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Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Cesare J, Bhattacharya S, Arvindekar S, Lange JJ, Xie Y, Garcia BA, Slaughter BD, Unruh JR, Viswanath S, Florens L, Workman JL, Washburn MP. An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome. Proc Natl Acad Sci U S A 2024; 121:e2318601121. [PMID: 39116123 PMCID: PMC11331135 DOI: 10.1073/pnas.2318601121] [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: 11/06/2023] [Accepted: 06/21/2024] [Indexed: 08/10/2024] Open
Abstract
Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected 149 pairs of cross-links between WDR76, SPIN1, and histones, we then built an integrated structural model of the complex where SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we used the powerful Bayesian Integrative Modeling approach as implemented in the Integrative Modeling Platform to build a model of WDR76 and SPIN1 bound to the nucleosome.
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Affiliation(s)
- Xingyu Liu
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Zhihui Wen
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Joseph Cesare
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Medical Scientist Training Program, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66150
| | | | - Shreyas Arvindekar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University St. Louis School of Medicine, St. Louis, MO 63110
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University St. Louis School of Medicine, St. Louis, MO 63110
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Shruthi Viswanath
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110
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2
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Wang Y, Li M, Chen Y, Jiang Y, Zhang Z, Yan Z, Liu X, Wu C. SPIN1 facilitates chemoresistance and HR repair by promoting Tip60 binding to H3K9me3. EMBO Rep 2024:10.1038/s44319-024-00219-1. [PMID: 39090319 DOI: 10.1038/s44319-024-00219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
The tandem Tudor-like domain-containing protein Spindlin1 (SPIN1) is a transcriptional coactivator with critical functions in embryonic development and emerging roles in cancer. However, the involvement of SPIN1 in DNA damage repair has remained unclear. Our study shows that SPIN1 is recruited to DNA lesions through its N-terminal disordered region that binds to Poly-ADP-ribose (PAR), and facilitates homologous recombination (HR)-mediated DNA damage repair. SPIN1 promotes H3K9me3 accumulation at DNA damage sites and enhances the interaction between H3K9me3 and Tip60, thereby promoting the activation of ATM and HR repair. We also show that SPIN1 increases chemoresistance. These findings reveal a novel role for SPIN1 in the activation of H3K9me3-dependent DNA repair pathways, and suggest that SPIN1 may contribute to cancer chemoresistance by modulating the efficiency of double-strand break (DSB) repair.
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Affiliation(s)
- Yukun Wang
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - Mengyao Li
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - Yuhan Chen
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - Yuhan Jiang
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - Ziyu Zhang
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - Zhenzhen Yan
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China.
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China.
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3
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Moore T. X centromeric drive may explain the prevalence of polycystic ovary syndrome and other conditions: Genomic structure of the human X chromosome pericentromeric region is consistent with meiotic drive associated with PCOS and other conditions. Bioessays 2024:e2400056. [PMID: 39072829 DOI: 10.1002/bies.202400056] [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: 03/12/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024]
Abstract
X chromosome centromeric drive may explain the prevalence of polycystic ovary syndrome and contribute to oocyte aneuploidy, menopause, and other conditions. The mammalian X chromosome may be vulnerable to meiotic drive because of X inactivation in the female germline. The human X pericentromeric region contains genes potentially involved in meiotic mechanisms, including multiple SPIN1 and ZXDC paralogs. This is consistent with a multigenic drive system comprising differential modification of the active and inactive X chromosome centromeres in female primordial germ cells and preferential segregation of the previously inactivated X chromosome centromere to the polar body at meiosis I. The drive mechanism may explain differences in X chromosome regulation in the female germlines of the human and mouse and, based on the functions encoded by the genes in the region, the transmission of X pericentromeric genetic or epigenetic variants to progeny could contribute to preeclampsia, autism, and differences in sexual differentiation.
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Affiliation(s)
- Tom Moore
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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4
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Zhao F, Deng Y, Yang F, Yan Y, Feng F, Peng B, Gao J, Bedford MT, Li H. Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation. J Mol Biol 2024; 436:168371. [PMID: 37977297 DOI: 10.1016/j.jmb.2023.168371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Spindlin1 is a histone reader with three Tudor-like domains and its transcriptional co-activator activity could be attenuated by SPINDOC. The first two Tudors are involved in histone methylation readout, while the function of Tudor 3 is largely unknown. Here our structural and binding studies revealed an engagement mode of SPINDOC-Spindlin1, in which a hydrophobic motif of SPINDOC, DOCpep3, stably interacts with Spindlin1 Tudor 3, and two neighboring K/R-rich motifs, DOCpep1 and DOCpep2, bind to the acidic surface of Spindlin1 Tudor 2. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPINDOC fragment containing the K/R-rich region attenuates histone or TCF4 binding by Spindlin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 "K4me3-K9me3" bivalent mark. Further ChIP-seq and RT-qPCR indicated that SPINDOC could promote genomic relocation of Spindlin1, thus modulate downstream gene transcription. Collectively, we revealed multivalent engagement between SPINDOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPINDOC-Spindlin1 association, while K/R-rich region modulates the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activity of Spindlin1.
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Affiliation(s)
- Fan Zhao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yafang Deng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fen Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Yan Yan
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Fan Feng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo Peng
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China.
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Haitao Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, MOE Key Laboratory of Coal Environmental Pathogenesis and Prevention, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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5
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Dabrowski KR, Floris G, Gillespie A, Daws SE. Orbitofrontal intronic circular RNA from Nrxn3 mediates reward learning and motivation for reward. Prog Neurobiol 2024; 232:102546. [PMID: 38036039 PMCID: PMC10843848 DOI: 10.1016/j.pneurobio.2023.102546] [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: 07/17/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
The orbitofrontal cortex (OFC) is a vital component of brain reward circuitry that is important for reward seeking behavior. However, OFC-mediated molecular mechanisms underlying rewarding behavior are understudied. Here, we report the first circular RNA (circRNA) profile associated with appetitive reward and identify regulation of 92 OFC circRNAs by sucrose self-administration. Among these changes, we observed downregulation of circNrxn3, a circRNA originating from neurexin 3 (Nrxn3), a gene involved in synaptogenesis, learning, and memory. Transcriptomic profiling via RNA sequencing and qPCR of the OFC following in vivo knock-down of circNrxn3 revealed differential regulation of genes associated with pathways important for learning and memory and altered splicing of Nrxn3. Furthermore, circNrxn3 knock-down enhanced sucrose self-administration and motivation for sucrose. Using RNA-immunoprecipitation, we report binding of circNrxn3 to the known Nrxn3 splicing factor SAM68. circNrxn3 is the first reported circRNA capable of regulating reward behavior and circNrxn3-mediated interactions with SAM68 may impact subsequent downstream processing of RNAs such as the regulation of gene expression and splicing.
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Affiliation(s)
- Konrad R Dabrowski
- Center for Substance Abuse Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA; Department of Biology, Temple University, Philadelphia, PA, USA
| | - Gabriele Floris
- Center for Substance Abuse Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA; Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Aria Gillespie
- Center for Substance Abuse Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA; Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Stephanie E Daws
- Center for Substance Abuse Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA; Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
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6
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Drastichova Z, Trubacova R, Novotny J. Regulation of phosphosignaling pathways involved in transcription of cell cycle target genes by TRH receptor activation in GH1 cells. Biomed Pharmacother 2023; 168:115830. [PMID: 37931515 DOI: 10.1016/j.biopha.2023.115830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Thyrotropin-releasing hormone (TRH) is known to activate several cellular signaling pathway, but the activation of the TRH receptor (TRH-R) has not been reported to regulate gene transcription. The aim of this study was to identify phosphosignaling pathways and phosphoprotein complexes associated with gene transcription in GH1 pituitary cells treated with TRH or its analog, taltirelin (TAL), using label-free bottom-up mass spectrometry-based proteomics. Our detailed analysis provided insight into the mechanism through which TRH-R activation may regulate the transcription of genes related to the cell cycle and proliferation. It involves control of the signaling pathways for β-catenin/Tcf, Notch/RBPJ, p53/p21/Rbl2/E2F, Myc, and YY1/Rb1/E2F through phosphorylation and dephosphorylation of their key components. In many instances, the phosphorylation patterns of differentially phosphorylated phosphoproteins in TRH- or TAL-treated cells were identical or displayed a similar trend in phosphorylation. However, some phosphoproteins, especially components of the Wnt/β-catenin/Tcf and YY1/Rb1/E2F pathways, exhibited different phosphorylation patterns in TRH- and TAL-treated cells. This supports the notion that TRH and TAL may act, at least in part, as biased agonists. Additionally, the deficiency of β-arrestin2 resulted in a reduced number of alterations in phosphorylation, highlighting the critical role of β-arrestin2 in the signal transduction from TRH-R in the plasma membrane to transcription factors in the nucleus.
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Affiliation(s)
- Zdenka Drastichova
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia
| | - Radka Trubacova
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia; Institute of Physiology, Czech Academy of Sciences, 142 20 Prague, Czechia
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia.
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7
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Lui JC, Wagner J, Zhou E, Dong L, Barnes KM, Jee YH, Baron J. Loss-of-function variant in SPIN4 causes an X-linked overgrowth syndrome. JCI Insight 2023; 8:e167074. [PMID: 36927955 PMCID: PMC10243798 DOI: 10.1172/jci.insight.167074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
Overgrowth syndromes can be caused by pathogenic genetic variants in epigenetic writers, such as DNA and histone methyltransferases. However, no overgrowth disorder has previously been ascribed to variants in a gene that acts primarily as an epigenetic reader. Here, we studied a male individual with generalized overgrowth of prenatal onset. Exome sequencing identified a hemizygous frameshift variant in Spindlin 4 (SPIN4), with X-linked inheritance. We found evidence that SPIN4 binds specific histone modifications, promotes canonical WNT signaling, and inhibits cell proliferation in vitro and that the identified frameshift variant had lost all of these functions. Ablation of Spin4 in mice recapitulated the human phenotype with generalized overgrowth, including increased longitudinal bone growth. Growth plate analysis revealed increased cell proliferation in the proliferative zone and an increased number of progenitor chondrocytes in the resting zone. We also found evidence of decreased canonical Wnt signaling in growth plate chondrocytes, providing a potential explanation for the increased number of resting zone chondrocytes. Taken together, our findings provide strong evidence that SPIN4 is an epigenetic reader that negatively regulates mammalian body growth and that loss of SPIN4 causes an overgrowth syndrome in humans, expanding our knowledge of the epigenetic regulation of human growth.
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Affiliation(s)
- Julian C. Lui
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Jacob Wagner
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Elaine Zhou
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institute of Health, Bethesda, Maryland, USA
| | - Kevin M. Barnes
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Youn Hee Jee
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
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8
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Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Lange JJ, Cesare J, Bhattacharya S, Slaughter BD, Unruh JR, Florens L, Workman JL, Washburn MP. Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526478. [PMID: 36778327 PMCID: PMC9915617 DOI: 10.1101/2023.01.31.526478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response. Teaser In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.
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9
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Integrative and Comprehensive Pan-Cancer Analysis of Lymphocyte-Specific Protein Tyrosine Kinase in Human Tumors. Int J Mol Sci 2022; 23:ijms232213998. [PMID: 36430477 PMCID: PMC9697346 DOI: 10.3390/ijms232213998] [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: 09/06/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Lymphocyte-specific protein tyrosine kinase (LCK) is common in a variety of hematologic malignancies but comparatively less common in solid tumors. This study aimed to explore the potential diagnostic and prognostic value of LCK across tumors through integrative and comprehensive pan-cancer analysis, as well as experimental validation. Multiple databases were used to explore the expression, alteration, prognostic value, association with immune infiltration, and potential functional pathways of LCK in pan-cancers. The results were further validated by western blotting and qPCR of patient samples as well as tumor cell lines. High LCK expression typically represents a better prognosis. Notably, drug sensitivity prediction of LCK identified P-529 as a candidate for drug development. Gene Annotations (GO) and KEGG analyses showed significant enrichment of PD-L1 and the T-cell receptor pathway. The results from patient samples and tumor cell lines confirmed these conclusions in LIHC. In conclusion, LCK is differentially expressed in multiple tumors and normal tissues. Further analysis highlighted its association with prognostic implications, pan-cancer genetic alterations, and immune signatures. Our data provide evidence for a diagnostic marker of LCK and the possible use of LCK as a target for the treatment of tumors.
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10
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Tong W, Yang L, Liu L, Liu X, Luo N. SPINDOC is Highly Expressed in Pan-Cancer Samples and Can Promote the Proliferation, Invasion and Migration of Hepatocellular Carcinoma Cells by Activating Wnt/β-Catenin Signaling Pathway. Onco Targets Ther 2022; 15:555-570. [PMID: 35611367 PMCID: PMC9124522 DOI: 10.2147/ott.s348843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/26/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Methods Results Conclusion
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Affiliation(s)
- Wangxia Tong
- The Medical Department of Hepatology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, People’s Republic of China
| | - Lilan Yang
- The Medical Department of Hepatology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, People’s Republic of China
| | - Li Liu
- The Medical Department of Hepatology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, People’s Republic of China
| | - Xudong Liu
- The Medical Department of Hepatology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, People’s Republic of China
| | - Ning Luo
- RuiKang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, People’s Republic of China
- Correspondence: Ning Luo, RuiKang Hospital Affiliated to Guangxi University of Chinese Medicine, 10 Huadong Road, Nanning, People’s Republic of China, 530011, Tel +86 0771-2183191, Fax +86 0771-4733943, Email
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11
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Yang F, Chen J, Liu B, Gao G, Sebastian M, Jeter C, Shen J, Person MD, Bedford MT. SPINDOC binds PARP1 to facilitate PARylation. Nat Commun 2021; 12:6362. [PMID: 34737271 PMCID: PMC8568969 DOI: 10.1038/s41467-021-26588-y] [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: 02/28/2021] [Accepted: 09/30/2021] [Indexed: 11/12/2022] Open
Abstract
SPINDOC is tightly associated with the histone H3K4me3 effector protein SPIN1. To gain a better understanding of the biological roles of SPINDOC, we identified its interacting proteins. Unexpectedly, SPINDOC forms two mutually exclusive protein complexes, one with SPIN1 and the other with PARP1. Consistent with its ability to directly interact with PARP1, SPINDOC expression is induced by DNA damage, likely by KLF4, and recruited to DNA lesions with dynamics that follows PARP1. In SPINDOC knockout cells, the levels of PARylation are reduced, in both the absence and presence of DNA damage. The SPINDOC/PARP1 interaction promotes the clearance of PARP1 from damaged DNA, and also impacts the expression of known transcriptional targets of PARP1. To address the in vivo roles of SPINDOC in PARP1 regulation, we generate SPINDOC knockout mice, which are viable, but slightly smaller than their wildtype counterparts. The KO mice display reduced levels of PARylation and, like PARP1 KO mice, are hypersensitive to IR-induced DNA damage. The findings identify a SPIN1-independent role for SPINDOC in the regulation of PARP1-mediated PARylation and the DNA damage response. SPINDOC is known to interact with Spindlin1 (SPIN1), a histone code effector protein. Here, the authors show that SPINDOC is distributed between two distinct protein complexes, one comprising SPIN1 and the other one with PARP1. Their results suggest a role for SPINDOC in the regulation of PARP1- mediated PARylation and the DNA damage response.
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Affiliation(s)
- Fen Yang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Jianji Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Manu Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Collene Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Maria D Person
- Center for Biomedical Research Support The University of Texas at Austin, Austin, TX, 78712, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
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12
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Genetic risk model for in-stent restenosis of second-and third-generation drug-eluting stents. iScience 2021; 24:103082. [PMID: 34585120 PMCID: PMC8455661 DOI: 10.1016/j.isci.2021.103082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/20/2021] [Accepted: 08/31/2021] [Indexed: 12/02/2022] Open
Abstract
The new generation, i.e., second- and third-generation, drug-eluting stents (DESs) remain a risk of in-stent restenosis (ISR). We evaluated the power of a genetic risk score (GRS) model to identify high-risk populations for new generation DES ISR. We enrolled patients with coronary artery disease (CAD) treated with new generations DESs by a single-center cohort study in Taiwan and evaluated their genetic profile. After propensity score matching, there were 343 patients and 153 patients in the derivation and validation cohorts, respectively. Five selected single-nucleotide polymorphisms (SNPs), i.e., SNPs in CAMLG, GALNT2, C11orf84, THOC5, and SAMD11, were included to calculate the GRS for new generation DES ISR. In the derivation and the validation cohorts, patients with a GRS greater than or equal to 3 had significantly higher new generation DES ISR rates. We provide biological information for interventional cardiologists prior to percutaneous coronary intervention by specific five SNP-derived GRS. A validated GRS model identified high-risk population for new generation DES ISR This GRS includes 5 SNPs in exons: CAMLG, GALNT2, C11orf84, THOC5, and SAMD11 The patients with high GRSs (≥3) had higher rates of new generation DES ISR The GRS provides crucial information in shared decision-making process clinically
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Abstract
Determining the three-dimensional structures of protein complexes is critically important to guide biological research. Structural models of complexes can be built using powerful integrative approaches that combine emerging technologies in mass spectrometry, molecular modeling, and protein docking; however, preparing enriched biochemical samples suitable for analysis remains a major challenge. Here we describe serial capture affinity purification (SCAP), which can be used for the study of protein interactions in live cells and, when combined with cross-linking mass spectrometry, contribute distance restraints for integrative structural modeling. This broadly applicable technology can be used to study any protein complex in human tissue culture cells. We demonstrate SCAP capabilities on a poorly characterized epigenetic protein complex with roles in human cancer. Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.
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SPIN1 triggers abnormal lipid metabolism and enhances tumor growth in liver cancer. Cancer Lett 2019; 470:54-63. [PMID: 31790762 DOI: 10.1016/j.canlet.2019.11.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/24/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
Abnormal lipid metabolism plays crucial roles in the development of cancer. Spindlin 1 (SPIN1) involving the process of spindle organization and chromosomal stability serves as an important player in the carcinogenesis. In this study, we try to identify the new function of SPIN1 in lipid metabolism of liver cancer. Tissue microarray showed that 75% (60/80) of hepatocellular carcinoma (HCC) tissues were positive for SPIN1, which was highly expressed in clinical HCC samples and positively associated with malignancy of HCC. Strikingly, SPIN1 could modulate abnormal lipid metabolism by increasing intracellular triglycerides, cholesterols, and lipid droplets in hepatoma cells, which could remarkably enhance the proliferation of hepatoma cells. Mechanistically, SPIN1 up-regulated FASN in hepatoma cells. SPIN1 co-activated transcriptional factor SREBP1c in the promoter of FASN through interaction with SREBP1c. Moreover, SPIN1 promoted the growth of liver cancer in vitro and in vivo and the levels of intracellular triglycerides, cholesterols and lipid droplets were increased in the tumor tissues from mice. In conclusion, SPIN1 modulates abnormal lipid metabolism and enhances growth of liver cancer through SREBP1c-triggered FASN signaling. Therapeutically, SPIN1 may serve as a novel target for HCC.
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