crosstalk with Hmgb1 to amplify inflammation. This study explores the complex dialog between β cells and immune cells during development. It has implications for the initiation of type I diabetes in utero when altered gene expression that compromises genome stability invokes a localized inflammatory response.
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Affiliation(s)
- Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Dalia Martinez-Marin
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Immunology and Molecular Microbiology, Texas Tech University-Health Sciences Center, Lubbock, Texas, United States of America
| | - Souad R. Sennoune
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rachel L. Washburn
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation. Int J Mol Sci 2023; 24:ijms24043181. [PMID: 36834591 PMCID: PMC9968238 DOI: 10.3390/ijms24043181] [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: 12/02/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Deregulation of RNA metabolism has emerged as one of the key events leading to the degeneration of motor neurons (MNs) in Amyotrophic Lateral Sclerosis (ALS) disease. Indeed, mutations on RNA-binding proteins (RBPs) or on proteins involved in aspects of RNA metabolism account for the majority of familiar forms of ALS. In particular, the impact of the ALS-linked mutations of the RBP FUS on many aspects of RNA-related processes has been vastly investigated. FUS plays a pivotal role in splicing regulation and its mutations severely alter the exon composition of transcripts coding for proteins involved in neurogenesis, axon guidance, and synaptic activity. In this study, by using in vitro-derived human MNs, we investigate the effect of the P525L FUS mutation on non-canonical splicing events that leads to the formation of circular RNAs (circRNAs). We observed altered levels of circRNAs in FUSP525L MNs and a preferential binding of the mutant protein to introns flanking downregulated circRNAs and containing inverted Alu repeats. For a subset of circRNAs, FUSP525L also impacts their nuclear/cytoplasmic partitioning, confirming its involvement in different processes of RNA metabolism. Finally, we assess the potential of cytoplasmic circRNAs to act as miRNA sponges, with possible implications in ALS pathogenesis.
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Slota JA, Medina SJ, Frost KL, Booth SA. Neurons and Astrocytes Elicit Brain Region Specific Transcriptional Responses to Prion Disease in the Murine CA1 and Thalamus. Front Neurosci 2022; 16:918811. [PMID: 35651626 PMCID: PMC9149297 DOI: 10.3389/fnins.2022.918811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 01/14/2023] Open
Abstract
Progressive dysfunction and loss of neurons ultimately culminates in the symptoms and eventual fatality of prion disease, yet the pathways and mechanisms that lead to neuronal degeneration remain elusive. Here, we used RNAseq to profile transcriptional changes in microdissected CA1 and thalamus brain tissues from prion infected mice. Numerous transcripts were altered during clinical disease, whereas very few transcripts were reliably altered at pre-clinical time points. Prion altered transcripts were assigned to broadly defined brain cell types and we noted a strong transcriptional signature that was affiliated with reactive microglia and astrocytes. While very few neuronal transcripts were common between the CA1 and thalamus, we described transcriptional changes in both regions that were related to synaptic dysfunction. Using transcriptional profiling to compare how different neuronal populations respond during prion disease may help decipher mechanisms that lead to neuronal demise and should be investigated with greater detail.
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Affiliation(s)
- Jessy A. Slota
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Sarah J. Medina
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kathy L. Frost
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stephanie A. Booth
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Stephanie A. Booth
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Functional validation of variants of unknown significance using CRISPR gene editing and transcriptomics: A Kleefstra syndrome case study. Gene X 2022; 821:146287. [PMID: 35176430 DOI: 10.1016/j.gene.2022.146287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
There are an estimated > 400 million people living with a rare disease globally, with genetic variants the cause of approximately 80% of cases. Next Generation Sequencing (NGS) rapidly identifies genetic variants however they are often of unknown significance. Low throughput functional validation in specialist laboratories is the current ad hoc approach for functional validation of genetic variants, which creating major bottlenecks in patient diagnosis. This study investigates the application of CRISPR gene editing followed by genome wide transcriptomic profiling to facilitate patient diagnosis. As proof-of-concept, we introduced a variant in the Euchromatin histone methyl transferase (EHMT1) gene into HEK293T cells. We identified changes in the regulation of the cell cycle, neural gene expression and suppression of gene expression changes on chromosome 19 and chromosome X, that are in keeping with Kleefstra syndrome clinical phenotype and/or provide insight into disease mechanism. This study demonstrates the utility of genome editing followed by functional readouts to rapidly and systematically validating the function of variants of unknown significance in patients suffering from rare diseases.
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Umschweif G, Medrihan L, Guillén-Samander A, Wang W, Sagi Y, Greengard P. Identification of Neurensin-2 as a novel modulator of emotional behavior. Mol Psychiatry 2021; 26:2872-2885. [PMID: 33742167 PMCID: PMC8505262 DOI: 10.1038/s41380-021-01058-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 11/09/2022]
Abstract
Among the hallmarks of major depressive disorders (MDD) are molecular, functional, and morphological impairments in the hippocampus. Recent studies suggested a key role for hippocampal GABAergic interneurons both in depression and in the response to its treatments. These interneurons highly express the chromatin-remodeler SMARCA3 which mediates the response to chronic antidepressants in an unknown mechanism. Using cell-type-specific molecular and physiological approaches, we report that SMARCA3 mediates the glutamatergic signaling in interneurons by repressing the expression of the neuronal protein, Neurensin-2. This vesicular protein associates with endosomes and postsynaptic proteins and is highly and selectively expressed in subpopulations of GABAergic interneurons. Upregulation of Neurensin-2 in the hippocampus either by stress, viral overexpression, or by SMARCA3 deletion, results in depressive-like behaviors. In contrast, the deletion of Neurensin-2 confers resilience to stress and induces AMPA receptor localization to synapses. This pathway which bidirectionally affects emotional behavior could be involved in neuropsychiatric disorders, and suggests novel therapeutic approaches.
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Affiliation(s)
- Gali Umschweif
- Laboratory for Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Lucian Medrihan
- Laboratory for Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | | | - Wei Wang
- Laboratory for Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Yotam Sagi
- Laboratory for Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA.
| | - Paul Greengard
- Laboratory for Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
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Expression and function of Smad7 in autoimmune and inflammatory diseases. J Mol Med (Berl) 2021; 99:1209-1220. [PMID: 34059951 PMCID: PMC8367892 DOI: 10.1007/s00109-021-02083-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022]
Abstract
Transforming growth factor-β (TGF-β) plays a critical role in the pathological processes of various diseases. However, the signaling mechanism of TGF-β in the pathological response remains largely unclear. In this review, we discuss advances in research of Smad7, a member of the I-Smads family and a negative regulator of TGF-β signaling, and mainly review the expression and its function in diseases. Smad7 inhibits the activation of the NF-κB and TGF-β signaling pathways and plays a pivotal role in the prevention and treatment of various diseases. Specifically, Smad7 can not only attenuate growth inhibition, fibrosis, apoptosis, inflammation, and inflammatory T cell differentiation, but also promotes epithelial cells migration or disease development. In this review, we aim to summarize the various biological functions of Smad7 in autoimmune diseases, inflammatory diseases, cancers, and kidney diseases, focusing on the molecular mechanisms of the transcriptional and posttranscriptional regulation of Smad7.
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Helmer RA, Martinez-Zaguilan R, Kaur G, Smith LA, Dufour JM, Chilton BS. Helicase-like transcription factor-deletion from the tumor microenvironment in a cell line-derived xenograft model of colorectal cancer reprogrammed the human transcriptome-S-nitroso-proteome to promote inflammation and redirect metastasis. PLoS One 2021; 16:e0251132. [PMID: 34010296 PMCID: PMC8133447 DOI: 10.1371/journal.pone.0251132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Methylation of the HLTF gene in colorectal cancer (CRC) cells occurs more frequently in men than women. Progressive epigenetic silencing of HLTF in tumor cells is accompanied by negligible expression in the tumor microenvironment (TME). Cell line-derived xenografts (CDX) were established in control (Hltf+/+) and Hltf-deleted male Rag2-/-IL2rg-/- mice by direct orthotopic cell microinjection (OCMI) of HLTF+/+HCT116 Red-FLuc cells into the submucosa of the cecum. Combinatorial induction of IL6 and S100A8/A9 in the Hltf-deleted TME with ICAM-1 and IL8 in the primary tumor activated a positive feedback loop. The proinflammatory niche produced a major shift in CDX metastasis to peritoneal dissemination compared to controls. Inducible nitric oxide (iNOS) gene expression and transactivation of the iNOS-S100A8/A9 signaling complex in Hltf-deleted TME reprogrammed the human S-nitroso-proteome. POTEE, TRIM52 and UN45B were S-nitrosylated on the conserved I/L-X-C-X2-D/E motif indicative of iNOS-S100A8/A9-mediated S-nitrosylation. 2D-DIGE and protein identification by MALDI-TOF/TOF mass spectrometry authenticated S-nitrosylation of 53 individual cysteines in half-site motifs (I/L-X-C or C-X-X-D/E) in CDX tumors. POTEE in CDX tumors is both a general S-nitrosylation target and an iNOS-S100A8/A9 site-specific (Cys638) target in the Hltf-deleted TME. REL is an example of convergence of transcriptomic-S-nitroso-proteomic signaling. The gene is transcriptionally activated in CDX tumors with an Hltf-deleted TME, and REL-SNO (Cys143) was found in primary CDX tumors and all metastatic sites. Primary CDX tumors from Hltf-deleted TME shared 60% of their S-nitroso-proteome with all metastatic sites. Forty percent of SNO-proteins from primary CDX tumors were variably expressed at metastatic sites. Global S-nitrosylation of proteins in pathways related to cytoskeleton and motility was strongly implicated in the metastatic dissemination of CDX tumors. Hltf-deletion from the TME played a major role in the pathogenesis of inflammation and linked protein S-nitrosylation in primary CDX tumors with spatiotemporal continuity in metastatic progression when the tumor cells expressed HLTF.
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Affiliation(s)
- Rebecca A. Helmer
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Lisa A. Smith
- Department of Pathology, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Cancer Center, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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Joseph SA, Taglialatela A, Leuzzi G, Huang JW, Cuella-Martin R, Ciccia A. Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease. DNA Repair (Amst) 2020; 95:102943. [PMID: 32971328 DOI: 10.1016/j.dnarep.2020.102943] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Over the course of DNA replication, DNA lesions, transcriptional intermediates and protein-DNA complexes can impair the progression of replication forks, thus resulting in replication stress. Failure to maintain replication fork integrity in response to replication stress leads to genomic instability and predisposes to the development of cancer and other genetic disorders. Multiple DNA damage and repair pathways have evolved to allow completion of DNA replication following replication stress, thus preserving genomic integrity. One of the processes commonly induced in response to replication stress is fork reversal, which consists in the remodeling of stalled replication forks into four-way DNA junctions. In normal conditions, fork reversal slows down replication fork progression to ensure accurate repair of DNA lesions and facilitates replication fork restart once the DNA lesions have been removed. However, in certain pathological situations, such as the deficiency of DNA repair factors that protect regressed forks from nuclease-mediated degradation, fork reversal can cause genomic instability. In this review, we describe the complex molecular mechanisms regulating fork reversal, with a focus on the role of the SNF2-family fork remodelers SMARCAL1, ZRANB3 and HLTF, and highlight the implications of fork reversal for tumorigenesis and cancer therapy.
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Affiliation(s)
- Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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Vpr and Its Cellular Interaction Partners: R We There Yet? Cells 2019; 8:cells8111310. [PMID: 31652959 PMCID: PMC6912716 DOI: 10.3390/cells8111310] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Vpr is a lentiviral accessory protein that is expressed late during the infection cycle and is packaged in significant quantities into virus particles through a specific interaction with the P6 domain of the viral Gag precursor. Characterization of the physiologically relevant function(s) of Vpr has been hampered by the fact that in many cell lines, deletion of Vpr does not significantly affect viral fitness. However, Vpr is critical for virus replication in primary macrophages and for viral pathogenesis in vivo. It is generally accepted that Vpr does not have a specific enzymatic activity but functions as a molecular adapter to modulate viral or cellular processes for the benefit of the virus. Indeed, many Vpr interacting factors have been described by now, and the goal of this review is to summarize our current knowledge of cellular proteins targeted by Vpr.
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Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice. PLoS One 2019; 14:e0221751. [PMID: 31461471 PMCID: PMC6713344 DOI: 10.1371/journal.pone.0221751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022] Open
Abstract
The helicase-like transcription factor (HLTF) gene-a tumor suppressor in human colorectal cancer (CRC)-is regulated by alternative splicing and promoter hypermethylation. In this study, we used the AOM/DSS-induced mouse model to show Hltf-deletion caused poor survival concomitant with increased tumor multiplicity, and dramatically shifted the topographic distribution of lesions into the rectum. Differential isoform expression analysis revealed both the truncated isoform that lacks a DNA-repair domain and the full length isoform capable of DNA damage repair are present during adenocarcinoma formation in controls. iPathwayGuide identified 51 dynamically regulated genes of 10,967 total genes with measured expression. Oxidative Phosphorylation (Kegg: 00190), the top biological pathway perturbed by Hltf-deletion, resulted from increased transcription of Atp5e, Cox7c, Uqcr11, Ndufa4 and Ndufb6 genes, concomitant with increased endogenous levels of ATP (p = 0.0062). Upregulation of gene expression, as validated with qRT-PCR, accompanied a stable mtDNA/nDNA ratio. This is the first study to show Hltf-deletion in an inflammation-associated CRC model elevates mitochondrial bioenergetics.
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Liu L, Liu H, Zhou Y, He J, Liu Q, Wang J, Zeng M, Yuan D, Tan F, Zhou Y, Pei H, Zhu H. HLTF suppresses the migration and invasion of colorectal cancer cells via TGF‑β/SMAD signaling in vitro. Int J Oncol 2018; 53:2780-2788. [PMID: 30320371 DOI: 10.3892/ijo.2018.4591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/25/2019] [Indexed: 11/06/2022] Open
Abstract
Helicase‑like transcription factor (HLTF) has been identified as a tumor suppressor gene. The hypermethylation of HTLF is frequently observed in various types of cancer, including colorectal cancer (CRC). However, the mechanisms through which HLTF suppresses CRC progression remain unclear. Thus, the aim of the present study was to explore the biological function of HLTF in CRC cells and the underlying mechanisms. CRC tissues and cells were used to detect the expression of HLTF. Wound‑healing and Transwell assays were performed to assess the motility of CRC cells. The results revealed that HLTF expression was significantly associated with the differentiation status, invasion depth, lymph node metastasis and distant metastasis. A low HLTF expression was significantly associated with a poor survival. Furthermore, HTLF knockdown or ectopic overexpression significantly promoted or suppressed the motility of CRC cells, respectively. With regard to the underlying molecular mechanisms, the protein expression of HTLF was upregulated when the CRC cells were stimulated with transforming growth factor (TGF)‑β, and HLTF upregulation induced an increase in SMAD4 and p‑SMAD2/3 expression and a decrease in levels of the TGF‑β/SMAD pathway downstream genes, Vimentin and zinc finger e‑box binding homeobox 1 (ZEB1). On the whole, the findings of this study suggest that HLTF is negatively associated with the progression of CRC, and its overexpression suppresses the migration and invasion of CRC cells by targeting the TGF‑β/SMAD pathway.
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Affiliation(s)
- Li Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Huan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jiaofeng He
- Department of Oncology, Hunan Academy of Traditional Chinese Medicine Affiliated Hospital, Changsha, Hunan 410008, P.R. China
| | - Qiong Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jian Wang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Manting Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Dan Yuan
- Department of Oncology, Zhuzhou No. 2 Hospital, Zhuzhou, Hunan 412005, P.R. China
| | - Fengbo Tan
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yuan Zhou
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Haiping Pei
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hong Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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Kaur G, Helmer RA, Smith LA, Martinez-Zaguilan R, Dufour JM, Chilton BS. Alternative splicing of helicase-like transcription factor (Hltf): Intron retention-dependent activation of immune tolerance at the feto-maternal interface. PLoS One 2018; 13:e0200211. [PMID: 29975766 PMCID: PMC6033450 DOI: 10.1371/journal.pone.0200211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Hltf is regulated by intron retention, and global Hltf-deletion causes perinatal lethality from hypoglycemia. In heart, full-length Hltf is a transcriptional regulator of Hif-1α that controls transport systems. Thus, we tested the hypothesis that Hltf deletion from placenta caused or exacerbated neonatal hypoglycemia via Hif-1α regulation of nutrient transporters. RNA-seq data analyses identified significant changes in transcript expression and alternative splicing (AS) in E18.5 placentome. iPathwayGuide was used for gene ontology (GO) analysis of biological processes, molecular functions and cellular components. Elim pruning algorithm identified hierarchical relationships. The methylome was interrogated by Methyl-MiniSeq Epiquest analysis. GO analysis identified gene enrichment within biological processes. Protein expression was visualized with immunohistochemistry. Although two Hltf mRNA isoforms are quantifiable in most murine tissues, only the truncated Hltf isoform is expressed in placenta. The responsible intron retention event occurs in the absence of DNA methylation. iPathwayGuide analysis identified 157 target genes of 11,538 total genes with measured expression. These were obtained using a threshold of 0.05 for statistical significance (p-value) and a long fold change of expression with absolute value of at least 0.6. Hltf deletion altered transcription of trophoblast lineage-specific genes, and increased transcription of the Cxcr7 (p = 0.004) gene whose protein product is a co-receptor for human and simian immunodeficiency viruses. Concomitant increased Cxcr7 protein was identified with immunolabeling. Hltf deletion had no effect on transcription or site-specific methylation patterns of Hif-1α, the major glucose transporters, or System A amino acid transporters. There was no measureable evidence of uteroplacental dysfunction or fetal compromise. iPathGuide analysis revealed Hltf suppresses cytolysis (10/21 genes; p-value 1.900e-12; p-value correction: Elim pruning; GO:019835) including the perforin-granzyme pathway in uterine natural killer cells. Our findings 1) prove the truncated Hltf protein isoform is a transcription factor, 2) establish a functional link between AS of Hltf and immunosuppression at the feto-maternal interface, 3) correlate intron retention with the absence of DNA methylation, and 4) underscore the importance of differential splicing analysis to identify Hltf's functional diversity.
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Affiliation(s)
- Gurvinder Kaur
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Lisa A. Smith
- Department of Pathology, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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Elserafy M, Abugable AA, Atteya R, El-Khamisy SF. Rad5, HLTF, and SHPRH: A Fresh View of an Old Story. Trends Genet 2018; 34:574-577. [PMID: 29807746 PMCID: PMC6055012 DOI: 10.1016/j.tig.2018.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/13/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022]
Abstract
Not only have helicase-like transcription factor (HLTF) and SNF2 histone-linker PHD-finger RING-finger helicase (SHPRH) proved to be important players in post-replication repair like their yeast counterpart, Rad5, but they are also involved in multiple biological functions and are associated with several human disorders. We provide here an updated view of their functions, associated diseases, and potential therapeutic approaches.
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Affiliation(s)
- Menattallah Elserafy
- Krebs Institute, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Sheffield S10 2TN, UK; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; These authors contributed equally to the manuscript
| | - Arwa A Abugable
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; These authors contributed equally to the manuscript
| | - Reham Atteya
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Sherif F El-Khamisy
- Krebs Institute, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Sheffield S10 2TN, UK; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt.
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15
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Assessment of DNA repair susceptibility genes identified by whole exome sequencing in head and neck cancer. DNA Repair (Amst) 2018; 66-67:50-63. [PMID: 29747023 DOI: 10.1016/j.dnarep.2018.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/31/2022]
Abstract
Head and neck cancer (HNC), the sixth most common cancer globally, stands second in India. In Northeast (NE) India, it is the sixth most common cause of death in males and seventh in females. Prolonged tobacco and alcohol consumption constitute the major etiological factors for HNC development, which induce DNA damage. Therefore, DNA repair pathway is a crucial system in maintaining genomic integrity and preventing carcinogenesis. The present work was aimed to predict the consequence of significant germline variants of the DNA repair genes in disease predisposition. Whole exome sequencing was performed in Ion Proton™ platform on 15 case-control samples from the HNC-prevalent states of Manipur, Mizoram, and Nagaland. Variant annotation was done in Ion Reporter™ as well as wANNOVAR. Subsequent statistical and bioinformatics analysis identified significant exonic and intronic variants associated with HNC. Amongst our observed variants, 78.6% occurred in ExAC, 94% reported in dbSNP and 5.8% & 9.3% variants were present in ClinVar and HGMD, respectively. The total variants were dispersed among 199 genes with DSBR and FA pathway being the most mutated pathways. The allelic association test suggested that the intronic variants in HLTF and RAD52 gene significantly associated (P < 0.05) with the risk (OR > 5), while intronic variants in PARP4, RECQL5, EXO1 and PER1 genes and exonic variant in TDP2 gene showed protection (OR < 1) for HNC. MDR analysis proposed the exonic variants in MSH6, BRCA2, PALB2 and TP53 genes and intronic variant in RECQL5 genetic region working together during certain phase of DNA repair mechanism for HNC causation. In addition, other intronic and 3'UTR variations caused modifications in the transcription factor binding sites and miRNA target sites associated with HNC. Large-scale validation in NE Indian population, in-depth structure prediction and subsequent simulation of our recognized polymorphisms is necessary to identify true causal variants related to HNC.
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16
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Dhont L, Pintilie M, Kaufman E, Navab R, Tam S, Burny A, Shepherd F, Belayew A, Tsao MS, Mascaux C. Helicase-like transcription factor expression is associated with a poor prognosis in Non-Small-Cell Lung Cancer (NSCLC). BMC Cancer 2018; 18:429. [PMID: 29661164 PMCID: PMC5902896 DOI: 10.1186/s12885-018-4215-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 03/12/2018] [Indexed: 01/09/2023] Open
Abstract
Background The relapse rate in early stage non-small cell lung cancer (NSCLC) after surgical resection is high. Prognostic biomarkers may help identify patients who may benefit from additional therapy. The Helicase-like Transcription Factor (HLTF) is a tumor suppressor, altered in cancer either by gene hypermethylation or mRNA alternative splicing. This study assessed the expression and the clinical relevance of wild-type (WT) and variant forms of HLTF RNAs in NSCLC. Methods We analyzed online databases (TCGA, COSMIC) for HLTF alterations in NSCLC and assessed WT and spliced HLTF mRNAs expression by RT-ddPCR in 39 lung cancer cell lines and 171 patients with resected stage I-II NSCLC. Results In silico analyses identified HLTF gene alterations more frequently in lung squamous cell carcinoma than in adenocarcinoma. In cell lines and in patients, WT and I21R HLTF mRNAs were detected, but the latter at lower level. The subgroup of 25 patients presenting a combined low WT HLTF expression and a high I21R HLTF expression had a significantly worse disease-free survival than the other 146 patients in univariate (HR 1.96, CI 1.17–3.30; p = 0.011) and multivariate analyses (HR 1.98, CI 1.15–3.40; p = 0.014). Conclusion A low WT HLTF expression with a high I21R HLTF expression is associated with a poor DFS.
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Affiliation(s)
- Ludovic Dhont
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, Université de Mons, Mons, Belgium.,Princess Margaret Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Cellular and Molecular Epigenetics, Université de Liège-GIGA, Liège, Belgium
| | - Melania Pintilie
- Biostatistics Department, University of Toronto, Toronto, Canada
| | - Ethan Kaufman
- Princess Margaret Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Roya Navab
- Princess Margaret Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shirley Tam
- Princess Margaret Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Arsène Burny
- Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Frances Shepherd
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, Université de Mons, Mons, Belgium
| | - Ming-Sound Tsao
- Princess Margaret Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Céline Mascaux
- Department of Muldisciplinary Oncology and Therapeutic Innovations, Assistance Publique des Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Chemin des Bourrely, 13195, Marseille, Cedex 20, France. .,Centre de Recherche en Cancérologie de Marseille (CRCM, Cancer Research Center of Marseille), Inserm UMR1068, CNRS UMR7258 and Aix-Marseille University UM105, Marseille, France.
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Lugli N, Sotiriou SK, Halazonetis TD. The role of SMARCAL1 in replication fork stability and telomere maintenance. DNA Repair (Amst) 2017. [PMID: 28623093 DOI: 10.1016/j.dnarep.2017.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1), also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. Mutations in this gene are the cause of Schimke immune-osseous dysplasia (SIOD), an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. In this review, we summarize the main roles of SMARCAL1 in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress.
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Affiliation(s)
- Natalia Lugli
- Department of Molecular Biology, University of Geneva, Switzerland
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18
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Cheng CK, Chan NPH, Wan TSK, Lam LY, Cheung CHY, Wong THY, Ip RKL, Wong RSM, Ng MHL. Helicase-like transcription factor is a RUNX1 target whose downregulation promotes genomic instability and correlates with complex cytogenetic features in acute myeloid leukemia. Haematologica 2016; 101:448-57. [PMID: 26802049 DOI: 10.3324/haematol.2015.137125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/13/2016] [Indexed: 12/27/2022] Open
Abstract
Helicase-like transcription factor is a SWI/SNF chromatin remodeling factor involved in various biological processes. However, little is known about its role in hematopoiesis. In this study, we measured helicase-like transcription factor mRNA expression in the bone marrow of 204 adult patients with de novo acute myeloid leukemia. Patients were dichotomized into low and high expression groups at the median level for clinicopathological correlations. Helicase-like transcription factor levels were dramatically reduced in the low expression patient group compared to those in the normal controls (n=40) (P<0.0001). Low helicase-like transcription factor expression correlated positively with French-American-British M4/M5 subtypes (P<0.0001) and complex cytogenetic abnormalities (P=0.02 for ≥3 abnormalities;P=0.004 for ≥5 abnormalities) but negatively with CEBPA double mutations (P=0.012). Also, low expression correlated with poorer overall (P=0.005) and event-free (P=0.006) survival in the intermediate-risk cytogenetic subgroup. Consistent with the more aggressive disease associated with low expression, helicase-like transcription factor knockdown in leukemic cells promoted proliferation and chromosomal instability that was accompanied by downregulation of mitotic regulators and impaired DNA damage response. The significance of helicase-like transcription factor in genome maintenance was further indicated by its markedly elevated expression in normal human CD34(+)hematopoietic stem cells. We further demonstrated that helicase-like transcription factor was a RUNX1 target and transcriptionally repressed by RUNX1-ETO and site-specific DNA methylation through a duplicated RUNX1 binding site in its promoter. Taken together, our findings provide new mechanistic insights on genomic instability linked to helicase-like transcription factor deregulation, and strongly suggest a tumor suppressor function of the SWI/SNF protein in acute myeloid leukemia.
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Affiliation(s)
- Chi Keung Cheng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Natalie P H Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Thomas S K Wan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Lai Ying Lam
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Coty H Y Cheung
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Terry H Y Wong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Rosalina K L Ip
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Raymond S M Wong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina Sir Y. K. Pao Centre for Cancer, Prince of Wales Hospital, Hong Kong, Cina
| | - Margaret H L Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Cina
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19
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Dhont L, Mascaux C, Belayew A. The helicase-like transcription factor (HLTF) in cancer: loss of function or oncomorphic conversion of a tumor suppressor? Cell Mol Life Sci 2016; 73:129-47. [PMID: 26472339 PMCID: PMC11108516 DOI: 10.1007/s00018-015-2060-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 09/21/2015] [Accepted: 10/01/2015] [Indexed: 12/21/2022]
Abstract
The Helicase-like Transcription Factor (HLTF) belongs to the SWI/SNF family of proteins involved in chromatin remodeling. In addition to its role in gene transcription, HLTF has been implicated in DNA repair, which suggests that this protein acts as a tumor suppressor. Accumulating evidence indicates that HLTF expression is altered in various cancers via two mechanisms: gene silencing through promoter hypermethylation or alternative mRNA splicing, which leads to the expression of truncated proteins that lack DNA repair domains. In either case, the alteration of HLTF expression in cancer has a poor prognosis. In this review, we gathered published clinical and molecular data on HLTF. Our purposes are (a) to address whether HLTF alterations could be considered as cancer drivers or passengers and (b) to determine whether its different functions (transcription or DNA repair) could be diverted in clonal selection during cancer progression.
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Affiliation(s)
- Ludovic Dhont
- Laboratory of Molecular Biology, University of Mons, Avenue du Champ de Mars 6, Pentagone 3A, B-7000 Mons, Belgium
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto Medical Discovery Tower, 101 College Street, 14th floor, Toronto, ON M5G 1L7 Canada
| | - Céline Mascaux
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto Medical Discovery Tower, 101 College Street, 14th floor, Toronto, ON M5G 1L7 Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2L9 Canada
| | - Alexandra Belayew
- Laboratory of Molecular Biology, University of Mons, Avenue du Champ de Mars 6, Pentagone 3A, B-7000 Mons, Belgium
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20
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Horn S, Kirkegaard JS, Hoelper S, Seymour PA, Rescan C, Nielsen JH, Madsen OD, Jensen JN, Krüger M, Grønborg M, Ahnfelt-Rønne J. Research Resource: A Dual Proteomic Approach Identifies Regulated Islet Proteins During β-Cell Mass Expansion In Vivo. Mol Endocrinol 2015; 30:133-43. [PMID: 26649805 DOI: 10.1210/me.2015-1208] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Diabetes is characterized by insulin insufficiency due to a relative paucity of functional β-cell mass. Thus, strategies for increasing β-cell mass in situ are sought-after for therapeutic purposes. Pregnancy is a physiological state capable of inducing robust β-cell mass expansion, however, the mechanisms driving this expansion are not fully understood. Thus, the aim of this study was to characterize pregnancy-induced changes in the islet proteome at the peak of β-cell proliferation in mice. Islets from pregnant and nonpregnant littermates were compared via 2 proteomic strategies. In vivo pulsed stable isotope labeling of amino acids in cell culture was used to monitor de novo protein synthesis during the first 14.5 days of pregnancy. In parallel, protein abundance was determined using ex vivo dimethyl labelling at gestational day 14.5. Comparison of the 2 datasets revealed 170 islet proteins to be up regulated as a response to pregnancy. These included several proteins, not previously associated with pregnancy-induced islet expansion, such as CLIC1, STMN1, MCM6, PPIB, NEDD4, and HLTF. Confirming the validity of our approach, we also identified proteins encoded by genes known to be associated with pregnancy-induced islet expansion, such as CHGB, IGFBP5, MATN2, EHHADH, IVD, and BMP1. Bioinformatic analyses demonstrated enrichment and activation of the biological functions: "protein synthesis" and "proliferation," and predicted the transcription factors HNF4α, MYC, MYCN, E2F1, NFE2L2, and HNF1α as upstream regulators of the observed expressional changes. As the first characterization of the islet-proteome during pregnancy, this study provides novel insight into the mechanisms involved in promoting pregnancy-induced β-cell mass expansion and function.
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Affiliation(s)
- Signe Horn
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Jeannette S Kirkegaard
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Soraya Hoelper
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Philip A Seymour
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Claude Rescan
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Jens H Nielsen
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Ole D Madsen
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Jan N Jensen
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Marcus Krüger
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Mads Grønborg
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
| | - Jonas Ahnfelt-Rønne
- Global Research (S.Hor., J.S.K., C.R., O.D.M., J.N.J., M.G., J.A.-R.), Novo Nordisk A/S, 2870 Maaloev, Denmark; Department of Biomedical Sciences (S.Hor., J.S.K., J.H.N.), University of Copenhagen, 2200 Copenhagen N, Denmark; Max Planck Institute for Heart and Lung Research (S.Hoe.), 61231 Bad Nauheim, Germany; The Danish Stem Cell Center (P.A.S., O.D.M.), University of Copenhagen, 2200 Copenhagen N, Denmark; and Institute of Genetics (M.K.), Cluster of Excellence in Cellular Stress Responses, University of Cologne, 50931 Cologne, Germany
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Tomi NS, Davari K, Grotzky D, Loos F, Böttcher K, Frankenberger S, Jungnickel B. Analysis of SHPRH functions in DNA repair and immunoglobulin diversification. DNA Repair (Amst) 2014; 24:63-72. [PMID: 25311267 DOI: 10.1016/j.dnarep.2014.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 08/29/2014] [Accepted: 09/23/2014] [Indexed: 12/18/2022]
Abstract
During replication, bypass of DNA lesions is orchestrated by the Rad6 pathway. Monoubiquitination of proliferating cell nuclear antigen (PCNA) by Rad6/Rad18 leads to recruitment of translesion polymerases for direct and potentially mutagenic damage bypass. An error-free bypass pathway may be initiated via K63-linked PCNA polyubiquitination by Ubc13/Mms2 and the E3 ligase Rad5 in yeast, or HLTF/SHPRH in vertebrates. For the latter two enzymes, redundancy with a third E3 ligase and alternative functions have been reported. We have previously shown that the Rad6 pathway is involved in somatic hypermutation of immunoglobulin genes in B lymphocytes. Here, we have used knockout strategies targeting expression of the entire SHPRH protein or functionally significant domains in chicken DT40 cells that do not harbor a HLTF ortholog. We show that SHPRH is apparently redundant with another E3 ligase during DNA damage-induced PCNA modification. SHPRH plays no substantial role in cellular resistance to drugs initiating excision repair and the Rad6 pathway, but is important in survival of topoisomerase II inhibitor treatment. Removal of only the C-terminal RING domain does not interfere with this SHPRH function. SHPRH inactivation does not substantially impact on the overall efficacy of Ig diversification. Redundancy of E3 ligases in the Rad6 pathway may be linked to its different functions in genome maintenance and genetic plasticity.
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Affiliation(s)
- Nils-Sebastian Tomi
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University Jena, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Kathrin Davari
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University Jena, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - David Grotzky
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Friedemann Loos
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Katrin Böttcher
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University Jena, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Samantha Frankenberger
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University Jena, Hans-Knoell-Strasse 2, 07745 Jena, Germany.
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22
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Arcolia V, Paci P, Dhont L, Chantrain G, Sirtaine N, Decaestecker C, Remmelink M, Belayew A, Saussez S. Helicase-like transcription factor: a new marker of well-differentiated thyroid cancers. BMC Cancer 2014; 14:492. [PMID: 25005870 PMCID: PMC4107960 DOI: 10.1186/1471-2407-14-492] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The preoperative characterization of thyroid nodules is a challenge for the clinicians. Fine-needle aspiration (FNA) is the commonly used pre-operative technique for diagnosis of malignant thyroid tumor. However, many benign lesions, with indeterminate diagnosis following FNA, are referred to surgery. There is an urgent need to identify biomarkers that could be used with the FNA to distinguish benign thyroid nodules from malignant tumors. The purpose of the study is to examine the level of expression of the helicase-like transcription factor (HLTF) in relation to neoplastic progression of thyroid carcinomas. METHODS The presence of HLTF was investigated using quantitative and semi-quantitative immunohistochemistry in a series of 149 thyroid lesion specimens. Our first clinical series was composed of 80 patients, including 20 patients presenting thyroid adenoma, 40 patients presenting thyroid papillary carcinoma, 12 patients presenting thyroid follicular carcinoma and 8 patients presenting anaplastic carcinoma. These specimens were assessed quantitatively using computer assisted microscopy. Our initial results were validated on a second clinical series composed of 40 benign thyroid lesions and 29 malignant thyroid lesions using a semi-quantitative approach. Finally, the HLTF protein expression was investigated by Western blotting in four thyroid cancer cell lines. RESULTS The decrease of HLTF staining was statistically significant during thyroid tumor progression in terms of both the percentage of mean optical density (MOD), which corresponds to the mean staining intensity (Kruskall-Wallis: p < 0.0005), and the labelling index (LI), which corresponds to the percentage of immunopositive cells (Kruskall-Wallis: p < 10-6). Adenomas presented very pronounced nuclear HLTF immunostaining, whereas papillary carcinomas exhibited HLTF only in the cytoplasm. The number of HLTF positive nuclei was clearly higher in the adenomas group (30%) than in the papillary carcinomas group (5%).The 115-kDa full size HLTF protein was immunodetected in four studied thyroid cancer cell lines. Moreover, three truncated HLTF forms (95-kDa, 80-kDa and 70-kDa) were also found in these tumor cells. CONCLUSIONS This study reveals an association between HLTF expression level and thyroid neoplastic progression. Nuclear HLTF immunostaining could be used with FNA in an attempt to better distinguish benign thyroid nodules from malignant tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sven Saussez
- Laboratory of Anatomy and Cell Biology, Faculty of Medicine and Pharmacy, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium.
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23
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Helmer RA, Martínez-Zaguilán R, Dertien JS, Fulford C, Foreman O, Peiris V, Chilton BS. Helicase-like transcription factor (Hltf) regulates G2/M transition, Wt1/Gata4/Hif-1a cardiac transcription networks, and collagen biogenesis. PLoS One 2013; 8:e80461. [PMID: 24278285 PMCID: PMC3835564 DOI: 10.1371/journal.pone.0080461] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/03/2013] [Indexed: 12/22/2022] Open
Abstract
HLTF/Hltf regulates transcription, remodels chromatin, and coordinates DNA damage repair. Hltf is expressed in mouse brain and heart during embryonic and postnatal development. Silencing Hltf is semilethal. Seventy-four percent of congenic C57BL/6J Hltf knockout mice died, 75% within 12-24 hours of birth. Previous studies in neonatal (6-8 hour postpartum) brain revealed silencing Hltf disrupted cell cycle progression, and attenuated DNA damage repair. An RNA-Seq snapshot of neonatal heart transcriptome showed 1,536 of 20,000 total transcripts were altered (p < 0.05) - 10 up- and 1,526 downregulated. Pathway enrichment analysis with MetaCore™ showed Hltf’s regulation of the G2/M transition (p=9.726E-15) of the cell cycle in heart is nearly identical to its role in brain. In addition, Brca1 and 12 members of the Brca1 associated genome surveillance complex are also downregulated. Activation of caspase 3 coincides with transcriptional repression of Bcl-2. Hltf loss caused downregulation of Wt1/Gata4/Hif-1a signaling cascades as well as Myh7b/miR499 transcription. Hltf-specific binding to promoters and/or regulatory regions of these genes was authenticated by ChIP-PCR. Hif-1a targets for prolyl (P4ha1, P4ha2) and lysyl (Plod2) collagen hydroxylation, PPIase enzymes (Ppid, Ppif, Ppil3) for collagen trimerization, and lysyl oxidase (Loxl2) for collagen-elastin crosslinking were downregulated. However, transcription of genes for collagens, fibronectin, Mmps and their inhibitors (Timps) was unaffected. The collective downregulation of genes whose protein products control collagen biogenesis caused disorganization of the interstitial and perivascular myocardial collagen fibrillar network as viewed with picrosirius red-staining, and authenticated with spectral imaging. Wavy collagen bundles in control hearts contrasted with collagen fibers that were thin, short and disorganized in Hltf null hearts. Collagen bundles in Hltf null hearts were tangled and fragmented. Thus, silencing Hltf during heart organogenesis compromised DNA double-strand break repair, and caused aberrant collagen biogenesis altering the structural network that transmits cardiomyocyte force into muscle contraction.
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Affiliation(s)
- Rebecca A. Helmer
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martínez-Zaguilán
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Janet S. Dertien
- Department of Pharmacology & Neuroscience, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Candra Fulford
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Oded Foreman
- The Jackson Laboratory, Sacramento, California, United States of America
| | - Vasum Peiris
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- * E-mail:
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