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Naqvi S, Kim S, Tabatabaee S, Pampari A, Kundaje A, Pritchard JK, Wysocka J. Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596078. [PMID: 38853998 PMCID: PMC11160683 DOI: 10.1101/2024.05.28.596078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Deep learning approaches have made significant advances in predicting cell type-specific chromatin patterns from the identity and arrangement of transcription factor (TF) binding motifs. However, most models have been applied in unperturbed contexts, precluding a predictive understanding of how chromatin state responds to TF perturbation. Here, we used transfer learning to train and interpret deep learning models that use DNA sequence to predict, with accuracy approaching experimental reproducibility, how the concentration of two dosage-sensitive TFs (TWIST1, SOX9) affects regulatory element (RE) chromatin accessibility in facial progenitor cells. High-affinity motifs that allow for heterotypic TF co-binding and are concentrated at the center of REs buffer against quantitative changes in TF dosage and strongly predict unperturbed accessibility. In contrast, motifs with low-affinity or homotypic binding distributed throughout REs lead to sensitive responses with minimal contributions to unperturbed accessibility. Both buffering and sensitizing features show signatures of purifying selection. We validated these predictive sequence features using reporter assays and showed that a biophysical model of TF-nucleosome competition can explain the sensitizing effect of low-affinity motifs. Our approach of combining transfer learning and quantitative measurements of the chromatin response to TF dosage therefore represents a powerful method to reveal additional layers of the cis-regulatory code.
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Affiliation(s)
- Sahin Naqvi
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Lead contact
| | - Seungsoo Kim
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Saman Tabatabaee
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joanna Wysocka
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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Molin AN, Contentin R, Angelozzi M, Karvande A, Kc R, Haseeb A, Voskamp C, de Charleroy C, Lefebvre V. Skeletal growth is enhanced by a shared role for SOX8 and SOX9 in promoting reserve chondrocyte commitment to columnar proliferation. Proc Natl Acad Sci U S A 2024; 121:e2316969121. [PMID: 38346197 PMCID: PMC10895259 DOI: 10.1073/pnas.2316969121] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
SOX8 was linked in a genome-wide association study to human height heritability, but roles in chondrocytes for this close relative of the master chondrogenic transcription factor SOX9 remain unknown. We undertook here to fill this knowledge gap. High-throughput assays demonstrate expression of human SOX8 and mouse Sox8 in growth plate cartilage. In situ assays show that Sox8 is expressed at a similar level as Sox9 in reserve and early columnar chondrocytes and turned off when Sox9 expression peaks in late columnar and prehypertrophic chondrocytes. Sox8-/- mice and Sox8fl/flPrx1Cre and Sox9fl/+Prx1Cre mice (inactivation in limb skeletal cells) have a normal or near normal skeletal size. In contrast, juvenile and adult Sox8fl/flSox9fl/+Prx1Cre compound mutants exhibit a 15 to 20% shortening of long bones. Their growth plate reserve chondrocytes progress slowly toward the columnar stage, as witnessed by a delay in down-regulating Pthlh expression, in packing in columns and in elevating their proliferation rate. SOX8 or SOX9 overexpression in chondrocytes reveals not only that SOX8 can promote growth plate cell proliferation and differentiation, even upon inactivation of endogenous Sox9, but also that it is more efficient than SOX9, possibly due to greater protein stability. Altogether, these findings uncover a major role for SOX8 and SOX9 in promoting skeletal growth by stimulating commitment of growth plate reserve chondrocytes to actively proliferating columnar cells. Further, by showing that SOX8 is more chondrogenic than SOX9, they suggest that SOX8 could be preferred over SOX9 in therapies to promote cartilage formation or regeneration in developmental and degenerative cartilage diseases.
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Affiliation(s)
- Arnaud N. Molin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Romain Contentin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Marco Angelozzi
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Anirudha Karvande
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Ranjan Kc
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Abdul Haseeb
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Chantal Voskamp
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Charles de Charleroy
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Véronique Lefebvre
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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Takahashi M, Chong HB, Zhang S, Lazarov MJ, Harry S, Maynard M, White R, Murrey HE, Hilbert B, Neil JR, Gohar M, Ge M, Zhang J, Durr BR, Kryukov G, Tsou CC, Brooijmans N, Alghali ASO, Rubio K, Vilanueva A, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Assaad J, Makram F, Rachman I, Khandelwal N, Tien PC, Popoola G, Chen N, Vordermark K, Richter M, Patel H, Yang TY, Griesshaber H, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Fisher DE, Maheswaran S, Haber DA, Boland G, Sade-Feldman M, Jenkins R, Hata A, Bardeesy N, Suva ML, Martin B, Liau B, Ott C, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563287. [PMID: 37961514 PMCID: PMC10634688 DOI: 10.1101/2023.10.20.563287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed DrugMap , an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NFκB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NFκB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity.
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Warman-Chardon J, Hartley T, Marshall AE, McBride A, Couse M, Macdonald W, Mann MRW, Bourque PR, Breiner A, Lochmüller H, Woulfe J, Sampaio ML, Melkus G, Brais B, Dyment DA, Boycott KM, Kernohan K. Biallelic SOX8 Variants Associated With Novel Syndrome With Myopathy, Skeletal Deformities, Intellectual Disability, and Ovarian Dysfunction. Neurol Genet 2023; 9:e200088. [PMID: 38235364 PMCID: PMC10508790 DOI: 10.1212/nxg.0000000000200088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/30/2023] [Indexed: 01/19/2024]
Abstract
Background and Objectives The human genome contains ∼20,000 genes, each of which has its own set of complex regulatory systems to govern precise expression in each developmental stage and cell type. Here, we report a female patient with congenital weakness, respiratory failure, skeletal dysplasia, contractures, short stature, intellectual delay, respiratory failure, and amenorrhea who presented to Medical Genetics service with no known cause for her condition. Methods Whole-exome and whole-genome sequencing were conducted, as well as investigational functional studies to assess the effect of SOX8 variant. Results The patient was found to have biallelic SOX8 variants (NM_014587.3:c.422+5G>C; c.583dup p.(His195ProfsTer11)). SOX8 is a transcriptional regulator, which is predicted to be imprinted (expressed from only one parental allele), but this has not yet been confirmed. We provide evidence that while SOX8 was maternally expressed in adult-derived fibroblasts and lymphoblasts, it was biallelically expressed in other cell types and therefore suggest that biallelic variants are associated with this recessive condition. Functionally, we showed that the paternal variant had the capacity to affect mRNA splicing while the maternal variant resulted in low levels of a truncated protein, which showed decreased binding at and altered expression of SOX8 targets. Discussion Our findings associate SOX8 variants with this novel condition, highlight how complex genome regulation can complicate novel disease-gene identification, and provide insight into the molecular pathogenesis of this disease.
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Affiliation(s)
- Jodi Warman-Chardon
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Taila Hartley
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Aren Elizabeth Marshall
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Arran McBride
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Madeline Couse
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - William Macdonald
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Mellissa R W Mann
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Pierre R Bourque
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Ari Breiner
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Hanns Lochmüller
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - John Woulfe
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Marcos Loreto Sampaio
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Gerd Melkus
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Bernard Brais
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - David A Dyment
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kym M Boycott
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kristin Kernohan
- From the Department of Medicine (J.W.-C., P.R.B., A.B., H.L.), The Ottawa Hospital; The Ottawa Hospital Research Institute (J.W.-C., P.R.B., H.L., J.W., M.L.S., G.M.); Faculty of Medicine (J.W.-C., P.R.B., A.B., H.L., J.W., M.L.S., D.A.D., K.M.B.); Children's Hospital of Eastern Ontario Research Institute (J.W.-C., T.H., A.E.M., A.M., H.L., D.A.D., K.M.B., K.K.), University of Ottawa; Hospital for Sick Children (M.C.), Centre for Computational Medicine, Toronto, Canada; Department of Obstetrics (W.M., M.R.W.M.), Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine; Magee-Womens Research Institute (W.M., M.R.W.M.), Pittsburgh, PA; Department of Pathology and Laboratory Medicine (A.B., J.W.), The Ottawa Hospital; Department of Radiology (M.L.S., G.M.), Radiation Oncology and Medical Physics, University of Ottawa; Department of Neurology and Neurosurgery (B.B.), Montreal Neurological Institute and Hospital, McGill University; and Newborn Screening Ontario (K.K.), Children's Hospital of Eastern Ontario, Ottawa, Canada
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5
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Wang J, Wan X, Le Q. Cross-regulation between SOX9 and the canonical Wnt signalling pathway in stem cells. Front Mol Biosci 2023; 10:1250530. [PMID: 37664185 PMCID: PMC10469848 DOI: 10.3389/fmolb.2023.1250530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
SOX9, a member of the SRY-related HMG-box transcription factors, has been reported to critically regulate fetal development and stem cell homeostasis. Wnt signalling is a highly conserved signalling pathway that controls stem cell fate decision and stemness maintenance throughout embryonic development and adult life. Many studies have shown that the interactions between SOX9 and the canonical Wnt signalling pathway are involved in many of the physiological and pathological processes of stem cells, including organ development, the proliferation, differentiation and stemness maintenance of stem cells, and tumorigenesis. In this review, we summarize the already-known molecular mechanism of cross-interactions between SOX9 and the canonical Wnt signalling pathway, outline its regulatory effects on the maintenance of homeostasis in different types of stem cells, and explore its potential in translational stem cell therapy.
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Affiliation(s)
- Jiajia Wang
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
| | - Xichen Wan
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
| | - Qihua Le
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
- Research Center, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
- Myopia Key Laboratory of Ministry of Health, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
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6
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Wang L, Liu Z, Zhao S, Xu K, Aceves V, Qiu C, Troutwine B, Liu L, Ma S, Niu Y, Wang S, Yuan S, Li X, Zhao L, Liu X, Wu Z, Zhang TJ, Gray RS, Wu N. Variants in the SOX9 transactivation middle domain induce axial skeleton dysplasia and scoliosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.29.23290174. [PMID: 37398377 PMCID: PMC10312849 DOI: 10.1101/2023.05.29.23290174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
SOX9 is an essential transcriptional regulator of cartilage development and homeostasis. In humans, dysregulation of SOX9 is associated with a wide spectrum of skeletal disorders, including campomelic and acampomelic dysplasia, and scoliosis. The mechanism of how SOX9 variants contribute to the spectrum of axial skeletal disorders is not well understood. Here, we report four novel pathogenic variants of SOX9 identified in a large cohort of patients with congenital vertebral malformations. Three of these heterozygous variants are in the HMG and DIM domains, and for the first time, we report a pathogenic variant within the transactivation middle (TAM) domain of SOX9 . Probands with these variants exhibit variable skeletal dysplasia, ranging from isolated vertebral malformation to acampomelic dysplasia. We also generated a Sox9 hypomorphic mutant mouse model bearing a microdeletion within the TAM domain ( Sox9 Asp272del ). We demonstrated that disturbance of the TAM domain with missense mutation or microdeletion results in reduced protein stability but does not affect the transcriptional activity of SOX9. Homozygous Sox9 Asp272del mice exhibited axial skeletal dysplasia including kinked tails, ribcage anomalies, and scoliosis, recapitulating phenotypes observed in human, while heterozygous mutants display a milder phenotype. Analysis of primary chondrocytes and the intervertebral discs in Sox9 Asp272del mutant mice revealed dysregulation of a panel of genes with major contributions of the extracellular matrix, angiogenesis, and ossification-related processes. In summary, our work identified the first pathologic variant of SOX9 within the TAM domain and demonstrated that this variant is associated with reduced SOX9 protein stability. Our finding suggests that reduced SOX9 stability caused by variants in the TAM domain may be responsible for the milder forms of axial skeleton dysplasia in humans.
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7
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Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Precise modulation of transcription factor levels identifies features underlying dosage sensitivity. Nat Genet 2023; 55:841-851. [PMID: 37024583 PMCID: PMC10181932 DOI: 10.1038/s41588-023-01366-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Harold S Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ophir D Klein
- Departments of Orofacial Sciences and Pediatrics, Program in Craniofacial Biology, and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | | | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Zhang X, Tai Z, Miao F, Huang H, Zhu Q, Bao L, Chen Z. Metabolism heterogeneity in melanoma fuels deactivation of immunotherapy: Predict before protect. Front Oncol 2022; 12:1046102. [PMID: 36620597 PMCID: PMC9813867 DOI: 10.3389/fonc.2022.1046102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Malignant melanoma is widely acknowledged as the most lethal skin malignancy. The metabolic reprogramming in melanoma leads to alterations in glycolysis and oxidative phosphorylation (OXPHOS), forming a hypoxic, glucose-deficient and acidic tumor microenvironment which inhibits the function of immune cells, resulting in a low response rate to immunotherapy. Therefore, improving the tumor microenvironment by regulating the metabolism can be used to improve the efficacy of immunotherapy. However, the tumor microenvironment (TME) and the metabolism of malignant melanoma are highly heterogeneous. Therefore, understanding and predicting how melanoma regulates metabolism is important to improve the local immune microenvironment of the tumor, and metabolism regulators are expected to increase treatment efficacy in combination with immunotherapy. This article reviews the energy metabolism in melanoma and its regulation and prediction, the integration of immunotherapy and metabolism regulators, and provides a comprehensive overview of future research focal points in this field and their potential application in clinical treatment.
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Affiliation(s)
- Xinyue Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Pharmacy, Third Affiliated Hospital of Naval Medical University, Shanghai, China,Department of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zongguang Tai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fengze Miao
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hao Huang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China,Department of Pharmacy, Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Quangang Zhu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Leilei Bao
- Department of Pharmacy, Third Affiliated Hospital of Naval Medical University, Shanghai, China,Department of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, China,*Correspondence: Zhongjian Chen, ; Leilei Bao,
| | - Zhongjian Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China,*Correspondence: Zhongjian Chen, ; Leilei Bao,
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9
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Szeto IYY, Chu DKH, Chen P, Chu KC, Au TYK, Leung KKH, Huang YH, Wynn SL, Mak ACY, Chan YS, Chan WY, Jauch R, Fritzsch B, Sham MH, Lovell-Badge R, Cheah KSE. SOX9 and SOX10 control fluid homeostasis in the inner ear for hearing through independent and cooperative mechanisms. Proc Natl Acad Sci U S A 2022; 119:e2122121119. [PMID: 36343245 PMCID: PMC9674217 DOI: 10.1073/pnas.2122121119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Abstract
The in vivo mechanisms underlying dominant syndromes caused by mutations in SRY-Box Transcription Factor 9 (SOX9) and SOX10 (SOXE) transcription factors, when they either are expressed alone or are coexpressed, are ill-defined. We created a mouse model for the campomelic dysplasia SOX9Y440X mutation, which truncates the transactivation domain but leaves DNA binding and dimerization intact. Here, we find that SOX9Y440X causes deafness via distinct mechanisms in the endolymphatic sac (ES)/duct and cochlea. By contrast, conditional heterozygous Sox9-null mice are normal. During the ES development of Sox9Y440X/+ heterozygotes, Sox10 and genes important for ionic homeostasis are down-regulated, and there is developmental persistence of progenitors, resulting in fewer mature cells. Sox10 heterozygous null mutants also display persistence of ES/duct progenitors. By contrast, SOX10 retains its expression in the early Sox9Y440X/+ mutant cochlea. Later, in the postnatal stria vascularis, dominant interference by SOX9Y440X is implicated in impairing the normal cooperation of SOX9 and SOX10 in repressing the expression of the water channel Aquaporin 3, thereby contributing to endolymphatic hydrops. Our study shows that for a functioning endolymphatic system in the inner ear, SOX9 regulates Sox10, and depending on the cell type and target gene, it works either independently of or cooperatively with SOX10. SOX9Y440X can interfere with the activity of both SOXE factors, exerting effects that can be classified as haploinsufficient/hypomorphic or dominant negative depending on the cell/gene context. This model of disruption of transcription factor partnerships may be applicable to congenital deafness, which affects ∼0.3% of newborns, and other syndromic disorders.
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Affiliation(s)
- Irene Y. Y. Szeto
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Daniel K. H. Chu
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Peikai Chen
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Ka Chi Chu
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Tiffany Y. K. Au
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Keith K. H. Leung
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Yong-Heng Huang
- Genome Regulation Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Sarah L. Wynn
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Angel C. Y. Mak
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Ying-Shing Chan
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Wood Yee Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ralf Jauch
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
- Genome Regulation Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Bernd Fritzsch
- Department of Biology, College of Arts & Sciences, University of Iowa, Iowa City, IA 52242
- Department of Otolaryngology, College of Arts & Sciences, University of Iowa, Iowa City, IA 52242
| | - Mai Har Sham
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | | | - Kathryn S. E. Cheah
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
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10
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Islam Z, Aldous N, Choi S, Schmidt F, Mifsud B, Abdelalim EM, Kolatkar PR. Flavin Adenine Dinucleotide (FAD) and Pyridoxal 5'-Phosphate (PLP) Bind to Sox9 and Alter the Expression of Key Pancreatic Progenitor Transcription Factors. Int J Mol Sci 2022; 23:ijms232214051. [PMID: 36430529 PMCID: PMC9694089 DOI: 10.3390/ijms232214051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Cofactor flavin adenine dinucleotide (FAD), a compound with flavin moiety and a derivative of riboflavin (vitamin B2), is shown to bind to Sox9 (a key transcription factor in early pancreatic development) and, subsequently, induce a large increase in markers of pancreatic development, including Ngn3 and PTF1a. Pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, also binds to Sox9 and results in a similar increase in pancreatic development markers. Sox9 is known to be specifically important for pancreatic progenitors. Previously, there was no known link between FAD, PLP, or other co-factors and Sox9 for function. Thus, our findings show the mechanism by which FAD and PLP interact with Sox9 and result in the altered expression of pancreatic progenitor transcription factors involved in the pancreas development.
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Affiliation(s)
- Zeyaul Islam
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Noura Aldous
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Sunkyu Choi
- Proteomics Core, Weill Cornell Medicine, Doha P.O. Box 24144, Qatar
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine, Doha P.O. Box 24144, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Essam M. Abdelalim
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Prasanna R. Kolatkar
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- Correspondence: ; Tel.: +974-445-45889; Fax: +974-445-41770
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11
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Ming Z, Vining B, Bagheri-Fam S, Harley V. SOX9 in organogenesis: shared and unique transcriptional functions. Cell Mol Life Sci 2022; 79:522. [PMID: 36114905 PMCID: PMC9482574 DOI: 10.1007/s00018-022-04543-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/13/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]
Abstract
The transcription factor SOX9 is essential for the development of multiple organs including bone, testis, heart, lung, pancreas, intestine and nervous system. Mutations in the human SOX9 gene led to campomelic dysplasia, a haploinsufficiency disorder with several skeletal malformations frequently accompanied by 46, XY sex reversal. The mechanisms underlying the diverse SOX9 functions during organ development including its post-translational modifications, the availability of binding partners, and tissue-specific accessibility to target gene chromatin. Here we summarize the expression, activities, and downstream target genes of SOX9 in molecular genetic pathways essential for organ development, maintenance, and function. We also provide an insight into understanding the mechanisms that regulate the versatile roles of SOX9 in different organs.
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Affiliation(s)
- Zhenhua Ming
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia
| | - Brittany Vining
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia
| | - Stefan Bagheri-Fam
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia
| | - Vincent Harley
- Sex Development Laboratory, Hudson Institute of Medical Research, PO Box 5152, Melbourne, VIC, 3168, Australia.
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, 3800, Australia.
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12
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Lin JM, Mitchell TA, Rothstein M, Pehl A, Taroc EZM, Katreddi RR, Parra KE, Zuloaga DG, Simoes-Costa M, Forni PE. Sociosexual behavior requires both activating and repressive roles of Tfap2e/AP-2ε in vomeronasal sensory neurons. eLife 2022; 11:e77259. [PMID: 36111787 PMCID: PMC9525060 DOI: 10.7554/elife.77259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Neuronal identity dictates the position in an epithelium, and the ability to detect, process, and transmit specific signals to specified targets. Transcription factors (TFs) determine cellular identity via direct modulation of genetic transcription and recruiting chromatin modifiers. However, our understanding of the mechanisms that define neuronal identity and their magnitude remain a critical barrier to elucidate the etiology of congenital and neurodegenerative disorders. The rodent vomeronasal organ provides a unique system to examine in detail the molecular mechanisms underlying the differentiation and maturation of chemosensory neurons. Here, we demonstrated that the identity of postmitotic/maturing vomeronasal sensory neurons (VSNs), and vomeronasal-dependent behaviors can be reprogrammed through the rescue of Tfap2e/AP-2ε expression in the Tfap2eNull mice, and partially reprogrammed by inducing ectopic Tfap2e expression in mature apical VSNs. We suggest that the TF Tfap2e can reprogram VSNs bypassing cellular plasticity restrictions, and that it directly controls the expression of batteries of vomeronasal genes.
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Affiliation(s)
- Jennifer M Lin
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Tyler A Mitchell
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Megan Rothstein
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Alison Pehl
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Ed Zandro M Taroc
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Raghu R Katreddi
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Katherine E Parra
- Department of Psychology, University at Albany, State University of New YorkAlbanyUnited States
| | - Damian G Zuloaga
- Department of Psychology, University at Albany, State University of New YorkAlbanyUnited States
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Paolo Emanuele Forni
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
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13
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Fuglerud BM, Drissler S, Lotto J, Stephan TL, Thakur A, Cullum R, Hoodless PA. SOX9 reprograms endothelial cells by altering the chromatin landscape. Nucleic Acids Res 2022; 50:8547-8565. [PMID: 35904801 PMCID: PMC9410909 DOI: 10.1093/nar/gkac652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 01/08/2023] Open
Abstract
The transcription factor SOX9 is activated at the onset of endothelial-to-mesenchymal transition (EndMT) during embryonic development and in pathological conditions. Its roles in regulating these processes, however, are not clear. Using human umbilical vein endothelial cells (HUVECs) as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal genes and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 displays features of a pioneer transcription factor, such as opening of chromatin and leading to deposition of active histone modifications at silent chromatin regions, guided by SOX dimer motifs and H2A.Z enrichment. We further observe highly transient and dynamic SOX9 binding, possibly promoted through its eviction by histone phosphorylation. However, while SOX9 binding is dynamic, changes in the chromatin landscape and cell fate induced by SOX9 are persistent. Finally, our analysis of single-cell chromatin accessibility indicates that SOX9 opens chromatin to drive EndMT in atherosclerotic lesions in vivo. This study provides new insight into key molecular functions of SOX9 and mechanisms of EndMT and highlights the crucial developmental role of SOX9 and relevance to human disease.
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Affiliation(s)
- Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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14
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Functional in vivo characterization of sox10 enhancers in neural crest and melanoma development. Commun Biol 2021; 4:695. [PMID: 34099848 PMCID: PMC8184803 DOI: 10.1038/s42003-021-02211-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
The role of a neural crest developmental transcriptional program, which critically involves Sox10 upregulation, is a key conserved aspect of melanoma initiation in both humans and zebrafish, yet transcriptional regulation of sox10 expression is incompletely understood. Here we used ATAC-Seq analysis of multiple zebrafish melanoma tumors to identify recurrently open chromatin domains as putative melanoma-specific sox10 enhancers. Screening in vivo with EGFP reporter constructs revealed 9 of 11 putative sox10 enhancers with embryonic activity in zebrafish. Focusing on the most active enhancer region in melanoma, we identified a region 23 kilobases upstream of sox10, termed peak5, that drives EGFP reporter expression in a subset of neural crest cells, Kolmer-Agduhr neurons, and early melanoma patches and tumors with high specificity. A ~200 base pair region, conserved in Cyprinidae, within peak5 is required for transgenic reporter activity in neural crest and melanoma. This region contains dimeric SoxE/Sox10 dimeric binding sites essential for peak5 neural crest and melanoma activity. We show that deletion of the endogenous peak5 conserved genomic locus decreases embryonic sox10 expression and disrupts adult stripe patterning in our melanoma model background. Our work demonstrates the power of linking developmental and cancer models to better understand neural crest identity in melanoma.
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15
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Mares L, Ramos L. Harderian SOX9: Molecular characterization and its dimorphic expression in hamster. Comp Biochem Physiol A Mol Integr Physiol 2021; 258:110981. [PMID: 34000431 DOI: 10.1016/j.cbpa.2021.110981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
The molecular action of SOX9 can promote lipogenesis. Because the hamster Harderian gland (HG) synthesizes lipids and exhibits sexual dimorphism, this study aimed to identify and characterize Harderian SOX9. We examined the tissue distribution and expression profiles of SOX9 in hamster Mesocricetus auratus HGs. The full-length SOX9 cDNA sequence [3649-base pairs (bp)] contains an 81-bp 5' untranslated region (UTR), a 3' UTR of 2044-bp, an open reading frame (ORF) of 1524-bp, and a polyadenylation signal (AATAAA) at 19-bp upstream of poly(A) tail. The cDNA encodes a 507 amino acid protein containing the potential DNA-binding domain known as the HMG box. BLAST analysis revealed 99%, 99%, and 97% identity with the SOX9 of mouse, rat, and human, respectively. High expression levels were also observed in the testis, cerebellum, and hypothalamus. qPCR analysis demonstrated that SOX9 is expressed more abundantly in the HGs of males than in females. Sexually dimorphic expression of SOX9 suggests that differential expression between male and female HGs could be under the regulation of sex steroids. SOX9 might play a similar role in regulating exocrine secretions of lipids; these could occur downstream of FGF signaling - as found during embryogenesis - and/or androgen signaling.
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Affiliation(s)
- L Mares
- Department of Reproductive Biology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - L Ramos
- Department of Reproductive Biology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico.
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16
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Al-Zahrani KN, Abou-Hamad J, Pascoal J, Labrèche C, Garland B, Sabourin LA. AKT-mediated phosphorylation of Sox9 induces Sox10 transcription in a murine model of HER2-positive breast cancer. Breast Cancer Res 2021; 23:55. [PMID: 33985544 PMCID: PMC8120776 DOI: 10.1186/s13058-021-01435-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
Background Approximately 5–10% of HER2-positive breast cancers can be defined by low expression of the Ste20-like kinase, SLK, and high expression of SOX10. Our lab has observed that genetic deletion of SLK results in the induction of Sox10 and significantly accelerates tumor initiation in a HER2-induced mammary tumor model. However, the mechanism responsible for the induction of SOX10 gene expression in this context remains unknown. Methods Using tumor-derived cell lines from MMTV-Neu mice lacking SLK and biochemical approaches, we have characterized the signaling mechanisms and relevant DNA elements driving Sox10 expression. Results Biochemical and genetic analyses of the SOX10 regulatory region in SLK-deficient mammary tumor cells show that Sox10 expression is dependent on a novel −7kb enhancer that harbors three SoxE binding sites. ChIP analyses demonstrate that Sox9 is bound to those elements in vivo. Our data show that AKT can directly phosphorylate Sox9 in vitro at serine 181 and that AKT inhibition blocks Sox9 phosphorylation and Sox10 expression in SLK(-/-) tumor cells. AKT-mediated Sox9 phosphorylation increases its transcriptional activity on the Sox10 −7kb enhancer without altering its DNA-binding activity. Interestingly, analysis of murine and human mammary tumors reveals a direct correlation between the levels of active phospho-Sox9 S181 and Sox10 expression. Conclusions Our results have identified a novel Sox10 enhancer and validated Sox9 as a direct target for AKT. As Sox10 is a biomarker for triple-negative breast cancers (TNBC), these findings might have major implications in the targeting and treatment of those cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01435-6.
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Affiliation(s)
- Khalid N Al-Zahrani
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - John Abou-Hamad
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Julia Pascoal
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
| | - Cédrik Labrèche
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Brennan Garland
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Luc A Sabourin
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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17
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Enhancing the chondrogenic potential of chondrogenic progenitor cells by deleting RAB5C. iScience 2021; 24:102464. [PMID: 34013174 PMCID: PMC8113995 DOI: 10.1016/j.isci.2021.102464] [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: 11/17/2020] [Revised: 02/24/2021] [Accepted: 04/21/2021] [Indexed: 11/21/2022] Open
Abstract
Osteoarthritis (OA) is the most prevalent chronic joint disease that affects a large proportion of the elderly population. Chondrogenic progenitor cells (CPCs) reside in late-stage OA cartilage tissue, producing a fibrocartilaginous extracellular matrix; these cells can be manipulated in vitro to deposit proteins of healthy articular cartilage. CPCs are under the control of SOX9 and RUNX2. In our earlier studies, we showed that a knockdown of RUNX2 enhanced the chondrogenic potential of CPCs. Here we demonstrate that CPCs carrying a knockout of RAB5C, a protein involved in endosomal trafficking, exhibited elevated expression of multiple chondrogenic markers, including the SOX trio, and increased COL2 deposition, whereas no changes in COL1 deposition were observed. We report RAB5C as an attractive target for future therapeutic approaches designed to increase the COL2 content in the diseased joint.
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18
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Vining B, Ming Z, Bagheri-Fam S, Harley V. Diverse Regulation but Conserved Function: SOX9 in Vertebrate Sex Determination. Genes (Basel) 2021; 12:genes12040486. [PMID: 33810596 PMCID: PMC8066042 DOI: 10.3390/genes12040486] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Sex determination occurs early during embryogenesis among vertebrates. It involves the differentiation of the bipotential gonad to ovaries or testes by a fascinating diversity of molecular switches. In most mammals, the switch is SRY (sex determining region Y); in other vertebrates it could be one of a variety of genes including Dmrt1 or dmy. Downstream of the switch gene, SOX9 upregulation is a central event in testes development, controlled by gonad-specific enhancers across the 2 Mb SOX9 locus. SOX9 is a ‘hub’ gene of gonadal development, regulated positively in males and negatively in females. Despite this diversity, SOX9 protein sequence and function among vertebrates remains highly conserved. This article explores the cellular, morphological, and genetic mechanisms initiated by SOX9 for male gonad differentiation.
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Affiliation(s)
- Brittany Vining
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
| | - Zhenhua Ming
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
| | - Vincent Harley
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
- Correspondence: ; Tel.: +61-3-8572-2527
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19
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Liu Y, Guo W. SOX factors as cell-state regulators in the mammary gland and breast cancer. Semin Cell Dev Biol 2021; 114:126-133. [PMID: 33583737 DOI: 10.1016/j.semcdb.2021.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 12/27/2022]
Abstract
Emerging evidence has shown that several SOX family transcription factors are key regulators of stem/progenitor cell fates in the mammary gland. These cell-fate regulators are often upregulated in breast cancer and contribute to tumor initiation and progression. They induce lineage plasticity and the epithelial-mesenchymal transition, which promotes tumor invasion, metastasis, and therapeutic resistance. SOX factors act through modulating multiple oncogenic signaling pathways in breast cancer. In addition to the cell-autonomous functions, new evidence suggests they can shape the tumor immune microenvironment. Here, we will review the molecular and functional evidence linking SOX factors with mammary gland development and discuss how these cell-fate regulators are co-opted in breast cancer.
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Affiliation(s)
- Yu Liu
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wenjun Guo
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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20
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Tanaka J, Takamatsu K, Yukimori A, Kujiraoka S, Ishida S, Takakura I, Yasuhara R, Mishima K. Sox9 function in salivary gland development. J Oral Biosci 2021; 63:8-13. [PMID: 33497841 DOI: 10.1016/j.job.2021.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Organogenesis is regulated by morphogen signaling and transcription networks. These networks differ between organs, and identifying the organ-specific network is important to clarify the molecular mechanisms of development and regeneration of organs. Several studies have been conducted to identify salivary gland-specific networks using a mouse submandibular gland model. The submandibular glands (SMGs) of mice manifest as a thickening of the oral epithelium at embryonic day 11.5 and invaginate into the underlying mesenchyme. The network between Fgf10 and Sox9 is involved in SMG development in mice. HIGHLIGHT Sox9, a member of the Sox family, is expressed in the SMG in mice from the embryonic stage to the adult stage, although the distribution changes during development. A null mutation of mouse Sox9 is lethal during the neonatal period due to respiratory failure, whereas deletion of Sox9 in the oral epithelium using the Cre/lox P system, can lead to smaller initial buds of SMGs in conditional knockout (cKO) mice than in normal mice. In addition, we showed that adenoviral transduction of Sox9 and Foxc1 genes into mouse embryonic stem cell-derived oral ectoderm could induce salivary gland rudiment in an organoid culture system. ChIP-sequencing revealed that Sox9 possibly regulates several tube- and branching-formation-related genes. CONCLUSION Sox9 may serve as an essential transcription factor for salivary gland development. The Sox9-mediated pathway can be a promising candidate for regenerating damaged salivary glands.
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Affiliation(s)
- Junichi Tanaka
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Koki Takamatsu
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Akane Yukimori
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Satoko Kujiraoka
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Shoko Ishida
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Ikuko Takakura
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Rika Yasuhara
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
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21
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Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, de Martin Garrido N, Marquez JA, Cordeiro TN, Pluta R, Macias MJ. Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes. Comput Struct Biotechnol J 2021; 19:632-646. [PMID: 33510867 PMCID: PMC7810915 DOI: 10.1016/j.csbj.2020.12.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
MH1 domains of BMP-activated Smads populate a dimer-monomer equilibrium. Swapping loop1 between BMP- and TGFβ Smads turns dimers into monomers and vice versa. BMP-responsive genomic regions have a lower average count of motifs than TGFβ ones.
Smad transcription factors are the main downstream effectors of the Transforming growth factor β superfamily (TGFβ) signalling network. The DNA complexes determined here by X-ray crystallography for the Bone Morphogenetic Proteins (BMP) activated Smad5 and Smad8 proteins reveal that all MH1 domains bind [GGC(GC)|(CG)] motifs similarly, although TGFβ-activated Smad2/3 and Smad4 MH1 domains bind as monomers whereas Smad1/5/8 form helix-swapped dimers. Dimers and monomers are also present in solution, as revealed by NMR. To decipher the characteristics that defined these dimers, we designed chimeric MH1 domains and characterized them using X-ray crystallography. We found that swapping the loop1 between TGFβ- and BMP- activated MH1 domains switches the dimer/monomer propensities. When we scanned the distribution of Smad-bound motifs in ChIP-Seq peaks (Chromatin immunoprecipitation followed by high-throughput sequencing) in Smad-responsive genes, we observed specific site clustering and spacing depending on whether the peaks correspond to BMP- or TGFβ-responsive genes. We also identified significant correlations between site distribution and monomer or dimer propensities. We propose that the MH1 monomer or dimer propensity of Smads contributes to the distinct motif selection genome-wide and together with the MH2 domain association, help define the composition of R-Smad/Smad4 trimeric complexes.
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Affiliation(s)
- Lidia Ruiz
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Zuzanna Kaczmarska
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France.,International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, Warsaw 02-109, Poland
| | - Tiago Gomes
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Eric Aragon
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Carles Torner
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Regina Freier
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Blazej Baginski
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Natàlia de Martin Garrido
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - José A Marquez
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Radoslaw Pluta
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain.,ICREA, Passeig Lluís Companys 23, Barcelona 08010, Spain
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22
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Schock EN, LaBonne C. Sorting Sox: Diverse Roles for Sox Transcription Factors During Neural Crest and Craniofacial Development. Front Physiol 2020; 11:606889. [PMID: 33424631 PMCID: PMC7793875 DOI: 10.3389/fphys.2020.606889] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
Sox transcription factors play many diverse roles during development, including regulating stem cell states, directing differentiation, and influencing the local chromatin landscape. Of the twenty vertebrate Sox factors, several play critical roles in the development the neural crest, a key vertebrate innovation, and the subsequent formation of neural crest-derived structures, including the craniofacial complex. Herein, we review the specific roles for individual Sox factors during neural crest cell formation and discuss how some factors may have been essential for the evolution of the neural crest. Additionally, we describe how Sox factors direct neural crest cell differentiation into diverse lineages such as melanocytes, glia, and cartilage and detail their involvement in the development of specific craniofacial structures. Finally, we highlight several SOXopathies associated with craniofacial phenotypes.
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Affiliation(s)
- Elizabeth N Schock
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, United States
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23
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Yu L, Peng F, Dong X, Chen Y, Sun D, Jiang S, Deng C. Sex-Determining Region Y Chromosome-Related High-Mobility-Group Box 10 in Cancer: A Potential Therapeutic Target. Front Cell Dev Biol 2020; 8:564740. [PMID: 33344444 PMCID: PMC7744619 DOI: 10.3389/fcell.2020.564740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/17/2020] [Indexed: 01/20/2023] Open
Abstract
Sex-determining region Y-related high mobility group-box 10 (SOX10), a member of the SOX family, has recently been highlighted as an essential transcriptional factor involved in developmental biology. Recently, the functionality of SOX 10 has been increasingly revealed by researchers worldwide. It has been reported that SOX10 significantly regulates the proliferation, migration, and apoptosis of tumors and is closely associated with the progression of cancer. In this review, we first introduce the basic background of the SOX family and SOX10 and then discuss the pathophysiological roles of SOX10 in cancer. Besides, we enumerate the application of SOX10 in the pathological diagnosis and therapeutic potential of cancer. Eventually, we summarize the potential directions and perspectives of SOX10 in neoplastic theranostics. The information compiled herein may assist in additional studies and increase the potential of SOX10 as a therapeutic target for cancer.
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Affiliation(s)
- Liming Yu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang, China
| | - Fan Peng
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Xue Dong
- Outpatient Department of Liaoning Military Region, General Hospital of Northern Theater Command, Shenyang, China
| | - Ying Chen
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dongdong Sun
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Shuai Jiang
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Chao Deng
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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24
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Williams CAC, Soufi A, Pollard SM. Post-translational modification of SOX family proteins: Key biochemical targets in cancer? Semin Cancer Biol 2020; 67:30-38. [PMID: 31539559 PMCID: PMC7703692 DOI: 10.1016/j.semcancer.2019.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/23/2019] [Accepted: 09/15/2019] [Indexed: 12/15/2022]
Abstract
Sox proteins are a family of lineage-associated transcription factors. They regulate expression of genes involved in control of self-renewal and multipotency in both developmental and adult stem cells. Overexpression of Sox proteins is frequently observed in many different human cancers. Despite their importance as therapeutic targets, Sox proteins are difficult to 'drug' using structure-based design. However, Sox protein localisation, activity and interaction partners are regulated by a plethora of post-translational modifications (PTMs), such as: phosphorylation, acetylation, sumoylation, methylation, and ubiquitylation. Here we review the various reported post-translational modifications of Sox proteins and their potential functional importance in guiding cell fate processes. The enzymes that regulate these PTMs could be useful targets for anti-cancer drug discovery.
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Affiliation(s)
- Charles A C Williams
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, EH16 4UU, Edinburgh, United Kingdom
| | - Abdenour Soufi
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, EH16 4UU, Edinburgh, United Kingdom
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, EH16 4UU, Edinburgh, United Kingdom.
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25
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Ashrafizadeh M, Taeb S, Hushmandi K, Orouei S, Shahinozzaman M, Zabolian A, Moghadam ER, Raei M, Zarrabi A, Khan H, Najafi M. Cancer and SOX proteins: New insight into their role in ovarian cancer progression/inhibition. Pharmacol Res 2020; 161:105159. [PMID: 32818654 DOI: 10.1016/j.phrs.2020.105159] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Transcription factors are potential targets in disease therapy, particularly in cancer. This is due to the fact that transcription factors regulate a variety of cellular events, and their modulation has opened a new window in cancer therapy. Sex-determining region Y (SRY)-related high-mobility group (HMG) box (SOX) proteins are potential transcription factors that are involved in developmental processes such as embryogenesis. It has been reported that abnormal expression of SOX proteins is associated with development of different cancers, particularly ovarian cancer (OC). In the present review, our aim is to provide a mechanistic review of involvement of SOX members in OC. SOX members may suppress and/or promote aggressiveness and proliferation of OC cells. Clinical studies have also confirmed the potential of transcription factors as diagnostic and prognostic factors in OC. Notably, studies have demonstrated the relationship between SOX members and other molecular pathways such as ST6Ga1-I, PI3K, ERK and so on, leading to more complexity. Furthermore, SOX members can be affected by upstream mediators such as microRNAs, long non-coding RNAs, and so on. It is worth mentioning that the expression of each member of SOX proteins is corelated with different stages of OC. Furthermore, their expression determines the response of OC cells to chemotherapy. These topics are discussed in this review to shed some light on role of SOX transcription factors in OC.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Shahram Taeb
- Ionizing and Non-Ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Sima Orouei
- MSc. Student, Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Md Shahinozzaman
- Department of Nutrition and Food Science, University of Maryland, College Park, MD, 20742, USA
| | - Amirhossein Zabolian
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Raei
- Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul, 34956, Turkey; Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, 34956, Turkey.
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, 23200, Pakistan
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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26
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Hou L, Wei Y, Lin Y, Wang X, Lai Y, Yin M, Chen Y, Guo X, Wu S, Zhu Y, Yuan J, Tariq M, Li N, Sun H, Wang H, Zhang X, Chen J, Bao X, Jauch R. Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2. Nucleic Acids Res 2020; 48:3869-3887. [PMID: 32016422 PMCID: PMC7144947 DOI: 10.1093/nar/gkaa067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 02/03/2023] Open
Abstract
Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate that the transcription factor Sox2 is able to directly bind RNA in vitro as well as in mouse and human cells. Sox2 targets RNA via a 60-amino-acid RNA binding motif (RBM) positioned C-terminally of the DNA binding high mobility group (HMG) box. Sox2 can associate with RNA and DNA simultaneously to form ternary RNA/Sox2/DNA complexes. Deletion of the RBM does not affect selection of target genes but mitigates binding to pluripotency related transcripts, switches exon usage and impairs the reprogramming of somatic cells to a pluripotent state. Our findings designate Sox2 as a multi-functional factor that associates with RNA whilst binding to cognate DNA sequences, suggesting that it may co-transcriptionally regulate RNA metabolism during somatic cell reprogramming.
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Affiliation(s)
- Linlin Hou
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangzhou/Shenzhen, China.,CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuanjie Wei
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yingying Lin
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangzhou/Shenzhen, China.,Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiwei Wang
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yiwei Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Menghui Yin
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China
| | - Yanpu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Xiangpeng Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Senbin Wu
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | | | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Muqddas Tariq
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaofei Zhang
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,CAS Key Laboratory of Regenerative Biology, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Laboratory of RNA Molecular Biology, 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 and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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27
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Christin JR, Wang C, Chung CY, Liu Y, Dravis C, Tang W, Oktay MH, Wahl GM, Guo W. Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer. Cell Rep 2020; 31:107742. [PMID: 32521267 PMCID: PMC7658810 DOI: 10.1016/j.celrep.2020.107742] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/08/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022] Open
Abstract
Lineage plasticity is important for the development of basal-like breast cancer (BLBC), an aggressive cancer subtype. While BLBC is likely to originate from luminal progenitor cells, it acquires substantial basal cell features and contains a heterogenous collection of cells exhibiting basal, luminal, and hybrid phenotypes. Why luminal progenitors are prone to BLBC transformation and what drives luminal-to-basal reprogramming remain unclear. Here, we show that the transcription factor SOX9 acts as a determinant for estrogen-receptor-negative (ER-) luminal stem/progenitor cells (LSPCs). SOX9 controls LSPC activity in part by activating both canonical and non-canonical nuclear factor κB (NF-κB) signaling. Inactivation of TP53 and RB via expression of SV40 TAg in a BLBC mouse tumor model leads to upregulation of SOX9, which drives luminal-to-basal reprogramming in vivo. Furthermore, SOX9 deletion inhibits the progression of ductal carcinoma in situ (DCIS)-like lesions to invasive carcinoma. These data show that ER- LSPC determinant SOX9 acts as a lineage plasticity driver for BLBC progression.
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Affiliation(s)
- John R Christin
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Chunhui Wang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Chi-Yeh Chung
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yu Liu
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christopher Dravis
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wei Tang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Maja H Oktay
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10467, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonic Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Integrated Imaging Program, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wenjun Guo
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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28
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Güven A, Kalebic N, Long KR, Florio M, Vaid S, Brandl H, Stenzel D, Huttner WB. Extracellular matrix-inducing Sox9 promotes both basal progenitor proliferation and gliogenesis in developing neocortex. eLife 2020; 9:49808. [PMID: 32191207 PMCID: PMC7105383 DOI: 10.7554/elife.49808] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 03/18/2020] [Indexed: 12/20/2022] Open
Abstract
Neocortex expansion is largely based on the proliferative capacity of basal progenitors (BPs), which is increased by extracellular matrix (ECM) components via integrin signaling. Here we show that the transcription factor Sox9 drives expression of ECM components and that laminin 211 increases BP proliferation in embryonic mouse neocortex. We show that Sox9 is expressed in human and ferret BPs and is required for BP proliferation in embryonic ferret neocortex. Conditional Sox9 expression in the mouse BP lineage, where it normally is not expressed, increases BP proliferation, reduces Tbr2 levels and induces Olig2 expression, indicative of premature gliogenesis. Conditional Sox9 expression also results in cell-non-autonomous stimulation of BP proliferation followed by increased upper-layer neuron production. Our findings demonstrate that Sox9 exerts concerted effects on transcription, BP proliferation, neuron production, and neurogenic vs. gliogenic BP cell fate, suggesting that Sox9 may have contributed to promote neocortical expansion.
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Affiliation(s)
- Ayse Güven
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nereo Kalebic
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Human Technopole, Milan, Italy
| | - Katherine R Long
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marta Florio
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Samir Vaid
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Holger Brandl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Denise Stenzel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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29
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Thierry GR, Gentek R, Bajenoff M. Remodeling of reactive lymph nodes: Dynamics of stromal cells and underlying chemokine signaling. Immunol Rev 2020; 289:42-61. [PMID: 30977194 DOI: 10.1111/imr.12750] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 01/28/2019] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
Abstract
Lymph nodes (LNs) are secondary immune organs dispersed throughout the body. They are primarily composed of lymphocytes, "transient passengers" that are only present for a few hours. During this time, they extensively interact with a meshwork of stromal cells. Although these cells constitute less than 5% of all LN cells, they are integral to LN function: Stromal cells create a three-dimensional network that provides a rigid backbone for the transport of lymph and generates "roads" for lymphocyte migration. Beyond structural support, the LN stroma also produces survival signals for lymphocytes and provides nutrients, soluble factors, antigens, and immune cells collectively required for immune surveillance and the generation of adaptive immune responses. A unique feature of LNs is their ability to considerably and rapidly change size: the volume and cellularity of inflamed LNs can increase up to 20-fold before returning to homeostatic levels. This cycle will be repeated many times during life and is accommodated by stromal cells. The dynamics underlying this dramatic remodeling are subject of this review. We will first introduce the main types of LN stromal cells and explain their known functions. We will then discuss how these cells enable LN growth during immune responses, with a particular focus on underlying cellular mechanisms and molecular cues. Similarly, we will elaborate on stromal dynamics mediating the return to LN homeostasis, a process that is mechanistically much less understood than LN expansion.
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Affiliation(s)
- Guilhem R Thierry
- Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, Marseille, France
| | - Rebecca Gentek
- Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, Marseille, France
| | - Marc Bajenoff
- Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, Marseille, France
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30
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Bulanenkova SS, Snezhkov EV, Akopov SB. SOX9 as One of the Central Units of Regulation Axis of Pancreas Embryogenesis and Cancer Progression. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2020. [DOI: 10.3103/s0891416819030030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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31
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Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J, Zaugg JB. Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. Nat Commun 2020; 11:124. [PMID: 31913281 PMCID: PMC6949242 DOI: 10.1038/s41467-019-13888-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/28/2019] [Indexed: 11/25/2022] Open
Abstract
Recent high-throughput transcription factor (TF) binding assays revealed that TF cooperativity is a widespread phenomenon. However, a global mechanistic and functional understanding of TF cooperativity is still lacking. To address this, here we introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data. We identify DNA shape as driver for cooperativity, with a particularly strong effect for Forkhead-Ets pairs. Follow-up experiments reveal a local shape preference at the Ets-DNA-Forkhead interface and decreased cooperativity upon loss of the interaction. Additionally, we discover many functional associations for cooperatively bound TFs. Examination of the link between FOXO1:ETV6 and lymphomas reveals that their joint expression levels improve patient clinical outcome stratification. Altogether, our results demonstrate that inter-family cooperative TF binding is driven by position-specific DNA readout mechanisms, which provides an additional regulatory layer for downstream biological functions. Although transcription factor (TF) cooperativity is widespread, a global mechanistic understanding of the role of TF cooperativity is still lacking. Here the authors introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data and provide mechanistic insights into TF cooperativity and its impact on protein-phenotype interactions.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Nele M Hollmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sandra Augsten
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Britta Velten
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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32
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Jana S, Madhu Krishna B, Singhal J, Horne D, Awasthi S, Salgia R, Singhal SS. SOX9: The master regulator of cell fate in breast cancer. Biochem Pharmacol 2020; 174:113789. [PMID: 31911091 DOI: 10.1016/j.bcp.2019.113789] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
SRY-related high-mobility group box 9 (SOX9) is an indispensable transcription factor that regulates multiple developmental pathways related to stemness, differentiation, and progenitor development. Previous studies have demonstrated that the SOX9 protein directs pathways involved in tumor initiation, proliferation, migration, chemoresistance, and stem cell maintenance, thereby regulating tumorigenesis as an oncogene. SOX9 overexpression is a frequent event in breast cancer (BC) subtypes. Of note, the molecular mechanisms and functional regulation underlying SOX9 upregulation during BC progression are still being uncovered. The focus of this review is to appraise recent advances regarding the involvement of SOX9 in BC pathogenesis. First, we provide a general overview of SOX9 structure and function, as well as its involvement in various kinds of cancer. Next, we discuss pathways of SOX9 regulation, particularly its miRNA-mediated regulation, in BC. Finally, we describe the involvement of SOX9 in BC pathogenesis via its regulation of pathways involved in regulating cancer hallmarks, as well as its clinical and therapeutic importance. In general, this review article aims to serve as an ample source of knowledge on the involvement of SOX9 in BC progression. Targeting SOX9 activity may improve therapeutic strategies to treat BC, but precisely inhibiting SOX9 using drugs and/or small peptides remains a huge challenge for forthcoming cancer research.
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Affiliation(s)
- Samir Jana
- Department of Medical Oncology, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - B Madhu Krishna
- Department of Medical Oncology, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Jyotsana Singhal
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sanjay Awasthi
- Department of Internal Medicine, Division of Hematology & Oncology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Ravi Salgia
- Department of Medical Oncology, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sharad S Singhal
- Department of Medical Oncology, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA.
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33
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Francis M, Cheng H, Ma P, Grider A. Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658. Biol Trace Elem Res 2019; 192:83-90. [PMID: 30734197 PMCID: PMC6685770 DOI: 10.1007/s12011-019-1650-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022]
Abstract
The zinc transcriptional regulatory element (ZTRE) is a newly reported binding motif for human zinc finger protein ZNF658, which alters gene expression in response to cellular zinc. The ZTRE has two nucleotide components-the palindromic flanking pairs and the bridging "N" bases between these flanks that range in number from 0 to 100. There are 12 pairs of ZTRE flanks (designated A-L). Three thousand five hundred twenty-five genes contain one or more ZTREs - 1000 to + 200 bp from their transcriptional start site (TSS). ZTRE-E is observed at a greater frequency, and ZTRE containing 25 bridging bases are less frequent, within - 200 bp from the TSS. The genes with ZTREs in this range are enriched in processes that may compensate zinc deficiency, while other genes with ZTREs outside this range are enriched in transcriptional activation processes. The division of ZTREs into two groups may imply a dual role of ZNF658, similar to the homologous yeast protein Zap1, via binding to low or high affinity sequences dependent upon cellular zinc. The KLF/Sp1-family binding motif is prevalent within the ZTRE "N" bridging bases, suggesting ZNF658 may compete with Sp1-like transactivators to suppress transcription.
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Affiliation(s)
- Michael Francis
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Huimin Cheng
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - Arthur Grider
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA.
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34
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Fufa TD, Baxter LL, Wedel JC, Gildea DE, Loftus SK, Pavan WJ. MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells. Epigenetics Chromatin 2019; 12:50. [PMID: 31399133 PMCID: PMC6688322 DOI: 10.1186/s13072-019-0297-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/28/2019] [Indexed: 01/03/2023] Open
Abstract
Background The MAPK/ERK signaling pathway is an essential regulator of numerous cell processes that are crucial for normal development as well as cancer progression. While much is known regarding MAPK/ERK signal conveyance from the cell membrane to the nucleus, the transcriptional and epigenetic mechanisms that govern gene expression downstream of MAPK signaling are not fully elucidated. Results This study employed an integrated epigenome analysis approach to interrogate the effects of MAPK/ERK pathway inhibition on the global transcriptome, the active chromatin landscape, and protein–DNA interactions in 501mel melanoma cells. Treatment of these cells with the small-molecule MEK inhibitor AZD6244 induces hyperpigmentation, widespread gene expression changes including alteration of genes linked to pigmentation, and extensive epigenomic reprogramming of transcriptionally distinct regulatory regions associated with the active chromatin mark H3K27ac. Regulatory regions with differentially acetylated H3K27ac regions following AZD6244 treatment are enriched in transcription factor binding motifs of ETV/ETS and ATF family members as well as the lineage-determining factors MITF and SOX10. H3K27ac-dense enhancer clusters known as super-enhancers show similar transcription factor motif enrichment, and furthermore, these super-enhancers are associated with genes encoding MITF, SOX10, and ETV/ETS proteins. Along with genome-wide resetting of the active enhancer landscape, MEK inhibition also results in widespread SOX10 recruitment throughout the genome, including increased SOX10 binding density at H3K27ac-marked enhancers. Importantly, these MEK inhibitor-responsive enhancers marked by H3K27ac and occupied by SOX10 are located near melanocyte lineage-specific and pigmentation genes and overlap numerous human SNPs associated with pigmentation and melanoma phenotypes, highlighting the variants located within these regions for prioritization in future studies. Conclusions These results reveal the epigenetic reprogramming underlying the re-activation of melanocyte pigmentation and developmental transcriptional programs in 501mel cells in response to MEK inhibition and suggest extensive involvement of a MEK-SOX10 axis in the regulation of these processes. The dynamic chromatin changes identified here provide a rich genomic resource for further analyses of the molecular mechanisms governing the MAPK pathway in pigmentation- and melanocyte-associated diseases. Electronic supplementary material The online version of this article (10.1186/s13072-019-0297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Temesgen D Fufa
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Derek E Gildea
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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35
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SOX9 in cartilage development and disease. Curr Opin Cell Biol 2019; 61:39-47. [PMID: 31382142 DOI: 10.1016/j.ceb.2019.07.008] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 07/06/2019] [Indexed: 12/18/2022]
Abstract
SOX9 is a pivotal transcription factor in chondrocytes, a lineage essential in skeletogenesis. Its mandatory role in transactivating many cartilage-specific genes is well established, whereas its pioneer role in lineage specification, which along with transactivation defines master transcription factors, remains to be better defined. Abundant, but yet incomplete evidence exists that intricate molecular networks control SOX9 activity during the multi-step chondrogenesis pathway. They include a highly modular genetic regulation, post-transcriptional and post-translational modifications, and varying sets of functional partners. Fully uncovering SOX9 actions and regulation is fundamental to explain mechanisms underlying many diseases that directly or indirectly affect SOX9 activities and to design effective disease treatments. We here review current knowledge, highlight recent discoveries, and propose new research directions to answer remaining questions.
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36
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Wang X, Srivastava Y, Jankowski A, Malik V, Wei Y, Del Rosario RC, Cojocaru V, Prabhakar S, Jauch R. DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1. Nucleic Acids Res 2019; 46:5470-5486. [PMID: 29669022 PMCID: PMC6009666 DOI: 10.1093/nar/gky259] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2018] [Indexed: 12/16/2022] Open
Abstract
FOXA1 is a transcription factor capable to bind silenced chromatin to direct context-dependent cell fate conversion. Here, we demonstrate that a compact palindromic DNA element (termed 'DIV' for its diverging half-sites) induces the homodimerization of FOXA1 with strongly positive cooperativity. Alternative structural models are consistent with either an indirect DNA-mediated cooperativity or a direct protein-protein interaction. The cooperative homodimer formation is strictly constrained by precise half-site spacing. Re-analysis of chromatin immunoprecipitation sequencing data indicates that the DIV is effectively targeted by FOXA1 in the context of chromatin. Reporter assays show that FOXA1-dependent transcriptional activity declines when homodimeric binding is disrupted. In response to phosphatidylinositol-3 kinase inhibition DIV sites pre-bound by FOXA1 such as at the PVT1/MYC locus exhibit a strong increase in accessibility suggesting a role of the DIV configuration in the chromatin closed-open dynamics. Moreover, several disease-associated single nucleotide polymorphisms map to DIV elements and show allelic differences in FOXA1 homodimerization, reporter gene expression and are annotated as quantitative trait loci. This includes the rs541455835 variant at the MAPT locus encoding the Tau protein associated with Parkinson's disease. Collectively, the DIV guides chromatin engagement and regulation by FOXA1 and its perturbation could be linked to disease etiologies.
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Affiliation(s)
- Xuecong Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yogesh Srivastava
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aleksander Jankowski
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warszawa, Poland.,Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanjie Wei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ricardo Ch Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge MA 02142, USA
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany.,Center for Multiscale Theory and Computation, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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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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38
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Aguilar-Medina M, Avendaño-Félix M, Lizárraga-Verdugo E, Bermúdez M, Romero-Quintana JG, Ramos-Payan R, Ruíz-García E, López-Camarillo C. SOX9 Stem-Cell Factor: Clinical and Functional Relevance in Cancer. JOURNAL OF ONCOLOGY 2019; 2019:6754040. [PMID: 31057614 PMCID: PMC6463569 DOI: 10.1155/2019/6754040] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/15/2022]
Abstract
Transcriptional and epigenetic embryonic programs can be reactivated in cancer cells. As result, a specific subset of undifferentiated cells with stem-cells properties emerges and drives tumorigenesis. Recent findings have shown that ectoderm- and endoderm-derived tissues continue expressing stem-cells related transcription factors of the SOX-family of proteins such as SOX2 and SOX9 which have been implicated in the presence of cancer stem-like cells (CSCs) in tumors. Currently, there is enough evidence suggesting an oncogenic role for SOX9 in different types of human cancers. This review provides a summary of the current knowledge about the involvement of SOX9 in development and progression of cancer. Understanding the functional roles of SOX9 and clinical relevance is crucial for developing novel treatments targeting CSCs in cancer.
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Affiliation(s)
- Maribel Aguilar-Medina
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Mariana Avendaño-Félix
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Erik Lizárraga-Verdugo
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Mercedes Bermúdez
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | | | - Rosalío Ramos-Payan
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Erika Ruíz-García
- Laboratorio de Medicina Traslacional y Departamento de Tumores Gastro-Intestinales, Instituto Nacional de Cancerología. CDMX, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX, Mexico
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39
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Domenici G, Aurrekoetxea-Rodríguez I, Simões BM, Rábano M, Lee SY, Millán JS, Comaills V, Oliemuller E, López-Ruiz JA, Zabalza I, Howard BA, Kypta RM, Vivanco MDM. A Sox2-Sox9 signalling axis maintains human breast luminal progenitor and breast cancer stem cells. Oncogene 2019; 38:3151-3169. [PMID: 30622340 PMCID: PMC6756022 DOI: 10.1038/s41388-018-0656-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/12/2018] [Accepted: 12/07/2018] [Indexed: 01/02/2023]
Abstract
Increased cancer stem cell content during development of resistance to tamoxifen in breast cancer is driven by multiple signals, including Sox2-dependent activation of Wnt signalling. Here, we show that Sox2 increases and estrogen reduces the expression of the transcription factor Sox9. Gain and loss of function assays indicate that Sox9 is implicated in the maintenance of human breast luminal progenitor cells. CRISPR/Cas knockout of Sox9 reduces growth of tamoxifen-resistant breast tumours in vivo. Mechanistically, Sox9 acts downstream of Sox2 to control luminal progenitor cell content and is required for expression of the cancer stem cell marker ALDH1A3 and Wnt signalling activity. Sox9 is elevated in breast cancer patients after endocrine therapy failure. This new regulatory axis highlights the relevance of SOX family transcription factors as potential therapeutic targets in breast cancer.
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Affiliation(s)
| | | | - Bruno M Simões
- CIC bioGUNE, Technological Park Bizkaia, Derio, 48160, Spain
| | - Miriam Rábano
- CIC bioGUNE, Technological Park Bizkaia, Derio, 48160, Spain
| | - So Young Lee
- CIC bioGUNE, Technological Park Bizkaia, Derio, 48160, Spain
| | | | | | - Erik Oliemuller
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ignacio Zabalza
- Department of Pathology, Galdakao-Usansolo Hospital, Galdakao, Spain
| | - Beatrice A Howard
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Robert M Kypta
- CIC bioGUNE, Technological Park Bizkaia, Derio, 48160, Spain.,Department of Surgery and Cancer, Imperial College London, London, UK
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40
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sox9b is required in cardiomyocytes for cardiac morphogenesis and function. Sci Rep 2018; 8:13906. [PMID: 30224706 PMCID: PMC6141582 DOI: 10.1038/s41598-018-32125-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/03/2018] [Indexed: 12/18/2022] Open
Abstract
The high mobility group transcription factor SOX9 is expressed in stem cells, progenitor cells, and differentiated cell-types in developing and mature organs. Exposure to a variety of toxicants including dioxin, di(2-ethylhexyl) phthalate, 6:2 chlorinated polyfluorinated ether sulfonate, and chlorpyrifos results in the downregulation of tetrapod Sox9 and/or zebrafish sox9b. Disruption of Sox9/sox9b function through environmental exposures or genetic mutations produce a wide range of phenotypes and adversely affect organ development and health. We generated a dominant-negative sox9b (dnsox9b) to inhibit sox9b target gene expression and used the Gal4/UAS system to drive dnsox9b specifically in cardiomyocytes. Cardiomyocyte-specific inhibition of sox9b function resulted in a decrease in ventricular cardiomyocytes, an increase in atrial cardiomyocytes, hypoplastic endothelial cushions, and impaired epicardial development, ultimately culminating in heart failure. Cardiomyocyte-specific dnsox9b expression significantly reduced end diastolic volume, which corresponded with a decrease in stroke volume, ejection fraction, and cardiac output. Further analysis of isolated cardiac tissue by RT-qPCR revealed cardiomyocyte-specific inhibition of sox9b function significantly decreased the expression of the critical cardiac development genes nkx2.5, nkx2.7, and myl7, as well as c-fos, an immediate early gene necessary for cardiomyocyte progenitor differentiation. Together our studies indicate sox9b transcriptional regulation is necessary for cardiomyocyte development and function.
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41
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Rodda LB, Lu E, Bennett ML, Sokol CL, Wang X, Luther SA, Barres BA, Luster AD, Ye CJ, Cyster JG. Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity. Immunity 2018; 48:1014-1028.e6. [PMID: 29752062 DOI: 10.1016/j.immuni.2018.04.006] [Citation(s) in RCA: 277] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/23/2017] [Accepted: 04/02/2018] [Indexed: 01/06/2023]
Abstract
Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing, we identified nine peripheral LN non-endothelial SC clusters. Included are the established subsets, Ccl19hi T-zone reticular cells (TRCs), marginal reticular cells, follicular dendritic cells (FDCs), and perivascular cells. We also identified Ccl19lo TRCs, likely including cholesterol-25-hydroxylase+ cells located at the T-zone perimeter, Cxcl9+ TRCs in the T-zone and interfollicular region, CD34+ SCs in the capsule and medullary vessel adventitia, indolethylamine N-methyltransferase+ SCs in the medullary cords, and Nr4a1+ SCs in several niches. These data help define how transcriptionally distinct LN SCs support niche-restricted immune functions and provide evidence that many SCs are in an activated state.
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Affiliation(s)
- Lauren B Rodda
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Erick Lu
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mariko L Bennett
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caroline L Sokol
- Center for Immunology & Inflammatory Diseases, Division of Rheumatology, Allergy & Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Xiaoming Wang
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Sanjiv A Luther
- Department of Biochemistry, Center for Immunity and Infection, University of Lausanne, 1066 Epalinges, Switzerland
| | - Ben A Barres
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew D Luster
- Center for Immunology & Inflammatory Diseases, Division of Rheumatology, Allergy & Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jason G Cyster
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
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42
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True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy. Nat Commun 2018; 9:1605. [PMID: 29686282 PMCID: PMC5913336 DOI: 10.1038/s41467-018-03977-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/16/2018] [Indexed: 01/31/2023] Open
Abstract
The complex patterns of gene expression in metazoans are controlled by selective binding of transcription factors (TFs) to regulatory DNA. To improve the quantitative understanding of this process, we have developed a novel method that uses fluorescence anisotropy measurements in a controlled delivery system to determine TF-DNA binding energies in solution with high sensitivity and throughput. Owing to its large dynamic range, the method, named high performance fluorescence anisotropy (HiP-FA), allows for reliable quantification of both weak and strong binding; binding specificities are calculated on the basis of equilibrium constant measurements for mutational DNA variants. We determine the binding preference landscapes for 26 TFs and measure high absolute affinities, but mostly lower binding specificities than reported by other methods. The revised binding preferences give rise to improved predictions of in vivo TF occupancy and enhancer expression. Our approach provides a powerful new tool for the systems-biological analysis of gene regulation. Methods to measure selective transcription factor-DNA binding often lack sensitivity and are not performed in solution. Here the authors develop a method to perform fluorescence anisotropy measurements of transcription factor-DNA binding energies with high sensitivity and throughput.
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43
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Fontaine FR, Goodall S, Prokop JW, Howard CB, Moustaqil M, Kumble S, Rasicci DT, Osborne GW, Gambin Y, Sierecki E, Jones ML, Zuegg J, Mahler S, Francois M. Functional domain analysis of SOX18 transcription factor using a single-chain variable fragment-based approach. MAbs 2018; 10:596-606. [PMID: 29648920 PMCID: PMC5972640 DOI: 10.1080/19420862.2018.1451288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibodies are routinely used to study the activity of transcription factors, using various in vitro and in vivo approaches such as electrophoretic mobility shift assay, enzyme-linked immunosorbent assay, genome-wide method analysis coupled with next generation sequencing, or mass spectrometry. More recently, a new application for antibodies has emerged as crystallisation scaffolds for difficult to crystallise proteins, such as transcription factors. Only in a few rare cases, antibodies have been used to modulate the activity of transcription factors, and there is a real gap in our knowledge on how to efficiently design antibodies to interfere with transcription. The molecular function of transcription factors is underpinned by complex networks of protein-protein interaction and in theory, setting aside intra-cellular delivery challenges, developing antibody-based approaches to modulate transcription factor activity appears a viable option. Here, we demonstrate that antibodies or an antibody single-chain variable region fragments are powerful molecular tools to unravel complex protein-DNA and protein-protein binding mechanisms. In this study, we focus on the molecular mode of action of the transcription factor SOX18, a key modulator of endothelial cell fate during development, as well as an attractive target in certain pathophysiological conditions such as solid cancer metastasis. The engineered antibody we designed inhibits SOX18 transcriptional activity, by interfering specifically with an 8-amino-acid motif in the C-terminal region directly adjacent to α-Helix 3 of SOX18 HMG domain, thereby disrupting protein-protein interaction. This new approach establishes a framework to guide the study of transcription factors interactomes using antibodies as molecular handles.
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Affiliation(s)
- Frank R Fontaine
- a Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Stephen Goodall
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia
| | - Jeremy W Prokop
- c HudsonAlpha Institute for Biotechnology , Huntsville AL , USA.,d Department of Pediatrics and Human Development , Michigan State University , East Lansing , MI , USA
| | - Christopher B Howard
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia.,e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Mehdi Moustaqil
- f Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales , Sydney , NSW , Australia
| | - Sumukh Kumble
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia.,e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | | | - Geoffrey W Osborne
- e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Yann Gambin
- f Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales , Sydney , NSW , Australia
| | - Emma Sierecki
- f Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales , Sydney , NSW , Australia
| | - Martina L Jones
- e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Johannes Zuegg
- a Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Stephen Mahler
- b Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , QLD , Australia.,e ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia , QLD , Australia
| | - Mathias Francois
- a Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
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44
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Tan Z, Niu B, Tsang KY, Melhado IG, Ohba S, He X, Huang Y, Wang C, McMahon AP, Jauch R, Chan D, Zhang MQ, Cheah KSE. Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PLoS Genet 2018; 14:e1007346. [PMID: 29659575 PMCID: PMC5919691 DOI: 10.1371/journal.pgen.1007346] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/26/2018] [Accepted: 03/29/2018] [Indexed: 11/18/2022] Open
Abstract
The growth plate mediates bone growth where SOX9 and GLI factors control chondrocyte proliferation, differentiation and entry into hypertrophy. FOXA factors regulate hypertrophic chondrocyte maturation. How these factors integrate into a Gene Regulatory Network (GRN) controlling these differentiation transitions is incompletely understood. We adopted a genome-wide whole tissue approach to establish a Growth Plate Differential Gene Expression Library (GP-DGEL) for fractionated proliferating, pre-hypertrophic, early and late hypertrophic chondrocytes, as an overarching resource for discovery of pathways and disease candidates. De novo motif discovery revealed the enrichment of SOX9 and GLI binding sites in the genes preferentially expressed in proliferating and prehypertrophic chondrocytes, suggesting the potential cooperation between SOX9 and GLI proteins. We integrated the analyses of the transcriptome, SOX9, GLI1 and GLI3 ChIP-seq datasets, with functional validation by transactivation assays and mouse mutants. We identified new SOX9 targets and showed SOX9-GLI directly and cooperatively regulate many genes such as Trps1, Sox9, Sox5, Sox6, Col2a1, Ptch1, Gli1 and Gli2. Further, FOXA2 competes with SOX9 for the transactivation of target genes. The data support a model of SOX9-GLI-FOXA phasic GRN in chondrocyte development. Together, SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon hypertrophy, FOXA competes with SOX9, and control toward terminal differentiation passes to FOXA, RUNX, AP1 and MEF2 factors. In the development of the mammalian growth plate, while several transcription factors are individually well known for their key roles in regulating phases of chondrocyte differentiation, there is little information on how they interact and cooperate with each other. We took an unbiased genome wide approach to identify the transcription factors and signaling pathways that play dominant roles in the chondrocyte differentiation cascade. We developed a searchable library of differentially expressed genes, GP-DGEL, which has fine spatial resolution and global transcriptomic coverage for discovery of processes, pathways and disease candidates. Our work identifies a novel regulatory mechanism that integrates the action of three transcription factors, SOX9, GLI and FOXA. SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon entry into prehypertrophy, FOXA competes with SOX9, and control of hypertrophy passes to FOXA, RUNX, AP1 and MEF2 factors.
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Affiliation(s)
- Zhijia Tan
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Ben Niu
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Kwok Yeung Tsang
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Ian G. Melhado
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Shinsuke Ohba
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, United States of America
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, United States of America
| | - Yongheng Huang
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Cheng Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine of the University of Southern California, Los Angeles, California, United States of America
| | - Ralf Jauch
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Danny Chan
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
| | - Michael Q. Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Dallas, Texas, United States of America
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, China
| | - Kathryn S. E. Cheah
- School of Biomedical Sciences, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong
- * E-mail:
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Portnoi MF, Dumargne MC, Rojo S, Witchel SF, Duncan AJ, Eozenou C, Bignon-Topalovic J, Yatsenko SA, Rajkovic A, Reyes-Mugica M, Almstrup K, Fusee L, Srivastava Y, Chantot-Bastaraud S, Hyon C, Louis-Sylvestre C, Validire P, de Malleray Pichard C, Ravel C, Christin-Maitre S, Brauner R, Rossetti R, Persani L, Charreau EH, Dain L, Chiauzzi VA, Mazen I, Rouba H, Schluth-Bolard C, MacGowan S, McLean WHI, Patin E, Rajpert-De Meyts E, Jauch R, Achermann JC, Siffroi JP, McElreavey K, Bashamboo A. Mutations involving the SRY-related gene SOX8 are associated with a spectrum of human reproductive anomalies. Hum Mol Genet 2018; 27:1228-1240. [PMID: 29373757 PMCID: PMC6159538 DOI: 10.1093/hmg/ddy037] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/14/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022] Open
Abstract
SOX8 is an HMG-box transcription factor closely related to SRY and SOX9. Deletion of the gene encoding Sox8 in mice causes reproductive dysfunction but the role of SOX8 in humans is unknown. Here, we show that SOX8 is expressed in the somatic cells of the early developing gonad in the human and influences human sex determination. We identified two individuals with 46, XY disorders/differences in sex development (DSD) and chromosomal rearrangements encompassing the SOX8 locus and a third individual with 46, XY DSD and a missense mutation in the HMG-box of SOX8. In vitro functional assays indicate that this mutation alters the biological activity of the protein. As an emerging body of evidence suggests that DSDs and infertility can have common etiologies, we also analysed SOX8 in a cohort of infertile men (n = 274) and two independent cohorts of women with primary ovarian insufficiency (POI; n = 153 and n = 104). SOX8 mutations were found at increased frequency in oligozoospermic men (3.5%; P < 0.05) and POI (5.06%; P = 4.5 × 10-5) as compared with fertile/normospermic control populations (0.74%). The mutant proteins identified altered SOX8 biological activity as compared with the wild-type protein. These data demonstrate that SOX8 plays an important role in human reproduction and SOX8 mutations contribute to a spectrum of phenotypes including 46, XY DSD, male infertility and 46, XX POI.
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Affiliation(s)
- Marie-France Portnoi
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | | | - Sandra Rojo
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | - Selma F Witchel
- Division of Pediatric Endocrinology, Children’s Hospital of Pittsburgh
of UPMC, Pittsburgh, PA 15224, USA
| | - Andrew J Duncan
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of
Child Health, London WC1N 1EH, UK
| | - Caroline Eozenou
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | | | - Svetlana A Yatsenko
- Department of Obstetrics, Gynecology and Reproductive Sciences,
Magee-Women’s Research Institute
- Department of Human Genetics, University of Pittsburgh School of
Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine,
Pittsburgh, PA 15213, USA
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology and Reproductive Sciences,
Magee-Women’s Research Institute
- Department of Human Genetics, University of Pittsburgh School of
Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine,
Pittsburgh, PA 15213, USA
| | - Miguel Reyes-Mugica
- Department of Obstetrics, Gynecology and Reproductive Sciences,
Magee-Women’s Research Institute
- Department of Human Genetics, University of Pittsburgh School of
Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine,
Pittsburgh, PA 15213, USA
| | - Kristian Almstrup
- University Department of Growth and Reproduction, Rigshospitalet,
DK-2100 Copenhagen, Denmark
| | - Leila Fusee
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China
Institute for Stem Cell Biology and Regenerative Medicine, 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
| | - Sandra Chantot-Bastaraud
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | - Capucine Hyon
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | | | - Pierre Validire
- Département d’Anatomie Pathologique, Institut Mutualiste Montsouris,
Paris 75014, France
| | | | - Celia Ravel
- Biology of Reproduction, CHU Rennes, Rennes 35033, France
| | - Sophie Christin-Maitre
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
- Service d'Endocrinologie, Diabétologie et Endocrinologie de la
Reproduction, Hôpital Saint-Antoine, Paris 75012, France
| | - Raja Brauner
- Université Paris Descartes and Pediatric Endocrinology Unit, Fondation
Ophtalmologique Adolphe de Rothschild, Paris 75019, France
| | - Raffaella Rossetti
- Department of Clinical Sciences & Community Health, University of
Milan, Milan 20122, Italy
- Laboratory of Endocrine & Metabolic Research and Division of
Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan 20149,
Italy
| | - Luca Persani
- Department of Clinical Sciences & Community Health, University of
Milan, Milan 20122, Italy
- Laboratory of Endocrine & Metabolic Research and Division of
Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan 20149,
Italy
| | - Eduardo H Charreau
- Centro Nacional de Genética Médica, Administración Nacional de
Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires C1428ADN,
Argentina
- Department of Physiology, Instituto de Biología y Medicina
Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (IBYME-CONICET),
Buenos Aires C1428ADN, Argentina
| | - Liliana Dain
- Centro Nacional de Genética Médica, Administración Nacional de
Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires C1428ADN,
Argentina
- Department of Physiology, Instituto de Biología y Medicina
Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (IBYME-CONICET),
Buenos Aires C1428ADN, Argentina
| | - Violeta A Chiauzzi
- Centro Nacional de Genética Médica, Administración Nacional de
Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires C1428ADN,
Argentina
- Department of Physiology, Instituto de Biología y Medicina
Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (IBYME-CONICET),
Buenos Aires C1428ADN, Argentina
| | - Inas Mazen
- Department of Clinical Genetics, National Research Centre, Cairo 12622,
Egypt
| | - Hassan Rouba
- Human Genetics Unit, Institut Pasteur of Morocco, Casablanca 20250,
Morocco
| | | | - Stuart MacGowan
- Centre for Dermatology and Genetic Medicine, School of Life Sciences,
University of Dundee, Dundee DD1 5EH, UK
| | - W H Irwin McLean
- Centre for Dermatology and Genetic Medicine, School of Life Sciences,
University of Dundee, Dundee DD1 5EH, UK
| | - Etienne Patin
- Human Evolutionary Genetics, Institut Pasteur, Paris 75724,
France
| | - Ewa Rajpert-De Meyts
- University Department of Growth and Reproduction, Rigshospitalet,
DK-2100 Copenhagen, Denmark
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China
Institute for Stem Cell Biology and Regenerative Medicine, 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
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of
Child Health, London WC1N 1EH, UK
| | - Jean-Pierre Siffroi
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | - Ken McElreavey
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | - Anu Bashamboo
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
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46
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Cronin JC, Loftus SK, Baxter LL, Swatkoski S, Gucek M, Pavan WJ. Identification and functional analysis of SOX10 phosphorylation sites in melanoma. PLoS One 2018; 13:e0190834. [PMID: 29315345 PMCID: PMC5760019 DOI: 10.1371/journal.pone.0190834] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/20/2017] [Indexed: 12/17/2022] Open
Abstract
The transcription factor SOX10 plays an important role in vertebrate neural crest development, including the establishment and maintenance of the melanocyte lineage. SOX10 is also highly expressed in melanoma tumors, and SOX10 expression increases with tumor progression. The suppression of SOX10 in melanoma cells activates TGF-β signaling and can promote resistance to BRAF and MEK inhibitors. Since resistance to BRAF/MEK inhibitors is seen in the majority of melanoma patients, there is an immediate need to assess the underlying biology that mediates resistance and to identify new targets for combinatorial therapeutic approaches. Previously, we demonstrated that SOX10 protein is required for tumor initiation, maintenance and survival. Here, we present data that support phosphorylation as a mechanism employed by melanoma cells to tightly regulate SOX10 expression. Mass spectrometry identified eight phosphorylation sites contained within SOX10, three of which (S24, S45 and T240) were selected for further analysis based on their location within predicted MAPK/CDK binding motifs. SOX10 mutations were generated at these phosphorylation sites to assess their impact on SOX10 protein function in melanoma cells, including transcriptional activation on target promoters, subcellular localization, and stability. These data further our understanding of SOX10 protein regulation and provide critical information for identification of molecular pathways that modulate SOX10 protein levels in melanoma, with the ultimate goal of discovering novel targets for more effective combinatorial therapeutic approaches for melanoma patients.
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Affiliation(s)
- Julia C. Cronin
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Laura L. Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Steve Swatkoski
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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47
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Julian LM, McDonald AC, Stanford WL. Direct reprogramming with SOX factors: masters of cell fate. Curr Opin Genet Dev 2017; 46:24-36. [PMID: 28662445 DOI: 10.1016/j.gde.2017.06.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/25/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]
Abstract
Over the last decade significant advances have been made toward reprogramming the fate of somatic cells, typically by overexpression of cell lineage-determinant transcription factors. As key regulators of cell fate, the SOX family of transcription factors has emerged as potent drivers of direct somatic cell reprogramming into multiple lineages, in some cases as the sole overexpressed factor. The vast capacity of SOX factors, especially those of the SOXB1, E and F subclasses, to reprogram cell fate is enlightening our understanding of organismal development, cancer and disease, and offers tremendous potential for regenerative medicine and cell-based therapies. Understanding the molecular mechanisms through which SOX factors reprogram cell fate is essential to optimize the development of novel somatic cell transdifferentiation strategies.
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Affiliation(s)
- Lisa M Julian
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1L8L6, Canada
| | - Angela Ch McDonald
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G0A4, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S3G9, Canada
| | - William L Stanford
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1L8L6, Canada; Department of Cellular and Molecular Medicine, Faulty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faulty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada.
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48
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Symon A, Harley V. SOX9: A genomic view of tissue specific expression and action. Int J Biochem Cell Biol 2017; 87:18-22. [DOI: 10.1016/j.biocel.2017.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 03/09/2017] [Accepted: 03/11/2017] [Indexed: 11/29/2022]
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49
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Forés M, Simón-Carrasco L, Ajuria L, Samper N, González-Crespo S, Drosten M, Barbacid M, Jiménez G. A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer. PLoS Genet 2017; 13:e1006622. [PMID: 28278156 PMCID: PMC5344332 DOI: 10.1371/journal.pgen.1006622] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/08/2017] [Indexed: 11/19/2022] Open
Abstract
HMG-box proteins, including Sox/SRY (Sox) and TCF/LEF1 (TCF) family members, bind DNA via their HMG-box. This binding, however, is relatively weak and both Sox and TCF factors employ distinct mechanisms for enhancing their affinity and specificity for DNA. Here we report that Capicua (CIC), an HMG-box transcriptional repressor involved in Ras/MAPK signaling and cancer progression, employs an additional distinct mode of DNA binding that enables selective recognition of its targets. We find that, contrary to previous assumptions, the HMG-box of CIC does not bind DNA alone but instead requires a distant motif (referred to as C1) present at the C-terminus of all CIC proteins. The HMG-box and C1 domains are both necessary for binding specific TGAATGAA-like sites, do not function via dimerization, and are active in the absence of cofactors, suggesting that they form a bipartite structure for sequence-specific binding to DNA. We demonstrate that this binding mechanism operates throughout Drosophila development and in human cells, ensuring specific regulation of multiple CIC targets. It thus appears that HMG-box proteins generally depend on auxiliary DNA binding mechanisms for regulating their appropriate genomic targets, but that each sub-family has evolved unique strategies for this purpose. Finally, the key role of C1 in DNA binding also explains the fact that this domain is a hotspot for inactivating mutations in oligodendroglioma and other tumors, while being preserved in oncogenic CIC-DUX4 fusion chimeras associated to Ewing-like sarcomas.
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Affiliation(s)
- Marta Forés
- Institut de Biologia Molecular de Barcelona-CSIC, Barcelona, Spain
| | - Lucía Simón-Carrasco
- Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Leiore Ajuria
- Institut de Biologia Molecular de Barcelona-CSIC, Barcelona, Spain
| | - Núria Samper
- Institut de Biologia Molecular de Barcelona-CSIC, Barcelona, Spain
| | | | - Matthias Drosten
- Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Mariano Barbacid
- Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Gerardo Jiménez
- Institut de Biologia Molecular de Barcelona-CSIC, Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail:
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50
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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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