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Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
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Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
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Yu H, Lesch BJ. Functional Roles of H3K4 Methylation in Transcriptional Regulation. Mol Cell Biol 2024:1-11. [PMID: 39155435 DOI: 10.1080/10985549.2024.2388254] [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: 06/12/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Histone 3 lysine 4 methylation (H3K4me) is a highly evolutionary conserved chromatin modification associated with active transcription, and its three methylation states-mono, di, and trimethylation-mark distinct regulatory elements. However, whether H3K4me plays functional roles in transcriptional regulation or is merely a by-product of histone methyltransferases recruited to actively transcribed loci is still under debate. Here, we outline the studies that have addressed this question in yeast, Drosophila, and mammalian systems. We review evidence from histone residue mutation, histone modifier manipulation, and epigenetic editing, focusing on the relative roles of H3K4me1 and H3K4me3. We conclude that H3K4me1 and H3K4me3 may have convergent functions in establishing open chromatin and promoting transcriptional activation during cell differentiation.
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Affiliation(s)
- Haoming Yu
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Bluma J Lesch
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, USA
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Vidaurre V, Song A, Li T, Ku WL, Zhao K, Qian J, Chen X. The Drosophila histone methyltransferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation. Development 2024; 151:dev202729. [PMID: 39007366 DOI: 10.1242/dev.202729] [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: 01/25/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Many tissue-specific adult stem cell lineages maintain a balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase Set1 regulates early-stage male germ cells in Drosophila. Early-stage germline-specific knockdown of Set1 results in temporally progressive defects, arising as germ cell loss and developing into overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage non-cell-autonomously. Additionally, wild-type Set1, but not the catalytically inactive Set1, rescues the Set1 knockdown phenotypes, highlighting the functional importance of the methyltransferase activity of Set1. Further, RNA-sequencing experiments reveal key signaling pathway components, such as the JAK-STAT pathway gene Stat92E and the BMP pathway gene Mad, which are upregulated upon Set1 knockdown. Genetic interaction assays support the functional relationships between Set1 and JAK-STAT or BMP pathways, as both Stat92E and Mad mutations suppress the Set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The phenotype of germ cell loss followed by over-proliferation when inhibiting a histone methyltransferase also raises concerns about using their inhibitors in cancer therapy.
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Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Annabelle Song
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taibo Li
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Wai Lim Ku
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20814, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20814, USA
| | - Jiang Qian
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
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Ali A, Liang P. Transposable elements contribute to tissue-specific gene regulation in humans. Genes Genomics 2024:10.1007/s13258-024-01550-6. [PMID: 39088190 DOI: 10.1007/s13258-024-01550-6] [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: 06/03/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Transposable elements (TEs) contribute to approximately half of the human genome, and along with many other functions, they have been known to play a role in gene regulation in the genome. With TEs' active/repressed states varying across tissue and cell types, they have the potential to regulate gene expression in a tissue-specific manner. OBJECTIVE AND METHODS To provide a systematic analysis of TEs' contribution in tissue-specific gene regulation, we examined the regulatory elements and genes in association with TE-derived regulatory sequences in 14 human cell lines belonging to 10 different tissue types using the functional genomics data from the ENCODE project. Specifically, we separately analyzed regulatory regions identified by three different approaches (DNase hypersensitive sites (DHS), histone active sites (HA), and histone repressive sites (HR)). RESULTS These regulatory regions showed to be distinct from each other by sharing less than 2.5% among all three types and more than 95% showed to be cell line-specific. Despite a lower total TE content overall than the genome average, each regulatory sequence type showed enrichment for one or two specific TE type(s): DHS for long terminal repeats (LTRs) and DNA transposons, HA for short interspersed nucleotide elements (SINEs), and HR for LTRs. In contrast, SINE was shown to be overrepresented in all three types of regulatory sequences located in gene-neighboring regions. TE-regulated genes were mostly shown to have cell line specific pattern, and tissue-specific genes (TSGs) showed higher usage of TE regulatory sequences in the tissue of their expression. While TEs in the regulatory sequences showed to be older than their genome-wide counterparts, younger TEs were shown to be more likely used in cell line specific regulatory sequences. CONCLUSIONS Collectively, our study provided further evidence enforcing an important contribution of TEs to tissue-specific gene regulation in humans.
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Affiliation(s)
- Arsala Ali
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.
- Centre of Biotechnologies, Brock University, St. Catharines, ON, L2S 3A1, Canada.
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Xu H, Yan S, Gerhard E, Xie D, Liu X, Zhang B, Shi D, Ameer GA, Yang J. Citric Acid: A Nexus Between Cellular Mechanisms and Biomaterial Innovations. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2402871. [PMID: 38801111 PMCID: PMC11309907 DOI: 10.1002/adma.202402871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Citrate-based biodegradable polymers have emerged as a distinctive biomaterial platform with tremendous potential for diverse medical applications. By harnessing their versatile chemistry, these polymers exhibit a wide range of material and bioactive properties, enabling them to regulate cell metabolism and stem cell differentiation through energy metabolism, metabonegenesis, angiogenesis, and immunomodulation. Moreover, the recent US Food and Drug Administration (FDA) clearance of the biodegradable poly(octamethylene citrate) (POC)/hydroxyapatite-based orthopedic fixation devices represents a translational research milestone for biomaterial science. POC joins a short list of biodegradable synthetic polymers that have ever been authorized by the FDA for use in humans. The clinical success of POC has sparked enthusiasm and accelerated the development of next-generation citrate-based biomaterials. This review presents a comprehensive, forward-thinking discussion on the pivotal role of citrate chemistry and metabolism in various tissue regeneration and on the development of functional citrate-based metabotissugenic biomaterials for regenerative engineering applications.
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Affiliation(s)
- Hui Xu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Su Yan
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ethan Gerhard
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Denghui Xie
- Department of Histology and Embryology, School of Basic Medical Sciences, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Southern Medical University, Guangzhou, 510515, P. R. China
- Academy of Orthopedics of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Guangzhou, 510630, P. R. China
| | - Xiaodong Liu
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310030, P. R. China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, P. R. China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310030, P. R. China
- Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310030, P. R. China
| | - Bing Zhang
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310030, P. R. China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, P. R. China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310030, P. R. China
- Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310030, P. R. China
| | - Dongquan Shi
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, P. R. China
| | - Guillermo A Ameer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jian Yang
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, 310030, P. R. China
- Biomedical Engineering Program, School of Engineering, Westlake University, Hangzhou, Zhejiang, 310030, P. R. China
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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc transferase congenital disorder of glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024; 300:107599. [PMID: 39059494 DOI: 10.1016/j.jbc.2024.107599] [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: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification of O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee, UK; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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Liu H, Liu W, Wang Z, Li N, Xie Y, Zhao Y. Comprehensive analysis of Alfin-like transcription factors associated with drought and salt stresses in wheat (Triticum aestivum L.). BMC Genomics 2024; 25:701. [PMID: 39020295 PMCID: PMC11256656 DOI: 10.1186/s12864-024-10557-y] [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: 04/15/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Alfin-like proteins are a kind of plant-specific transcription factors, and play vital roles in plant growth, development and stress responses. RESULTS In this study, a total of 27 Alfin-like transcription factors were identified in wheat. TaAL genes were unevenly distributed on chromosome. Phylogenetic analysis showed TaAL genes were divided into AL-B and AL-C subfamilies, and TaALs with closer evolutionary relationships generally shared more similar exon-intron structures and conserved motifs. The cis-acting element analysis showed MBS, ABRE and CGTCA-motif were the most common in TaAL promoters. The interacting proteins and downstream target genes of TaAL genes were also investigated in wheat. The transcriptome data and real-time PCR results indicated TaAL genes were differentially expressed under drought and salt stresses, and TaAL1-B was significantly up-regulated in response to drought stress. In addition, association analysis revealed that TaAL1-B-Hap-I allelic variation had significantly higher survival rate compared to TaAL1-B-Hap-II under drought stress. CONCLUSIONS These results will provide vital information to increase our understanding of the Alfin-like gene family in wheat, and help us in breeding better wheat varieties in the future.
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Affiliation(s)
- Hao Liu
- College of Agriculture, Ludong University, Yantai, 264000, China
| | - Wenyan Liu
- College of Agriculture, Ludong University, Yantai, 264000, China
| | - Ziyi Wang
- College of Agriculture, Ludong University, Yantai, 264000, China
| | - Na Li
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, China.
| | - Yongfeng Xie
- College of Environment and Life Sciences, Weinan Normal University, Weinan, 714099, China.
| | - Yanhong Zhao
- College of Agriculture, Ludong University, Yantai, 264000, China.
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Noura M, Tomita S, Yasuda T, Tsuzuki S, Kiyoi H, Hayakawa F. NUP98-BPTF promotes oncogenic transformation through PIM1 upregulation. Cancer Med 2024; 13:e7445. [PMID: 38940430 PMCID: PMC11212001 DOI: 10.1002/cam4.7445] [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: 01/19/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
INTRODUCTION Nucleoporin 98 (NUP98) fusion proteins are recurrently found in leukemia and are associated with unfavorable clinical outcomes. They are distributed to the nucleus and contribute to leukemogenesis via aberrant transcriptional regulation. We previously identified NUP98-BPTF (NB) fusion in patients with T-cell acute lymphoblastic leukemia (T-ALL) using next-generation sequencing. The FG-repeat of NUP98 and the PHD finger and bromodomain of bromodomain PHD finger transcription factor (BPTF) are retained in the fusion. Like other NUP98 fusion proteins, NB is considered to regulate genes that are essential for leukemogenesis. However, its target genes or pathways remain unknown. MATERIALS AND METHODS To investigate the potential oncogenic properties of the NB fusion protein, we lentivirally transduced a doxycycline-inducible NB expression vector into mouse NIH3T3 fibroblasts and human Jurkat T-ALL cells. RESULTS NB promoted the transformation of mouse NIH3T3 fibroblasts by upregulating the proto-oncogene Pim1, which encodes a serine/threonine kinase. NB transcriptionally regulated Pim1 expression by binding to its promoter and activated MYC and mTORC1 signaling. PIM1 knockdown or pharmacological inhibition of mTORC1 signaling suppressed NB-induced NIH3T3 cell transformation. Furthermore, NB enhanced the survival of human Jurkat T-ALL cells by inactivating the pro-apoptotic protein BCL2-associated agonist of cell death (BAD). CONCLUSION We demonstrated the pivotal role of NB in cell transformation and survival and identified PIM1as a key downstream target of NB. These findings propose a promising therapeutic strategy for patients with NB fusion-positive leukemia.
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Affiliation(s)
- Mina Noura
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Sakura Tomita
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
| | - Takahiko Yasuda
- Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Shinobu Tsuzuki
- Department of BiochemistryAichi Medical University School of MedicineNagakuteJapan
| | - Hitoshi Kiyoi
- Department of Hematology and OncologyNagoya University Graduate School of MedicineNagoyaJapan
| | - Fumihiko Hayakawa
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
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Chen X, Li J, Guan X, Bai Y, Wang K. Abnormal activation of genomic LINE1 elements caused by DNA demethylation contributes to lncRNA CASC9 overexpression in esophageal squamous cell carcinoma. Heliyon 2024; 10:e32857. [PMID: 38975080 PMCID: PMC11226909 DOI: 10.1016/j.heliyon.2024.e32857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Long noncoding RNA (lncRNA) cancer susceptibility 9 (CASC9) has been found to be overexpressed and functions as an oncogene in many cancer types. We investigated the molecular mechanism underlying CASC9 overexpression in esophageal squamous cell carcinoma (ESCC). Transcripts containing exons 2 and 6 and exons 4 and 6 showed the highest CASC9 expression levels in ESCC, no transcripts were detected in the normal esophageal epithelial Het1A cell line. The Long Interspersed Nuclear Element-1 (LINE1 or L1) element in the genome was found to participate in the evolution of lncRNA CASC9, the antisense promoter (ASP) of L1 provides the cis-regulatory elements necessary for CASC9 activation, and the antisense chain of L1 participates in the formation of exons of CASC9. The activation of the antisense promoter was due to the aberrant hypomethylation of L1 elements. An active enhancer element was identified in the downstream region of CASC9 gene by ChIP-seq and ChIP-qPCR. The interaction between ASP and the enhancer elements was confirmed by chromosome conformation capture (3C). Thus, our results suggest that the L1 ASP activation due to aberrant hypomethylation and downstream enhancer interaction plays a key role in the overexpression of lncRNA CASC9 in ESCC.
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Affiliation(s)
- Xuedan Chen
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
| | - Juan Li
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
- Jinfeng Laboratory, Chongqing 400038, China
| | - Xingying Guan
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
| | - Yun Bai
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
| | - Kai Wang
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
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Anyetei-Anum CS, Leatham-Jensen MP, Fox GC, Smith BR, Krajewski K, Strahl BD, Dowen JM, Matera AG, Duronio RJ, McKay DJ. Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600669. [PMID: 38979215 PMCID: PMC11230394 DOI: 10.1101/2024.06.25.600669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4). However, there is no direct evidence that H3K4 regulates Polycomb group target genes in vivo . Here, we demonstrate two key roles for replication-dependent histone H3.2K4 in target control. We find that H3.2K4 antagonizes Polycomb group catalytic activity and that it is required for proper target gene activation. We conclude that H3.2K4 directly regulates expression of Polycomb targets.
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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12
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Ni Y, Shi M, Liu L, Lin D, Zeng H, Ong C, Wang Y. G9a in Cancer: Mechanisms, Therapeutic Advancements, and Clinical Implications. Cancers (Basel) 2024; 16:2175. [PMID: 38927881 PMCID: PMC11201431 DOI: 10.3390/cancers16122175] [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: 04/19/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
G9a, also named EHMT2, is a histone 3 lysine 9 (H3K9) methyltransferase responsible for catalyzing H3K9 mono- and dimethylation (H3K9me1 and H3K9me2). G9a contributes to various aspects of embryonic development and tissue differentiation through epigenetic regulation. Furthermore, the aberrant expression of G9a is frequently observed in various tumors, particularly in prostate cancer, where it contributes to cancer pathogenesis and progression. This review highlights the critical role of G9a in multiple cancer-related processes, such as epigenetic dysregulation, tumor suppressor gene silencing, cancer lineage plasticity, hypoxia adaption, and cancer progression. Despite the increased research on G9a in prostate cancer, there are still significant gaps, particularly in understanding its interactions within the tumor microenvironment and its broader epigenetic effects. Furthermore, this review discusses the recent advancements in G9a inhibitors, including the development of dual-target inhibitors that target G9a along with other epigenetic factors such as EZH2 and HDAC. It aims to bring together the existing knowledge, identify gaps in the current research, and suggest future directions for research and treatment strategies.
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Affiliation(s)
- Yuchao Ni
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China;
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Mingchen Shi
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Liangliang Liu
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Dong Lin
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Hao Zeng
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Christopher Ong
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada; (M.S.); (L.L.); (D.L.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC V5Z 1L3, Canada
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13
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Zhang Y, Xie G, Lee JE, Zandian M, Sudarshan D, Estavoyer B, Benz C, Viita T, Asgaritarghi G, Lachance C, Messmer C, Simonetti L, Sinha VK, Lambert JP, Chen YW, Wang SP, Ivarsson Y, Affar EB, Côté J, Ge K, Kutateladze TG. ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers. Nat Commun 2024; 15:4883. [PMID: 38849395 PMCID: PMC11161652 DOI: 10.1038/s41467-024-49391-x] [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: 10/09/2022] [Accepted: 05/31/2024] [Indexed: 06/09/2024] Open
Abstract
The human methyltransferase and transcriptional coactivator MLL4 and its paralog MLL3 are frequently mutated in cancer. MLL4 and MLL3 monomethylate histone H3K4 and contain a set of uncharacterized PHD fingers. Here, we report a novel function of the PHD2 and PHD3 (PHD2/3) fingers of MLL4 and MLL3 that bind to ASXL2, a component of the Polycomb repressive H2AK119 deubiquitinase (PR-DUB) complex. The structure of MLL4 PHD2/3 in complex with the MLL-binding helix (MBH) of ASXL2 and mutational analyses reveal the molecular mechanism which is conserved in homologous ASXL1 and ASXL3. The native interaction of the Trithorax MLL3/4 complexes with the PR-DUB complex in vivo depends solely on MBH of ASXL1/2, coupling the two histone modifying activities. ChIP-seq analysis in embryonic stem cells demonstrates that MBH of ASXL1/2 is required for the deubiquitinase BAP1 recruitment to MLL4-bound active enhancers. Our findings suggest an ASXL1/2-dependent functional link between the MLL3/4 and PR-DUB complexes.
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Affiliation(s)
- Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Guojia Xie
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Ji-Eun Lee
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Benjamin Estavoyer
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, H1T 2M4, Canada
| | - Caroline Benz
- Department of Chemistry, BMC, Uppsala University, Uppsala, 75237, Sweden
| | - Tiina Viita
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Golareh Asgaritarghi
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Clémence Messmer
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, H1T 2M4, Canada
| | - Leandro Simonetti
- Department of Chemistry, BMC, Uppsala University, Uppsala, 75237, Sweden
| | - Vikrant Kumar Sinha
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Jean-Philippe Lambert
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Yu-Wen Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Shu-Ping Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, 75237, Sweden
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada.
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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14
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Becht DC, Mohid SA, Lee JE, Zandian M, Benz C, Biswas S, Sinha VK, Ivarsson Y, Ge K, Zhang Y, Kutateladze TG. MLL4 binds TET3. Structure 2024; 32:706-714.e3. [PMID: 38579707 PMCID: PMC11162309 DOI: 10.1016/j.str.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/01/2024] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
Human mixed lineage leukemia 4 (MLL4), also known as KMT2D, regulates cell type specific transcriptional programs through enhancer activation. Along with the catalytic methyltransferase domain, MLL4 contains seven less characterized plant homeodomain (PHD) fingers. Here, we report that the sixth PHD finger of MLL4 (MLL4PHD6) binds to the hydrophobic motif of ten-eleven translocation 3 (TET3), a dioxygenase that converts methylated cytosine into oxidized derivatives. The solution NMR structure of the TET3-MLL4PHD6 complex and binding assays show that, like histone H4 tail, TET3 occupies the hydrophobic site of MLL4PHD6, and that this interaction is conserved in the seventh PHD finger of homologous MLL3 (MLL3PHD7). Analysis of genomic localization of endogenous MLL4 and ectopically expressed TET3 in mouse embryonic stem cells reveals a high degree overlap on active enhancers and suggests a potential functional relationship of MLL4 and TET3.
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Affiliation(s)
- Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sk Abdul Mohid
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ji-Eun Lee
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Soumi Biswas
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Vikrant Kumar Sinha
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Yi Zhang
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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15
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Verma P, Sánchez Alvarado A, Duncan EM. Chromatin remodeling protein BPTF regulates transcriptional stability in planarian stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595819. [PMID: 38826365 PMCID: PMC11142235 DOI: 10.1101/2024.05.24.595819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Trimethylation of histone H3 lysine 4 (H3K4me3) correlates strongly with gene expression in many different organisms, yet the question of whether it plays a causal role in transcriptional activity remains unresolved. Although H3K4me3 does not directly affect chromatin accessibility, it can indirectly affect genome accessibility by recruiting the ATP-dependent chromatin remodeling complex NuRF (Nucleosome Remodeling Factor). The largest subunit of NuRF, BPTF/NURF301, binds H3K4me3 specifically and recruits the NuRF complex to loci marked by this modification. Studies have shown that the strength and duration of BPTF binding likely also depends on additional chromatin features at these loci, such as lysine acetylation and variant histone proteins. However, the exact details of this recruitment mechanism vary between studies and have largely been tested in vitro. Here, we use stem cells isolated directly from live planarian animals to investigate the role of BPTF in regulating chromatin accessibility in vivo. We find that BPTF operates at gene promoters and is most effective at facilitating transcription at genes marked by Set1-dependent H3K4me3 peaks, which are significantly broader than those added by the lysine methyltransferase MLL1/2. Moreover, BPTF is essential for planarian stem cell biology and its loss of function phenotype mimics that of Set1 knockdown. Together, these data suggest that BPTF and H3K4me3 are important mediators of both transcription and in vivo stem cell function.
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16
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Sureshkumar S, Bandaranayake C, Lv J, Dent CI, Bhagat PK, Mukherjee S, Sarwade R, Atri C, York HM, Tamizhselvan P, Shamaya N, Folini G, Bergey BG, Yadav AS, Kumar S, Grummisch OS, Saini P, Yadav RK, Arumugam S, Rosonina E, Sadanandom A, Liu H, Balasubramanian S. SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana. NATURE PLANTS 2024; 10:749-759. [PMID: 38641663 DOI: 10.1038/s41477-024-01672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024]
Abstract
Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me2/3. Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me3 to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing.
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Affiliation(s)
- Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia.
| | - Champa Bandaranayake
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Junqing Lv
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Craig I Dent
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Sourav Mukherjee
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Rucha Sarwade
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Chhaya Atri
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Harrison M York
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory, Australia (EMBL Australia), Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Prashanth Tamizhselvan
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Giulia Folini
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Subhasree Kumar
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Oliver S Grummisch
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Prince Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Ram K Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory, Australia (EMBL Australia), Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, UK
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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17
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Khan I, Kashani-Sabet M. Bromodomain inhibition targeting BPTF in the treatment of melanoma and other solid tumors. Clin Exp Metastasis 2024:10.1007/s10585-024-10265-7. [PMID: 38683257 DOI: 10.1007/s10585-024-10265-7] [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: 06/20/2023] [Accepted: 01/06/2024] [Indexed: 05/01/2024]
Abstract
Epigenetic mechanisms have been shown to play an important role in the development of cancer. These include the activation of chromatin remodeling factors in various malignancies, including bromodomain plant homeodomain (PHD) finger transcription factor (BPTF), the largest component of the human nucleosome remodeling factor (NURF). In the last few years, BPTF has been identified as a pro-tumorigenic factor in melanoma, stimulated by research into the molecular mechanisms underlying BPTF function. Developing therapy targeting the BPTF bromodomain would represent a significant advance. Melanoma therapy has been revolutionized by the efficacy of immunotherapeutic and targeted strategies, but the development of drug resistance calls for alternative therapeutic approaches. Recent work has shown both a biomarker as well as functional role for BPTF in melanoma progression and as a possible target for its therapy. BPTF was shown to stimulate the mitogen-activated protein kinase pathway, which is targeted by selective BRAF inhibitors. The advent of small molecule inhibitors that target bromodomain motifs has shown that bromodomains are druggable. By combining the bromodomain inhibitor bromosporine with existing treatments that target mutant BRAF, BPTF targeting has emerged as a novel and promising therapeutic approach for metastatic melanoma. This article summarizes the functional role of BPTF in tumor progression, reviews the clinical experience to date with bromodomain inhibitors, and discusses the promise of BPTF targeting in melanoma and other solid tumors.
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Affiliation(s)
- Imran Khan
- California Pacific Medical Center Research Institute, 475 Brannan St, Suite 130, San Francisco, CA, 94107, USA
| | - Mohammed Kashani-Sabet
- California Pacific Medical Center Research Institute, 475 Brannan St, Suite 130, San Francisco, CA, 94107, USA.
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18
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Zhang C, Liu W, Xu L, Liu S, Che F. Abnormal H3K4 enzyme catalytic activity and neuronal morphology caused by ASH1L mutations in individuals with Tourette syndrome. Eur Child Adolesc Psychiatry 2024:10.1007/s00787-024-02437-3. [PMID: 38634863 DOI: 10.1007/s00787-024-02437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
ASH1L potentially contributes to Tourette syndrome (TS) and other neuropsychiatric disorders, as our previous studies have shown. It regulates essential developmental genes by counteracting polycomb-mediated transcriptional repression, which restricts chromatin accessibility at target genes. ASH1L is highly expressed in the adult brain, playing a crucial role in the early stage. However, it remains unclear how ASH1L mutations carried by patients with TS participate in regulating neuronal growth processes leading to TS traits. Five TS families recruited in our study underwent comprehensive physical examinations and questionnaires to record clinical phenotypes and environmental impact factors. We validated the variants via Sanger sequencing and constructed two mutants near the catalytic domain of ASH1L. We conducted molecular modeling, in vitro assays, and primary neuron cultures to find the role of ASH1L in neuronal development and its correlation with TS. In this study, we validated five pathogenic ASH1L rare variants and observed symptoms in patients with simple tics and behavioral comorbidities. Mutations near the catalytic domain of TS patients cause mental state abnormalities and disrupt ASH1L function by destabilizing its spatial conformation, leading to decreased activity of catalytic H3K4, thereby affecting the neurite growth. We need to conduct larger-scale studies on TS patients and perform additional neurological evaluations on mature neurons. We first reported the effects of ASH1L mutations in TS patients, including phenotypic heterogeneity, protein function, and neurological growth. This information contributes to understanding the neurodevelopmental pathogenesis of TS in patients with ASH1L mutations.
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Affiliation(s)
- Cheng Zhang
- Department of Neurology, The Second Affiliated Hospital of Shandong University, Jinan, 250033, Shandong, China
- Department of Neurology, Linyi People's Hospital, 27 East Section of Jiefang Road Lanshan District, Linyi, 276000, Shandong, China
| | - Wenmiao Liu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Lulu Xu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Shiguo Liu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China.
| | - Fengyuan Che
- Department of Neurology, Linyi People's Hospital, 27 East Section of Jiefang Road Lanshan District, Linyi, 276000, Shandong, China
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19
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Paniri A, Hosseini MM, Akhavan-Niaki H. Alzheimer's Disease-Related Epigenetic Changes: Novel Therapeutic Targets. Mol Neurobiol 2024; 61:1282-1317. [PMID: 37700216 DOI: 10.1007/s12035-023-03626-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Aging is a significant risk factor for Alzheimer's disease (AD), although the precise mechanism and molecular basis of AD are not yet fully understood. Epigenetic mechanisms, such as DNA methylation and hydroxymethylation, mitochondrial DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), play a role in regulating gene expression related to neuron plasticity and integrity, which are closely associated with learning and memory development. This review describes the impact of dynamic and reversible epigenetic modifications and factors on memory and plasticity throughout life, emphasizing their potential as target for therapeutic intervention in AD. Additionally, we present insight from postmortem and animal studies on abnormal epigenetics regulation in AD, as well as current strategies aiming at targeting these factors in the context of AD therapy.
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Affiliation(s)
- Alireza Paniri
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran.
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20
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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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21
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Vidaurre V, Song A, Li T, Ku WL, Zhao K, Qian J, Chen X. The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580277. [PMID: 38405894 PMCID: PMC10888844 DOI: 10.1101/2024.02.14.580277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Many cell types come from tissue-specific adult stem cells that maintain the balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase, Set1, regulates early-stage male germ cell proliferation and differentiation in Drosophila. Early-stage germline-specific knockdown of set1 results in a temporally progressed defects, arising as germ cell loss and developing to overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage in a non-cell-autonomous manner. Additionally, wild-type Set1, but not the catalytically inactive Set1, could rescue the set1 knockdown phenotypes, highlighting the functional importance of the methyl-transferase activity of the Set1 enzyme. Further, RNA-seq experiments reveal key signaling pathway components, such as the JAK-STAT pathway gene stat92E and the BMP pathway gene mad, that are upregulated upon set1 knockdown. Genetic interaction assays support the functional relationships between set1 and JAK-STAT or BMP pathways, as mutations of both the stat92E and mad genes suppress the set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The germ cell loss followed by over-proliferation phenotypes when inhibiting a histone methyl-transferase raise concerns about using their inhibitors in cancer therapy.
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Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Annabelle Song
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Taibo Li
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wai Lim Ku
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Jiang Qian
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Xin Chen
- Howard Hughes Medical Institute, Baltimore, Maryland, United States of America
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
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22
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Felipe I, Martínez-de-Villarreal J, Patel K, Martínez-Torrecuadrada J, Grossmann LD, Roncador G, Cubells M, Farrell A, Kendsersky N, Sabroso-Lasa S, Sancho-Temiño L, Torres K, Martinez D, Perez JM, García F, Pogoriler J, Moreno L, Maris JM, Real FX. BPTF cooperates with MYCN and MYC to link neuroblastoma cell cycle control to epigenetic cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579816. [PMID: 38405949 PMCID: PMC10888818 DOI: 10.1101/2024.02.11.579816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The nucleosome remodeling factor BPTF is required for the deployment of the MYC-driven transcriptional program. Deletion of one Bptf allele delays tumor progression in mouse models of pancreatic cancer and lymphoma. In neuroblastoma, MYCN cooperates with the transcriptional core regulatory circuitry (CRC). High BPTF levels are associated with high-risk features and decreased survival. BPTF depletion results in a dramatic decrease of cell proliferation. Bulk RNA-seq, single-cell sequencing, and tissue microarrays reveal a positive correlation of BPTF and CRC transcription factor expression. Immunoprecipitation/mass spectrometry shows that BPTF interacts with MYCN and the CRC proteins. Genome-wide distribution analysis of BPTF and CRC in neuroblastoma reveals a dual role for BPTF: 1) it co-localizes with MYCN/MYC at the promoter of genes involved in cell cycle and 2) it co-localizes with the CRC at super-enhancers to regulate cell identity. The critical role of BPTF across neuroblastoma subtypes supports its relevance as a therapeutic target.
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23
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Marunde MR, Fuchs HA, Burg JM, Popova IK, Vaidya A, Hall NW, Weinzapfel EN, Meiners MJ, Watson R, Gillespie ZB, Taylor HF, Mukhsinova L, Onuoha UC, Howard SA, Novitzky K, McAnarney ET, Krajewski K, Cowles MW, Cheek MA, Sun ZW, Venters BJ, Keogh MC, Musselman CA. Nucleosome conformation dictates the histone code. eLife 2024; 13:e78866. [PMID: 38319148 PMCID: PMC10876215 DOI: 10.7554/elife.78866] [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: 03/22/2022] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.
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Affiliation(s)
| | - Harrison A Fuchs
- Department of Biochemistry, University of Iowa Carver College of MedicineAuroraUnited States
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillChapel HillUnited States
| | | | | | | | | | | | - Catherine A Musselman
- Department of Biochemistry, University of Iowa Carver College of MedicineAuroraUnited States
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
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24
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Yogev Y, Schaffer M, Shlapobersky M, Jean MM, Wormser O, Drabkin M, Halperin D, Kassem R, Livoff A, Tsitrina AA, Asna N, Birk OS. A role of BPTF in viral oncogenicity delineated through studies of heritable Kaposi sarcoma. J Med Virol 2024; 96:e29436. [PMID: 38380509 DOI: 10.1002/jmv.29436] [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: 05/24/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Kaposi sarcoma (KS), caused by Herpesvirus-8 (HHV-8; KSHV), shows sporadic, endemic, and epidemic forms. While familial clustering of KS was previously recorded, the molecular basis of hereditary predilection to KS remains largely unknown. We demonstrate through genetic studies that a dominantly inherited missense mutation in BPTF segregates with a phenotype of classical KS in multiple immunocompetent individuals in two families. Using an rKSHV.219-infected CRISPR/cas9-model, we show that BPTFI2012T mutant cells exhibit higher latent-to-lytic ratio, decreased virion production, increased LANA staining, and latent phenotype in viral transcriptomics. RNA-sequencing demonstrated that KSHV infection dysregulated oncogenic-like response and P53 pathways, MAPK cascade, and blood vessel development pathways, consistent with KS. BPTFI2012T also enriched pathways of viral genome regulation and replication, immune response, and chemotaxis, including downregulation of IFI16, SHFL HLAs, TGFB1, and HSPA5, all previously associated with KSHV infection and tumorigenesis. Many of the differentially expressed genes are regulated by Rel-NF-κB, which regulates immune processes, cell survival, and proliferation and is pivotal to oncogenesis. We thus demonstrate BPTF mutation-mediated monogenic hereditary predilection of KSHV virus-induced oncogenesis, and suggest BPTF as a drug target.
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Affiliation(s)
- Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Moshe Schaffer
- Department of Oncology, Barzilai University Medical Center, Ashkelon, and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Mark Shlapobersky
- Department of Pathology, Barzilai University Medical Center, Ashkelon, and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Matan M Jean
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Riad Kassem
- Department of Dermatology, Sheba Medical Center, Ramat Gan, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Livoff
- Department of Pathology, Barzilai University Medical Center, Ashkelon, and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
- Department of Pathology, Galilee Medical Center, and The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Alexandra A Tsitrina
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Noam Asna
- Department of Oncology, Barzilai University Medical Center, Ashkelon, and Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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25
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Sotomayor-Lugo F, Iglesias-Barrameda N, Castillo-Aleman YM, Casado-Hernandez I, Villegas-Valverde CA, Bencomo-Hernandez AA, Ventura-Carmenate Y, Rivero-Jimenez RA. The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation. Int J Mol Sci 2024; 25:1459. [PMID: 38338738 PMCID: PMC10855761 DOI: 10.3390/ijms25031459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Mammalian fertilization initiates the reprogramming of oocytes and sperm, forming a totipotent zygote. During this intricate process, the zygotic genome undergoes a maternal-to-zygotic transition (MZT) and subsequent zygotic genome activation (ZGA), marking the initiation of transcriptional control and gene expression post-fertilization. Histone modifications are pivotal in shaping cellular identity and gene expression in many mammals. Recent advances in chromatin analysis have enabled detailed explorations of histone modifications during ZGA. This review delves into conserved and unique regulatory strategies, providing essential insights into the dynamic changes in histone modifications and their variants during ZGA in mammals. The objective is to explore recent advancements in leading mechanisms related to histone modifications governing this embryonic development phase in depth. These considerations will be useful for informing future therapeutic approaches that target epigenetic regulation in diverse biological contexts. It will also contribute to the extensive areas of evolutionary and developmental biology and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
| | | | | | | | | | | | | | - Rene Antonio Rivero-Jimenez
- Abu Dhabi Stem Cells Center, Abu Dhabi P.O. Box 4600, United Arab Emirates; (F.S.-L.); (N.I.-B.); (Y.M.C.-A.); (I.C.-H.); (C.A.V.-V.); (A.A.B.-H.); (Y.V.-C.)
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26
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Zhao Q, Zong H, Zhu P, Su C, Tang W, Chen Z, Jin S. Crosstalk between colorectal CSCs and immune cells in tumorigenesis, and strategies for targeting colorectal CSCs. Exp Hematol Oncol 2024; 13:6. [PMID: 38254219 PMCID: PMC10802076 DOI: 10.1186/s40164-024-00474-x] [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: 09/28/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Cancer immunotherapy has emerged as a promising strategy in the treatment of colorectal cancer, and relapse after tumor immunotherapy has attracted increasing attention. Cancer stem cells (CSCs), a small subset of tumor cells with self-renewal and differentiation capacities, are resistant to traditional therapies such as radiotherapy and chemotherapy. Recently, CSCs have been proven to be the cells driving tumor relapse after immunotherapy. However, the mutual interactions between CSCs and cancer niche immune cells are largely uncharacterized. In this review, we focus on colorectal CSCs, CSC-immune cell interactions and CSC-based immunotherapy. Colorectal CSCs are characterized by robust expression of surface markers such as CD44, CD133 and Lgr5; hyperactivation of stemness-related signaling pathways, such as the Wnt/β-catenin, Hippo/Yap1, Jak/Stat and Notch pathways; and disordered epigenetic modifications, including DNA methylation, histone modification, chromatin remodeling, and noncoding RNA action. Moreover, colorectal CSCs express abnormal levels of immune-related genes such as MHC and immune checkpoint molecules and mutually interact with cancer niche cells in multiple tumorigenesis-related processes, including tumor initiation, maintenance, metastasis and drug resistance. To date, many therapies targeting CSCs have been evaluated, including monoclonal antibodies, antibody‒drug conjugates, bispecific antibodies, tumor vaccines adoptive cell therapy, and small molecule inhibitors. With the development of CSC-/niche-targeting technology, as well as the integration of multidisciplinary studies, novel therapies that eliminate CSCs and reverse their immunosuppressive microenvironment are expected to be developed for the treatment of solid tumors, including colorectal cancer.
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Affiliation(s)
- Qi Zhao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hong Zong
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Pingping Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Chang Su
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, No. 2 Jing‑ba Road, Zhengzhou, 450014, China.
| | - Zhenzhen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Shuiling Jin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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27
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Janssens DH, Greene JE, Wu SJ, Codomo CA, Minot SS, Furlan SN, Ahmad K, Henikoff S. Scalable single-cell profiling of chromatin modifications with sciCUT&Tag. Nat Protoc 2024; 19:83-112. [PMID: 37935964 PMCID: PMC11229882 DOI: 10.1038/s41596-023-00905-9] [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: 02/06/2023] [Accepted: 08/18/2023] [Indexed: 11/09/2023]
Abstract
Cleavage under targets and tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune precipitation-based methods, such as chromatin immunoprecipitation-sequencing. The efficiency of the method enables chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution, high-throughput, single-cell chromatin profiling. In this single-cell combinatorial indexing CUT&Tag (sciCUT&Tag) protocol, lightly cross-linked nuclei are bound to magnetic beads and incubated with primary and secondary antibodies in bulk and then arrayed in a 96-well plate for a first round of cellular indexing by antibody-directed Tn5 tagmentation. The sample is then repooled, mixed and arrayed across 5,184 nanowells at a density of 12-24 nuclei per well for a second round of cellular indexing during PCR amplification of the sequencing-ready library. This protocol can be completed in 1.5 days by a research technician, and we illustrate the optimized protocol by profiling histone modifications associated with developmental gene repression (H3K27me3) as well as transcriptional activation (H3K4me1-2-3) in human peripheral blood mononuclear cells and use single-nucleotide polymorphisms to facilitate collision removal. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.
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Affiliation(s)
- Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob E Greene
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease (M3D) PhD Program, University of Washington, Seattle, WA, USA
| | - Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Christine A Codomo
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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28
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Radzisheuskaya A, Peña‐Rømer I, Lorenzini E, Koche R, Zhan Y, Shliaha PV, Cooper AJ, Fan Z, Shlyueva D, Johansen JV, Hendrickson RC, Helin K. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. EMBO J 2023; 42:e114221. [PMID: 37987160 PMCID: PMC10711654 DOI: 10.15252/embj.2023114221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
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Affiliation(s)
- Aliaksandra Radzisheuskaya
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Isabel Peña‐Rømer
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Eugenia Lorenzini
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Richard Koche
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Yingqian Zhan
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Pavel V Shliaha
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Zheng Fan
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Daria Shlyueva
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jens V Johansen
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
| | - Ronald C Hendrickson
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Kristian Helin
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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29
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Hu X, Wang Y, Zhang X, Li C, Zhang X, Yang D, Liu Y, Li L. DNA methylation of HOX genes and its clinical implications in cancer. Exp Mol Pathol 2023; 134:104871. [PMID: 37696326 DOI: 10.1016/j.yexmp.2023.104871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Homeobox (HOX) genes encode highly conserved transcription factors that play vital roles in embryonic development. DNA methylation is a pivotal regulatory epigenetic signaling mark responsible for regulating gene expression. Abnormal DNA methylation is largely associated with the aberrant expression of HOX genes, which is implicated in a broad range of human diseases, including cancer. Numerous studies have clarified the mechanisms of DNA methylation in both physiological and pathological processes. In this review, we focus on how DNA methylation regulates HOX genes and briefly discuss drug development approaches targeting these mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China; Laboratory of Precision Medicine, Zhangqiu District People's Hospital of Jinan, Jinan 250200, Shandong, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Chensheng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Xikun Zhang
- Department of Minimally Invasive Interventional, The Third Affiliated Hospital of Shandong First Medical University, Jinan 250031, Shandong, China
| | - Dongxia Yang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Yuanyuan Liu
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Lianlian Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China; Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
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30
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Wang D, Lu X, Jiang Y, Pan L, Zhu F, Yu A, Zhao M, Yang M, Bi J, He X, Liu H, Li J. The chromatin remodeling protein BPTF mediates cell cycle, proliferation and apoptosis in porcine ovarian granulosa cells. Theriogenology 2023; 211:172-181. [PMID: 37643502 DOI: 10.1016/j.theriogenology.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Bromodomain PHD finger transcription factor (BPTF), a core subunit of nucleosome-remodeling factor (NURF) complex, plays an important role in chromatin remodeling. However, few information of BPTF is available in pig, especially in mammalian follicular granulosa cells (GCs). The present study firstly confirmed that BPTF in porcine was relative close to human and mouse. The expression of BPTF could be detected in ovary, testes, lung, kidney, large intestine, and small intestine. And a relative high expression of BPTF was observed in ovarian follicles and GCs. When BPTF was knocked down (BPTF-siRNA), the viability of GCs was affected. And the expression level of CDK1, cyclin B1, CDK4 and CDK2 was higher than the control, which might indicate that the cell cycle of GCs was inhibited from S to G2/M phase. Although the apoptosis level was induced in the BPTF-siRNA GCs, the reduced level of H3K4 methylation was detected with the down regulation of SMYD3, EHMT2 and DPY30. Thereby, results in the present might provide the primary knowledge of BPTF in GCs and the follicular development in pig.
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Affiliation(s)
- Dayu Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinyue Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuan Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Linqing Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fuquan Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Aochen Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingyue Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Meng Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jiaying Bi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xu He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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31
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Dupouy G, Cashell R, Brychkova G, Tuteja R, McKeown PC, Spillane C. PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome. Genome Biol Evol 2023; 15:evad191. [PMID: 37931037 PMCID: PMC10630071 DOI: 10.1093/gbe/evad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.
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Affiliation(s)
- Gilles Dupouy
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Ronan Cashell
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Reetu Tuteja
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Agriculture & Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway H91 REW4, Ireland
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32
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Espinoza Pereira KN, Shan J, Licht JD, Bennett RL. Histone mutations in cancer. Biochem Soc Trans 2023; 51:1749-1763. [PMID: 37721138 PMCID: PMC10657182 DOI: 10.1042/bst20210567] [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: 11/30/2022] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Genes encoding histone proteins are recurrently mutated in tumor samples, and these mutations may impact nucleosome stability, histone post-translational modification, or chromatin dynamics. The prevalence of histone mutations across diverse cancer types suggest that normal chromatin structure is a barrier to tumorigenesis. Oncohistone mutations disrupt chromatin structure and gene regulatory mechanisms, resulting in aberrant gene expression and the development of cancer phenotypes. Examples of oncohistones include the histone H3 K27M mutation found in pediatric brain cancers that blocks post-translational modification of the H3 N-terminal tail and the histone H2B E76K mutation found in some solid tumors that disrupts nucleosome stability. Oncohistones may comprise a limited fraction of the total histone pool yet cause global effects on chromatin structure and drive cancer phenotypes. Here, we survey histone mutations in cancer and review their function and role in tumorigenesis.
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Affiliation(s)
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, U.S.A
| | - Jonathan D. Licht
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, U.S.A
| | - Richard L. Bennett
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, U.S.A
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33
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Buchholz C, Sneddon MS, McPherson JE, Das S, Gee CT, Grillo MJ, Chai SC, Lee RE, Chen T, Harki DA, Shelat AA, Pomerantz WCK. Fragment-Based NMR Screening of the BPTF PHD Finger Methyl Lysine Reader Leads to the First Small-Molecule Inhibitors. ACS Med Chem Lett 2023; 14:1441-1447. [PMID: 37849548 PMCID: PMC10577693 DOI: 10.1021/acsmedchemlett.3c00343] [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: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
Methyl lysine readers, specifically PHD fingers, are emerging epigenetic targets in human diseases. For example, several PHD finger fusions are implicated in clinical cases of acute myeloid leukemia, highlighting the potential for PHD inhibitors in disease regulation. However, limited chemical matter targeting PHD fingers exists. Here we report the first fragment-based screen against the BPTF PHD to identify several of the first reported BPTF PHD-targeting small-molecule ligands. We used ligand-observed NMR to first screen a fragment library, followed by biophysical validation to prioritize two scaffolds, pyrrolidine- and pyridazine-containing fragments. Structural predictions show that these respective scaffolds may engage two distinct subpockets on the protein. The demonstrated ligandability of the BPTF PHD supports the future development of methyl lysine reader chemical probes to study their oncogenic functions.
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Affiliation(s)
- Caroline
R. Buchholz
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Molly S. Sneddon
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Joseph E. McPherson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sourav Das
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Clifford T. Gee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Michael J. Grillo
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sergio C. Chai
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anang A. Shelat
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - William C. K. Pomerantz
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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34
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Kent D, Marchetti L, Mikulasova A, Russell LJ, Rico D. Broad H3K4me3 domains: Maintaining cellular identity and their implication in super-enhancer hijacking. Bioessays 2023; 45:e2200239. [PMID: 37350339 DOI: 10.1002/bies.202200239] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023]
Abstract
The human and mouse genomes are complex from a genomic standpoint. Each cell has the same genomic sequence, yet a wide array of cell types exists due to the presence of a plethora of regulatory elements in the non-coding genome. Recent advances in epigenomic profiling have uncovered non-coding gene proximal promoters and distal enhancers of transcription genome-wide. Extension of promoter-associated H3K4me3 histone mark across the gene body, known as a broad H3K4me3 domain (H3K4me3-BD), is a signature of constitutive expression of cell-type-specific regulation and of tumour suppressor genes in healthy cells. Recently, it has been discovered that the presence of H3K4me3-BDs over oncogenes is a cancer-specific feature associated with their dysregulated gene expression and tumourigenesis. Moreover, it has been shown that the hijacking of clusters of enhancers, known as super-enhancers (SE), by proto-oncogenes results in the presence of H3K4me3-BDs over the gene body. Therefore, H3K4me3-BDs and SE crosstalk in healthy and cancer cells therefore represents an important mechanism to identify future treatments for patients with SE driven cancers.
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Affiliation(s)
- Daniel Kent
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Letizia Marchetti
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Aneta Mikulasova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lisa J Russell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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35
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Li X, Wu F, Günther S, Looso M, Kuenne C, Zhang T, Wiesnet M, Klatt S, Zukunft S, Fleming I, Poschet G, Wietelmann A, Atzberger A, Potente M, Yuan X, Braun T. Inhibition of fatty acid oxidation enables heart regeneration in adult mice. Nature 2023; 622:619-626. [PMID: 37758950 PMCID: PMC10584682 DOI: 10.1038/s41586-023-06585-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Postnatal maturation of cardiomyocytes is characterized by a metabolic switch from glycolysis to fatty acid oxidation, chromatin reconfiguration and exit from the cell cycle, instating a barrier for adult heart regeneration1,2. Here, to explore whether metabolic reprogramming can overcome this barrier and enable heart regeneration, we abrogate fatty acid oxidation in cardiomyocytes by inactivation of Cpt1b. We find that disablement of fatty acid oxidation in cardiomyocytes improves resistance to hypoxia and stimulates cardiomyocyte proliferation, allowing heart regeneration after ischaemia-reperfusion injury. Metabolic studies reveal profound changes in energy metabolism and accumulation of α-ketoglutarate in Cpt1b-mutant cardiomyocytes, leading to activation of the α-ketoglutarate-dependent lysine demethylase KDM5 (ref. 3). Activated KDM5 demethylates broad H3K4me3 domains in genes that drive cardiomyocyte maturation, lowering their transcription levels and shifting cardiomyocytes into a less mature state, thereby promoting proliferation. We conclude that metabolic maturation shapes the epigenetic landscape of cardiomyocytes, creating a roadblock for further cell divisions. Reversal of this process allows repair of damaged hearts.
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Affiliation(s)
- Xiang Li
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Fan Wu
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ting Zhang
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Marion Wiesnet
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stephan Klatt
- Institute for Vascular Signaling, Centre for Molecular Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Sven Zukunft
- Institute for Vascular Signaling, Centre for Molecular Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Ingrid Fleming
- Institute for Vascular Signaling, Centre for Molecular Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Astrid Wietelmann
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ann Atzberger
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michael Potente
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Max Delbrück Center for Molecular Medicine, Helmholtz Association of German Research Centres, Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xuejun Yuan
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Instituto de Investigacion en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Instituto de Investigacion en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
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36
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Namitz KEW, Showalter SA, Cosgrove MS. Phase separation promotes a highly active oligomeric scaffold of the MLL1 core complex for regulation of histone H3K4 methylation. J Biol Chem 2023; 299:105204. [PMID: 37660926 PMCID: PMC10551905 DOI: 10.1016/j.jbc.2023.105204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Enzymes that regulate the degree of histone H3 lysine 4 (H3K4) methylation are crucial for proper cellular differentiation and are frequently mutated in cancer. The Mixed lineage leukemia (MLL) family of enzymes deposit H3K4 mono-, di-, or trimethylation at distinct genomic locations, requiring precise spatial and temporal control. Despite evidence that the degree of H3K4 methylation is controlled in part by a hierarchical assembly pathway with key subcomplex components, we previously found that the assembled state of the MLL1 core complex is not favored at physiological temperature. To better understand this paradox, we tested the hypothesis that increasing the concentration of subunits in a biomolecular condensate overcomes this thermodynamic barrier via mass action. Here, we demonstrate that MLL1 core complex phase separation stimulates enzymatic activity up to 60-fold but not primarily by concentrating subunits into droplets. Instead, we found that stimulated activity is largely due to the formation of an altered oligomeric scaffold that greatly reduces substrate Km. We posit that phase separation-induced scaffolding of the MLL1 core complex is a potential "switch-like" mechanism for spatiotemporal control of H3K4 methylation through the rapid formation or dissolution of biomolecular condensates within RNA Pol II transcription factories.
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Affiliation(s)
- Kevin E W Namitz
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | - Scott A Showalter
- Department of Chemistry, Penn State University, University Park, Pennsylvania, USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA.
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37
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Fields JK, Hicks CW, Wolberger C. Diverse modes of regulating methyltransferase activity by histone ubiquitination. Curr Opin Struct Biol 2023; 82:102649. [PMID: 37429149 PMCID: PMC10527252 DOI: 10.1016/j.sbi.2023.102649] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/29/2023] [Accepted: 06/11/2023] [Indexed: 07/12/2023]
Abstract
Post-translational modification of histones plays a central role in regulating transcription. Methylation of histone H3 at lysines 4 (H3K4) and 79 (H3K79) play roles in activating transcription whereas methylation of H3K27 is a repressive mark. These modifications, in turn, depend upon prior monoubiquitination of specific histone residues in a phenomenon known as histone crosstalk. Earlier work had provided insights into the mechanism by which monoubiquitination histone H2BK120 stimulates H3K4 methylation by COMPASS/MLL1 and H3K79 methylation by DOT1L, and monoubiquitinated H2AK119 stimulates methylation of H3K27 by the PRC2 complex. Recent studies have shed new light on the role of individual subunits and paralogs in regulating the activity of PRC2 and how additional post-translational modifications regulate yeast Dot1 and human DOT1L, as well as provided new insights into the regulation of MLL1 by H2BK120ub.
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Affiliation(s)
- James K Fields
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Chad W Hicks
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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38
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Gebicke-Haerter PJ. The computational power of the human brain. Front Cell Neurosci 2023; 17:1220030. [PMID: 37608987 PMCID: PMC10441807 DOI: 10.3389/fncel.2023.1220030] [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: 05/19/2023] [Accepted: 07/05/2023] [Indexed: 08/24/2023] Open
Abstract
At the end of the 20th century, analog systems in computer science have been widely replaced by digital systems due to their higher computing power. Nevertheless, the question keeps being intriguing until now: is the brain analog or digital? Initially, the latter has been favored, considering it as a Turing machine that works like a digital computer. However, more recently, digital and analog processes have been combined to implant human behavior in robots, endowing them with artificial intelligence (AI). Therefore, we think it is timely to compare mathematical models with the biology of computation in the brain. To this end, digital and analog processes clearly identified in cellular and molecular interactions in the Central Nervous System are highlighted. But above that, we try to pinpoint reasons distinguishing in silico computation from salient features of biological computation. First, genuinely analog information processing has been observed in electrical synapses and through gap junctions, the latter both in neurons and astrocytes. Apparently opposed to that, neuronal action potentials (APs) or spikes represent clearly digital events, like the yes/no or 1/0 of a Turing machine. However, spikes are rarely uniform, but can vary in amplitude and widths, which has significant, differential effects on transmitter release at the presynaptic terminal, where notwithstanding the quantal (vesicular) release itself is digital. Conversely, at the dendritic site of the postsynaptic neuron, there are numerous analog events of computation. Moreover, synaptic transmission of information is not only neuronal, but heavily influenced by astrocytes tightly ensheathing the majority of synapses in brain (tripartite synapse). At least at this point, LTP and LTD modifying synaptic plasticity and believed to induce short and long-term memory processes including consolidation (equivalent to RAM and ROM in electronic devices) have to be discussed. The present knowledge of how the brain stores and retrieves memories includes a variety of options (e.g., neuronal network oscillations, engram cells, astrocytic syncytium). Also epigenetic features play crucial roles in memory formation and its consolidation, which necessarily guides to molecular events like gene transcription and translation. In conclusion, brain computation is not only digital or analog, or a combination of both, but encompasses features in parallel, and of higher orders of complexity.
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Affiliation(s)
- Peter J. Gebicke-Haerter
- Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine, University of Heidelberg, Mannheim, Germany
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39
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Xiao C, Fan T, Zheng Y, Tian H, Deng Z, Liu J, Li C, He J. H3K4 trimethylation regulates cancer immunity: a promising therapeutic target in combination with immunotherapy. J Immunother Cancer 2023; 11:e005693. [PMID: 37553181 PMCID: PMC10414074 DOI: 10.1136/jitc-2022-005693] [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] [Accepted: 05/03/2023] [Indexed: 08/10/2023] Open
Abstract
With the advances in cancer immunity regulation and immunotherapy, the effects of histone modifications on establishing antitumor immunological ability are constantly being uncovered. Developing combination therapies involving epigenetic drugs (epi-drugs) and immune checkpoint blockades or chimeric antigen receptor-T cell therapies are promising to improve the benefits of immunotherapy. Histone H3 lysine 4 trimethylation (H3K4me3) is a pivotal epigenetic modification in cancer immunity regulation, deeply involved in modulating tumor immunogenicity, reshaping tumor immune microenvironment, and regulating immune cell functions. However, how to integrate these theoretical foundations to create novel H3K4 trimethylation-based therapeutic strategies and optimize available therapies remains uncertain. In this review, we delineate the mechanisms by which H3K4me3 and its modifiers regulate antitumor immunity, and explore the therapeutic potential of the H3K4me3-related agents combined with immunotherapies. Understanding the role of H3K4me3 in cancer immunity will be instrumental in developing novel epigenetic therapies and advancing immunotherapy-based combination regimens.
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Affiliation(s)
- Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziqin Deng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingjing Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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40
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Gaurav N, Kutateladze TG. Non-histone binding functions of PHD fingers. Trends Biochem Sci 2023; 48:610-617. [PMID: 37061424 PMCID: PMC10330121 DOI: 10.1016/j.tibs.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/17/2023]
Abstract
Plant homeodomain (PHD) fingers comprise a large and well-established family of epigenetic readers that recognize histone H3. A typical PHD finger binds to the unmodified or methylated amino-terminal tail of H3. This interaction is highly specific and can be regulated by post-translational modifications (PTMs) in H3 and other domains present in the protein. However, a set of PHD fingers has recently been shown to bind non-histone proteins, H3 mimetics, and DNA. In this review, we highlight the molecular mechanisms by which PHD fingers interact with ligands other than the amino terminus of H3 and discuss similarities and differences in engagement with histone and non-histone binding partners.
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Affiliation(s)
- Nitika Gaurav
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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41
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [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: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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42
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Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, Churchill GA, Trowbridge JJ, Stitzel ML, Paigen K, Petkov PM, Carter GW. Variation in histone configurations correlates with gene expression across nine inbred strains of mice. Genome Res 2023; 33:857-871. [PMID: 37217254 PMCID: PMC10519406 DOI: 10.1101/gr.277467.122] [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: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The Diversity Outbred (DO) mice and their inbred founders are widely used models of human disease. However, although the genetic diversity of these mice has been well documented, their epigenetic diversity has not. Epigenetic modifications, such as histone modifications and DNA methylation, are important regulators of gene expression and, as such, are a critical mechanistic link between genotype and phenotype. Therefore, creating a map of epigenetic modifications in the DO mice and their founders is an important step toward understanding mechanisms of gene regulation and the link to disease in this widely used resource. To this end, we performed a strain survey of epigenetic modifications in hepatocytes of the DO founders. We surveyed four histone modifications (H3K4me1, H3K4me3, H3K27me3, and H3K27ac), as well as DNA methylation. We used ChromHMM to identify 14 chromatin states, each of which represents a distinct combination of the four histone modifications. We found that the epigenetic landscape is highly variable across the DO founders and is associated with variation in gene expression across strains. We found that epigenetic state imputed into a population of DO mice recapitulated the association with gene expression seen in the founders, suggesting that both histone modifications and DNA methylation are highly heritable mechanisms of gene expression regulation. We illustrate how DO gene expression can be aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide a data resource that documents strain-specific variation in the chromatin state and DNA methylation in hepatocytes across nine widely used strains of laboratory mice.
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Affiliation(s)
- Anna L Tyler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Catrina Spruce
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Annat Haber
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Robyn L Ball
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Wendy A Pitman
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Alexander D Fine
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael Walker
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - J Matthew Mahoney
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Kenneth Paigen
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Petko M Petkov
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA;
| | - Gregory W Carter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
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43
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You M, Xie Z, Zhang N, Zhang Y, Xiao D, Liu S, Zhuang W, Li L, Tao Y. Signaling pathways in cancer metabolism: mechanisms and therapeutic targets. Signal Transduct Target Ther 2023; 8:196. [PMID: 37164974 PMCID: PMC10172373 DOI: 10.1038/s41392-023-01442-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 03/20/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023] Open
Abstract
A wide spectrum of metabolites (mainly, the three major nutrients and their derivatives) can be sensed by specific sensors, then trigger a series of signal transduction pathways and affect the expression levels of genes in epigenetics, which is called metabolite sensing. Life body regulates metabolism, immunity, and inflammation by metabolite sensing, coordinating the pathophysiology of the host to achieve balance with the external environment. Metabolic reprogramming in cancers cause different phenotypic characteristics of cancer cell from normal cell, including cell proliferation, migration, invasion, angiogenesis, etc. Metabolic disorders in cancer cells further create a microenvironment including many kinds of oncometabolites that are conducive to the growth of cancer, thus forming a vicious circle. At the same time, exogenous metabolites can also affect the biological behavior of tumors. Here, we discuss the metabolite sensing mechanisms of the three major nutrients and their derivatives, as well as their abnormalities in the development of various cancers, and discuss the potential therapeutic targets based on metabolite-sensing signaling pathways to prevent the progression of cancer.
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Affiliation(s)
- Mengshu You
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Zhuolin Xie
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Nan Zhang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Yixuan Zhang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Wei Zhuang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, People's Republic of China.
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Ma Liu Shui, Hong Kong.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China.
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China.
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China.
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, 410011, Changsha, China.
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Bhootra S, Jill N, Rajak R, Shanmugam G, Rakshit S, Kannanthodi S, Thakkar V, George M, Sarkar K. Diospyros malabarica fruit preparation mediates immunotherapeutic modulation and epigenetic regulation to evoke protection against non-small cell lung cancer (NSCLC). JOURNAL OF ETHNOPHARMACOLOGY 2023; 314:116525. [PMID: 37149067 DOI: 10.1016/j.jep.2023.116525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Diospyros malabarica is an ethnomedicinal plant with hypoglycaemic, anti-bacterial, and anti-cancer properties and it belongs to the Ebenaceae family which is well known for its medicinal uses since ancient times and application of its bark and unripened fruit has been significantly mentioned in Ayurvedic texts. The Diospyros malabarica species which is known as the Gaub in Hindi and Indian Persimmon in English is native to India, however, it is distributed throughout the tropics. AIM OF THE STUDY As Diospyros malabarica fruit preparation (DFP) possesses medicinal values, the study aims to evaluate its role as natural, non-toxic, and cost-effective dendritic cells (DCs) maturing immunomodulatory agent and also as an epigenetic regulator to combat Non-small cell lung cancer (NSCLC) which is a type of lung cancer whose treatment options such as chemotherapy, radiation therapy, etc. are accompanied with some adverse side effects. Thus, immunotherapeutic strategies are in high demand to evoke tumor protective immunity against NSCLC without causing such side effects. MATERIALS AND METHODS Peripheral Mononuclear Cells (PBMCs) derived monocytes of normal subjects and NSCLC patients were utilized to generate DCs matured with either LPS (LPSDC) or DFP (DFPDC). Mixed Lymphocyte Reaction (MLR) was carried out with the differentially matured DCs co-culturing T cells and cytotoxicity of lung cancer cells (A549) was measured through LDH release assay and cytokine profiling was carried out via ELISA respectively. PBMCs of normal subjects and NSCLC patients have transfected separately in vitrowith CRISPR-activation plasmid of p53 and CRISPR-Cas9 knockout plasmid of c-Myc to analyze epigenetic mechanism(s) in the presence and absence of DFP. RESULTS Diospyros malabarica fruit preparation (DFP) treated DC upregulates the secretion of T helper (TH)1 cell specific cytokines (IFN-γ and IL-12) and signal transducer and activator of transcription molecules (STAT1 and STAT4). Furthermore, it also downregulates the secretion of TH2-specific cytokines (IL-4 and IL-10). Diospyros malabarica fruit preparation (DFP) enhances p53 expression by reducing methylation levels at the CpG island of the promoter region. Upon c-Myc knockout, epigenetic markers such as H3K4Me3, p53, H3K14Ac, BRCA1, and WASp were enhanced whereas H3K27Me3, JMJD3, and NOTCH1 were downregulated. CONCLUSION Diospyros malabarica fruit preparation (DFP) not only increases the expression of type 1 specific cytokines but also augments tumor suppression modulating various epigenetic markers to evoke tumor protective immunity without any toxic activities.
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Affiliation(s)
- Sannidhi Bhootra
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Nandana Jill
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Rohit Rajak
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Sudeshna Rakshit
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Samiyah Kannanthodi
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Vidhi Thakkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Melvin George
- Department of Clinical Pharmacology, SRM Medical College Hospital and Research Centre, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India.
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Sun G, Wei Y, Zhou B, Wang M, Luan R, Bai Y, Li H, Wang S, Zheng D, Wang C, Wang S, Zeng K, Liu S, Lin L, He M, Zhang Q, Zhao Y. BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer. Cell Death Differ 2023; 30:1260-1278. [PMID: 36828916 PMCID: PMC10154423 DOI: 10.1038/s41418-023-01135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
The estrogen receptor alpha (ERα) signaling pathway is a crucial target for ERα-positive breast cancer therapeutic strategies. Co-regulators and other transcription factors cooperate for effective ERα-related enhancer activation. Recent studies demonstrate that the transcription factor CTCF is essential to participate in ERα/E2-induced enhancer transactivation. However, the mechanism of how CTCF is achieved remains unknown. Here, we provided evidence that BAP18 is required for CTCF recruitment on ERα-enriched enhancers, facilitating CTCF-mediated chromatin accessibility to promote enhancer RNAs transcription. Consistently, GRO-seq demonstrates that the enhancer activity is positively correlated with BAP18 enrichment. Furthermore, BAP18 interacts with SMARCA1/BPTF to accelerate the recruitment of CTCF to ERα-related enhancers. Interestingly, BAP18 is involved in chromatin accessibility within enhancer regions, thereby increasing enhancer transactivation and enhancer-promoter looping. BAP18 depletion increases the sensitivity of anti-estrogen and anti-enhancer treatment in MCF7 cells. Collectively, our study indicates that BAP18 coordinates with CTCF to enlarge the transactivation of ERα-related enhancers, providing a better understanding of BAP18/CTCF coupling chromatin remodeling and E-P looping in the regulation of enhancer transcription.
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Affiliation(s)
- Ge Sun
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Yuntao Wei
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang City, 110042, Liaoning Province, China
| | - Baosheng Zhou
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Manlin Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Ruina Luan
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Yu Bai
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Hao Li
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shan Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Dantong Zheng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Shuchang Liu
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Mingcong He
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang City, 110042, Liaoning Province, China
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City, 110122, Liaoning Province, China.
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Devaraj A, Singh M, Narayanavari SA, Yong G, Chen J, Wang J, Becker M, Walisko O, Schorn A, Cseresznyés Z, Raskó T, Radscheit K, Selbach M, Ivics Z, Izsvák Z. HMGXB4 Targets Sleeping Beauty Transposition to Germinal Stem Cells. Int J Mol Sci 2023; 24:ijms24087283. [PMID: 37108449 PMCID: PMC10138897 DOI: 10.3390/ijms24087283] [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: 12/02/2022] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
Transposons are parasitic genetic elements that frequently hijack vital cellular processes of their host. HMGXB4 is a known Wnt signaling-regulating HMG-box protein, previously identified as a host-encoded factor of Sleeping Beauty (SB) transposition. Here, we show that HMGXB4 is predominantly maternally expressed, and marks both germinal progenitor and somatic stem cells. SB piggybacks HMGXB4 to activate transposase expression and target transposition to germinal stem cells, thereby potentiating heritable transposon insertions. The HMGXB4 promoter is located within an active chromatin domain, offering multiple looping possibilities with neighboring genomic regions. HMGXB4 is activated by ERK2/MAPK1, ELK1 transcription factors, coordinating pluripotency and self-renewal pathways, but suppressed by the KRAB-ZNF/TRIM28 epigenetic repression machinery, also known to regulate transposable elements. At the post-translational level, SUMOylation regulates HMGXB4, which modulates binding affinity to its protein interaction partners and controls its transcriptional activator function via nucleolar compartmentalization. When expressed, HMGXB4 can participate in nuclear-remodeling protein complexes and transactivate target gene expression in vertebrates. Our study highlights HMGXB4 as an evolutionarily conserved host-encoded factor that assists Tc1/Mariner transposons to target the germline, which was necessary for their fixation and may explain their abundance in vertebrate genomes.
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Affiliation(s)
- Anantharam Devaraj
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Manvendra Singh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Suneel A Narayanavari
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Guo Yong
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Mareike Becker
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Oliver Walisko
- Division of Hematology, Gene and Cell Therapy, Paul-Ehrlich-Institute, Paul-Ehrlich-Strasse 51-59, 63225 Langen, Germany
| | - Andrea Schorn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Zoltán Cseresznyés
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Tamás Raskó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Kathrin Radscheit
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Matthias Selbach
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Zoltán Ivics
- Division of Hematology, Gene and Cell Therapy, Paul-Ehrlich-Institute, Paul-Ehrlich-Strasse 51-59, 63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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McBride DA, Kerr MD, Johnson WT, Nguyen A, Zoccheddu M, Yao M, Prideaux EB, Dorn NC, Wang W, Svensson MN, Bottini N, Shah NJ. Immunomodulatory Microparticles Epigenetically Modulate T Cells and Systemically Ameliorate Autoimmune Arthritis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2202720. [PMID: 36890657 PMCID: PMC10104670 DOI: 10.1002/advs.202202720] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 01/09/2023] [Indexed: 05/10/2023]
Abstract
Disease modifying antirheumatic drugs (DMARDs) have improved the prognosis of autoimmune inflammatory arthritides but a large fraction of patients display partial or nonresponsiveness to front-line DMARDs. Here, an immunoregulatory approach based on sustained joint-localized release of all-trans retinoic acid (ATRA), which modulates local immune activation and enhances disease-protective T cells and leads to systemic disease control is reported. ATRA imprints a unique chromatin landscape in T cells, which is associated with an enhancement in the differentiation of naïve T cells into anti-inflammatory regulatory T cells (Treg ) and suppression of Treg destabilization. Sustained release poly-(lactic-co-glycolic) acid (PLGA)-based biodegradable microparticles encapsulating ATRA (PLGA-ATRA MP) are retained in arthritic mouse joints after intra-articular (IA) injection. IA PLGA-ATRA MP enhance migratory Treg which in turn reduce inflammation and modify disease in injected and uninjected joints, a phenotype that is also reproduced by IA injection of Treg . PLGA-ATRA MP reduce proteoglycan loss and bone erosions in the SKG and collagen-induced arthritis mouse models of autoimmune arthritis. Strikingly, systemic disease modulation by PLGA-ATRA MP is not associated with generalized immune suppression. PLGA-ATRA MP have the potential to be developed as a disease modifying agent for autoimmune arthritis.
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Affiliation(s)
- David A. McBride
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Matthew D. Kerr
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Wade T. Johnson
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Anders Nguyen
- Department of Rheumatology and Inflammation ResearchSahlgrenska AcademyInstitute of MedicineUniversity of GothenburgGothenburg41346Sweden
| | - Martina Zoccheddu
- Department of MedicineDivision of RheumatologyAllergy and ImmunologyUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Mina Yao
- Department of Chemistry and BiochemistryUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Edward B. Prideaux
- Department of Chemistry and BiochemistryUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Nicholas C. Dorn
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Wei Wang
- Department of Chemistry and BiochemistryUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Department of Cellular and Molecular MedicineUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Mattias N.D. Svensson
- Department of Rheumatology and Inflammation ResearchSahlgrenska AcademyInstitute of MedicineUniversity of GothenburgGothenburg41346Sweden
| | - Nunzio Bottini
- Department of MedicineDivision of RheumatologyAllergy and ImmunologyUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Nisarg J. Shah
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
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48
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Choi EY, Franco D, Stapf CA, Gordin M, Chow A, Cover KK, Chandra R, Lobo MK. Inducible CRISPR Epigenome Systems Mimic Cocaine Induced Bidirectional Regulation of Nab2 and Egr3. J Neurosci 2023; 43:2242-2259. [PMID: 36849419 PMCID: PMC10072301 DOI: 10.1523/jneurosci.1802-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 03/01/2023] Open
Abstract
Substance use disorder is a chronic disease and a leading cause of disability around the world. The NAc is a major brain hub mediating reward behavior. Studies demonstrate exposure to cocaine is associated with molecular and functional imbalance in NAc medium spiny neuron subtypes (MSNs), dopamine receptor 1 and 2 enriched D1-MSNs and D2-MSNs. We previously reported repeated cocaine exposure induced transcription factor early growth response 3 (Egr3) mRNA in NAc D1-MSNs, and reduced it in D2-MSNs. Here, we report our findings of repeated cocaine exposure in male mice inducing MSN subtype-specific bidirectional expression of the Egr3 corepressor NGFI-A-binding protein 2 (Nab2). Using CRISPR activation and interference (CRISPRa and CRISPRi) tools combined with Nab2 or Egr3-targeted sgRNAs, we mimicked these bidirectional changes in Neuro2a cells. Furthermore, we investigated D1-MSN- and D2-MSN-specific expressional changes of histone lysine demethylases Kdm1a, Kdm6a, and Kdm5c in NAc after repeated cocaine exposure in male mice. Since Kdm1a showed bidirectional expression patterns in D1-MSNs and D2-MSNs, like Egr3, we developed a light-inducible Opto-CRISPR-KDM1a system. We were able to downregulate Egr3 and Nab2 transcripts in Neuro2A cells and cause similar bidirectional expression changes we observed in D1-MSNs and D2-MSNs of mouse repeated cocaine exposure model. Contrastingly, our Opto-CRISPR-p300 activation system induced the Egr3 and Nab2 transcripts and caused opposite bidirectional transcription regulations. Our study sheds light on the expression patterns of Nab2 and Egr3 in specific NAc MSNs in cocaine action and uses CRISPR tools to further mimic these expression patterns.SIGNIFICANCE STATEMENT Substance use disorder is a major societal issue. The lack of medication to treat cocaine addiction desperately calls for a treatment development based on precise understanding of molecular mechanisms underlying cocaine addiction. In this study, we show that Egr3 and Nab2 are bidirectionally regulated in mouse NAc D1-MSNs and D2-MSNs after repeated exposure to cocaine. Furthermore, histone lysine demethylations enzymes with putative EGR3 binding sites showed bidirectional regulation in D1- and D2-MSNs after repeated exposure to cocaine. Using Cre- and light-inducible CRISPR tools, we show that we can mimic this bidirectional regulation of Egr3 and Nab2 in Neuro2a cells.
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Affiliation(s)
- Eric Y Choi
- Department of Anatomy and Neurobiology
- Graduate Program in Life Sciences, Biochemistry and Molecular Biology
| | - Daniela Franco
- Department of Anatomy and Neurobiology
- Program in Neuroscience, Graduate Program in Life Sciences
| | - Catherine A Stapf
- Department of Anatomy and Neurobiology
- Program in Neuroscience, Graduate Program in Life Sciences
| | | | | | - Kara K Cover
- Department of Anatomy and Neurobiology
- Program in Neuroscience, Graduate Program in Life Sciences
| | - Ramesh Chandra
- Department of Anatomy and Neurobiology
- Center for Innovative Biomedical Resources, Virus Vector Core, University of Maryland School of Medicine Baltimore, Maryland, 21201
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49
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Zhao T, Wang M, Li Z, Li H, Yuan D, Zhang X, Guo M, Qian W, Cheng D. Wds-Mediated H3K4me3 Modification Regulates Lipid Synthesis and Transport in Drosophila. Int J Mol Sci 2023; 24:ijms24076125. [PMID: 37047100 PMCID: PMC10093852 DOI: 10.3390/ijms24076125] [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: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
Lipid homeostasis is essential for insect growth and development. The complex of proteins associated with Set 1 (COMPASS)-catalyzed Histone 3 lysine 4 trimethylation (H3K4me3) epigenetically activates gene transcription and is involved in various biological processes, but the role and molecular mechanism of H3K4me3 modification in lipid homeostasis remains largely unknown. In the present study, we showed in Drosophila that fat body-specific knockdown of will die slowly (Wds) as one of the COMPASS complex components caused a decrease in lipid droplet (LD) size and triglyceride (TG) levels. Mechanistically, Wds-mediated H3K4me3 modification in the fat body targeted several lipogenic genes involved in lipid synthesis and the Lpp gene associated with lipid transport to promote their expressions; the transcription factor heat shock factor (Hsf) could interact with Wds to modulate H3K4me3 modification within the promoters of these targets; and fat body-specific knockdown of Hsf phenocopied the effects of Wds knockdown on lipid homeostasis in the fat body. Moreover, fat body-specific knockdown of Wds or Hsf reduced high-fat diet (HFD)-induced oversized LDs and high TG levels. Altogether, our study reveals that Wds-mediated H3K4me3 modification is required for lipid homeostasis during Drosophila development and provides novel insights into the epigenetic regulation of insect lipid metabolism.
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Affiliation(s)
- Tujing Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Min Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Zheng Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Hao Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Dongqin Yuan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Xing Zhang
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Mengge Guo
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Wenliang Qian
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
| | - Daojun Cheng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
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50
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Martinelli P, Schaaf O, Mantoulidis A, Martin LJ, Fuchs JE, Bader G, Gollner A, Wolkerstorfer B, Rogers C, Balıkçı E, Lipp JJ, Mischerikow N, Doebel S, Gerstberger T, Sommergruber W, Huber KVM, Böttcher J. Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments. ChemMedChem 2023; 18:e202200686. [PMID: 36649575 DOI: 10.1002/cmdc.202200686] [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: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
The bromodomain and PHD-finger containing transcription factor (BPTF) is part of the nucleosome remodeling factor (NURF) complex and has been implicated in multiple cancer types. Here, we report the discovery of a potent and selective chemical probe targeting the bromodomain of BPTF with an attractive pharmacokinetic profile enabling cellular and in vivo experiments in mice. Microarray-based transcriptomics in presence of the probe in two lung cancer cell lines revealed only minor effects on the transcriptome. Profiling against a panel of cancer cell lines revealed that the antiproliferative effect does not correlate with BPTF dependency score in depletion screens. Both observations and the multi-domain architecture of BPTF suggest that depleting the protein by proteolysis targeting chimeras (PROTACs) could be a promising strategy to target cancer cell proliferation. We envision that the presented chemical probe and the related negative control will enable the research community to further explore scientific hypotheses with respect to BPTF bromodomain inhibition.
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Affiliation(s)
- Paola Martinelli
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Otmar Schaaf
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Andreas Mantoulidis
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Laetitia J Martin
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Andreas Gollner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Catherine Rogers
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Esra Balıkçı
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Nikolai Mischerikow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Sandra Doebel
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Wolfgang Sommergruber
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Kilian V M Huber
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
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