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Tourigny DS, Altieri B, Secener KA, Sbiera S, Schauer MP, Arampatzi P, Herterich S, Sauer S, Fassnacht M, Ronchi CL. Cellular landscape of adrenocortical carcinoma at single-nuclei resolution. Mol Cell Endocrinol 2024; 590:112272. [PMID: 38759836 DOI: 10.1016/j.mce.2024.112272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Adrenocortical carcinoma (ACC) is a rare yet devastating tumour of the adrenal gland with a molecular pathology that remains incompletely understood. To gain novel insights into the cellular landscape of ACC, we generated single-nuclei RNA sequencing (snRNA-seq) data sets from twelve ACC tumour samples and analysed these alongside snRNA-seq data sets from normal adrenal glands (NAGs). We find the ACC tumour microenvironment to be relatively devoid of immune cells compared to NAG tissues, consistent with known high tumour purity values for ACC as an immunologically "cold" tumour. Our analysis identifies three separate groups of ACC samples that are characterised by different relative compositions of adrenocortical cell types. These include cell populations that are specifically enriched in the most clinically aggressive and hormonally active tumours, displaying hallmarks of reorganised cell mechanobiology and dysregulated steroidogenesis, respectively. We also identified and validated a population of mitotically active adrenocortical cells that strongly overexpress genes POLQ, DIAPH3 and EZH2 to support tumour expansion alongside an LGR4+ progenitor-like or cell-of-origin candidate for adrenocortical carcinogenesis. Trajectory inference suggests the fate adopted by malignant adrenocortical cells upon differentiation is associated with the copy number or allelic balance state of the imprinted DLK1/MEG3 genomic locus, which we verified by assessing bulk tumour DNA methylation status. In conclusion, our results therefore provide new insights into the clinical and cellular heterogeneity of ACC, revealing how genetic perturbations to healthy adrenocortical renewal and zonation provide a molecular basis for disease pathogenesis.
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Affiliation(s)
- David S Tourigny
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Kerim A Secener
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany; Institute of Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, 14195, Germany
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Marc P Schauer
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany; Center for Cellular Immunotherapy, Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, 97080, Germany
| | | | - Sabine Herterich
- Central Laboratory, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Cristina L Ronchi
- Institute of Metabolism and System Research, University of Birmingham, Birmingham, B15 2TT, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, B15 2GW, UK.
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2
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Wang Y, Yang J, Wu C, Guo Y, Ding Y, Zou X. LncRNA SNHG14 silencing attenuates the progression of diabetic nephropathy via the miR-30e-5p/SOX4 axis. J Diabetes 2024; 16:e13565. [PMID: 38751373 PMCID: PMC11096814 DOI: 10.1111/1753-0407.13565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/05/2024] [Accepted: 03/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) is a diabetic complication. LncRNAs are reported to participate in the pathophysiology of DN. Here, the function and mechanism of lncRNA small nucleolar RNA host gene 14 (SNHG14) in DN were explored. METHODS Streptozotocin (STZ)-induced DN mouse models and high glucose (HG)-treated human mesangial cells (MCs) were used to detect SNHG14 expression. SNHG14 silencing plasmids were applied to examine the function of SNHG14 on proliferation and fibrosis in HG-treated MCs. Potential targets of SNHG14 were predicted using bioinformatics tools and verified by luciferase reporter, RNA pulldown, and northern blotting assays. The functional role of SNHG14 in DN in vivo was detected by injection with adenoviral vector carrying sh-SNHG14 into DN mice. Serum creatinine, blood urea nitrogen, blood glucose, 24-h proteinuria, relative kidney weight, and renal pathological changes were examined in DN mice. RESULTS SNHG14 expression was elevated in the kidneys of DN mice and HG-treated MCs. SNHG14 silencing inhibited proliferation and fibrosis of HG-stimulated MCs. SNHG14 bound to miR-30e-5p to upregulate SOX4 expression. In rescue assays, SOX4 elevation diminished the effects of SNHG14 silencing in HG-treated MCs, and SOX4 silencing reversed the effects of SNHG14 overexpression. In in vivo studies, SNHG14 downregulation significantly ameliorated renal injuries and renal interstitial fibrosis in DN mice. CONCLUSIONS SNHG14 silencing attenuates kidney injury in DN mice and reduces proliferation and fibrotic phenotype of HG-stimulated MCs via the miR-30e-5p/SOX4 axis.
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Affiliation(s)
- YunXia Wang
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - JiaJia Yang
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Chun Wu
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Yuqin Guo
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Yuan Ding
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Xiujuan Zou
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
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3
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Singleton KS, Silva-Rodriguez P, Cunningham DD, Silva EM. Xenopus Sox11 Partner Proteins and Functional Domains in Neurogenesis. Genes (Basel) 2024; 15:243. [PMID: 38397232 PMCID: PMC10887758 DOI: 10.3390/genes15020243] [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: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Sox11, a member of the SoxC family of transcription factors, has distinct functions at different times in neural development. Studies in mouse, frog, chick, and zebrafish show that Sox11 promotes neural fate, neural differentiation, and neuron maturation in the central nervous system. These diverse roles are controlled in part by spatial and temporal-specific protein interactions. However, the partner proteins and Sox11-interaction domains underlying these diverse functions are not well defined. Here, we identify partner proteins and the domains of Xenopus laevis Sox11 required for protein interaction and function during neurogenesis. Our data show that Sox11 co-localizes and interacts with Pou3f2 and Neurog2 in the anterior neural plate and in early neurons, respectively. We also demonstrate that Sox11 does not interact with Neurog1, a high-affinity partner of Sox11 in the mouse cortex, suggesting that Sox11 has species-specific partner proteins. Additionally, we determined that the N-terminus including the HMG domain of Sox11 is necessary for interaction with Pou3f2 and Neurog2, and we established a novel role for the N-terminal 46 amino acids in the specification of placodal progenitors. This is the first identification of partner proteins for Sox11 and of domains required for partner-protein interactions and distinct roles in neurogenesis.
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Affiliation(s)
- Kaela S. Singleton
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
| | - Pablo Silva-Rodriguez
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Doreen D. Cunningham
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Elena M. Silva
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
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4
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Narayan G, Ronima K R, Agrawal A, Thummer RP. An Insight into Vital Genes Responsible for β-cell Formation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1450:1-27. [PMID: 37432546 DOI: 10.1007/5584_2023_778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The regulation of glucose homeostasis and insulin secretion by pancreatic β-cells, when disturbed, will result in diabetes mellitus. Replacement of dysfunctional or lost β-cells with fully functional ones can tackle the problem of β-cell generation in diabetes mellitus. Various pancreatic-specific genes are expressed during different stages of development, which have essential roles in pancreatogenesis and β-cell formation. These factors play a critical role in cellular-based studies like transdifferentiation or de-differentiation of somatic cells to multipotent or pluripotent stem cells and their differentiation into functional β-cells. This work gives an overview of crucial transcription factors expressed during various stages of pancreas development and their role in β-cell specification. In addition, it also provides a perspective on the underlying molecular mechanisms.
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Affiliation(s)
- Gloria Narayan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ronima K R
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Akriti Agrawal
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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5
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Diawara M, Martin LJ. Regulatory mechanisms of SoxD transcription factors and their influences on male fertility. Reprod Biol 2023; 23:100823. [PMID: 37979495 DOI: 10.1016/j.repbio.2023.100823] [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: 09/22/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Members of the SRY-related box (SOX) subfamily D (SoxD) of transcription factors are well conserved among vertebrate species and play important roles in different stages of male reproductive development. In mammals, the SoxD subfamily contains three members: SOX5, SOX6 and SOX13. Here, we describe their implications in testicular development and spermatogenesis, contributing to fertility. We also cover the mechanisms of action of SoxD transcription factors in gene regulation throughout male development. The specificity of activation of target genes by SoxD members depends, in part, on their post-translational modifications and interactions with other partners. Sperm production in adult males requires the coordination in the regulation of gene expression by different members of the SoxD subfamily of transcription factors in the testis. Specifically, the regulation of genes promoting adequate spermatogenesis by SoxD members is discussed in comparison between species.
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Affiliation(s)
- Mariama Diawara
- Biology Department, Université de Moncton, Moncton, New Brunswick E1A 3E9, Canada
| | - Luc J Martin
- Biology Department, Université de Moncton, Moncton, New Brunswick E1A 3E9, Canada.
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6
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Zhu C, Fu Y, Xia L, Li F, Huang K, Sun X. Expression Profiles, Prognosis, and ceRNA Regulation of SRY-Related HMG-Box Genes in Stomach Adenocarcinoma. J Environ Pathol Toxicol Oncol 2023; 42:79-91. [PMID: 36749091 DOI: 10.1615/jenvironpatholtoxicoloncol.2022044640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aberrant expression of the SRY-related HMG-box (SOX) genes contributes to tumor development and progression. This research aimed to identify the regulation of the SOX genes in stomach adenocarcinoma (STAD). Expression profiles downloaded from The Cancer Genome Atlas (TCGA) were conducted to analyze the expression and function of the SOX genes. A competing endogenous RNAs (ceRNA) network mediated by the SOX genes was effectively constructed consisting of 64 lncRNAs, 29 miRNAs, and 11 SOX genes based on predicted miRNAs shared by lncRNAs and mRNAs using miRDB, TargetScan, miRTarBase, miRcode, and starBase v2.0. SOX9 was identified as a prognostic signature, which showed the usefulness of diagnosis and prognosis of STAD by the receiver operating characteristic (ROC) and Kaplan-Meier curves. SOX9 was also shown specifically in STAD and identified as highly expressed in the gastrointestinal tract. Gene Ontology (GO) enrichment analysis showed that SOX9 might influence the genes related to the pattern specification process, sodium ion homeostasis, and potassium ion transport, mainly including FEZF1, HOXC13, HOXC10, HOXC9, HOXA11, DPP6, ATP4B, CASQ2, KCNA1, ATP4A, and SFRP1. Furthermore, HOTAIR knockdown, miR-206-mimic transfection, the Cell Count Kit-8 (CCK-8) assay were performed to verify the function of HOTAIR/miR-206/SOX9 axis, which was identified in the ceRNA network analysis. HOTAIR could induce proliferation potentially by competitively binding miR-206/SOX9 axis in STAD. These findings provide new clues with prognostic and therapeutic implications in STAD and suggest that HOTAIR/miR-206/SOX9 might be a potential new strategy for therapeutic targeting of gastric cancer.
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Affiliation(s)
- Chang Zhu
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Yuxiang Fu
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Ligang Xia
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Fang Li
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Kaibin Huang
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Xiao Sun
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
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7
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Chaudhary A, Raza SS, Haque R. Transcriptional factors targeting in cancer stem cells for tumor modulation. Semin Cancer Biol 2023; 88:123-137. [PMID: 36603792 DOI: 10.1016/j.semcancer.2022.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
Cancer Stem Cells (CSCs) are now considered the primary "seeds" for the onset, development, metastasis, and recurrence of tumors. Despite therapeutic breakthroughs, cancer remains the leading cause of death worldwide. This is because the tumor microenvironment contains a key population of cells known as CSCs, which promote tumor aggression. CSCs are self-renewing cells that aid tumor recurrence by promoting tumor growth and persisting in patients after many traditional cancer treatments. According to reports, numerous transcription factors (TF) play a key role in maintaining CSC pluripotency and its self-renewal property. The understanding of the functions, structures, and interactional dynamics of these transcription factors with DNA has modified the hypothesis, paving the way for novel transcription factor-targeted therapies. These TFs, which are crucial and are required by cancer cells, play a vital function in the etiology of human cancer. Such CSC TFs will help with gene expression profiling, which provides crucial data for predicting the prognosis of patients. To overcome anti-cancer medication resistance and completely eradicate cancer, a potent therapy combining TFs-based CSC targets with traditional chemotherapy may be developed. In order to develop therapies that could eliminate CSCs, we here concentrated on the effect of TFs and other components of signalling pathways on cancer stemness.
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Affiliation(s)
- Archana Chaudhary
- Department of Biotechnology, School of Earth Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Rizwanul Haque
- Department of Biotechnology, School of Earth Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India.
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8
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Comparative role of SOX10 gene in the gliogenesis of central, peripheral, and enteric nervous systems. Differentiation 2022; 128:13-25. [DOI: 10.1016/j.diff.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/10/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022]
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9
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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10
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Wei H, Gu Q. SOX4 promotes high-glucose-induced inflammation and angiogenesis of retinal endothelial cells by activating NF-κB signaling pathway. Open Life Sci 2022; 17:393-400. [PMID: 35573654 PMCID: PMC9041534 DOI: 10.1515/biol-2022-0045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/26/2021] [Accepted: 01/03/2022] [Indexed: 11/25/2022] Open
Abstract
Diabetic retinopathy (DR) is a type of main microvascular complication of diabetes mellitus (DM) and an important factor that causes blindness in adults. SOX4 is a transcription factor expressed in the pancreas and is essential for normal endocrine pancreatic development. However, the effect and the regulatory mechanism of SOX4 on DR have not been reported. In the present study, upregulation of SOX4 was found in DM patients, particularly in DR patients and mice models. The in vitro experiments showed that SOX4 depletion increased the viability and inhibited the inflammation level of human retinal endothelial cells (HRCECs) induced by high glucose. Besides, SOX4 knockdown inhibited the migration and angiogenesis of HRCECs upon high glucose treatment. Mechanically, depletion of SOX4 inhibited the NF-κB pathway. Therefore, SOX4 could serve as a promising target for DR treatment.
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Affiliation(s)
- Haifeng Wei
- Department of Ophthalmology, Tongxiang First People’s Hospital , No. 1918 Jiaochang East Road , Jiaxing , Zhejiang Province, 314500 , China
| | - Quan Gu
- Department of Ophthalmology, Tongxiang First People’s Hospital , No. 1918 Jiaochang East Road , Jiaxing , Zhejiang Province, 314500 , China
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11
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Nan J, Hu X, Guo B, Xu M, Yao Y. Inhibition of endoplasmic reticulum stress alleviates triple-negative breast cancer cell viability, migration, and invasion by Syntenin/SOX4/Wnt/β-catenin pathway via regulation of heat shock protein A4. Bioengineered 2022; 13:10564-10577. [PMID: 35442158 PMCID: PMC9161907 DOI: 10.1080/21655979.2022.2062990] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Endoplasmic reticulum stress (ER stress) is a double-edged sword in the occurrence and development of malignant cancer. The aim of this study was to explore the roles of ER stress in metastasis and epithelial-mesenchymal transitionin triple-negative breast cancer (TNBC) and potential mechanisms. In this study, 4-PBA was administrated to inhibit the ER stress. Cell viability was evaluated using a cell counting kit-8 assay. Cell migration and invasion were identified by wound healing and transwell assay, respectively. Levels of MMP2 and MMP9 were measured by enzyme-linked immunosorbent assay and immunohistochemical staining. Western blot assay was used to assess the levels of ER stress-related proteins, Syndecan-1 (SDC-1)/Syntenin-1 (SDCBP-1)/SRY-related HMG-box 4 (SOX4) signaling and Wnt/β-catenin signaling. Moreover, a xenograft mice model was conducted to confirm the role of ER stress in TNBC. The data indicate that the ability of viability and metastasis of breast cancer cells were stronger than normal mammary epithelial cells. More aggressiveness was manifested in TNBC cells than that in non-TNBC cells. 4-PBA significantly suppressed the viability, migration, and invasion in BC cells and inhibited the SDC/SDCBP/SOX4 axis and Wnt/β-catenin signaling. Furthermore, heat shock protein A4 (HSPA4) overexpression stimulated ER stress and activated the SDC-1/SDCBP-1/SOX4 pathway and Wnt/β-catenin signaling. Animal experiments showed similar results that 4-PBA repressed tumor growth and inactivated the two pathways, while HSPA4 overexpression reversed the effects of 4-PBA. In summary, inhibition of ER stress inhibited TNBC viability, migration, and invasion by Syntenin/SOX4/Wnt/β-catenin pathway via regulation of HSPA4 in vivo and in vitro.
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Affiliation(s)
- Jinniang Nan
- School of Clinical Medicine, Nanchang Medical College, Jiangxi Province, Nanchang, P.R.China
| | - Xuguang Hu
- Department of Organ Transplantation, Jiangxi Provincial People's Hospital, Nanchang, Jiangxi Province, P.R.China
| | - Binbin Guo
- School of Clinical Medicine, Nanchang Medical College, Jiangxi Province, Nanchang, P.R.China
| | - Meiyun Xu
- School of Clinical Medicine, Nanchang Medical College, Jiangxi Province, Nanchang, P.R.China
| | - Yufeng Yao
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanchang, Jiangxi Province, P.R.China
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12
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Chaves-Moreira D, Mitchell MA, Arruza C, Rawat P, Sidoli S, Nameki R, Reddy J, Corona RI, Afeyan LK, Klein IA, Ma S, Winterhoff B, Konecny GE, Garcia BA, Brady DC, Lawrenson K, Morin PJ, Drapkin R. The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17. Sci Signal 2022; 15:eabm2496. [PMID: 35380877 DOI: 10.1126/scisignal.abm2496] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PAX8 is a master transcription factor that is essential during embryogenesis and promotes neoplastic growth. It is expressed by the secretory cells lining the female reproductive tract, and its deletion during development results in atresia of reproductive tract organs. Nearly all ovarian carcinomas express PAX8, and its knockdown results in apoptosis of ovarian cancer cells. To explore the role of PAX8 in these tissues, we purified the PAX8 protein complex from nonmalignant fallopian tube cells and high-grade serous ovarian carcinoma cell lines. We found that PAX8 was a member of a large chromatin remodeling complex and preferentially interacted with SOX17, another developmental transcription factor. Depleting either PAX8 or SOX17 from cancer cells altered the expression of factors involved in angiogenesis and functionally disrupted tubule and capillary formation in cell culture and mouse models. PAX8 and SOX17 in ovarian cancer cells promoted the secretion of angiogenic factors by suppressing the expression of SERPINE1, which encodes a proteinase inhibitor with antiangiogenic effects. The findings reveal a non-cell-autonomous function of these transcription factors in regulating angiogenesis in ovarian cancer.
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Affiliation(s)
- Daniele Chaves-Moreira
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Marilyn A Mitchell
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Cristina Arruza
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Priyanka Rawat
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, Suite 9-124, Philadelphia, PA 19104, USA
| | - Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica Reddy
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sisi Ma
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, Division of Gynecologic Oncology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gottfried E Konecny
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, Suite 9-124, Philadelphia, PA 19104, USA
| | - Donita C Brady
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 612, Philadelphia, PA 19104, USA.,Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 612, Philadelphia, PA 19104, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Patrice J Morin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Ronny Drapkin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
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13
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Dynamics of sexual development in teleosts with a note on Mugil cephalus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Pouremamali F, Vahedian V, Hassani N, Mirzaei S, Pouremamali A, Kazemzadeh H, Faridvand Y, Jafari-gharabaghlou D, Nouri M, Maroufi NF. The role of SOX family in cancer stem cell maintenance: With a focus on SOX2. Pathol Res Pract 2022; 231:153783. [DOI: 10.1016/j.prp.2022.153783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
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15
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Advance of SOX Transcription Factors in Hepatocellular Carcinoma: From Role, Tumor Immune Relevance to Targeted Therapy. Cancers (Basel) 2022; 14:cancers14051165. [PMID: 35267473 PMCID: PMC8909699 DOI: 10.3390/cancers14051165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is one of the deadliest human health burdens worldwide. However, the molecular mechanism of HCC development is still not fully understood. Sex determining region Y-related high-mobility group box (SOX) transcription factors not only play pivotal roles in cell fate decisions during development but also participate in the initiation and progression of cancer. Given the significance of SOX factors in cancer and their ‘undruggable’ properties, we summarize the role and molecular mechanism of SOX family members in HCC and the regulatory effect of SOX factors in the tumor immune microenvironment (TIME) of various cancers. For the first time, we analyze the association between the levels of SOX factors and that of immune components in HCC, providing clues to the pivotal role of SOX factors in the TIME of HCC. We also discuss the opportunities and challenges of targeting SOX factors for cancer. Abstract Sex determining region Y (SRY)-related high-mobility group (HMG) box (SOX) factors belong to an evolutionarily conserved family of transcription factors that play essential roles in cell fate decisions involving numerous developmental processes. In recent years, the significance of SOX factors in the initiation and progression of cancers has been gradually revealed, and they act as potential therapeutic targets for cancer. However, the research involving SOX factors is still preliminary, given that their effects in some leading-edge fields such as tumor immune microenvironment (TIME) remain obscure. More importantly, as a class of ‘undruggable’ molecules, targeting SOX factors still face considerable challenges in achieving clinical translation. Here, we mainly focus on the roles and regulatory mechanisms of SOX family members in hepatocellular carcinoma (HCC), one of the fatal human health burdens worldwide. We then detail the role of SOX members in remodeling TIME and analyze the association between SOX members and immune components in HCC for the first time. In addition, we emphasize several alternative strategies involved in the translational advances of SOX members in cancer. Finally, we discuss the alternative strategies of targeting SOX family for cancer and propose the opportunities and challenges they face based on the current accumulated studies and our understanding.
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Lin ZB, Li J, Ye L, Sun HS, Yu AY, Chen SH, Li FF. Novel SOX2 mutation in autosomal dominant cataract-microcornea syndrome. BMC Ophthalmol 2022; 22:70. [PMID: 35148715 PMCID: PMC8840263 DOI: 10.1186/s12886-022-02291-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 12/04/2022] Open
Abstract
Background Congenital cataract-microcornea syndrome (CCMC) is characterized by the association of congenital cataract and microcornea without any other systemic anomaly or dysmorphism. Although several causative genes have been reported in patients with CCMC, the genetic etiology of CCMC is yet to be clearly understood. Purpose To unravel the genetic cause of autosomal dominant family with CCMC. Methods All patients and available family members underwent a comprehensive ophthalmologic clinical examination in the hospital by expert ophthalmologists and carried out to clinically diagnosis. All the patients were screened by whole-exome sequencing and then validated using co-segregation by Sanger sequencing. Results Four CCMC patients from a Chinese family and five unaffected family members were enrolled in this study. Using whole-exome sequencing, a missense mutation c.295G > T (p.A99S, NM_003106.4) in the SOX2 gene was identified and validated by segregation analysis. In addition, this missense mutation was predicted to be damaging by multiple predictive tools. Variant p.Ala99Ser was located in a conservation high mobility group (HMG)-box domain in SOX2 protein, with a potential pathogenic impact of p.Ala99Ser on protein level. Conclusions A novel missense mutation (c.295G > T, p.Ala99Ser) in the SOX2 gene was found in this Han Chinese family with congenital cataract and microcornea. Our study determined that mutations in SOX2 were associated with CCMC, warranting further investigations on the pathogenesis of this disorder. This result expands the mutation spectrum of SOX2 and provides useful information to study the molecular pathogenesis of CCMC.
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Affiliation(s)
- Zhi-Bo Lin
- The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jin Li
- The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lu Ye
- Shanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated Guangren Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Hai-Sen Sun
- The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - A-Yong Yu
- The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shi-Hao Chen
- The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Fen-Fen Li
- The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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17
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Biallelic in-frame deletion of SOX4 is associated with developmental delay, hypotonia and intellectual disability. Eur J Hum Genet 2022; 30:243-247. [PMID: 34750527 PMCID: PMC8821644 DOI: 10.1038/s41431-021-00968-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) represents an extremely heterogeneous group of disorders, characterized by significant limitations in intellectual function and adaptive behavior. Among the monogenic causes, autosomal recessive genes (ARID) are responsible for more than 50% of ID. Here, we report a novel in-frame homozygous deletion variant [c.730_753del; p.(Ala244_Gly251del)] in SOX4 (sex-determining region Y-related high-mobility group box 4), segregating with moderate to severe ID, hypotonia, and developmental delay in a Pakistani family. Our identified variant p.(Ala244_Gly251del) is predicted to remove evolutionarily conserved residues from the interdomain region and may destabilize the protein secondary structure. SOX4 belongs to group C of the SOX transcription regulating family known to be involved in early embryo development. Single-cell RNA data analysis of developing telencephalon revealed highly overlapping expression of SOX4 with SOX11 and DCX, known neurogenesis regulators. Our study expands the mutational landscape of SOX4 and the repertoire of the known genetic causes of ARID.
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18
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Choi EB, Vodnala M, Zerbato M, Wang J, Ho JJ, Inouye C, Ding L, Fong YW. ATP-binding cassette protein ABCF1 couples transcription and genome surveillance in embryonic stem cells through low-complexity domain. SCIENCE ADVANCES 2021; 7:eabk2775. [PMID: 34714667 PMCID: PMC8555894 DOI: 10.1126/sciadv.abk2775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
OCT4 and SOX2 confer pluripotency by recruiting coactivators to activate stem cell–specific transcription. However, the composition of coactivator complexes and their roles in maintaining stem cell fidelity remain unclear. Here, we report the ATP-binding cassette subfamily F member 1 (ABCF1) as a coactivator for OCT4/SOX2 critical for stem cell self-renewal. The intrinsically disordered low-complexity domain (LCD) of ABCF1 contributes to phase separation in vitro and transcriptional activation of pluripotency genes by mediating multivalent interactions with SOX2 and co-dependent coactivators XPC and DKC1. These LCD-driven transcription factor–coactivator interactions critical for pluripotency gene expression are disrupted by DNA damage, likely due to LCD-dependent binding of ABCF1 to damage-generated intracellular DNA fragments instead of SOX2. This study identifies a transcriptional coactivator that uses its LCD to form selective multivalent interactions to regulate stem cell self-renewal and exit from pluripotency when genome integrity is compromised.
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Affiliation(s)
- Eun-Bee Choi
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Munender Vodnala
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Madeleine Zerbato
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jianing Wang
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jaclyn J. Ho
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Lai Ding
- Department of Neurology, Program for Interdisciplinary Neuroscience, Brigham and Women’s Hospital, Boston, MA, USA
| | - Yick W. Fong
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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Epigenetic Silencing of SOX15 Is Controlled by miRNAs rather than Methylation in Papillary Thyroid Cancer. DISEASE MARKERS 2021; 2021:1588220. [PMID: 34603557 PMCID: PMC8486500 DOI: 10.1155/2021/1588220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/11/2021] [Accepted: 09/11/2021] [Indexed: 11/17/2022]
Abstract
Methods In this study, qRT-PCR was used to investigate the expression levels of the SOX15 gene and of miR-182, miR-183, miR-375, and miR-96 in thyroid tumors and adjacent noncancerous tissues. We also investigated the methylation status of the SOX15 promoter by methylation-specific PCR in tumors and adjacent noncancerous tissues. Results We observed a statistically significant downregulation of SOX15 expression in tumors compared to noncancerous tissue samples. The methylation levels of tumors and matched noncancerous tissues were similar, but miR-182, miR-183, and miR-375 expression levels were elevated in tumor tissues compared to noncancerous tissue samples. Conclusions Our results indicate that SOX15 gene expression is associated with the pathogenesis of papillary thyroid carcinoma (PTC), and the epigenetic control of the SOX15 gene is regulated by miRNAs rather than by promoter methylation.
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Design and Characterization of a Cell-Penetrating Peptide Derived from the SOX2 Transcription Factor. Int J Mol Sci 2021; 22:ijms22179354. [PMID: 34502261 PMCID: PMC8431565 DOI: 10.3390/ijms22179354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022] Open
Abstract
SOX2 is an oncogenic transcription factor overexpressed in nearly half of the basal-like triple-negative breast cancers associated with very poor outcomes. Targeting and inhibiting SOX2 is clinically relevant as high SOX2 mRNA levels are positively correlated with decreased overall survival and progression-free survival in patients affected with breast cancer. Given its key role as a master regulator of cell proliferation, SOX2 represents an important scaffold for the engineering of dominant-negative synthetic DNA-binding domains (DBDs) that act by blocking or interfering with the oncogenic activity of the endogenous transcription factor in cancer cells. We have synthesized an interference peptide (iPep) encompassing a truncated 24 amino acid long C-terminus of SOX2 containing a potential SOX-specific nuclear localization sequence, and the determinants of the binding of SOX2 to the DNA and to its transcription factor binding partners. We found that the resulting peptide (SOX2-iPep) possessed intrinsic cell penetration and promising nuclear localization into breast cancer cells, and decreased cellular proliferation of SOX2 overexpressing cell lines. The novel SOX2-iPep was found to exhibit a random coil conformation predominantly in solution. Molecular dynamics simulations were used to characterize the interactions of both the SOX2 transcription factor and the SOX2-iPep with FGF4-enhancer DNA in the presence of the POU domain of the partner transcription factor OCT4. Predictions of the free energy of binding revealed that the iPep largely retained the binding affinity for DNA of parental SOX2. This work will enable the future engineering of novel dominant interference peptides to transport different therapeutic cargo molecules such as anti-cancer drugs into cells.
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Circular RNA Pleiotrophin promotes carcinogenesis in glioma via regulation of microRNA-122/SRY-box transcription factor 6 axis. Eur J Cancer Prev 2021; 29:165-173. [PMID: 31609809 DOI: 10.1097/cej.0000000000000535] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) are recently identified as gene regulators in mammals and play important roles in carcinogenesis of cancer. For example, circRNA_PTN has been recognized as a biomarker of human cancer and is overexpressed in glioma. The molecular function of circRNA_PTN and its downstream targets in glioma, however, remains elusive. METHODS Quantitative polymerase chain reaction analysis was used to measure the expression of circular RNA pleiotrophin (circ_PTN) and miR-122. 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, propidium iodide and Annexin-V/propidium iodide assay were performed to determine cell proliferation and apoptosis of glioma cells. Circular RNA Interactome and TargetScan were used to predict the potential microRNA targeting of circ_PTN and the potential targets of miR-122, respectively. Luciferase activity assay was used to validate these interactions. Downstream molecular mechanisms, including SRY-box transcription factor 6 (SOX6), extracellular regulated protein kinases (ERK), Cyclin D1, B-cell lymphoma-2 (BCL-2) and BCL2 associated X, apoptosis regulator (BAX), were determined by western blot. RESULTS Circ_PTN was overexpressed in glioma cells, and its knockdown induced cell proliferation inhibition, cell cycle arrest and apoptosis in glioma cells. The target microRNA of circ_PTN was predicted to be miR-122, the expression of which was negatively correlated with circ_PTN in glioma cells. Moreover, SOX6 was predicted as a potential target of miR-122, and miR-122 overexpression decreased SOX6 expression. MiR-122 inhibitor reversed the tumor-suppressing effects of circ_PTN knockdown, while overexpression of SOX6 impaired the miR-122 overexpression-induced cell growth inhibition and apoptosis. In addition, mitogen activated kinase-like protein (MAPK)/ERK pathway was involved in circ_PTN/miR-122/SOX6 axis. CONCLUSIONS Circ_PTN acted as a sponge of miR-122 and upregulated miR-122 target SOX6, thus promoting carcinogenesis of glioma cells.
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Schmidt H, Putnam A, Rasoloson D, Seydoux G. Protein-based condensation mechanisms drive the assembly of RNA-rich P granules. eLife 2021; 10:63698. [PMID: 34106046 PMCID: PMC8238508 DOI: 10.7554/elife.63698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Germ granules are protein-RNA condensates that segregate with the embryonic germline. In Caenorhabditis elegans embryos, germ (P) granule assembly requires MEG-3, an intrinsically disordered protein that forms RNA-rich condensates on the surface of PGL condensates at the core of P granules. MEG-3 is related to the GCNA family and contains an N-terminal disordered region (IDR) and a predicted ordered C-terminus featuring an HMG-like motif (HMGL). We find that MEG-3 is a modular protein that uses its IDR to bind RNA and its C-terminus to drive condensation. The HMGL motif mediates binding to PGL-3 and is required for co-assembly of MEG-3 and PGL-3 condensates in vivo. Mutations in HMGL cause MEG-3 and PGL-3 to form separate condensates that no longer co-segregate to the germline or recruit RNA. Our findings highlight the importance of protein-based condensation mechanisms and condensate-condensate interactions in the assembly of RNA-rich germ granules.
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Affiliation(s)
- Helen Schmidt
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Andrea Putnam
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Dominique Rasoloson
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
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Structures of chromatin modulators in complex with nucleosome. Curr Opin Chem Biol 2021; 63:105-114. [PMID: 33823458 DOI: 10.1016/j.cbpa.2021.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/17/2022]
Abstract
The chromatin structure is dynamically regulated by many different modulators that post-translationally modify histones, replace canonical histones with histone variants, and unwind nucleosomal DNA, thereby modulating the accessibility of nucleosomal DNA and facilitating downstream DNA-templated nuclear processes. To understand how these modulators change the chromatin structure, it is essential to determine the 3D structures of chromatin modulators in complex with nucleosome. Here, we review the very recent progress in structural studies of some selected chromatin modulators in complex with nucleosome, including those of histone demethylases LSD1/2, some pioneer transcription factors, and the PWWP domain-containing protein LEDGF.
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25
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Shan B, Liu Y, Yang C, Zhao Y, Sun D. Comparative transcriptomic analysis for identification of candidate sex-related genes and pathways in Crimson seabream (Parargyrops edita). Sci Rep 2021; 11:1077. [PMID: 33441831 PMCID: PMC7806868 DOI: 10.1038/s41598-020-80282-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Teleost fishes display the largest array of sex-determining systems among animals, resulting in various reproductive strategies. Research on sex-related genes in teleosts will broaden our understanding of the process, and provide important insight into the plasticity of the sex determination process in vertebrates in general. Crimson seabream (Parargyrops edita Tanaka, 1916) is one of the most valuable and abundant fish resources throughout Asia. However, little genomic information on P. edita is available. In the present study, the transcriptomes of male and female P. edita were sequenced with RNA-seq technology. A total of 388,683,472 reads were generated from the libraries. After filtering and assembling, a total of 79,775 non redundant unigenes were obtained with an N50 of 2,921 bp. The unigenes were annotated with multiple public databases, including NT (53,556, 67.13%), NR (54,092, 67.81%), Swiss-Prot (45,265, 56.74%), KOG (41,274, 51.74%), KEGG (46,302, 58.04%), and GO (11,056, 13.86%) databases. Comparison of the unigenes of different sexes of P. edita revealed that 11,676 unigenes (9,335 in females, 2,341 in males) were differentially expressed between males and females. Of these, 5,463 were specifically expressed in females, and 1,134 were specifically expressed in males. In addition, the expression levels of ten unigenes were confirmed to validate the transcriptomic data by qRT-PCR. Moreover, 34,473 simple sequence repeats (SSRs) were identified in SSR-containing sequences, and 50 loci were randomly selected for primer development. Of these, 36 loci were successfully amplified, and 19 loci were polymorphic. Finally, our comparative analysis identified many sex-related genes (zps, amh, gsdf, sox4, cyp19a, etc.) and pathways (MAPK signaling pathway, p53 signaling pathway, etc.) of P. edita. This informative transcriptomic analysis provides valuable data to increase genomic resources of P. edita. The results will be useful for clarifying the molecular mechanism of sex determination and for future functional analyses of sex-associated genes.
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Affiliation(s)
- Binbin Shan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Yan Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Changping Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Yu Zhao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Dianrong Sun
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China.
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.
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Anani M, Nobuhisa I, Taga T. Sry-related High Mobility Group Box 17 Functions as a Tumor Suppressor by Antagonizing the Wingless-related Integration Site Pathway. J Cancer Prev 2020; 25:204-212. [PMID: 33409253 PMCID: PMC7783240 DOI: 10.15430/jcp.2020.25.4.204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 11/16/2022] Open
Abstract
A transcription factor Sry-related high mobility group box (Sox) 17 is involved in developmental processes including spermatogenesis, cardiovascular system, endoderm formation, and so on. In this article, we firstly review the studies on the relation between the Sox17 expression and tumor malignancy. Although Sox17 positively promotes various tissue development, most of the cancers associated with Sox17 show decreased expression levels of Sox17, and an inverse correlation between Sox17 expression and malignancy is revealed. We briefly discuss the mechanism of such Sox17 down-regulation by focusing on DNA methylation of CpG sites located in the Sox17 gene promoter. Next, we overview the function of Sox17 in the fetal hematopoiesis, particularly in the dorsal aorta in midgestation mouse embryos. The Sox17 expression in hematopoietic stem cell (HSC)-containing intra-aortic hematopoietic cell cluster (IAHCs) is important for the cluster formation with the hematopoietic ability. The sustained expression of Sox17 in adult bone marrow HSCs and the cells in IAHCs of the dorsal aorta indicate abnormalities that are low lymphocyte chimerism and the aberrant proliferation of common myeloid progenitors in transplantation experiments. We then summarize the perspectives of Sox17 research in cancer control.
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Affiliation(s)
- Maha Anani
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Ikuo Nobuhisa
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tetsuya Taga
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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27
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Tan DS, Holzner M, Weng M, Srivastava Y, Jauch R. SOX17 in cellular reprogramming and cancer. Semin Cancer Biol 2020; 67:65-73. [DOI: 10.1016/j.semcancer.2019.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/19/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
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28
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McAninch D, Thomson EP, Thomas PQ. Genome-wide DNA-binding profile of SRY-box transcription factor 3 (SOX3) in mouse testes. Reprod Fertil Dev 2020; 32:1260-1270. [PMID: 33166488 DOI: 10.1071/rd20108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
Spermatogenesis is the male version of gametogenesis, where germ cells are transformed into haploid spermatozoa through a tightly controlled series of mitosis, meiosis and differentiation. This process is reliant on precisely timed changes in gene expression controlled by several different hormonal and transcriptional mechanisms. One important transcription factor is SRY-box transcription factor 3 (SOX3), which is transiently expressed within the uncommitted spermatogonial stem cell population. Sox3-null mouse testes exhibit a block in spermatogenesis, leading to infertility or subfertility. However, the molecular role of SOX3 during spermatogonial differentiation remains poorly understood because the genomic regions targeted by this transcription factor have not been identified. In this study we used chromatin immunoprecipitation sequencing to identify and characterise the endogenous genome-wide binding profile of SOX3 in mouse testes at Postnatal Day 7. We show that neurogenin3 (Neurog3 or Ngn3) is directly targeted by SOX3 in spermatogonial stem cells via a novel testes-specific binding site. We also implicate SOX3, for the first time, in direct regulation of histone gene expression and demonstrate that this function is shared by both neural progenitors and testes, and with another important transcription factor required for spermatogenesis, namely promyelocytic leukaemia zinc-finger (PLZF). Together, these data provide new insights into the function of SOX3 in different stem cell contexts.
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Affiliation(s)
- Dale McAninch
- School of Biological Sciences and Robinson Research Institute, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Ella P Thomson
- School of Biological Sciences and Robinson Research Institute, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Paul Q Thomas
- School of Biological Sciences and Robinson Research Institute, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia; and Adelaide Medical School, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia; and Precision Medicine Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; and Corresponding author.
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29
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Feng M, Fang F, Fang T, Jiao H, You S, Wang X, Zhao W. Sox13 promotes hepatocellular carcinoma metastasis by transcriptionally activating Twist1. J Transl Med 2020; 100:1400-1410. [PMID: 32461589 DOI: 10.1038/s41374-020-0445-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
SRY (sex-determining region Y)-box 13 (Sox13), a member of group D of the SRY-related high mobility group (HMG) box (Sox) family, is a critical regulator of embryonic development and cartilage formation. Few studies have investigated the role of Sox13 in tumorigenesis. The present study reveals the clinical significance and biological function of Sox13 in hepatocellular carcinoma (HCC). First, the expression of Sox13 in HCC samples was evaluated by qRT-PCR and western blotting, and its association with clinicopathological features and prognosis was determined. We found that Sox13 expression was higher in tumor tissue than in paired nontumor tissue. The upregulation of Sox13 was associated with poor differentiation, metastasis, recurrence and poor overall, and tumor-free survival of HCC patients. The function of Sox13 on HCC cell migration and invasion was then assessed by Transwell assay, and the results demonstrated that Sox13 promoted HCC cell invasion, migration, and epithelial-to-mesenchymal transition (EMT). Notably, the invasion, migration, and EMT of HCC cells induced by Sox13 overexpression could be abolished by Twist1 depletion, and Sox13 was positively correlated with Twist1 at both the mRNA and protein levels. Mechanistically, we revealed that Sox13 activated Twist1 transcription and consequently upregulated Twist1 expression. Furthermore, Sox13 formed a heterodimer with Sox5, and this heterodimer functionally cooperated to enhance the transcriptional activity of Twist1. Our findings suggest that Sox13 serves as an oncogene in HCC, and might be a novel prognostic and therapeutic candidate.
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Affiliation(s)
- Min Feng
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China
| | - Fei Fang
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China
| | - Ting Fang
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China
| | - Hui Jiao
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China
| | - Song You
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China
| | - Xiaomin Wang
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China.
| | - Wenxiu Zhao
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhongshan Hospital, Xiamen University, Building 6, No. 209, South Hubin Road, 361004, Xiamen, China.
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30
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Yang H, Geng YH, Wang P, Yang H, Zhou YT, Zhang HQ, He HY, Fang WG, Tian XX. Extracellular ATP promotes breast cancer invasion and chemoresistance via SOX9 signaling. Oncogene 2020; 39:5795-5810. [PMID: 32724162 DOI: 10.1038/s41388-020-01402-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/09/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
Our previous research demonstrated that extracellular adenosine 5'-triphosphate (ATP) could promote breast cancer cell invasion. However, the impact of extracellular ATP on chemoresistance and the mechanisms behind ATP pro-invasion and pro-chemoresistance remain unclear. Here we aimed to determine the molecules or signaling pathways involved. cDNA microarray was performed to identify the differentially expressed genes before and after ATP treatment. As a result, Sex-determining region Y-box 9 (SOX9) was up-regulated after ATP treatment in breast cancer cells. In vitro invasion and migration assays demonstrated that knocking down SOX9 attenuated ATP-driven invasive capability. Mass spectrometry and co-IP revealed that SOX9 interacted with Janus kinase 1 (JAK1). Afterward, IL-6-JAK1-STAT3 signaling was demonstrated to promote SOX9 expression and invasion following ATP treatment. Notably, ATP-IL-6-SOX9 signaling was shown to stimulate chemoresistance in breast cancer cells. ChIP assays identified some potential SOX9 target genes, among which carcinoembryonic antigen-related cell adhesion molecule 5/6 (CEACAM5/6) was demonstrated to mediate ATP pro-invasive function, while ATP-binding cassette subfamily B member 1 (ABCB1) and ATP-binding cassette subfamily G member 2 (ABCG2) mediated ATP-driven chemoresistance. In addition, SOX9-knockdown and apyrase (an ATP hydrolase)-treated MDA-MB-231 cells illustrated decreased tumor growth and enhanced drug sensitivity in nude mice. In vitro spheroid formation assays also proved the significance of ATP-SOX9 in mediating chemoresistance. Moreover, molecules involved in ATP-SOX9 signaling were up-regulated in human breast carcinoma specimens and were associated with poor prognosis. Altogether, SOX9 signaling is vital in ATP-driven invasion and chemoresistance, which may serve as a potential target for breast cancer therapies.
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Affiliation(s)
- Hui Yang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China
| | - Yue-Hang Geng
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China
| | - Peng Wang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Han Yang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China
| | - Yan-Ting Zhou
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China
| | - Hong-Quan Zhang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Hui-Ying He
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China
| | - Wei-Gang Fang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China.
| | - Xin-Xia Tian
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing 100191, China.
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31
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Schaefer T, Lengerke C. SOX2 protein biochemistry in stemness, reprogramming, and cancer: the PI3K/AKT/SOX2 axis and beyond. Oncogene 2020; 39:278-292. [PMID: 31477842 PMCID: PMC6949191 DOI: 10.1038/s41388-019-0997-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/20/2019] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
Research of the past view years expanded our understanding of the various physiological functions the cell-fate determining transcription factor SOX2 exerts in ontogenesis, reprogramming, and cancer. However, while scientific reports featuring novel and exciting aspects of SOX2-driven biology are published in near weekly routine, investigations in the underlying protein-biochemical processes that transiently tailor SOX2 activity to situational demand are underrepresented and have not yet been comprehensively summarized. Largely unrecognizable to modern array or sequencing-based technology, various protein secondary modifications and concomitant function modulations have been reported for SOX2. The chemical modifications imposed onto SOX2 are inherently heterogeneous, comprising singular or clustered events of phosphorylation, methylation, acetylation, ubiquitination, SUMOylation, PARPylation, and O-glycosylation that reciprocally affect each other and critically impact SOX2 functionality, often in a tissue and species-specific manner. One recurring regulatory principle though is the canonical PI3K/AKT signaling axis to which SOX2 relates in various entangled, albeit not exclusive ways. Here we provide a comprehensive review of the current knowledge on SOX2 protein modifications, their proposed relationship to the PI3K/AKT pathway, and regulatory influence on SOX2 with regards to stemness, reprogramming, and cancer.
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Affiliation(s)
- Thorsten Schaefer
- University of Basel and University Hospital Basel, Department of Biomedicine, Basel, Switzerland.
| | - Claudia Lengerke
- University of Basel and University Hospital Basel, Department of Biomedicine, Basel, Switzerland
- University Hospital Basel, Division of Hematology, Basel, Switzerland
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32
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Sun Y, Lei B, Huang Q. SOX18 Affects Cell Viability, Migration, Invasiveness, and Apoptosis in Hepatocellular Carcinoma (HCC) Cells by Participating in Epithelial-to-Mesenchymal Transition (EMT) Progression and Adenosine Monophosphate Activated Protein Kinase (AMPK)/Mammalian Target of Rapamycin (mTOR). Med Sci Monit 2019; 25:6244-6254. [PMID: 31427562 PMCID: PMC6713035 DOI: 10.12659/msm.915729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignancies around the world. It has been verified that the expression of SOX18 is correlated to poor clinical prognosis in patients with ovarian cancer, non-small cell lung cancer, or breast invasive ductal carcinoma. However, the expression pattern and biological function of SOX18 in HCC tissues remains unclear. In this study, we set out to investigate the associated biological function and potential molecular mechanism of the SOX18 gene in HCC cells. Material/Methods The mRNA and protein expression levels of experimental related genes were detected by real-time polymerase chain reaction and western blotting assay, respectively. The MTT method was used to assess cell viability, and cell apoptosis analysis was performed by means of FACScan flow cytometry. Wound-healing assay and Transwell analysis were performed to evaluate the ability of cell migration and invasiveness, respectively. Results SOX18 was highly expressed in various HCC cell lines. In addition, SOX18 promoted cell viability, migration, and invasion and simultaneously induce cell apoptosis. SOX18 promoted epithelial-to-mesenchymal transition (EMT) progression, and SOX18 downregulation activated the autophagy signaling pathway AMPK/mTOR in HCC cells. Conclusions SOX18 downregulation in HCC cells suppressed cell viability and metastasis, induced cell apoptosis and hindered the occurrence and progression of tumor cells by participating in the EMT process and regulating the autophagy signaling pathway AMPK/mTOR.
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Affiliation(s)
- Yanni Sun
- Department of Hepatology, Yantai City Hospital for Infectious Diseases, Yantai, Shandong, China (mainland)
| | - Bo Lei
- Department of Hepatology, Yantai City Hospital for Infectious Diseases, Yantai, Shandong, China (mainland)
| | - Qingxian Huang
- Department of Hepatobiliary Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China (mainland)
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33
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Shibayama H, Yamamoto T, Oshima K, Matsuda T, Nadano D. Transcription Factor Sox4 as a Potential Player in Mammary Gland Involution. DNA Cell Biol 2019; 38:1125-1133. [PMID: 31408364 DOI: 10.1089/dna.2019.4700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mammary gland involution is a regressive process for the gland to return to its prepregnancy state after lactation and comprises an initial reversible and second remodeling stage. Although many genes and the multiple expression profiles of their mRNAs have been found in this process, the mechanisms controlling the profiles are largely unknown. In this study, we identified and analyzed transcription factor Sox4 in mammary gland involution. Elevated expression of Sox4 gene in the first stage (48 h after weaning) was observed at the mRNA and protein levels in the mouse mammary gland. Immunohistochemistry of the involuting gland indicated that Sox4 was located in the nuclei of epithelial cells. Nuclear Sox4 was also detected in the second stage, but unlikely to be involved in cell death, one of the characteristic events of involution. To clarify the functional roles of Sox4 in involution, we introduced a model, including a normal mammary epithelial cell line, for finding candidate target genes of this transcription factor and examined its effect on tenascin C mRNA expression.
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Affiliation(s)
- Hirohisa Shibayama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomomi Yamamoto
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzi Oshima
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tsukasa Matsuda
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Daita Nadano
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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34
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Moustaqil M, Fontaine F, Overman J, McCann A, Bailey TL, Rudolffi Soto P, Bhumkar A, Giles N, Hunter DJB, Gambin Y, Francois M, Sierecki E. Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor. Nucleic Acids Res 2019; 46:11381-11395. [PMID: 30335167 PMCID: PMC6265484 DOI: 10.1093/nar/gky897] [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: 02/08/2018] [Accepted: 09/26/2018] [Indexed: 01/24/2023] Open
Abstract
During embryogenesis, vascular development relies on a handful of transcription factors that instruct cell fate in a distinct sub-population of the endothelium (1). The SOXF proteins that comprise SOX7, 17 and 18, are molecular switches modulating arterio-venous and lymphatic endothelial differentiation (2,3). Here, we show that, in the SOX-F family, only SOX18 has the ability to switch between a monomeric and a dimeric form. We characterized the SOX18 dimer in binding assays in vitro, and using a split-GFP reporter assay in a zebrafish model system in vivo. We show that SOX18 dimerization is driven by a novel motif located in the vicinity of the C-terminus of the DNA binding region. Insertion of this motif in a SOX7 monomer forced its assembly into a dimer. Genome-wide analysis of SOX18 binding locations on the chromatin revealed enrichment for a SOX dimer binding motif, correlating with genes with a strong endothelial signature. Using a SOX18 small molecule inhibitor that disrupts dimerization, we revealed that dimerization is important for transcription. Overall, we show that dimerization is a specific feature of SOX18 that enables the recruitment of key endothelial transcription factors, and refines the selectivity of the binding to discrete genomic locations assigned to endothelial specific genes.
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Affiliation(s)
- Mehdi Moustaqil
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeroen Overman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alex McCann
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy L Bailey
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Paulina Rudolffi Soto
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Akshay Bhumkar
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Nichole Giles
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Dominic J B Hunter
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yann Gambin
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Mathias Francois
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Emma Sierecki
- EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia
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35
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Vervoort SJ, de Jong OG, Roukens MG, Frederiks CL, Vermeulen JF, Lourenço AR, Bella L, Vidakovic AT, Sandoval JL, Moelans C, van Amersfoort M, Dallman MJ, Bruna A, Caldas C, Nieuwenhuis E, van der Wall E, Derksen P, van Diest P, Verhaar MC, Lam EWF, Mokry M, Coffer PJ. Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesis. eLife 2018; 7:e27706. [PMID: 30507376 PMCID: PMC6277201 DOI: 10.7554/elife.27706] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/07/2018] [Indexed: 12/30/2022] Open
Abstract
The expression of the transcription factor SOX4 is increased in many human cancers, however, the pro-oncogenic capacity of SOX4 can vary greatly depending on the type of tumor. Both the contextual nature and the mechanisms underlying the pro-oncogenic SOX4 response remain unexplored. Here, we demonstrate that in mammary tumorigenesis, the SOX4 transcriptional network is dictated by the epigenome and is enriched for pro-angiogenic processes. We show that SOX4 directly regulates endothelin-1 (ET-1) expression and can thereby promote tumor-induced angiogenesis both in vitro and in vivo. Furthermore, in breast tumors, SOX4 expression correlates with blood vessel density and size, and predicts poor-prognosis in patients with breast cancer. Our data provide novel mechanistic insights into context-dependent SOX4 target gene selection, and uncover a novel pro-oncogenic role for this transcription factor in promoting tumor-induced angiogenesis. These findings establish a key role for SOX4 in promoting metastasis through exploiting diverse pro-tumorigenic pathways.
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Affiliation(s)
- Stephin J Vervoort
- Department of Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Olivier G de Jong
- Department of Nephrology and HypertensionUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - M Guy Roukens
- Department of Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Cynthia L Frederiks
- Department of Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Jeroen F Vermeulen
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Ana Rita Lourenço
- Department of Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Laura Bella
- Department of Surgery and CancerImperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | | | - José L Sandoval
- Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Cathy Moelans
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Margaret J Dallman
- Department of Life Sciences, Division of Cell and Molecular BiologyImperial College LondonLondonUnited Kingdom
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Edward Nieuwenhuis
- Division of Pediatrics, Wilhelmina Children’s HospitalUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Patrick Derksen
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Paul van Diest
- Department of PathologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Marianne C Verhaar
- Department of Nephrology and HypertensionUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Eric W-F Lam
- Department of Surgery and CancerImperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Michal Mokry
- Division of Pediatrics, Wilhelmina Children’s HospitalUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Paul J Coffer
- Department of Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
- Division of Pediatrics, Wilhelmina Children’s HospitalUniversity Medical Center UtrechtUtrechtThe Netherlands
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36
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Wang X, Li X, Wang T, Wu SP, Jeong JW, Kim TH, Young SL, Lessey BA, Lanz RB, Lydon JP, DeMayo FJ. SOX17 regulates uterine epithelial-stromal cross-talk acting via a distal enhancer upstream of Ihh. Nat Commun 2018; 9:4421. [PMID: 30356064 PMCID: PMC6200785 DOI: 10.1038/s41467-018-06652-w] [Citation(s) in RCA: 53] [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: 03/06/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023] Open
Abstract
Mammalian pregnancy depends on the ability of the uterus to support embryo implantation. Previous studies reveal the Sox17 gene as a downstream target of the Pgr-Gata2-dependent transcription network that directs genomic actions in the uterine endometrium receptive for embryo implantation. Here, we report that ablating Sox17 in the uterine epithelium impairs leukemia inhibitory factor (LIF) and Indian hedgehog homolog (IHH) signaling, leading to failure of embryo implantation. In vivo deletion of the SOX17-binding region 19 kb upstream of the Ihh locus by CRISPR-Cas technology reduces Ihh expression specifically in the uterus and alters proper endometrial epithelial-stromal interactions, thereby impairing pregnancy. This SOX17-binding interval is also bound by GATA2, FOXA2, and PGR. This cluster of transcription factor binding is common in 737 uterine genes and may represent a key regulatory element essential for uterine epithelial gene expression.
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Affiliation(s)
- Xiaoqiu Wang
- Reproductive and Development Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Xilong Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - San-Pin Wu
- Reproductive and Development Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jae-Wook Jeong
- Department of Obstetrics and Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, USA
| | - Tae Hoon Kim
- Department of Obstetrics and Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, USA
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce A Lessey
- Deptartment of Obstetrics and Gynecology, University of South Carolina School of Medicine, Greenville, SC, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - John P Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Francesco J DeMayo
- Reproductive and Development Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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Vervoort SJ, Lourenço A, Tufegdzic Vidakovic A, Mocholi E, Sandoval J, Rueda OM, Frederiks C, Pals C, Peeters JGC, Caldas C, Bruna A, Coffer PJ. SOX4 can redirect TGF-β-mediated SMAD3-transcriptional output in a context-dependent manner to promote tumorigenesis. Nucleic Acids Res 2018; 46:9578-9590. [PMID: 30137431 PMCID: PMC6182182 DOI: 10.1093/nar/gky755] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 07/26/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
Expression of the transcription factor SOX4 is often elevated in human cancers, where it generally correlates with tumor-progression and poor-disease outcome. Reduction of SOX4 expression results in both diminished tumor-incidence and metastasis. In breast cancer, TGF-β-mediated induction of SOX4 has been shown to contribute to epithelial-to-mesenchymal transition (EMT), which controls pro-metastatic events. Here, we identify SMAD3 as a novel, functionally relevant SOX4 interaction partner. Genome-wide analysis showed that SOX4 and SMAD3 co-occupy a large number of genomic loci in a cell-type specific manner. Moreover, SOX4 expression was required for TGF-β-mediated induction of a subset of SMAD3/SOX4-co-bound genes regulating migration and extracellular matrix-associated processes, and correlating with poor-prognosis. These findings identify SOX4 as an important SMAD3 co-factor controlling transcription of pro-metastatic genes and context-dependent shaping of the cellular response to TGF-β. Targeted disruption of the interaction between these factors may have the potential to disrupt pro-oncogenic TGF-β signaling, thereby impairing tumorigenesis.
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Affiliation(s)
- Stephin J Vervoort
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht Uppsalalaan 6, Utrecht, The Netherlands
| | - Ana Rita Lourenço
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht Uppsalalaan 6, Utrecht, The Netherlands
| | | | - Enric Mocholi
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht Uppsalalaan 6, Utrecht, The Netherlands
| | - José L Sandoval
- Cancer Research UK Cambridge Institute, and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Cynthia Frederiks
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht Uppsalalaan 6, Utrecht, The Netherlands
| | - Cornelieke Pals
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht Uppsalalaan 6, Utrecht, The Netherlands
| | - Janneke G C Peeters
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, 3508 AB Utrecht, The Netherlands
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3484 EA Utrecht, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
- Cancer Research UK Cancer Centre, Cambridge Biomedical Campus, Cambridge CB2 2QQ, UK
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Paul J Coffer
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht Uppsalalaan 6, Utrecht, The Netherlands
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3484 EA Utrecht, The Netherlands
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A role for SOX9 in post-transcriptional processes: insights from the amphibian oocyte. Sci Rep 2018; 8:7191. [PMID: 29740094 PMCID: PMC5940923 DOI: 10.1038/s41598-018-25356-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Sox9 is a member of the gene family of SOX transcription factors, which is highly conserved among vertebrates. It is involved in different developmental processes including gonadogenesis. In all amniote species examined thus far, Sox9 is expressed in the Sertoli cells of the male gonad, suggesting an evolutionarily conserved role in testis development. However, in the anamniotes, fishes and amphibians, it is also expressed in the oocyte but the significance of such an expression remains to be elucidated. Here, we have investigated the nuclear localization of the SOX9 protein in the oocyte of three amphibian species, the urodelan Pleurodeles waltl, and two anurans, Xenopus laevis and Xenopus tropicalis. We demonstrate that SOX9 is associated with ribonucleoprotein (RNP) transcripts of lampbrush chromosomes in an RNA-dependent manner. This association can be visualized by Super-resolution Structured Illumination Microscopy (SIM). Our results suggest that SOX9, known to bind DNA, also carries an additional function in the posttranscriptional processes. We also discuss the significance of the acquisition or loss of Sox9 expression in the oocyte during evolution at the transition between anamniotes and amniotes.
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39
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Malik V, Zimmer D, Jauch R. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming. Cell Mol Life Sci 2018; 75:1587-1612. [PMID: 29335749 PMCID: PMC11105716 DOI: 10.1007/s00018-018-2748-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite 'two-in-one' DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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40
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Mistri TK, Arindrarto W, Ng WP, Wang C, Lim LH, Sun L, Chambers I, Wohland T, Robson P. Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision through Fgf4/ Fgfr2 signaling in preimplantation mouse embryos. Biochem J 2018; 475:1075-1089. [PMID: 29487166 PMCID: PMC5896025 DOI: 10.1042/bcj20170418] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/22/2022]
Abstract
Oct4 and Sox2 regulate the expression of target genes such as Nanog, Fgf4, and Utf1, by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerize on adjacent cis regulatory motifs, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In the present study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy. We found that the synergistic binding interaction is driven mainly by the level of Sox2 in the case of the Fgf4 Sox/Oct motif. Taking into account Sox2 expression levels fluctuate more than Oct4, our finding provides an explanation on how Sox2 controls the segregation of the epiblast and primitive endoderm populations within the inner cell mass of the developing rodent blastocyst.
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Affiliation(s)
- Tapan Kumar Mistri
- School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
- Department of Chemistry, National University of Singapore, Singapore
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, U.K
| | - Wibowo Arindrarto
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Wei Ping Ng
- Department of Chemistry, National University of Singapore, Singapore
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Choayang Wang
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Leng Hiong Lim
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Lili Sun
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, U.K.
| | - Thorsten Wohland
- Department of Chemistry, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore
| | - Paul Robson
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, U.S.A
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41
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Pugongchai A, Bychkov A, Sampatanukul P. Promoter hypermethylation of SOX11 correlates with adverse clinicopathological features of human prostate cancer. Int J Exp Pathol 2017; 98:341-346. [PMID: 29315911 PMCID: PMC5826943 DOI: 10.1111/iep.12257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/04/2017] [Indexed: 12/16/2022] Open
Abstract
Currently available tools for early diagnosis and prognosis of prostate cancer lack sufficient accuracy. There is a need to identify novel biomarkers for this common malignancy. SOX family genes play an important role in embryogenesis and are also implicated in various cancers. SOX11 has been recently recognized as a potential tumour suppressor that is downregulated in prostate cancer. We hypothesized that hypermethylation may be responsible for SOX11 silencing in human prostate cancer. The aim of the study was to investigate SOX11 promoter methylation in prostate adenocarcinoma by comparing it with benign prostatic hyperplasia (BPH). A total of 143 human prostate tissue samples, 62 from patients with prostate cancer and 81 from patients with BPH were examined by methylation-specific PCR. Associations between SOX11 promoter methylation and clinicopathological parameters were assessed by univariate statistics. Detection rates of SOX11 promoter methylation were 80.6% and 35.8% in prostate cancer and BPH respectively (P < 0.001). SOX11 hypermethylation was associated with adverse clinicopathological characteristics of prostate cancer, including higher PSA level (P < 0.01), Gleason score ≥ 7 (P = 0.03) and perineural invasion (P = 0.03). SOX11 methylation was positively correlated with the PSA level (P = 0.001). Our data indicated that SOX11 can be a promising methylation marker candidate for differential diagnosis and risk stratification for prostate cancer.
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Affiliation(s)
- Apiwat Pugongchai
- Department of PathologyFaculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Andrey Bychkov
- Department of PathologyFaculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Pichet Sampatanukul
- Department of PathologyFaculty of MedicineChulalongkorn UniversityBangkokThailand
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42
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Zhang JJ, Zhu Y, Zhang XF, Liu DF, Wang Y, Yang C, Shi GD, Peng YP, Zhang K, Tian L, Miao Y, Jiang KR. Yin Yang-1 suppresses pancreatic ductal adenocarcinoma cell proliferation and tumor growth by regulating SOX2OT-SOX2 axis. Cancer Lett 2017; 408:144-154. [DOI: 10.1016/j.canlet.2017.08.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/12/2022]
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43
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Tatè R, Zona E, De Cicco R, Trotta V, Urciuoli M, Morelli A, Baiano S, Carnuccio R, Fuggetta MP, Morelli F. Simvastatin inhibits the expression of stemness-related genes and the metastatic invasion of human cancer cells via destruction of the cytoskeleton. Int J Oncol 2017; 51:1851-1859. [DOI: 10.3892/ijo.2017.4158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/15/2017] [Indexed: 11/06/2022] Open
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44
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She ZY, Yang WX. Nucleocytoplasmic shuttling of SOX14A and SOX14B transcription factors. Oncotarget 2017; 8:46955-46968. [PMID: 28187450 PMCID: PMC5564536 DOI: 10.18632/oncotarget.15134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/11/2017] [Indexed: 01/23/2023] Open
Abstract
The nucleocytoplasmic shuttling of SOX transcription factors play a crucial role in the regulation of SOX protein functions during development. In this study, we have demonstrated two nuclear localization signals in the HMG box of Eriocheir sinensis SOX14A and SOX14B. These two conserved nuclear localization signals mediate nuclear transport. The N-termini nuclear localization signal mediates the calmodulin-dependent pathway and the C-termini nuclear localization signal interacts with the importin-β pathway. The targeted deletion of nuclear localization signals of SOX14A/B dramatically inhibits the nuclear accumulation. We have first time revealed a non-classic nuclear export signal in the HMG box of E. sinensis SOX14A/B proteins is responds to leptomycin B. E. sinensis SOX14A/B is transported from the nucleus to the cytoplasm via a CRM1-dependent nuclear export pathway. And E. sinensis SOX14A/B are not belong to the subgroup E SOX proteins. Furthermore, these findings could shed a light on the mechanisms involved in the nuclear export of SOX proteins. The imperfect nuclear export signal on other SOX proteins, rather than just those of the SOXE group, may also be functional for nuclear export.
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Affiliation(s)
- Zhen-Yu She
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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45
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Liu Y, Zeng S, Jiang X, Lai D, Su Z. SOX4 induces tumor invasion by targeting EMT-related pathway in prostate cancer. Tumour Biol 2017; 39:1010428317694539. [PMID: 28466783 DOI: 10.1177/1010428317694539] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
SOX4 (sex-determining region Y-related high-mobility group box 4) is associated with tumor progression and poor clinical outcome in several cancers. This study aims to evaluate whether SOX4 affects the biological behaviors of prostate cancer and further elucidate whether this effect works through the epithelial-mesenchymal transition pathway. We investigated the expression of SOX4 in a series of prostate cancer tissues and adjacent noncancerous tissues, as well as in a panel of prostate cancer cell lines. Cell proliferation, migration, and invasion were evaluated in SOX4 knockdown prostate cancer cell lines by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and Transwell assay. Our results showed that the expression of SOX4 was remarkably upregulated both in prostate cancer tissues and in cell lines. Knockdown of SOX4 repressed the ability of cell proliferation and migration of DU145 cells. Moreover, inhibition of SOX4 could reverse the epithelial-mesenchymal transition processes through upregulation of E-cadherin and downregulation of vimentin. This study provided evidence that SOX4 could serve as a potential therapeutic target in prostate cancer.
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Affiliation(s)
- Yifan Liu
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Zeng
- 2 Department of Pharmacy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xianhan Jiang
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dehui Lai
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhengming Su
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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46
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Higashiyama H, Ozawa A, Sumitomo H, Uemura M, Fujino K, Igarashi H, Imaimatsu K, Tsunekawa N, Hirate Y, Kurohmaru M, Saijoh Y, Kanai-Azuma M, Kanai Y. Embryonic cholecystitis and defective gallbladder contraction in the Sox17-haploinsufficient mouse model of biliary atresia. Development 2017; 144:1906-1917. [PMID: 28432216 DOI: 10.1242/dev.147512] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 04/12/2017] [Indexed: 12/15/2022]
Abstract
The gallbladder excretes cytotoxic bile acids into the duodenum through the cystic duct and common bile duct system. Sox17 haploinsufficiency causes biliary atresia-like phenotypes and hepatitis in late organogenesis mouse embryos, but the molecular and cellular mechanisms underlying this remain unclear. In this study, transcriptomic analyses revealed the early onset of cholecystitis in Sox17+/- embryos, together with the appearance of ectopic cystic duct-like epithelia in their gallbladders. The embryonic hepatitis showed positive correlations with the severity of cholecystitis in individual Sox17+/- embryos. Embryonic hepatitis could be induced by conditional deletion of Sox17 in the primordial gallbladder epithelia but not in fetal liver hepatoblasts. The Sox17+/- gallbladder also showed a drastic reduction in sonic hedgehog expression, leading to aberrant smooth muscle formation and defective contraction of the fetal gallbladder. The defective gallbladder contraction positively correlated with the severity of embryonic hepatitis in Sox17+/- embryos, suggesting a potential contribution of embryonic cholecystitis and fetal gallbladder contraction in the early pathogenesis of congenital biliary atresia.
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Affiliation(s)
- Hiroki Higashiyama
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Aisa Ozawa
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Sumitomo
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mami Uemura
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,Center for Experimental Animals, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ko Fujino
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hitomi Igarashi
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kenya Imaimatsu
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoki Tsunekawa
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshikazu Hirate
- Center for Experimental Animals, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Masamichi Kurohmaru
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukio Saijoh
- Department of Neurobiology and Anatomy, The University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Masami Kanai-Azuma
- Center for Experimental Animals, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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47
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Lilly AJ, Lacaud G, Kouskoff V. SOXF transcription factors in cardiovascular development. Semin Cell Dev Biol 2017; 63:50-57. [PMID: 27470491 DOI: 10.1016/j.semcdb.2016.07.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/19/2016] [Accepted: 07/23/2016] [Indexed: 12/24/2022]
Abstract
Cardiovascular development during embryogenesis involves complex changes in gene regulatory networks regulated by a variety of transcription factors. In this review we discuss the various reported roles of the SOXF factors: SOX7, SOX17 and SOX18 in cardiac, vascular and lymphatic development. SOXF factors have pleiotropic roles during these processes, and there is significant redundancy and functional compensation between SOXF family members. Despite this, evidence suggests that there is some specificity in the transcriptional programs they regulate which is necessary to control the differentiation and behaviour of endothelial subpopulations. Furthermore, SOXF factors appear to have an indirect role in regulating cardiac mesoderm specification and differentiation. Understanding how SOXF factors are regulated, as well as their downstream transcriptional target genes, will be important for unravelling their roles in cardiovascular development and related diseases.
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Affiliation(s)
- Andrew J Lilly
- Cancer Research UK, Stem Cell Hematopoiesis, The University of Manchester, Wilmslow road, M20 4BX, UK
| | - Georges Lacaud
- Cancer Research UK, Stem Cell Biology group Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow road, M20 4BX, UK.
| | - Valerie Kouskoff
- Cancer Research UK, Stem Cell Hematopoiesis, The University of Manchester, Wilmslow road, M20 4BX, UK.
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48
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Molecular basis for the genome engagement by Sox proteins. Semin Cell Dev Biol 2017; 63:2-12. [DOI: 10.1016/j.semcdb.2016.08.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 01/11/2023]
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49
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Banerjee A, Ray S. Structural insight, mutation and interactions in human Beta-catenin and SOX17 protein: A molecular-level outlook for organogenesis. Gene 2017; 610:118-126. [PMID: 28132771 DOI: 10.1016/j.gene.2017.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 10/20/2022]
Abstract
Essential human proteins; SOX17-HMG domain and beta-catenin uphold a major responsibility for vertebrate gastrulation and embryonic development. Earlier experimental assays document their interaction and states that upon M76A and G103R mutation, their interaction varied. Till date, there was no computational analysis for either of proteins as well as their respective residues for the interaction. The present study extracted and analyzed the experimentally validated 3D models of SOX17-HMG domain and beta-catenin. After analysis of the evolutionarily conserved residues and the sequence-level alteration, the mutated SOX17-HMG protein was re-modeled, demonstrated and energy minimized. Molecular dynamics simulation was performed upon the docked complex of beta-catenin with wild-type and mutant-type protein, individually. Comparable analysis for interaction studies revealed reduction of predominant ionic interactions from 16 (wild-type) to 5 (mutant-type). Glu residues from wild-type protein played a pivotal role forming 50% of the ionic interactions alone. Fascinatingly, statistically significant deductions for several stability calculations deduced the mutant-type protein/complex to form unsteady interaction with beta-catenin. Again, helix-to-coil transition in mutant-type protein supported its weaker conformation. This probe depicts the paramount molecular-level detailed scrutiny for the essential human proteins and disclosure of the mutational analysis, which might tend to hinder the signal transduction. It instigates the future development for the pharmaceutical research.
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Affiliation(s)
- Arundhati Banerjee
- Department of Biotechnology, National Institute of Technology, Durgapur, West Bengal, India.
| | - Sujay Ray
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India; Amity Institute of Biotechnology, Amity University, Kolkata, West Bengal, India.
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50
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Chang YK, Srivastava Y, Hu C, Joyce A, Yang X, Zuo Z, Havranek JJ, Stormo GD, Jauch R. Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq. Nucleic Acids Res 2016; 45:832-845. [PMID: 27915232 PMCID: PMC5314778 DOI: 10.1093/nar/gkw1198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/30/2022] Open
Abstract
Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.
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Affiliation(s)
- Yiming K Chang
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Caizhen Hu
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Adam Joyce
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoxiao Yang
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zheng Zuo
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - James J Havranek
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gary D Stormo
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China .,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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