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Zhang C, Jian M, Li W, Yao X, Tan C, Qian Q, Hu Y, Liu X, Hou X. Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis. THE PLANT CELL 2023; 35:3470-3484. [PMID: 37294919 PMCID: PMC10473208 DOI: 10.1093/plcell/koad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/11/2023]
Abstract
Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.
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Affiliation(s)
- Chunyu Zhang
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyang Jian
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weijun Li
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiani Yao
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Cuirong Tan
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Qian
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yilong Hu
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Liu
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
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102
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Liu PP, Lu SP, Li X, Tang GB, Liu X, Dai SK, Jiao LF, Lin XW, Li XG, Hu B, Jiao J, Teng ZQ, Han CS, Liu CM. Abnormal chromatin remodeling caused by ARID1A deletion leads to malformation of the dentate gyrus. Cell Death Differ 2023; 30:2187-2199. [PMID: 37543710 PMCID: PMC10483045 DOI: 10.1038/s41418-023-01199-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/15/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
ARID1A, an SWI/SNF chromatin-remodeling gene, is commonly mutated in cancer and hypothesized to be a tumor suppressor. Recently, loss-of-function of ARID1A gene has been shown to cause intellectual disability. Here we generate Arid1a conditional knockout mice and investigate Arid1a function in the hippocampus. Disruption of Arid1a in mouse forebrain significantly decreases neural stem/progenitor cells (NSPCs) proliferation and differentiation to neurons within the dentate gyrus (DG), increasing perinatal and postnatal apoptosis, leading to reduced hippocampus size. Moreover, we perform single-cell RNA sequencing (scRNA-seq) to investigate cellular heterogeneity and reveal that Arid1a is necessary for the maintenance of the DG progenitor pool and survival of post-mitotic neurons. Transcriptome and ChIP-seq analysis data demonstrate that ARID1A specifically regulates Prox1 by altering the levels of histone modifications. Overexpression of downstream target Prox1 can rescue proliferation and differentiation defects of NSPCs caused by Arid1a deletion. Overall, our results demonstrate a critical role for Arid1a in the development of the hippocampus and may also provide insight into the genetic basis of intellectual disabilities such as Coffin-Siris syndrome, which is caused by germ-line mutations or microduplication of Arid1a.
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Affiliation(s)
- Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Shi-Ping Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiao Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gang-Bin Tang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin-Fei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Wen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences, China Medical University, No.91, Hsueh-Shih Road, Taichung, 40402, Taiwan
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chun-Sheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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103
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Gong H, Xue B, Ru J, Pei G, Li Y. Targeted Therapy for EWS-FLI1 in Ewing Sarcoma. Cancers (Basel) 2023; 15:4035. [PMID: 37627063 PMCID: PMC10452796 DOI: 10.3390/cancers15164035] [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: 05/28/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare and predominantly pediatric malignancy of bone and soft tissue in children and adolescents. Although international collaborations have greatly improved the prognosis of most EwS, the occurrence of macrometastases or relapse remains challenging. The prototypic oncogene EWS-FLI1 acts as an aberrant transcription factor that drives the cellular transformation of EwS. In addition to its involvement in RNA splicing and the DNA damage response, this chimeric protein directly binds to GGAA repeats, thereby modifying the transcriptional profile of EwS. Direct pharmacological targeting of EWS-FLI1 is difficult because of its intrinsically disordered structure. However, targeting the EWS-FLI1 protein complex or downstream pathways provides additional therapeutic options. This review describes the EWS-FLI1 protein partners and downstream pathways, as well as the related target therapies for the treatment of EwS.
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Affiliation(s)
- Helong Gong
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
| | - Busheng Xue
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Guoqing Pei
- Department of Orthopedics, Xijing Hospital, Air Force Medical University, Xi’an 710032, China;
| | - Yan Li
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
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104
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Malla AB, Yu H, Farris D, Kadimi S, Lam TT, Cox AL, Smith ZD, Lesch BJ. DOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres. EMBO Rep 2023; 24:e56492. [PMID: 37317657 PMCID: PMC10398668 DOI: 10.15252/embr.202256492] [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: 11/16/2022] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Repetitive DNA elements are packaged in heterochromatin, but many require bursts of transcription to initiate and maintain long-term silencing. The mechanisms by which these heterochromatic genome features are transcribed remain largely unknown. Here, we show that DOT1L, a conserved histone methyltransferase that modifies lysine 79 of histone H3 (H3K79), has a specialized role in transcription of major satellite repeats to maintain pericentromeric heterochromatin and genome stability. We find that H3K79me3 is selectively enriched relative to H3K79me2 at repetitive elements in mouse embryonic stem cells (mESCs), that DOT1L loss compromises pericentromeric satellite transcription, and that this activity involves possible coordination between DOT1L and the chromatin remodeler SMARCA5. Stimulation of transcript production from pericentromeric repeats by DOT1L participates in stabilization of heterochromatin structures in mESCs and cleavage-stage embryos and is required for preimplantation viability. Our findings uncover an important role for DOT1L as a bridge between transcriptional activation of repeat elements and heterochromatin stability, advancing our understanding of how genome integrity is maintained and how chromatin state is set up during early development.
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Affiliation(s)
- Aushaq B Malla
- Department of GeneticsYale School of MedicineNew HavenCTUSA
| | - Haoming Yu
- Department of GeneticsYale School of MedicineNew HavenCTUSA
| | - Delaney Farris
- Department of GeneticsYale School of MedicineNew HavenCTUSA
| | | | - TuKiet T Lam
- Keck MS & Proteomics ResourceYale School of MedicineNew HavenCTUSA
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
| | - Andy L Cox
- Department of GeneticsYale School of MedicineNew HavenCTUSA
| | - Zachary D Smith
- Department of GeneticsYale School of MedicineNew HavenCTUSA
- Yale Stem Cell CenterYale School of MedicineNew HavenCTUSA
| | - Bluma J Lesch
- Department of GeneticsYale School of MedicineNew HavenCTUSA
- Yale Cancer CenterYale School of MedicineNew HavenCTUSA
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105
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Stefanova ME, Volokh OI, Chertkov OV, Armeev GA, Shaytan AK, Feofanov AV, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET. Int J Mol Sci 2023; 24:12127. [PMID: 37569503 PMCID: PMC10419094 DOI: 10.3390/ijms241512127] [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: 05/17/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Formation of compact dinucleosomes (CODIs) occurs after collision between adjacent nucleosomes at active regulatory DNA regions. Although CODIs are likely dynamic structures, their structural heterogeneity and dynamics were not systematically addressed. Here, single-particle Förster resonance energy transfer (spFRET) and electron microscopy were employed to study the structure and dynamics of CODIs. spFRET microscopy in solution and in gel revealed considerable uncoiling of nucleosomal DNA from the histone octamer in a fraction of CODIs, suggesting that at least one of the nucleosomes is destabilized in the presence of the adjacent closely positioned nucleosome. Accordingly, electron microscopy analysis suggests that up to 30 bp of nucleosomal DNA are involved in transient uncoiling/recoiling on the octamer. The more open and dynamic nucleosome structure in CODIs cannot be stabilized by histone chaperone Spt6. The data suggest that proper internucleosomal spacing is an important determinant of chromatin stability and support the possibility that CODIs could be intermediates of chromatin disruption.
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Affiliation(s)
- Maria E. Stefanova
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Olesya I. Volokh
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Oleg V. Chertkov
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Grigory A. Armeev
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Alexey K. Shaytan
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Alexey V. Feofanov
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Mikhail P. Kirpichnikov
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Olga S. Sokolova
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
- Biological Faculty, MSU-BIT Shenzhen University, Shenzhen 518115, China
| | - Vasily M. Studitsky
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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106
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Sun D, Ding Z, Hai Y, Cheng Y. Advances in epigenetic research of adolescent idiopathic scoliosis and congenital scoliosis. Front Genet 2023; 14:1211376. [PMID: 37564871 PMCID: PMC10411889 DOI: 10.3389/fgene.2023.1211376] [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: 04/24/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
Scoliosis is a three-dimensional structural deformity of the spine; more than 80% of scoliosis has no specific pathogenesis but is understood to be closely related to genetic, hormonal, and environmental factors. In recent years, the epigenetic alterations observed in scoliosis have been analyzed in numerous studies to determine the pathogenesis and progression of this condition, however, there is currently no comprehensive review of the epigenetic factors to date. We searched PubMed, Embase, and Web of Science databases for relative studies without language and date restrictions in March 2023. Twenty-five studies were included in this review and analyzed from the four main aspects of epigenetic alteration: DNA methylation, non-coding RNAs, histone modifications, and chromatin remodeling. The relationship between DNA methylation, non-coding RNAs, and scoliosis was considerably reported in the literature, and the corresponding related signaling pathways and novel biomarkers observed in scoliosis provide insights into innovative prevention and treatment strategies. However, the role of histone modifications is rarely reported in scoliosis, and few studies have investigated the relationship between scoliosis and chromatin remodeling. Therefore, these related fields need to be further explored to elucidate the overall effects of epigenetics in scoliosis.
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Affiliation(s)
| | | | - Yong Hai
- Department of Orthopedic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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107
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Wu H, Muñoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y. Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Science 2023; 381:319-324. [PMID: 37384669 PMCID: PMC10480058 DOI: 10.1126/science.adf4197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
Abstract
Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of Saccharomyces cerevisiae INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6 and SHL -7, as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes such that Ino80 is maximally active near SHL -2. The SHL -2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles.
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Affiliation(s)
- Hao Wu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elise N. Muñoz
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Laura J. Hsieh
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Un Seng Chio
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Muryam A. Gourdet
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
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108
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Padilla-Benavides T, Olea-Flores M, Sharma T, Syed SA, Witwicka H, Zuñiga-Eulogio MD, Zhang K, Navarro-Tito N, Imbalzano AN. Differential Contributions of mSWI/SNF Chromatin Remodeler Sub-Families to Myoblast Differentiation. Int J Mol Sci 2023; 24:11256. [PMID: 37511016 PMCID: PMC10378909 DOI: 10.3390/ijms241411256] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Mammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions. mSWI/SNF enzymes are classified into three sub-families based on the presence of specific subunit proteins. The sub-families are Brm- or Brg1-associated factor (BAF), ncBAF (non-canonical BAF), and polybromo-associated BAF (PBAF). The biological roles for the different enzyme sub-families are poorly described. We knocked down the expression of genes encoding unique subunit proteins for each sub-family, Baf250A, Brd9, and Baf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that Baf250A and the BAF complex were required to drive lineage-specific gene expression. KD of Brd9 delayed differentiation. However, while the Baf250A-dependent gene expression profile included myogenic genes, the Brd9-dependent gene expression profile did not, suggesting Brd9 and the ncBAF complex indirectly contributed to differentiation. Baf180 was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme sub-families during myoblast differentiation.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Monserrat Olea-Flores
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Tapan Sharma
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Miriam D. Zuñiga-Eulogio
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Kexin Zhang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
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Sharma T, Olea-Flores M, Imbalzano AN. Regulation of the Wnt signaling pathway during myogenesis by the mammalian SWI/SNF ATPase BRG1. Front Cell Dev Biol 2023; 11:1160227. [PMID: 37484913 PMCID: PMC10360407 DOI: 10.3389/fcell.2023.1160227] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Skeletal muscle differentiation is a tightly regulated process, and the importance of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling family for regulation of genes involved in skeletal myogenesis is well-established. Our prior work showed that bromodomains of mSWI/SNF ATPases BRG1 and BRM contribute to myogenesis by facilitating the binding of mSWI/SNF enzymes to regulatory regions of myogenic and other target genes. Here, we report that pathway analyses of differentially expressed genes from that study identified an additional role for mSWI/SNF enzymes via the regulation of the Wnt signaling pathway. The Wnt pathway has been previously shown to be important for skeletal muscle development. To investigate the importance of mSWI/SNF enzymes for the regulation of the Wnt pathway, individual and dual knockdowns were performed for BRG1 and BRM followed by RNA-sequencing. The results show that BRG1, but not BRM, is a regulator of Wnt pathway components and downstream genes. Reactivation of Wnt pathway by stabilization of β-catenin could rescue the defect in myogenic gene expression and differentiation due to BRG1 knockdown or bromodomain inhibition using a specific small molecule inhibitor, PFI-3. These results demonstrate that BRG1 is required upstream of β-catenin function. Chromatin immunoprecipitation of BRG1, BRM and β-catenin at promoters of Wnt pathway component genes showed binding of BRG1 and β-catenin, which provides further mechanistic insight to the transcriptional regulation of these genes.
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Affiliation(s)
| | | | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, United States
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110
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Banks OGB, Harms MJ, McKnight JN, McKnight LE. Simultaneous Mapping of DNA Binding and Nucleosome Positioning with SpLiT-ChEC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547581. [PMID: 37461563 PMCID: PMC10349973 DOI: 10.1101/2023.07.03.547581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The organization of chromatin - including the positions of nucleosomes and the binding of other proteins to DNA - helps define transcriptional profiles in eukaryotic organisms. While techniques like ChIP-Seq and MNase-Seq can map protein-DNA and nucleosome localization separately, assays designed to simultaneously capture nucleosome positions and protein-DNA interactions can produce a detailed picture of the chromatin landscape. Most assays that monitor chromatin organization and protein binding rely on antibodies, which often exhibit nonspecific binding, and/or the addition of bulky adducts to the DNA-binding protein being studied, which can affect their expression and activity. Here, we describe SpyCatcher Linked Targeting of Chromatin Endogenous Cleavage (SpLiT-ChEC), where a 13-amino acid SpyTag peptide, appended to a protein of interest, serves as a highly-specific targeting moiety for in situ enzymatic digestion. The SpyTag/SpyCatcher system forms a covalent bond, linking the target protein and a co-expressed MNase-SpyCatcher fusion construct. SpyTagged proteins are expressed from endogenous loci, whereas MNase-SpyCatcher expression is induced immediately before harvesting cultures. MNase is activated with high concentrations of calcium, which primarily digests DNA near target protein binding sites. By sequencing the DNA fragments released by targeted MNase digestion, we found that this method recovers information on protein binding and proximal nucleosome positioning. SpLiT-ChEC provides precise temporal control that we anticipate can be used to monitor chromatin under various conditions and at distinct points in the cell cycle.
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Affiliation(s)
- Orion G. B. Banks
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
| | - Michael J. Harms
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene OR 97403, USA
| | - Jeffrey. N. McKnight
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
- Knight Campus for Accelerated Research, University of Oregon, Eugene OR 97403, USA
| | - Laura E. McKnight
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
- Knight Campus for Accelerated Research, University of Oregon, Eugene OR 97403, USA
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Zimmer K, Kocher F, Untergasser G, Kircher B, Amann A, Baca Y, Xiu J, Korn WM, Berger MD, Lenz HJ, Puccini A, Fontana E, Shields AF, Marshall JL, Hall M, El-Deiry WS, Hsiehchen D, Macarulla T, Tabernero J, Pichler R, Khushman M, Manne U, Lou E, Wolf D, Sokolova V, Schnaiter S, Zeimet AG, Gulhati P, Widmann G, Seeber A. PBRM1 mutations might render a subtype of biliary tract cancers sensitive to drugs targeting the DNA damage repair system. NPJ Precis Oncol 2023; 7:64. [PMID: 37400502 DOI: 10.1038/s41698-023-00409-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
Polybromo-1 (PBRM1) loss of function mutations are present in a fraction of biliary tract cancers (BTCs). PBRM1, a subunit of the PBAF chromatin-remodeling complex, is involved in DNA damage repair. Herein, we aimed to decipher the molecular landscape of PBRM1 mutated (mut) BTCs and to define potential translational aspects. Totally, 1848 BTC samples were analyzed using next-generation DNA-sequencing and immunohistochemistry (Caris Life Sciences, Phoenix, AZ). siRNA-mediated knockdown of PBRM1 was performed in the BTC cell line EGI1 to assess the therapeutic vulnerabilities of ATR and PARP inhibitors in vitro. PBRM1 mutations were identified in 8.1% (n = 150) of BTCs and were more prevalent in intrahepatic BTCs (9.9%) compared to gallbladder cancers (6.0%) or extrahepatic BTCs (4.5%). Higher rates of co-mutations in chromatin-remodeling genes (e.g., ARID1A 31% vs. 16%) and DNA damage repair genes (e.g., ATRX 4.4% vs. 0.3%) were detected in PBRM1-mutated (mut) vs. PBRM1-wildtype (wt) BTCs. No difference in real-world overall survival was observed between PBRM1-mut and PBRM1-wt patients (HR 1.043, 95% CI 0.821-1.325, p = 0.731). In vitro, experiments suggested that PARP ± ATR inhibitors induce synthetic lethality in the PBRM1 knockdown BTC model. Our findings served as the scientific rationale for PARP inhibition in a heavily pretreated PBRM1-mut BTC patient, which induced disease control. This study represents the largest and most extensive molecular profiling study of PBRM1-mut BTCs, which in vitro sensitizes to DNA damage repair inhibiting compounds. Our findings might serve as a rationale for future testing of PARP/ATR inhibitors in PBRM1-mut BTCs.
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Affiliation(s)
- Kai Zimmer
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria
| | - Florian Kocher
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria
| | - Gerold Untergasser
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria
- Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Brigitte Kircher
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria
- Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Arno Amann
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria
| | | | | | | | - Martin D Berger
- Department of Medical Oncology, Inselspital, University of Bern, Bern, Switzerland
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alberto Puccini
- Medical Oncology Unit 1, Ospedale Policlinico San Martino, Genoa, Italy
| | - Elisa Fontana
- Drug Development Unit, Sarah Cannon Research Institute UK, Marylebone, London, UK
| | - Anthony F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - John L Marshall
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Michael Hall
- Department of Hematology and Oncology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, USA
| | - Wafik S El-Deiry
- Department of Pathology and Laboratory Medicine, Cancer Center at Brown University, Providence, RI, USA
| | - David Hsiehchen
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Teresa Macarulla
- Medical Oncology Department, Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), IOB-Quiron, Barcelona, Spain
| | - Josep Tabernero
- Medical Oncology Department, Vall d'Hebron Hospital Campus and Institute of Oncology (VHIO), IOB-Quiron, Barcelona, Spain
| | - Renate Pichler
- Department of Urology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Moh'd Khushman
- O'Neal Comprehensive Cancer Center, the University of Alabama at Birmingham, Birmingham, Al, USA
| | - Upender Manne
- O'Neal Comprehensive Cancer Center, the University of Alabama at Birmingham, Birmingham, Al, USA
| | - Emil Lou
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Dominik Wolf
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria
| | - Viktorija Sokolova
- Department of Nuclear Medicine, Provincial Hospital of Bolzano (SABES-ASDAA), Teaching Hospital of the Paracelsus Medical Private University, Bolzano-Bozen, Italy
| | - Simon Schnaiter
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alain G Zeimet
- Department of Obstetrics and Gynaecology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Pat Gulhati
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Gerlig Widmann
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Seeber
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck (CCCI), Medical University Innsbruck (MUI), Innsbruck, Austria.
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Xu X, Peng Q, Jiang X, Tan S, Yang Y, Yang W, Han Y, Chen Y, Oyang L, Lin J, Xia L, Peng M, Wu N, Tang Y, Li J, Liao Q, Zhou Y. Metabolic reprogramming and epigenetic modifications in cancer: from the impacts and mechanisms to the treatment potential. Exp Mol Med 2023:10.1038/s12276-023-01020-1. [PMID: 37394582 PMCID: PMC10394076 DOI: 10.1038/s12276-023-01020-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 07/04/2023] Open
Abstract
Metabolic reprogramming and epigenetic modifications are hallmarks of cancer cells. In cancer cells, metabolic pathway activity varies during tumorigenesis and cancer progression, indicating regulated metabolic plasticity. Metabolic changes are often closely related to epigenetic changes, such as alterations in the expression or activity of epigenetically modified enzymes, which may exert a direct or an indirect influence on cellular metabolism. Therefore, exploring the mechanisms underlying epigenetic modifications regulating the reprogramming of tumor cell metabolism is important for further understanding tumor pathogenesis. Here, we mainly focus on the latest studies on epigenetic modifications related to cancer cell metabolism regulations, including changes in glucose, lipid and amino acid metabolism in the cancer context, and then emphasize the mechanisms related to tumor cell epigenetic modifications. Specifically, we discuss the role played by DNA methylation, chromatin remodeling, noncoding RNAs and histone lactylation in tumor growth and progression. Finally, we summarize the prospects of potential cancer therapeutic strategies based on metabolic reprogramming and epigenetic changes in tumor cells.
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Affiliation(s)
- Xuemeng Xu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- University of South China, Hengyang, 421001, Hunan, China
| | - Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yiqing Yang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Wenjuan Yang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yuyu Chen
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Mingjing Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Jinyun Li
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
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113
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Fu W, Yu Y, Shu J, Yu Z, Zhong Y, Zhu T, Zhang Z, Liang Z, Cui Y, Chen C, Li C. Organization, genomic targeting, and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis. THE PLANT CELL 2023; 35:2464-2483. [PMID: 37062961 PMCID: PMC10291025 DOI: 10.1093/plcell/koad111] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
Switch defective/sucrose nonfermentable (SWI/SNF) complexes are evolutionarily conserved multisubunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes are poorly understood. Here, we report the organization, genomic targeting, and assembly of 3 distinct SWI/SNF complexes in Arabidopsis thaliana: BRAHMA-Associated SWI/SNF complexes (BAS), SPLAYED-Associated SWI/SNF complexes (SAS), and MINUSCULE-Associated SWI/SNF complexes (MAS). We show that BAS complexes are equivalent to human ncBAF, whereas SAS and MAS complexes evolve in multiple subunits unique to plants, suggesting plant-specific functional evolution of SWI/SNF complexes. We further show overlapping and specific genomic targeting of the 3 plant SWI/SNF complexes on chromatin and reveal that SAS complexes are necessary for the correct genomic localization of the BAS complexes. Finally, we define the role of the core module subunit in the assembly of plant SWI/SNF complexes and highlight that ATPase module subunit is required for global complex stability and the interaction of core module subunits in Arabidopsis SAS and BAS complexes. Together, our work highlights the divergence of SWI/SNF chromatin remodelers during eukaryote evolution and provides a comprehensive landscape for understanding plant SWI/SNF complex organization, assembly, genomic targeting, and function.
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Affiliation(s)
- Wei Fu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Shu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zewang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yixiong Zhong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhihao Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada N5V 4T3
| | - Chen Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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114
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Smith CM, Grow EJ, Shadle SC, Cairns BR. Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534786. [PMID: 37034731 PMCID: PMC10081216 DOI: 10.1101/2023.03.29.534786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The embryonic transcription factor DUX regulates chromatin opening and gene expression in totipotent cleavage-stage mouse embryos, and its expression in embryonic stem cells promotes their conversion to 2-cell embryo-like cells (2CLCs) with extraembryonic potential. However, little is known regarding which domains within mouse DUX interact with particular chromatin and transcription regulators. Here, we reveal that the C-terminus of mouse DUX contains five uncharacterized ~100 amino acid (aa) repeats followed by an acidic 14 amino acid tail. Unexpectedly, structure-function approaches classify two repeats as 'active' and three as 'inactive' in cleavage/2CLC transcription program enhancement, with differences narrowed to a key 6 amino acid section. Our proximity dependent biotin ligation (BioID) approach identified factors selectively associated with active DUX repeat derivatives (including the 14aa 'tail'), including transcription and chromatin factors such as SWI/SNF (BAF) complex, as well as nucleolar factors that have been previously implicated in regulating the Dux locus. Finally, our mechanistic studies reveal cooperativity between DUX active repeats and the acidic tail in cofactor recruitment, DUX target opening, and transcription. Taken together, we provide several new insights into DUX structure-function, and mechanisms of chromatin and gene regulation.
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Affiliation(s)
- Christina M. Smith
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Edward J. Grow
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Green Center for Reproductive Biological Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean C. Shadle
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bradley R. Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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115
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Davidson RK, Kanojia S, Wu W, Kono T, Xu J, Osmulski M, Bone RN, Casey N, Evans-Molina C, Sims EK, Spaeth JM. The Chd4 Helicase Regulates Chromatin Accessibility and Gene Expression Critical for β-Cell Function In Vivo. Diabetes 2023; 72:746-757. [PMID: 36913741 PMCID: PMC10202766 DOI: 10.2337/db22-0939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/01/2023] [Indexed: 03/15/2023]
Abstract
The transcriptional activity of Pdx1 is modulated by a diverse array of coregulatory factors that govern chromatin accessibility, histone modifications, and nucleosome distribution. We previously identified the Chd4 subunit of the nucleosome remodeling and deacetylase complex as a Pdx1-interacting factor. To identify how loss of Chd4 impacts glucose homeostasis and gene expression programs in β-cells in vivo, we generated an inducible β-cell-specific Chd4 knockout mouse model. Removal of Chd4 from mature islet β-cells rendered mutant animals glucose intolerant, in part due to defects in insulin secretion. We observed an increased ratio of immature-to-mature insulin granules in Chd4-deficient β-cells that correlated with elevated levels of proinsulin both within isolated islets and from plasma following glucose stimulation in vivo. RNA sequencing and assay for transposase-accessible chromatin with sequencing showed that lineage-labeled Chd4-deficient β-cells have alterations in chromatin accessibility and altered expression of genes critical for β-cell function, including MafA, Slc2a2, Chga, and Chgb. Knockdown of CHD4 from a human β-cell line revealed similar defects in insulin secretion and alterations in several β-cell-enriched gene targets. These results illustrate how critical Chd4 activities are in controlling genes essential for maintaining β-cell function. ARTICLE HIGHLIGHTS Pdx1-Chd4 interactions were previously shown to be compromised in β-cells from human donors with type 2 diabetes. β-Cell-specific removal of Chd4 impairs insulin secretion and leads to glucose intolerance in mice. Expression of key β-cell functional genes and chromatin accessibility are compromised in Chd4-deficient β-cells. Chromatin remodeling activities enacted by Chd4 are essential for β-cell function under normal physiological conditions.
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Affiliation(s)
- Rebecca K. Davidson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Sukrati Kanojia
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Wenting Wu
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Tatsuyoshi Kono
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Jerry Xu
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Meredith Osmulski
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Robert N. Bone
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Nolan Casey
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Carmella Evans-Molina
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN
- Richard L. Roudebush Veterans’ Administration Medical Center, Indianapolis, IN
| | - Emily K. Sims
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Jason M. Spaeth
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN
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116
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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117
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Yang J, Xu J, Wang W, Zhang B, Yu X, Shi S. Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets. Signal Transduct Target Ther 2023; 8:210. [PMID: 37217462 DOI: 10.1038/s41392-023-01480-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/17/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Over decades, researchers have focused on the epigenetic control of DNA-templated processes. Histone modification, DNA methylation, chromatin remodeling, RNA modification, and noncoding RNAs modulate many biological processes that are crucial to the development of cancers. Dysregulation of the epigenome drives aberrant transcriptional programs. A growing body of evidence suggests that the mechanisms of epigenetic modification are dysregulated in human cancers and might be excellent targets for tumor treatment. Epigenetics has also been shown to influence tumor immunogenicity and immune cells involved in antitumor responses. Thus, the development and application of epigenetic therapy and cancer immunotherapy and their combinations may have important implications for cancer treatment. Here, we present an up-to-date and thorough description of how epigenetic modifications in tumor cells influence immune cell responses in the tumor microenvironment (TME) and how epigenetics influence immune cells internally to modify the TME. Additionally, we highlight the therapeutic potential of targeting epigenetic regulators for cancer immunotherapy. Harnessing the complex interplay between epigenetics and cancer immunology to develop therapeutics that combine thereof is challenging but could yield significant benefits. The purpose of this review is to assist researchers in understanding how epigenetics impact immune responses in the TME, so that better cancer immunotherapies can be developed.
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Affiliation(s)
- Jing Yang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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118
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Chen Q, Shi X, Ai L, Tian X, Zhang H, Tian J, Wang Q, Zhang M, Cui S, Yang C, Zhao H. Genome-wide identification of genes encoding SWI/SNF components in soybean and the functional characterization of GmLFR1 in drought-stressed plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1176376. [PMID: 37255551 PMCID: PMC10225534 DOI: 10.3389/fpls.2023.1176376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
ATP-dependent SWI/SNF chromatin remodeling complexes (CRCs) are evolutionarily conserved multi-component machines that regulate transcription, replication, and genome stability in eukaryotes. SWI/SNF components play pivotal roles in development and various stress responses in plants. However, the compositions and biological functions of SWI/SNF complex subunits remain poorly understood in soybean. In this study, we used bioinformatics to identify 39 genes encoding SWI/SNF subunit distributed on the 19 chromosomes of soybean. The promoter regions of the genes were enriched with several cis-regulatory elements that are responsive to various hormones and stresses. Digital expression profiling and qRT-PCR revealed that most of the SWI/SNF subunit genes were expressed in multiple tissues of soybean and were sensitive to drought stress. Phenotypical, physiological, and molecular genetic analyses revealed that GmLFR1 (Leaf and Flower-Related1) plays a negative role in drought tolerance in soybean and Arabidopsis thaliana. Together, our findings characterize putative components of soybean SWI/SNF complex and indicate possible roles for GmLFR1 in plants under drought stress. This study offers a foundation for comprehensive analyses of soybean SWI/SNF subunit and provides mechanistic insight into the epigenetic regulation of drought tolerance in soybean.
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Affiliation(s)
- Qiang Chen
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Ministry of Agriculture and Rural Affairs, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Ministry of Agriculture and Rural Affairs, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Lijuan Ai
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
| | - Xuan Tian
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
| | - Hongwei Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
| | - Jiawang Tian
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
| | - Qianying Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Ministry of Agriculture and Rural Affairs, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Ministry of Agriculture and Rural Affairs, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, Shijiazhuang, Hebei, China
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119
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Xun Q, Song Y, Mei M, Ding Y, Ding C. The SMC5/6 complex subunit MMS21 regulates stem cell proliferation in rice. PLANT CELL REPORTS 2023:10.1007/s00299-023-03030-9. [PMID: 37178216 DOI: 10.1007/s00299-023-03030-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE SMC5/6 complex subunit OsMMS21 is involved in cell cycle and hormone signaling and required for stem cell proliferation during shoot and root development in rice. The structural maintenance of chromosome (SMC)5/6 complex is required for nucleolar integrity and DNA metabolism. Moreover, METHYL METHANESULFONATE SENSITIVITY GENE 21 (MMS21), a SUMO E3 ligase that is part of the SMC5/6 complex, is essential for the root stem cell niche and cell cycle transition in Arabidopsis. However, its specific role in rice remains unclear. Here, OsSMC5 and OsSMC6 single heterozygous mutants were generated using CRISPR/Cas9 technology to elucidate the function of SMC5/6 subunits, including OsSMC5, OsSMC6, and OsMMS21, in cell proliferation in rice. ossmc5/ + and ossmc6/ + heterozygous single mutants did not yield homozygous mutants in their progeny, indicating that OsSMC5 and OsSMC6 both play necessary roles during embryo formation. Loss of OsMMS21 caused severe defects in both the shoot and roots in rice. Transcriptome analysis showed a significant decrease in the expression of genes involved in auxin signaling in the roots of osmms21 mutants. Moreover, the expression levels of the cycB2-1 and MCM genes, which are involved the cell cycle, were significantly lower in the shoots of the mutants, indicating that OsMMS21 was involved in both hormone signaling pathways and the cell cycle. Overall, these findings indicate that the SUMO E3 ligase OsMMS21 is required for both shoot and root stem cell niches, improving the understanding of the function of the SMC5/6 complex in rice.
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Affiliation(s)
- Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ye Song
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Mei
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China.
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120
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Prozzillo Y, Fattorini G, Ferreri D, Leo M, Dimitri P, Messina G. Knockdown of DOM/Tip60 Complex Subunits Impairs Male Meiosis of Drosophila melanogaster. Cells 2023; 12:1348. [PMID: 37408183 DOI: 10.3390/cells12101348] [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: 03/27/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 07/07/2023] Open
Abstract
ATP-dependent chromatin remodeling complexes are involved in nucleosome sliding and eviction and/or the incorporation of histone variants into chromatin to facilitate several cellular and biological processes, including DNA transcription, replication and repair. The DOM/TIP60 chromatin remodeling complex of Drosophila melanogaster contains 18 subunits, including the DOMINO (DOM), an ATPase that catalyzes the exchange of the canonical H2A with its variant (H2A.V), and TIP60, a lysine-acetyltransferase that acetylates H4, H2A and H2A.V histones. In recent decades, experimental evidence has shown that ATP-dependent chromatin remodeling factors, in addition to their role in chromatin organization, have a functional relevance in cell division. In particular, emerging studies suggested the direct roles of ATP-dependent chromatin remodeling complex subunits in controlling mitosis and cytokinesis in both humans and D. melanogaster. However, little is known about their possible involvement during meiosis. The results of this work show that the knockdown of 12 of DOM/TIP60 complex subunits generates cell division defects that, in turn, cause total/partial sterility in Drosophila males, providing new insights into the functions of chromatin remodelers in cell division control during gametogenesis.
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Affiliation(s)
- Yuri Prozzillo
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Gaia Fattorini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), Sapienza University of Rome, 00185 Rome, Italy
| | - Diego Ferreri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Manuela Leo
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy
| | - Patrizio Dimitri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Giovanni Messina
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Pasteur Institute, Fondazione Cenci-Bolognetti, 00161 Rome, Italy
- Department of Biotechnology and Biosciences, Milano-Bicocca University, 20126 Milan, Italy
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121
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Singh A, Modak SB, Chaturvedi MM, Purohit JS. SWI/SNF Chromatin Remodelers: Structural, Functional and Mechanistic Implications. Cell Biochem Biophys 2023:10.1007/s12013-023-01140-5. [PMID: 37119511 DOI: 10.1007/s12013-023-01140-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
The nuclear events of a eukaryotic cell, such as replication, transcription, recombination and repair etc. require the transition of the compactly arranged chromatin into an uncompacted state and vice-versa. This is mediated by post-translational modification of the histones, exchange of histone variants and ATP-dependent chromatin remodeling. The SWI/SNF chromatin remodeling complexes are one of the most well characterized families of chromatin remodelers. In addition to their role in modulating chromatin, they have also been assigned roles in cancer and health-related anomalies such as developmental, neurocognitive, and intellectual disabilities. Owing to their vital cellular and medical connotations, developing an understanding of the structural and functional aspects of the complex becomes imperative. However, due to the intricate nature of higher-order chromatin as well as compositional heterogeneity of the SWI/SNF complex, intra-species isoforms and inter-species homologs, this often becomes challenging. To this end, the present review attempts to present an amalgamated perspective on the discovery, structure, function, and regulation of the SWI/SNF complex.
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Affiliation(s)
- Abhilasha Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Madan M Chaturvedi
- Department of Zoology, University of Delhi, Delhi, 110007, India
- SGT University, Gurugram (Delhi-NCR), Haryana, 122505, India
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122
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Bure IV, Nemtsova MV. Mutual Regulation of ncRNAs and Chromatin Remodeling Complexes in Normal and Pathological Conditions. Int J Mol Sci 2023; 24:ijms24097848. [PMID: 37175555 PMCID: PMC10178202 DOI: 10.3390/ijms24097848] [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: 03/23/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Chromatin remodeling is the one of the main epigenetic mechanisms of gene expression regulation both in normal cells and in pathological conditions. In recent years, a growing number of investigations have confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. Genes encoding protein subunits of chromatin remodeling complexes are often mutated and change their expression in diseases, as well as non-coding RNAs (ncRNAs). Moreover, different mechanisms of their mutual regulation have already been described. Further understanding of these processes may help apply their clinical potential for establishment of the diagnosis, prognosis, and treatment of the diseases. The therapeutic targeting of the chromatin structure has many limitations because of the complexity of its regulation, with the involvement of a large number of genes, proteins, non-coding transcripts, and other intermediary molecules. However, several successful strategies have been proposed to target subunits of chromatin remodeling complexes and genes encoding them, as well as the ncRNAs that regulate the operation of these complexes and direct them to the target gene regions. In our review, we focus on chromatin remodeling complexes and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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Affiliation(s)
- Irina V Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Marina V Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
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123
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Wang J, Sun Z, Liu H, Yue L, Wang F, Liu S, Su B, Liu B, Kong F, Fang C. Genome-Wide Identification and Characterization of the Soybean Snf2 Gene Family and Expression Response to Rhizobia. Int J Mol Sci 2023; 24:ijms24087250. [PMID: 37108411 PMCID: PMC10138738 DOI: 10.3390/ijms24087250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Sucrose nonfermenting 2 (Snf2) family proteins are the core component of chromatin remodeling complexes that can alter chromatin structure and nucleosome position by utilizing the energy of ATP, playing a vital role in transcription regulation, DNA replication, and DNA damage repair. Snf2 family proteins have been characterized in various species including plants, and they have been found to regulate development and stress responses in Arabidopsis. Soybean (Glycine max) is an important food and economic crop worldwide, unlike other non-leguminous crops, soybeans can form a symbiotic relationship with rhizobia for biological nitrogen fixation. However, little is known about Snf2 family proteins in soybean. In this study, we identified 66 Snf2 family genes in soybean that could be classified into six groups like Arabidopsis, unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis with Arabidopsis revealed that these 66 Snf2 family genes could be divided into 18 subfamilies. Collinear analysis showed that segmental duplication was the main mechanism for expansion of Snf2 genes rather than tandem repeats. Further evolutionary analysis indicated that the duplicated gene pairs had undergone purifying selection. All Snf2 proteins contained seven domains, and each Snf2 protein had at least one SNF2_N domain and one Helicase_C domain. Promoter analysis revealed that most Snf2 genes had cis-elements associated with jasmonic acid, abscisic acid, and nodule specificity in their promoter regions. Microarray data and real-time quantitative PCR (qPCR) analysis revealed that the expression profiles of most Snf2 family genes were detected in both root and nodule tissues, and some of them were found to be significantly downregulated after rhizobial infection. In this study, we conducted a comprehensive analysis of the soybean Snf2 family genes and demonstrated their responsiveness to Rhizobia infection. This provides insight into the potential roles of Snf2 family genes in soybean symbiotic nodulation.
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Affiliation(s)
- Jianhao Wang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhihui Sun
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Huan Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lin Yue
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fan Wang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Shuangrong Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Bohong Su
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Baohui Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chao Fang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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124
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Gutiérrez-Santiago F, Navarro F. Transcription by the Three RNA Polymerases under the Control of the TOR Signaling Pathway in Saccharomyces cerevisiae. Biomolecules 2023; 13:biom13040642. [PMID: 37189389 DOI: 10.3390/biom13040642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Ribosomes are the basis for protein production, whose biogenesis is essential for cells to drive growth and proliferation. Ribosome biogenesis is highly regulated in accordance with cellular energy status and stress signals. In eukaryotic cells, response to stress signals and the production of newly-synthesized ribosomes require elements to be transcribed by the three RNA polymerases (RNA pols). Thus, cells need the tight coordination of RNA pols to adjust adequate components production for ribosome biogenesis which depends on environmental cues. This complex coordination probably occurs through a signaling pathway that links nutrient availability with transcription. Several pieces of evidence strongly support that the Target of Rapamycin (TOR) pathway, conserved among eukaryotes, influences the transcription of RNA pols through different mechanisms to ensure proper ribosome components production. This review summarizes the connection between TOR and regulatory elements for the transcription of each RNA pol in the budding yeast Saccharomyces cerevisiae. It also focuses on how TOR regulates transcription depending on external cues. Finally, it discusses the simultaneous coordination of the three RNA pols through common factors regulated by TOR and summarizes the most important similarities and differences between S. cerevisiae and mammals.
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Affiliation(s)
- Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
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125
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Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Mol Cell 2023; 83:1350-1367.e7. [PMID: 37028419 DOI: 10.1016/j.molcel.2023.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/07/2023] [Accepted: 03/10/2023] [Indexed: 04/09/2023]
Abstract
The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes play critical roles in regulating DNA accessibility and gene expression. The three final-form subcomplexes-cBAF, PBAF, and ncBAF-are distinct in biochemical componentry, chromatin targeting, and roles in disease; however, the contributions of their constituent subunits to gene expression remain incompletely defined. Here, we performed Perturb-seq-based CRISPR-Cas9 knockout screens targeting mSWI/SNF subunits individually and in select combinations, followed by single-cell RNA-seq and SHARE-seq. We uncovered complex-, module-, and subunit-specific contributions to distinct regulatory networks and defined paralog subunit relationships and shifted subcomplex functions upon perturbations. Synergistic, intra-complex genetic interactions between subunits reveal functional redundancy and modularity. Importantly, single-cell subunit perturbation signatures mapped across bulk primary human tumor expression profiles both mirror and predict cBAF loss-of-function status in cancer. Our findings highlight the utility of Perturb-seq to dissect disease-relevant gene regulatory impacts of heterogeneous, multi-component master regulatory complexes.
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Affiliation(s)
- Jordan E Otto
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Oana Ursu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander P Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Evan B Winter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sai Ma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kristin Qian
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Brittany C Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Bonnie Berger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, UA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Chemical Biology Program, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, UA.
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To KKW, Xing E, Larue RC, Li PK. BET Bromodomain Inhibitors: Novel Design Strategies and Therapeutic Applications. Molecules 2023; 28:molecules28073043. [PMID: 37049806 PMCID: PMC10096006 DOI: 10.3390/molecules28073043] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
The mammalian bromodomain and extra-terminal domain (BET) family of proteins consists of four conserved members (Brd2, Brd3, Brd4, and Brdt) that regulate numerous cancer-related and immunity-associated genes. They are epigenetic readers of histone acetylation with broad specificity. BET proteins are linked to cancer progression due to their interaction with numerous cellular proteins including chromatin-modifying factors, transcription factors, and histone modification enzymes. The spectacular growth in the clinical development of small-molecule BET inhibitors underscores the interest and importance of this protein family as an anticancer target. Current approaches targeting BET proteins for cancer therapy rely on acetylation mimics to block the bromodomains from binding chromatin. However, bromodomain-targeted agents are suffering from dose-limiting toxicities because of their effects on other bromodomain-containing proteins. In this review, we provided an updated summary about the evolution of small-molecule BET inhibitors. The design of bivalent BET inhibitors, kinase and BET dual inhibitors, BET protein proteolysis-targeting chimeras (PROTACs), and Brd4-selective inhibitors are discussed. The novel strategy of targeting the unique C-terminal extra-terminal (ET) domain of BET proteins and its therapeutic significance will also be highlighted. Apart from single agent treatment alone, BET inhibitors have also been combined with other chemotherapeutic modalities for cancer treatment demonstrating favorable clinical outcomes. The investigation of specific biomarkers for predicting the efficacy and resistance of BET inhibitors is needed to fully realize their therapeutic potential in the clinical setting.
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Ma T, Wang S, Sun C, Tian J, Guo H, Cui S, Zhao H. Arabidopsis LFR, a SWI/SNF complex component, interacts with ICE1 and activates ICE1 and CBF3 expression in cold acclimation. FRONTIERS IN PLANT SCIENCE 2023; 14:1097158. [PMID: 37025149 PMCID: PMC10070696 DOI: 10.3389/fpls.2023.1097158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Low temperatures restrict the growth and geographic distribution of plants, as well as crop yields. Appropriate transcriptional regulation is critical for cold acclimation in plants. In this study, we found that the mutation of Leaf and flower related (LFR), a component of SWI/SNF chromatin remodeling complex (CRC) important for transcriptional regulation in Arabidopsis (Arabidopsis thaliana), resulted in hypersensitivity to freezing stress in plants with or without cold acclimation, and this defect was successfully complemented by LFR. The expression levels of CBFs and COR genes in cold-treated lfr-1 mutant plants were lower than those in wild-type plants. Furthermore, LFR was found to interact directly with ICE1 in yeast and plants. Consistent with this, LFR was able to directly bind to the promoter region of CBF3, a direct target of ICE1. LFR was also able to bind to ICE1 chromatin and was required for ICE1 transcription. Together, these results demonstrate that LFR interacts directly with ICE1 and activates ICE1 and CBF3 gene expression in response to cold stress. Our work enhances our understanding of the epigenetic regulation of cold responses in plants.
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Singh AK, Viviano S, Allington G, McGee S, Kiziltug E, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Ma S, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.19.23287455. [PMID: 36993720 PMCID: PMC10055611 DOI: 10.1101/2023.03.19.23287455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design setting and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)", characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a "neural stem cell" paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk genes for congenital structural brain disorders and suggest WES may be a valuable adjunct in the clinical management of CH patients. KEY POINTS Question: What is the role of SMARCC1 , a core component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)? Findings: SMARCC1 harbored an exome-wide significant burden of rare, protein-damaging de novo mutations (DNMs) (p = 5.83 × 10 -9 ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios). SMARCC1 contained four loss-of-function DNMs and two identical canonical splice site DNMs in a total of six unrelated patients. Patients exhibited developmental delay, aqueductal stenosis, and other structural brain and cardiac defects. Xenopus Smarcc1 mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant SMARCC1 . Hydrocephalic SMARCC1 -mutant human brain and Smarcc1 -mutant Xenopus brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation. Meaning: SMARCC1 is essential for human brain morphogenesis and is a bona fide CH risk gene. SMARCC1 mutations cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)". These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.
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Zhu W, Xie Z, Chu Z, Ding Y, Shi G, Chen W, Wei X, Yuan Y, Wei F, Tian B. The Chromatin Remodeling Factor BrCHR39 Targets DNA Methylation to Positively Regulate Apical Dominance in Brassica rapa. PLANTS (BASEL, SWITZERLAND) 2023; 12:1384. [PMID: 36987072 PMCID: PMC10051476 DOI: 10.3390/plants12061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa.
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Affiliation(s)
- Wei Zhu
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenni Chu
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yakun Ding
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gongyao Shi
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Weiwei Chen
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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The SMARCA4 R1157W mutation facilitates chromatin remodeling and confers PRMT1/SMARCA4 inhibitors sensitivity in colorectal cancer. NPJ Precis Oncol 2023; 7:28. [PMID: 36922568 PMCID: PMC10017700 DOI: 10.1038/s41698-023-00367-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
Genomic studies have demonstrated a high frequency of genetic alterations in components of the SWI/SNF complex including the core subunit SMARCA4. However, the mechanisms of tumorigenesis driven by SMARCA4 mutations, particularly in colorectal cancer (CRC), remain largely unknown. In this study, we identified a specific, hotspot mutation in SMARCA4 (c. 3721C>T) which results in a conversion from arginine to tryptophan at residue 1157 (R1157W) in human CRC tissues associated with higher-grade tumors and controls CRC progression. Mechanistically, we found that the SMARCA4R1157W mutation facilitated its recruitment to PRMT1-mediated H4R3me2a (asymmetric dimethylation of Arg 3 in histone H4) and enhanced the ATPase activity of SWI/SNF complex to remodel chromatin in CRC cells. We further showed that the SMARCA4R1157W mutant reinforced the transcriptional expression of EGFR and TNS4 to promote the proliferation of CRC cells and patient-derived tumor organoids. Importantly, we demonstrated that SMARCA4R1157W CRC cells and mutant cell-derived xenografts were more sensitive to the combined inhibition of PRMT1 and SMARCA4 which act synergistically to suppress cell proliferation. Together, our findings show that SMARCA4-R1157W is a critical activating mutation, which accelerates CRC progression through facilitating chromatin recruitment and remodeling. Our results suggest a potential precision therapeutic strategy for the treatment of CRC patients carrying the SMARCA4R1157W mutation.
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Nucleosome Remodeling at the Yeast PHO8 and PHO84 Promoters without the Putatively Essential SWI/SNF Remodeler. Int J Mol Sci 2023; 24:ijms24054949. [PMID: 36902382 PMCID: PMC10003099 DOI: 10.3390/ijms24054949] [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: 12/05/2022] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 03/08/2023] Open
Abstract
Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, removal of budding yeast PHO8 and PHO84 promoter nucleosomes upon physiological gene induction by phosphate starvation essentially requires the SWI/SNF remodeling complex. This dependency on SWI/SNF may indicate specificity in remodeler recruitment, in recognition of nucleosomes as remodeling substrate or in remodeling outcome. By in vivo chromatin analyses of wild type and mutant yeast under various PHO regulon induction conditions, we found that overexpression of the remodeler-recruiting transactivator Pho4 allowed removal of PHO8 promoter nucleosomes without SWI/SNF. For PHO84 promoter nucleosome removal in the absence of SWI/SNF, an intranucleosomal Pho4 site, which likely altered the remodeling outcome via factor binding competition, was required in addition to such overexpression. Therefore, an essential remodeler requirement under physiological conditions need not reflect substrate specificity, but may reflect specific recruitment and/or remodeling outcomes.
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Liu Y, Wen D, Ho C, Yu L, Zheng D, O'Reilly S, Gao Y, Li Q, Zhang Y. Epigenetics as a versatile regulator of fibrosis. J Transl Med 2023; 21:164. [PMID: 36864460 PMCID: PMC9983257 DOI: 10.1186/s12967-023-04018-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Fibrosis, a process caused by excessive deposition of extracellular matrix (ECM), is a common cause and outcome of organ failure and even death. Researchers have made many efforts to understand the mechanism of fibrogenesis and to develop therapeutic strategies; yet, the outcome remains unsatisfactory. In recent years, advances in epigenetics, including chromatin remodeling, histone modification, DNA methylation, and noncoding RNA (ncRNA), have provided more insights into the fibrotic process and have suggested the possibility of novel therapy for organ fibrosis. In this review, we summarize the current research on the epigenetic mechanisms involved in organ fibrosis and their possible clinical applications.
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Affiliation(s)
- Yangdan Liu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Dongsheng Wen
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Chiakang Ho
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Li Yu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Danning Zheng
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | | | - Ya Gao
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Yifan Zhang
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
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Toward the Development of Epigenome Editing-Based Therapeutics: Potentials and Challenges. Int J Mol Sci 2023; 24:ijms24054778. [PMID: 36902207 PMCID: PMC10003136 DOI: 10.3390/ijms24054778] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The advancement in epigenetics research over the past several decades has led to the potential application of epigenome-editing technologies for the treatment of various diseases. In particular, epigenome editing is potentially useful in the treatment of genetic and other related diseases, including rare imprinted diseases, as it can regulate the expression of the epigenome of the target region, and thereby the causative gene, with minimal or no modification of the genomic DNA. Various efforts are underway to successfully apply epigenome editing in vivo, such as improving target specificity, enzymatic activity, and drug delivery for the development of reliable therapeutics. In this review, we introduce the latest findings, summarize the current limitations and future challenges in the practical application of epigenome editing for disease therapy, and introduce important factors to consider, such as chromatin plasticity, for a more effective epigenome editing-based therapy.
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Yu W, Wang HL, Zhang J, Yin C. The effects of epigenetic modifications on bone remodeling in age-related osteoporosis. Connect Tissue Res 2023; 64:105-116. [PMID: 36271658 DOI: 10.1080/03008207.2022.2120392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE As the population ages, there is an increased risk of fracture and morbidity diseases associated with aging, such as age-related osteoporosis and other bone diseases linked to aging skeletons. RESULTS Several bone-related cells, including multipotent bone mesenchymal stem cells, osteoblasts that form bone tissue, and osteoclasts that break it down, are in symbiotic relationships throughout life. Growing evidence indicates that epigenetic modifications of cells caused by aging contribute to compromised bone remodeling and lead to osteoporosis. A number of epigenetic mechanisms are at play, including DNA/RNA modifications, histone modifications, microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), as well as chromatin remodeling. CONCLUSION In this review, we summarized the epigenetic modifications of different bone-related cells during the development and progression of osteoporosis associated with aging. Additionally, we described a compensatory recovery mechanism under epigenetic regulation that may lead to new strategies for regulating bone remodeling in age-related osteoporosis.
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Affiliation(s)
- Wenyue Yu
- School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, China
| | - He-Ling Wang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Jianying Zhang
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Chengcheng Yin
- School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, China
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135
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Asadauskaitė G, Morkūnienė A, Utkus A, Burnytė B. Identification of a novel BICRA variant leading to the newly described Coffin-Siris syndrome 12. Brain Dev 2023; 45:185-190. [PMID: 36437209 DOI: 10.1016/j.braindev.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pathogenic heterozygous variants in BICRA have recently been identified in patients with SWI/SNF-related intellectual disability (SSRIDD) - Coffin-Siris syndrome 12. So far, only one article reported SSRIDD associated with pathogenic variants in BICRA. CASE PRESENTATION The patient's phenotype include low birth weight, microcephaly, neurodevelopment delay, visual, gastrointestinal, urinary tract impairment, and craniofacial dysmorphism. Whole exome sequencing revealed a novel pathogenic heterozygous variant in exon 6 of BICRA gene c.535C > T (p.(Gln179*)). Sanger sequencing confirmed de novo origin. CONCLUSION The clinical findings confirm and supplement the previous study which showed that pathogenic variant in BICRA is commonly characterized by neurodevelopmental, gastrointestinal, and ophthalmologic symptoms, growth retardation, as well as craniofacial dysmorphism.
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Affiliation(s)
| | - Aušra Morkūnienė
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Algirdas Utkus
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Birutė Burnytė
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
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136
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Wei J, Patil A, Collings CK, Alfajaro MM, Liang Y, Cai WL, Strine MS, Filler RB, DeWeirdt PC, Hanna RE, Menasche BL, Ökten A, Peña-Hernández MA, Klein J, McNamara A, Rosales R, McGovern BL, Luis Rodriguez M, García-Sastre A, White KM, Qin Y, Doench JG, Yan Q, Iwasaki A, Zwaka TP, Qi J, Kadoch C, Wilen CB. Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Nat Genet 2023; 55:471-483. [PMID: 36894709 PMCID: PMC10011139 DOI: 10.1038/s41588-023-01307-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes, specifically canonical BRG1/BRM-associated factor (cBAF) complexes, promote severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and represent host-directed therapeutic targets. The catalytic activity of SMARCA4 is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, ACE2 expression and virus susceptibility. The transcription factors HNF1A/B interact with and recruit mSWI/SNF complexes to ACE2 enhancers, which contain high HNF1A motif density. Notably, small-molecule mSWI/SNF ATPase inhibitors or degraders abrogate angiotensin-converting enzyme 2 (ACE2) expression and confer resistance to SARS-CoV-2 variants and a remdesivir-resistant virus in three cell lines and three primary human cell types, including airway epithelial cells, by up to 5 logs. These data highlight the role of mSWI/SNF complex activities in conferring SARS-CoV-2 susceptibility and identify a potential class of broad-acting antivirals to combat emerging coronaviruses and drug-resistant variants.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arya Ökten
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew McNamara
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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137
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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138
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Xu JJ, Viny AD. Till SMARCA5 loss do nucleosomes part. Mol Cell 2023; 83:500-501. [PMID: 36804911 PMCID: PMC11104060 DOI: 10.1016/j.molcel.2023.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/18/2023]
Abstract
In this issue of Molecular Cell, Bomber et al. demonstrate that acute loss of SMARCA5 in human cells leads to eviction of CTCF and an increase in nucleosome repeat length without direct impact on transcriptional activity.
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Affiliation(s)
- Jane Jialu Xu
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA; Department of Medicine, Division of Hematology & Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron D Viny
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA; Department of Medicine, Division of Hematology & Oncology, Columbia University Irving Medical Center, New York, NY, USA.
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139
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Long J, Carter B, Johnson ET, Ogas J. Contribution of the histone variant H2A.Z to expression of responsive genes in plants. Semin Cell Dev Biol 2023; 135:85-92. [PMID: 35474148 PMCID: PMC9588091 DOI: 10.1016/j.semcdb.2022.04.006] [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: 01/10/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/19/2022]
Abstract
The histone variant H2A.Z plays a critical role in chromatin-based processes such as transcription, replication, and repair in eukaryotes. Although many H2A.Z-associated processes and features are conserved in plants and animals, a distinguishing feature of plant chromatin is the enrichment of H2A.Z in the bodies of genes that exhibit dynamic expression, particularly in response to differentiation and the environment. Recent work sheds new light on the plant machinery that enables dynamic changes in H2A.Z enrichment and identifies additional chromatin-based pathways that contribute to transcriptional properties of H2A.Z-enriched chromatin. In particular, analysis of a variety of responsive loci reveals a repressive role for H2A.Z in expression of responsive genes and identifies roles for SWR1 and INO80 chromatin remodelers in enabling dynamic regulation of H2A.Z levels and transcription. These studies lay the groundwork for understanding how this ancient histone variant is harnessed by plants to enable responsive and dynamic gene expression (Graphical Abstract).
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Affiliation(s)
- Jiaxin Long
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Benjamin Carter
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Emily T Johnson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA.
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140
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BRM Complex in Arabidopsis Adopts ncBAF-like Composition and Requires BRD Subunits for Assembly and Stability. Int J Mol Sci 2023; 24:ijms24043917. [PMID: 36835328 PMCID: PMC9967331 DOI: 10.3390/ijms24043917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
ATP-dependent SWI/SNF chromatin remodelling complexes are conserved multi-subunit assemblies that control genome activity. Functions of SWI/SNF complexes in plant development and growth have been well established, but the architecture of particular assemblies is unclear. In this study, we elucidate the organization of Arabidopsis SWI/SNF complexes formed around a BRM catalytic subunit, and define the requirement of bromodomain-containing proteins BRD1/2/13 for the formation and stability of the entire complex. Using affinity purification followed by mass spectrometry, we identify a set of BRM-associated subunits and demonstrate that the BRM complexes strongly resemble mammalian non-canonical BAF complexes. Furthermore, we identify BDH1 and 2 proteins as components of the BRM complex and, using mutant analyses, show that BDH1/2 are important for vegetative and generative development, as well as hormonal responses. We further show that BRD1/2/13 represent unique subunits of the BRM complexes, and their depletion severely affects the integrity of the complex, resulting in the formation of residual assemblies. Finally, analyses of BRM complexes after proteasome inhibition revealed the existence of a module consisting of the ATPase, ARP, and BDH proteins, assembled with other subunits in a BRD-dependent manner. Together, our results suggest modular organization of plant SWI/SNF complexes and provide a biochemical explanation for mutant phenotypes.
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141
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Suraweera TL, Merlin JPJ, Dellaire G, Xu Z, Rupasinghe HPV. Genistein and Procyanidin B2 Reduce Carcinogen-Induced Reactive Oxygen Species and DNA Damage through the Activation of Nrf2/ARE Cell Signaling in Bronchial Epithelial Cells In Vitro. Int J Mol Sci 2023; 24:ijms24043676. [PMID: 36835090 PMCID: PMC9961944 DOI: 10.3390/ijms24043676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide. Chemotherapy and radiation therapy are currently providing the basis for cancer therapies, although both are associated with significant side effects. Thus, cancer prevention through dietary modifications has been receiving growing interest. The potential of selected flavonoids in reducing carcinogen-induced reactive oxygen species (ROS) and DNA damage through the activation of nuclear factor erythroid 2 p45 (NF-E2)-related factor (Nrf2)/antioxidant response element (ARE) pathway was studied in vitro. Dose-dependent effects of pre-incubated flavonoids on pro-carcinogen 4-[(acetoxymethyl)nitrosamino]-1-(3-pyridyl)-1-butanone (NNKAc)-induced ROS and DNA damage in human bronchial epithelial cells were studied in comparison to non-flavonoids. The most effective flavonoids were assessed for the activation of Nrf2/ARE pathway. Genistein, procyanidin B2 (PCB2), and quercetin significantly suppressed the NNKAc-induced ROS and DNA damage. Quercetin significantly upregulated the phosphorylated protein kinase B/Akt. PCB2 significantly upregulated the activation of Nrf2 and Akt through phosphorylation. Genistein and PCB2 significantly upregulated the phospho-Nrf2 nuclear translocation and catalase activity. In summary, genistein and PCB2 reduced the NNKAc-induced ROS and DNA damage through the activation of Nrf2. Further studies are required to understand the role of dietary flavonoids on the regulation of the Nrf2/ARE pathway in relation to carcinogenesis.
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Affiliation(s)
- Tharindu L. Suraweera
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 2R8, Canada
| | - J. P. Jose Merlin
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 2R8, Canada
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Zhaolin Xu
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4H7, Canada
- QEII Health Sciences Centre, Division of Anatomical Pathology and Cytopathology, Nova Scotia Health Authority, Halifax, NS B3H 1V8, Canada
| | - H. P. Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 2R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4H7, Canada
- Correspondence:
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142
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Colarusso E, Ceccacci S, Monti MC, Gazzillo E, Giordano A, Chini MG, Ferraro MG, Piccolo M, Ruggiero D, Irace C, Terracciano S, Bruno I, Bifulco G, Lauro G. Identification of 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based small molecules as selective BRD9 binders. Eur J Med Chem 2023; 247:115018. [PMID: 36577218 DOI: 10.1016/j.ejmech.2022.115018] [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: 06/28/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Targeting bromodomain-containing protein 9 (BRD9) represents a promising strategy for the development of new agents endowed with anticancer properties. With this aim, a set of 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based compounds was investigated following a combined approach that relied on in silico studies, chemical synthesis, biophysical and biological evaluation of the most promising items. The protocol was initially based on molecular docking experiments, accounting a library of 1896 potentially synthesizable items tested in silico against the bromodomain of BRD9. A first set of 21 compounds (1-21) was selected and the binding on BDR9 was assessed through AlphaScreen assays. The obtained results disclosed compounds 17 and 20 able to bind BRD9 in the submicromolar range (IC50 = 0.35 ± 0.18 μM and IC50 = 0.14 ± 0.03 μM, respectively) showing a promising selectivity profile when tested against further nine bromodomains. Taking advantage of 3D structure-based pharmacophore models, additional 10 derivatives were selected in silico for the synthetic step and binding assessment, highlighting seven compounds (22, 23, 25, 26, 28, 29, 31) able to selectively bind BRD9 among different bromodomains. The ability of the identified BRD9 binders to cross artificial membranes in vitro was also assessed, revealing a very good passive permeability profile. Preliminary studies were carried out on a panel of healthy and cancer human cell lines to explore the biological behavior of the selected compounds, disclosing a moderate activity and significant selectivity profile towards leukaemia cells. These results highlighted the applicability of the reported multidisciplinary approach for accelerating the selection of promising items and for driving the chemical synthesis of novel selective BRD9 binders. Moreover, the low molecular weight of the reported 2,4,5-trisubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one-based BRD9 binders suggests the possibility for further exploring the chemical space in order to obtain new analogues with improved potency.
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Affiliation(s)
- Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Sara Ceccacci
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Assunta Giordano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy; Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale Delle Ricerche (CNR), Via Campi Flegrei 34, I-80078, Pozzuoli, Napoli, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Maria Grazia Ferraro
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Dafne Ruggiero
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples "Federico II", Via Domenico Montesano 49, Naples, 80131, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy.
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143
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SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett 2023; 554:216022. [PMID: 36450331 DOI: 10.1016/j.canlet.2022.216022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
SMARCA4, also known as transcription activator, is an ATP-dependent catalytic subunit of SWI/SNF (SWItch/Sucrose NonFermentable) chromatin-remodeling complexes that participates in the regulation of chromatin structure and gene expression by supplying energy. As a tumor suppressor that has aberrant expression in ∼10% of non-small-cell lung cancers (NSCLCs), SMARCA4 possesses many biological functions, including regulating gene expression, differentiation and transcription. Furthermore, NSCLC patients with SMARCA4 alterations have a weak response to conventional chemotherapy and poor prognosis. Therefore, the mechanisms of SMARCA4 in NSCLC development urgently need to be explored to identify novel biomarkers and precise therapeutic strategies for this subtype. This review systematically describes the biological functions of SMARCA4 and its role in NSCLC development, metastasis, functional epigenetics and potential therapeutic approaches for NSCLCs with SMARCA4 alterations. Additionally, this paper explores the relationship and regulatory mechanisms shared by SMARCA4 and its mutually exclusive catalytic subunit SMARCA2. We aim to provide innovative treatment strategies and improve clinical outcomes for NSCLC patients with SMARCA4 alterations.
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144
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Liu X, Wang A, Shi Y, Dai M, Liu M, Cai HB. PROTACs in Epigenetic Cancer Therapy: Current Status and Future Opportunities. Molecules 2023; 28:molecules28031217. [PMID: 36770884 PMCID: PMC9919707 DOI: 10.3390/molecules28031217] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
The epigenetic regulation of gene functions has been proven to be strongly associated with the development and progression of cancer. Reprogramming the cancer epigenome landscape is one of the most promising target therapies in both treatments and in reversing drug resistance. Proteolytic targeted chimeras (PROTACs) are an emerging therapeutic modality for selective degradation via the native ubiquitin-proteasome system. Rapid advances in PROTACs have facilitated the exploration of targeting epigenetic proteins, a lot of PROTAC degraders have already been designed in the field of epigenetic cancer therapy, and PROTACs targeting epigenetic proteins can better exploit target druggability and improve the mechanistic understanding of the epigenetic regulation of cancer. Thus, this review focuses on the progress made in the development of PROTAC degraders and PROTAC drugs targeting epigenetics in cancer and discusses challenges and future opportunities for the field.
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Affiliation(s)
- Xuelian Liu
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Anjin Wang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Yuying Shi
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Mengyuan Dai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
- Correspondence: (M.D.); (H.-B.C.)
| | - Miao Liu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hong-Bing Cai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
- Correspondence: (M.D.); (H.-B.C.)
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145
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Peng J, Zhang WJ, Zhang Q, Su YH, Tang LP. The dynamics of chromatin states mediated by epigenetic modifications during somatic cell reprogramming. Front Cell Dev Biol 2023; 11:1097780. [PMID: 36727112 PMCID: PMC9884706 DOI: 10.3389/fcell.2023.1097780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023] Open
Abstract
Somatic cell reprogramming (SCR) is the conversion of differentiated somatic cells into totipotent or pluripotent cells through a variety of methods. Somatic cell reprogramming also provides a platform to investigate the role of chromatin-based factors in establishing and maintaining totipotency or pluripotency, since high expression of totipotency- or pluripotency-related genes usually require an active chromatin state. Several studies in plants or mammals have recently shed light on the molecular mechanisms by which epigenetic modifications regulate the expression of totipotency or pluripotency genes by altering their chromatin states. In this review, we present a comprehensive overview of the dynamic changes in epigenetic modifications and chromatin states during reprogramming from somatic cells to totipotent or pluripotent cells. In addition, we illustrate the potential role of DNA methylation, histone modifications, histone variants, and chromatin remodeling during somatic cell reprogramming, which will pave the way to developing reliable strategies for efficient cellular reprogramming.
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Affiliation(s)
| | | | | | - Ying Hua Su
- *Correspondence: Ying Hua Su, ; Li Ping Tang,
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146
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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147
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Li W, Yuan J. Targeting RIPK1 kinase for modulating inflammation in human diseases. Front Immunol 2023; 14:1159743. [PMID: 36969188 PMCID: PMC10030951 DOI: 10.3389/fimmu.2023.1159743] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Receptor-Interacting Serine/Threonine-Protein Kinase 1 (RIPK1) is a master regulator of TNFR1 signaling in controlling cell death and survival. While the scaffold of RIPK1 participates in the canonical NF-κB pathway, the activation of RIPK1 kinase promotes not only necroptosis and apoptosis, but also inflammation by mediating the transcriptional induction of inflammatory cytokines. The nuclear translocation of activated RIPK1 has been shown to interact BAF-complex to promote chromatin remodeling and transcription. This review will highlight the proinflammatory role of RIPK1 kinase with focus on human neurodegenerative diseases. We will discuss the possibility of targeting RIPK1 kinase for the treatment of inflammatory pathology in human diseases.
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Affiliation(s)
- Wanjin Li
- *Correspondence: Wanjin Li, ; Junying Yuan,
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148
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Appiah CO, Singh M, May L, Bakshi I, Vaidyanathan A, Dent P, Ginder G, Grant S, Bear H, Landry J. The epigenetic regulation of cancer cell recovery from therapy exposure and its implications as a novel therapeutic strategy for preventing disease recurrence. Adv Cancer Res 2023; 158:337-385. [PMID: 36990536 DOI: 10.1016/bs.acr.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ultimate goal of cancer therapy is the elimination of disease from patients. Most directly, this occurs through therapy-induced cell death. Therapy-induced growth arrest can also be a desirable outcome, if prolonged. Unfortunately, therapy-induced growth arrest is rarely durable and the recovering cell population can contribute to cancer recurrence. Consequently, therapeutic strategies that eliminate residual cancer cells reduce opportunities for recurrence. Recovery can occur through diverse mechanisms including quiescence or diapause, exit from senescence, suppression of apoptosis, cytoprotective autophagy, and reductive divisions resulting from polyploidy. Epigenetic regulation of the genome represents a fundamental regulatory mechanism integral to cancer-specific biology, including the recovery from therapy. Epigenetic pathways are particularly attractive therapeutic targets because they are reversible, without changes in DNA, and are catalyzed by druggable enzymes. Previous use of epigenetic-targeting therapies in combination with cancer therapeutics has not been widely successful because of either unacceptable toxicity or limited efficacy. The use of epigenetic-targeting therapies after a significant interval following initial cancer therapy could potentially reduce the toxicity of combination strategies, and possibly exploit essential epigenetic states following therapy exposure. This review examines the feasibility of targeting epigenetic mechanisms using a sequential approach to eliminate residual therapy-arrested populations, that might possibly prevent recovery and disease recurrence.
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Affiliation(s)
- Christiana O Appiah
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States; Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, United States
| | - Manjulata Singh
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Lauren May
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Ishita Bakshi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Ashish Vaidyanathan
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Paul Dent
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Gordon Ginder
- Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Steven Grant
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States; Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States; Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States; Department of Microbiology & Immunology, Virginia Commonwealth University School of Medicine, Massey Cancer Center, Richmond, Richmond, VA, United States
| | - Harry Bear
- Department of Surgery, Virginia Commonwealth University School of Medicine, Massey Cancer Center, Richmond, VA, United States; Department of Microbiology & Immunology, Virginia Commonwealth University School of Medicine, Massey Cancer Center, Richmond, Richmond, VA, United States
| | - Joseph Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, United States.
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149
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Naqvi AAT, Rizvi SAM, Hassan MI. Pan-cancer analysis of Chromobox (CBX) genes for prognostic significance and cancer classification. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166561. [PMID: 36183965 DOI: 10.1016/j.bbadis.2022.166561] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the polycomb group involved in chromatin remodelling. Aberrations in CBX expression are linked to various cancers. To assess their biomarker significance, we performed a pan-cancer analysis of CBX mRNA levels in 18 cancer types. We also performed cancer classification using CBX genes as distinctive features for machine learning model development. Logistic regression (L.R.), support vector machine (SVM), random forest (R.F.), decision tree (D.T.), and XGBoost (XGB) algorithms for model training and classification. The expression of CBX genes was significantly changed in four cancer types, i.e., cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). The fold change (FC) values suggest that CBX2 was significantly upregulated in CHOL (FC = 1.639), COAD (FC = 1.734), and LUSC (FC = 1.506). On the other hand, CBX7 was found downregulated in COAD (FC = -1.209), LUAD (FC = -1.190), and LUSC (FC = -1.214). The performance of machine learning models for classification was excellent. L.R., R.F., SVM, and XGB obtained a prediction accuracy of 100 % for most cancers. However, D.T. performed comparatively poorly in prediction accuracy. The results suggest that CBX expression is significantly altered in all the cancers studied; therefore, they might be treated as potential biomarkers for therapeutic intervention of these cancers.
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Affiliation(s)
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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150
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Tong A, Di X, Zhao X, Liang X. Review the progression of ovarian clear cell carcinoma from the perspective of genomics and epigenomics. Front Genet 2023; 14:952379. [PMID: 36873929 PMCID: PMC9978161 DOI: 10.3389/fgene.2023.952379] [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: 05/25/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a rare subtype of epithelial ovarian cancer with unique molecular characteristics, specific biological and clinical behavior, poor prognosis and high resistance to chemotherapy. Pushed by the development of genome-wide technologies, our knowledge about the molecular features of OCCC has been considerably advanced. Numerous studies are emerging as groundbreaking, and many of them are promising treatment strategies. In this article, we reviewed studies about the genomics and epigenetics of OCCC, including gene mutation, copy number variations, DNA methylation and histone modifications.
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Affiliation(s)
- An Tong
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiangjie Di
- Clinical Trial Center, NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drugs, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Liang
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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