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Liu TY, Yan JS, Li X, Xu L, Hao JL, Zhao SY, Hu QL, Na FJ, Li HM, Zhao Y, Zhao MF. FGL1: a novel biomarker and target for non-small cell lung cancer, promoting tumor progression and metastasis through KDM4A/STAT3 transcription mechanism. J Exp Clin Cancer Res 2024; 43:213. [PMID: 39085849 PMCID: PMC11293164 DOI: 10.1186/s13046-024-03140-6] [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: 04/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is characterized by a high incidence rate and poor prognosis worldwide. A deeper insight into the pathogenesis of NSCLC and identification of novel therapeutic targets are essential to improve the prognosis of NSCLC. In this study, we revealed that fibrinogen-like protein 1 (FGL1) promotes proliferation, migration, and invasion of NSCLC cells. Mechanistically, we found that Stat3 acts as a transcription factor and can be recruited to the FGL1 promoter, enhancing FGL1 promoter activity. Lysine-specific demethylase 4A (KDM4A) interacts with Stat3 and facilitates the removal of methyl groups from H3K9me3, thereby enhancing Stat3-mediated transcription of FGL1. Furthermore, we observed that Stat3 and KDM4A promote NSCLC cell proliferation, migration, and invasion partly by upregulating FGL1 expression. Additionally, the expression of FGL1 was significantly higher in cancer tissues (n = 90) than in adjacent non-cancerous tissues (n = 90). Furthermore, patients with high FGL1 expression had a shorter overall survival (OS) compared to those with low FGL1 expression. We measured the expression levels of FGL1 on circulating tumor cells (CTCs) in 65 patients and found that patients with a dynamic decrease in FGL1 expression on CTCs exhibited a better therapeutic response. These findings suggest that the dynamic changes in FGL1 expression can serve as a potential biomarker for predicting treatment efficacy in NSCLC. Overall, this study revealed the significant role and regulatory mechanisms of FGL1 in the development of NSCLC, suggesting its potential as a therapeutic target for patients with NSCLC. Future studies should provide more personalized and effective treatment options for patients with NSCLC to improve clinical outcomes.
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Affiliation(s)
- Tian Yao Liu
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Jin Shan Yan
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Xin Li
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Lu Xu
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Jun Li Hao
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Su Ya Zhao
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Qi Lin Hu
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China
| | - Fang Jian Na
- Network Information Center, China Medical University, Shenyang, China
| | - He Ming Li
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China.
- Guangdong Association of Clinical Trials (GACT)/Chinese Thoracic Oncology Group (CTONG) and Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangzhou, 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, Liaoning Province, 110122, China.
| | - Ming Fang Zhao
- Department of Medical Oncology, The First Hospital of China Medical University, No.155 Nanjingbei Road, Shenyang, Liaoning, 110001, People's Republic of China.
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2
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Hou A, Luo H, Liu H, Luo L, Ding P. Multi-scale DNA language model improves 6 mA binding sites prediction. Comput Biol Chem 2024; 112:108129. [PMID: 39067351 DOI: 10.1016/j.compbiolchem.2024.108129] [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: 03/04/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/30/2024]
Abstract
DNA methylation at the N6 position of adenine (N6-methyladenine, 6 mA), which refers to the attachment of a methyl group to the N6 site of the adenine (A) of DNA, is an important epigenetic modification in prokaryotic and eukaryotic genomes. Accurately predicting the 6 mA binding sites can provide crucial insights into gene regulation, DNA repair, disease development and so on. Wet experiments are commonly used for analyzing 6 mA binding sites. However, they suffer from high cost and expensive time. Therefore, various deep learning methods have been widely used to predict 6 mA binding sites recently. In this study, we develop a framework based on multi-scale DNA language model named "iDNA6mA-MDL". "iDNA6mA-MDL" integrates multiple kmers and the nucleotide property and frequency method for feature embedding, which can capture a full range of DNA sequence context information. At the prediction stage, it also leverages DNABERT to compensate for the incomplete capture of global DNA information. Experiments show that our framework obtains average AUC of 0.981 on a classic 6 mA rice gene dataset, going beyond all existing advanced models under fivefold cross-validations. Moreover, "iDNA6mA-MDL" outperforms most of the popular state-of-the-art methods on another 11 6 mA datasets, demonstrating its effectiveness in 6 mA binding sites prediction.
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Affiliation(s)
- Anlin Hou
- School of Computer Science, University of South China, Hengyang 421001, China
| | - Hanyu Luo
- School of Computer Science, University of South China, Hengyang 421001, China
| | - Huan Liu
- School of Computer Science, University of South China, Hengyang 421001, China
| | - Lingyun Luo
- School of Computer Science, University of South China, Hengyang 421001, China.
| | - Pingjian Ding
- School of Computer Science, University of South China, Hengyang 421001, China
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3
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DeCotiis-Mauro J, Han SM, Mello H, Goyeneche C, Marchesini-Tovar G, Jin L, Bellofatto V, Lukac DM. The cellular Notch1 protein promotes KSHV reactivation in an Rta-dependent manner. J Virol 2024:e0078824. [PMID: 38975769 DOI: 10.1128/jvi.00788-24] [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: 05/06/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024] Open
Abstract
The cellular Notch signal transduction pathway is intimately associated with infections by Kaposi's sarcoma-associated herpesvirus (KSHV) and other gamma-herpesviruses. RBP-Jk, the cellular DNA binding component of the canonical Notch pathway, is the key Notch downstream effector protein in virus-infected and uninfected animal cells. Reactivation of KSHV from latency requires the viral lytic switch protein, Rta, to form complexes with RBP-Jk on numerous sites within the viral DNA. Constitutive Notch activity is essential for KSHV pathophysiology in models of Kaposi's sarcoma (KS) and Primary Effusion Lymphoma (PEL), and we demonstrate that Notch1 is also constitutively active in infected Vero cells. Although the KSHV genome contains >100 RBP-Jk DNA motifs, we show that none of the four isoforms of activated Notch can productively reactivate the virus from latency in a highly quantitative trans-complementing reporter virus system. Nevertheless, Notch contributed positively to reactivation because broad inhibition of Notch1-4 with gamma-secretase inhibitor (GSI) or expression of dominant negative mastermind-like1 (dnMAML1) coactivators severely reduced production of infectious KSHV from Vero cells. Reduction of KSHV production is associated with gene-specific reduction of viral transcription in both Vero and PEL cells. Specific inhibition of Notch1 by siRNA partially reduces the production of infectious KSHV, and NICD1 forms promoter-specific complexes with viral DNA during reactivation. We conclude that constitutive Notch activity is required for the robust production of infectious KSHV, and our results implicate activated Notch1 as a pro-viral member of a MAML1/RBP-Jk/DNA complex during viral reactivation. IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) manipulates the host cell oncogenic Notch signaling pathway for viral reactivation from latency and cell pathogenesis. KSHV reactivation requires that the viral protein Rta functionally interacts with RBP-Jk, the DNA-binding component of the Notch pathway, and with promoter DNA to drive transcription of productive cycle genes. We show that the Notch pathway is constitutively active during KSHV reactivation and is essential for robust production of infectious virus progeny. Inhibiting Notch during reactivation reduces the expression of specific viral genes yet does not affect the growth of the host cells. Although Notch cannot reactivate KSHV alone, the requisite expression of Rta reveals a previously unappreciated role for Notch in reactivation. We propose that activated Notch cooperates with Rta in a promoter-specific manner that is partially programmed by Rta's ability to redistribute RBP-Jk DNA binding to the virus during reactivation.
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Affiliation(s)
- Jennifer DeCotiis-Mauro
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Sun M Han
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Helena Mello
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Corey Goyeneche
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Giuseppina Marchesini-Tovar
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Lianhua Jin
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - Vivian Bellofatto
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
| | - David M Lukac
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Health Science Campus at Newark, Rutgers University, Newark, New Jersey, USA
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4
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Cameron DP, Sornkom J, Alsahafi S, Drygin D, Poortinga G, McArthur GA, Hein N, Hannan R, Panov KI. CX-5461 Preferentially Induces Top2α-Dependent DNA Breaks at Ribosomal DNA Loci. Biomedicines 2024; 12:1514. [PMID: 39062087 PMCID: PMC11275095 DOI: 10.3390/biomedicines12071514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
While genotoxic chemotherapeutic agents are among the most effective tools to combat cancer, they are often associated with severe adverse effects caused by indiscriminate DNA damage in non-tumor tissue as well as increased risk of secondary carcinogenesis. This study builds on our previous work demonstrating that the RNA Polymerase I (Pol I) transcription inhibitor CX-5461 elicits a non-canonical DNA damage response and our discovery of a critical role for Topoisomerase 2α (Top2α) in the initiation of Pol I-dependent transcription. Here, we identify Top2α as a mediator of CX-5461 response in the murine Eµ-Myc B lymphoma model whereby sensitivity to CX-5461 is dependent on cellular Top2α expression/activity. Most strikingly, and in contrast to canonical Top2α poisons, we found that the Top2α-dependent DNA damage induced by CX-5461 is preferentially localized at the ribosomal DNA (rDNA) promoter region, thereby highlighting CX-5461 as a loci-specific DNA damaging agent. This mechanism underpins the efficacy of CX-5461 against certain types of cancer and can be used to develop effective non-genotoxic anticancer drugs.
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Affiliation(s)
- Donald P. Cameron
- ACRF Department of Cancer Biology and Therapeutics, Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia; (D.P.C.); (N.H.)
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
| | - Jirawas Sornkom
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Sameerh Alsahafi
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
| | - Denis Drygin
- Pimera Therapeutics, 7875 Highland Village Place, Suite 412, San Diego, CA 92129, USA;
| | - Gretchen Poortinga
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
| | - Grant A. McArthur
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics, Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia; (D.P.C.); (N.H.)
| | - Ross Hannan
- ACRF Department of Cancer Biology and Therapeutics, Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia; (D.P.C.); (N.H.)
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3053, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Konstantin I. Panov
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
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5
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Cheng Y, Wang S, Zhang H, Lee JS, Ni C, Guo J, Chen E, Wang S, Acharya A, Chang TC, Buszczak M, Zhu H, Mendell JT. A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence. Cell 2024:S0092-8674(24)00693-7. [PMID: 38981482 DOI: 10.1016/j.cell.2024.06.019] [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: 05/31/2023] [Revised: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
Cellular senescence is an irreversible state of cell-cycle arrest induced by various stresses, including aberrant oncogene activation, telomere shortening, and DNA damage. Through a genome-wide screen, we discovered a conserved small nucleolar RNA (snoRNA), SNORA13, that is required for multiple forms of senescence in human cells and mice. Although SNORA13 guides the pseudouridylation of a conserved nucleotide in the ribosomal decoding center, loss of this snoRNA minimally impacts translation. Instead, we found that SNORA13 negatively regulates ribosome biogenesis. Senescence-inducing stress perturbs ribosome biogenesis, resulting in the accumulation of free ribosomal proteins (RPs) that trigger p53 activation. SNORA13 interacts directly with RPL23, decreasing its incorporation into maturing 60S subunits and, consequently, increasing the pool of free RPs, thereby promoting p53-mediated senescence. Thus, SNORA13 regulates ribosome biogenesis and the p53 pathway through a non-canonical mechanism distinct from its role in guiding RNA modification. These findings expand our understanding of snoRNA functions and their roles in cellular signaling.
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Affiliation(s)
- Yujing Cheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Siwen Wang
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jong-Sun Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jason Guo
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric Chen
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shenming Wang
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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6
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Serra-Cardona A, Hua X, McNutt SW, Zhou H, Toda T, Jia S, Chu F, Zhang Z. The PCNA-Pol δ complex couples lagging strand DNA synthesis to parental histone transfer for epigenetic inheritance. SCIENCE ADVANCES 2024; 10:eadn5175. [PMID: 38838138 PMCID: PMC11152121 DOI: 10.1126/sciadv.adn5175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Inheritance of epigenetic information is critical for maintaining cell identity. The transfer of parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications on histone proteins, represents a crucial yet poorly understood step in the inheritance of epigenetic information. Here, we show the lagging strand DNA polymerase, Pol δ, interacts directly with H3-H4 and that the interaction between Pol δ and the sliding clamp PCNA regulates parental histone transfer to lagging strands, most likely independent of their roles in DNA synthesis. When combined, mutations at Pol δ and Mcm2 that compromise parental histone transfer result in a greater reduction in nucleosome occupancy at nascent chromatin than mutations in either alone. Last, PCNA contributes to nucleosome positioning on nascent chromatin. On the basis of these results, we suggest that the PCNA-Pol δ complex couples lagging strand DNA synthesis to parental H3-H4 transfer, facilitating epigenetic inheritance.
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Affiliation(s)
- Albert Serra-Cardona
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
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7
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Karri S, Yang Y, Zhou J, Dickinson Q, Jia J, Huang Y, Wang Z, Gan H, Yu C. Defective transfer of parental histone decreases frequency of homologous recombination by increasing free histone pools in budding yeast. Nucleic Acids Res 2024; 52:5138-5151. [PMID: 38554108 PMCID: PMC11109958 DOI: 10.1093/nar/gkae205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging strands, respectively. Single Dpb3 deletion (dpb3Δ) or Mcm2 mutation (mcm2-3A), which each disrupts one parental histone transfer pathway, leads to the other's predominance. However, the biological impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3Δ mcm2-3A double mutant did not exhibit the asymmetric parental histone patterns caused by a single dpb3Δ or mcm2-3A mutation, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3Δ, mcm2-3A and dpb3Δ mcm2-3A mutants, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones during DNA replication is essential for maintaining chromatin structure and that lower homologous recombination activity due to parental histone transfer defects is detrimental to cells.
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Affiliation(s)
- Srinivasu Karri
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yi Yang
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Jiaqi Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Quinn Dickinson
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Jing Jia
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yuxin Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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8
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Zhang J, Yu Y, Zou X, Du Y, Liang Q, Gong M, He Y, Luo J, Wu D, Jiang X, Sinclair M, Tajkhorshid E, Chen HZ, Hou Z, Zheng Y, Chen LF, Yang XD. WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination. Nucleic Acids Res 2024; 52:4969-4984. [PMID: 38452206 PMCID: PMC11109945 DOI: 10.1093/nar/gkae161] [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: 06/06/2023] [Revised: 02/08/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Proteasome-mediated degradation of chromatin-bound NF-κB is critical in terminating the transcription of pro-inflammatory genes and can be triggered by Set9-mediated lysine methylation of the RelA subunit. However, the E3 ligase targeting methylated RelA remains unknown. Here, we find that two structurally similar substrate-recognizing components of Cullin-RING E3 ligases, WSB1 and WSB2, can recognize chromatin-bound methylated RelA for polyubiquitination and proteasomal degradation. We showed that WSB1/2 negatively regulated a subset of NF-κB target genes via associating with chromatin where they targeted methylated RelA for ubiquitination, facilitating the termination of NF-κB-dependent transcription. WSB1/2 specifically interacted with methylated lysines (K) 314 and 315 of RelA via their N-terminal WD-40 repeat (WDR) domains, thereby promoting ubiquitination of RelA. Computational modeling further revealed that a conserved aspartic acid (D) at position 158 within the WDR domain of WSB2 coordinates K314/K315 of RelA, with a higher affinity when either of the lysines is methylated. Mutation of D158 abolished WSB2's ability to bind to and promote ubiquitination of methylated RelA. Together, our study identifies a novel function and the underlying mechanism for WSB1/2 in degrading chromatin-bound methylated RelA and preventing sustained NF-κB activation, providing potential new targets for therapeutic intervention of NF-κB-mediated inflammatory diseases.
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Affiliation(s)
- Jie Zhang
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yuanyuan Yu
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiuqun Zou
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yaning Du
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Qiankun Liang
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mengyao Gong
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yurong He
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Junqi Luo
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dandan Wu
- Shanghai Institute of Immunology, and Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoli Jiang
- Shanghai Institute of Immunology, and Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hong-Zhuan Chen
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shuguang lab of Future Health, Shanghai Frontiers Science Center of TCM Chemical Biology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhaoyuan Hou
- Hongqiao Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
- Linyi University-Shanghai Jiaotong University Joint Institute of Translational Medicine, Linyi University, Shandong 276000, China
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xiao-Dong Yang
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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9
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Arends T, Tsuchida H, Adeyemi RO, Tapscott SJ. DUX4-induced HSATII transcription causes KDM2A/B-PRC1 nuclear foci and impairs DNA damage response. J Cell Biol 2024; 223:e202303141. [PMID: 38451221 PMCID: PMC10919155 DOI: 10.1083/jcb.202303141] [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: 03/30/2023] [Revised: 11/02/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
Polycomb repressive complexes regulate developmental gene programs, promote DNA damage repair, and mediate pericentromeric satellite repeat repression. Expression of pericentromeric satellite repeats has been implicated in several cancers and diseases, including facioscapulohumeral dystrophy (FSHD). Here, we show that DUX4-mediated transcription of HSATII regions causes nuclear foci formation of KDM2A/B-PRC1 complexes, resulting in a global loss of PRC1-mediated monoubiquitination of histone H2A. Loss of PRC1-ubiquitin signaling severely impacts DNA damage response. Our data implicate DUX4-activation of HSATII and sequestration of KDM2A/B-PRC1 complexes as a mechanism of regulating epigenetic and DNA repair pathways.
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Affiliation(s)
- Tessa Arends
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hiroshi Tsuchida
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Richard O. Adeyemi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stephen J. Tapscott
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
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10
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Delegard J, Patel A, Ellenbogen RG, Ramakrishna R, Rostomily R. Analysis of gliomas DNA methylation: Assessment of pre-analytical variables. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586350. [PMID: 38586048 PMCID: PMC10996653 DOI: 10.1101/2024.03.26.586350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Precision oncology is driven by molecular biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase ( MGMT ) gene DNA promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage before fixing, sampling, and processing are major sources of errors and batch effects, that are further confounded by intra-tumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL) and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter CpG methylation was examined in 173 surgical samples from 90 individuals, 50 of these were used for intra-tumor heterogeneity studies. MGMT promoter methylation levels in paired frozen and formalin fixed paraffin embedded (FFPE) samples were very close, confirming suitability of FFPE for MGMT promoter methylation analysis in clinical settings. Matrix MeDIP-qPCR yielded similar results to methylation specific PCR (MS-PCR). Warm ex-vivo ischemia (37°C up to 4hrs) and 3 cycles of repeated sample thawing and freezing did not alter 5mC levels at MGMT promoter, exon and upstream enhancer regions, demonstrating the resistance of DNA methylation to the most common variations in sample processing conditions that might be encountered in research and clinical settings. 20-30% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. Collectively these data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have significant impact on assessment of MGMT promoter methylation status. However, intratumor methylation heterogeneity underscores the need for histologic verification and value of multiple biopsies at different GBM geographic tumor sites in assessment of MGMT promoter methylation. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs), that are likewise resilient to variation in above post-resection pre-analytical conditions. These MGMT -associated global DNA methylation patterns offer new opportunities to validate more granular data-based epigenetic GBM clinical biomarkers where the CryoGrid-PIXUL-Matrix toolbox could prove to be useful.
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11
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Zhang J, Chen F, Tang M, Xu W, Tian Y, Liu Z, Shu Y, Yang H, Zhu Q, Lu X, Peng B, Liu X, Xu X, Gullerova M, Zhu WG. The ARID1A-METTL3-m6A axis ensures effective RNase H1-mediated resolution of R-loops and genome stability. Cell Rep 2024; 43:113779. [PMID: 38358891 DOI: 10.1016/j.celrep.2024.113779] [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: 07/12/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
R-loops are three-stranded structures that can pose threats to genome stability. RNase H1 precisely recognizes R-loops to drive their resolution within the genome, but the underlying mechanism is unclear. Here, we report that ARID1A recognizes R-loops with high affinity in an ATM-dependent manner. ARID1A recruits METTL3 and METTL14 to the R-loop, leading to the m6A methylation of R-loop RNA. This m6A modification facilitates the recruitment of RNase H1 to the R-loop, driving its resolution and promoting DNA end resection at DSBs, thereby ensuring genome stability. Depletion of ARID1A, METTL3, or METTL14 leads to R-loop accumulation and reduced cell survival upon exposure to cytotoxic agents. Therefore, ARID1A, METTL3, and METTL14 function in a coordinated, temporal order at DSB sites to recruit RNase H1 and to ensure efficient R-loop resolution. Given the association of high ARID1A levels with resistance to genotoxic therapies in patients, these findings open avenues for exploring potential therapeutic strategies for cancers with ARID1A abnormalities.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Yuxin Shu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Hui Yang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Bin Peng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China; Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China; School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China; Department of Biochemistry and Molecular Biology, Peking University Health Science Centre, Beijing 100191, China.
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12
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Karri S, Dickinson Q, Jia J, Gan H, Wang Z, Deng Y, Yu C. The Role of Hexokinases in Epigenetic Regulation: Altered Hexokinase Expression and Chromatin Stability in Yeast. RESEARCH SQUARE 2024:rs.3.rs-3899124. [PMID: 38352584 PMCID: PMC10862943 DOI: 10.21203/rs.3.rs-3899124/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Background . Human hexokinase 2 ( HK2 ) plays an important role in regulating Warburg effect, which metabolizes glucose to lactate acid even in the presence of ample oxygen and provides intermediate metabolites to support cancer cell proliferation and tumor growth. HK2 overexpression has been observed in various types of cancers and targeting HK2 -driven Warburg effect has been suggested as a potential cancer therapeutic strategy. Given that epigenetic enzymes utilize metabolic intermediates as substrates or co-factors to carry out post-translational modification of DNA and histones in cells, we hypothesized that altering HK2 expression-mediated cellular glycolysis rates could impact the epigenome and, consequently, genome stability in yeast. To test this hypothesis, we established genetic models with different yeast hexokinase 2 ( HXK2) expression in Saccharomyces cerevisiae yeast cells and investigated the effect of HXK2 -dependent metabolism on parental nucleosome transfer, a key DNA replication-coupled epigenetic inheritance process, and chromatin stability. Results . By comparing the growth of mutant yeast cells carrying single deletion of hxk1Δ , hxk2Δ , or double-loss of hxk1Δ hxk2Δ to wild-type cells, we demonstrated that HXK2 is the dominant HXK in yeast cell growth. Surprisingly, manipulating HXK2 expression in yeast, whether through overexpression or deletion, had only a marginal impact on parental nucleosome assembly, but a noticeable trend with decrease chromatin instability. However, targeting yeast cells with 2-deoxy-D-glucose (2-DG), a HK2 inhibitor that has been proposed as an anti-cancer treatment, significantly increased chromatin instability. Conclusion . Our findings suggest that in yeast cells lacking HXK2 , alternative HXK s such as HXK1 or glucokinase 1 ( GLK1 ) play a role in supporting glycolysis at a level that adequately maintain epigenomic stability. While our study demonstrated an increase in epigenetic instability with 2-DG treatment, the observed effect seemed to occur independently of Hxk2-mediated glycolysis inhibition. Thus, additional research is needed to identify the molecular mechanism through which 2-DG influences chromatin stability.
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Feng R, Tong C, Lin T, Liu H, Shao C, Li Y, Sticht C, Kan K, Li X, Liu R, Wang S, Wang S, Munker S, Niess H, Meyer C, Liebe R, Ebert MP, Dooley S, Wang H, Ding H, Weng HL. Insulin Determines Transforming Growth Factor β Effects on Hepatocyte Nuclear Factor 4α Transcription in Hepatocytes. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:52-70. [PMID: 37820926 DOI: 10.1016/j.ajpath.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Loss of hepatocyte nuclear factor 4α (HNF4α) expression is frequently observed in end-stage liver disease and associated with loss of vital liver functions, thus increasing mortality. Loss of HNF4α expression is mediated by inflammatory cytokines, such as transforming growth factor (TGF)-β. However, details of how HNF4α is suppressed are largely unknown to date. Herein, TGF-β did not directly inhibit HNF4α but contributed to its transcriptional regulation by SMAD2/3 recruiting acetyltransferase CREB-binding protein/p300 to the HNF4α promoter. The recruitment of CREB-binding protein/p300 is indispensable for CCAAT/enhancer-binding protein α (C/EBPα) binding, another essential requirement for constitutive HNF4α expression in hepatocytes. Consistent with the in vitro observation, 67 of 98 patients with hepatic HNF4α expressed both phospho-SMAD2 and C/EBPα, whereas 22 patients without HNF4α expression lacked either phospho-SMAD2 or C/EBPα. In contrast to the observed induction of HNF4α, SMAD2/3 inhibited C/EBPα transcription. Long-term TGF-β incubation resulted in C/EBPα depletion, which abrogated HNF4α expression. Intriguingly, SMAD2/3 inhibitory binding to the C/EBPα promoter was abolished by insulin. Two-thirds of patients without C/EBPα lacked membrane glucose transporter type 2 expression in hepatocytes, indicating insulin resistance. Taken together, these data indicate that hepatic insulin sensitivity is essential for hepatic HNF4α expression in the condition of inflammation.
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Affiliation(s)
- Rilu Feng
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chenhao Tong
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tao Lin
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hui Liu
- Department of Pathology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Chen Shao
- Department of Pathology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yujia Li
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kejia Kan
- Department of Surgery, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiaofeng Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Rui Liu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Sai Wang
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shanshan Wang
- Beijing Institute of Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Stefan Munker
- Department of Medicine II, Liver Centre Munich, University Hospital, Campus Großhadern, Ludwig-Maximilians-University Munich, Munich, Germany; Liver Centre Munich, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Hanno Niess
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany; Biobank of the Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christoph Meyer
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Roman Liebe
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Clinical Cooperation Unit Healthy Metabolism, Center of Preventive Medicine and Digital Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Steven Dooley
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hua Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huiguo Ding
- Department of Gastroenterology and Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Hong-Lei Weng
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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14
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Luan R, He M, Li H, Bai Y, Wang A, Sun G, Zhou B, Wang M, Wang C, Wang S, Zeng K, Feng J, Lin L, Wei Y, Kato S, Zhang Q, Zhao Y. MYSM1 acts as a novel co-activator of ERα to confer antiestrogen resistance in breast cancer. EMBO Mol Med 2024; 16:10-39. [PMID: 38177530 PMCID: PMC10883278 DOI: 10.1038/s44321-023-00003-z] [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: 03/07/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024] Open
Abstract
Endocrine resistance is a crucial challenge in estrogen receptor alpha (ERα)-positive breast cancer (BCa). Aberrant alteration in modulation of E2/ERα signaling pathway has emerged as the putative contributor for endocrine resistance in BCa. Herein, we demonstrate that MYSM1 as a deubiquitinase participates in modulating ERα action via histone and non-histone deubiquitination. MYSM1 is involved in maintenance of ERα stability via ERα deubiquitination. MYSM1 regulates relevant histone modifications on cis regulatory elements of ERα-regulated genes, facilitating chromatin decondensation. MYSM1 is highly expressed in clinical BCa samples. MYSM1 depletion attenuates BCa-derived cell growth in xenograft models and increases the sensitivity of antiestrogen agents in BCa cells. A virtual screen shows that the small molecule Imatinib could potentially interact with catalytic MPN domain of MYSM1 to inhibit BCa cell growth via MYSM1-ERα axis. These findings clarify the molecular mechanism of MYSM1 as an epigenetic modifier in regulation of ERα action and provide a potential therapeutic target for endocrine resistance in BCa.
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Affiliation(s)
- Ruina Luan
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, 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, 110122, Shenyang City, 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, 110122, Shenyang City, 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, 110122, Shenyang City, Liaoning Province, China
| | - Anqi Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
- First Clinical Medical College, China Medical University, 110001, Shenyang City, Liaoning Province, China
| | - Ge Sun
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, 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, 110122, Shenyang City, 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, 110122, Shenyang City, 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, 110122, Shenyang City, 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, 110122, Shenyang City, 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, 110122, Shenyang City, Liaoning Province, China
| | - Jianwei Feng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, 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, 110122, Shenyang City, Liaoning Province, China
| | - Yuntao Wei
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, 110042, Shenyang City, Liaoning Province, China
| | - Shigeaki Kato
- Graduate School of Life Science and Engineering, Iryo Sosei University, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, 110042, Shenyang City, 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, 110122, Shenyang City, Liaoning Province, China.
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15
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Behrmann A, Zhong D, Li L, Xie S, Mead M, Sabaeifard P, Goodarzi M, Lemoff A, Kozlitina J, Towler DA. Wnt16 Promotes Vascular Smooth Muscle Contractile Phenotype and Function via Taz (Wwtr1) Activation in Male LDLR-/- Mice. Endocrinology 2023; 165:bqad192. [PMID: 38123514 PMCID: PMC10765280 DOI: 10.1210/endocr/bqad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Wnt16 is expressed in bone and arteries, and maintains bone mass in mice and humans, but its role in cardiovascular physiology is unknown. We show that Wnt16 protein accumulates in murine and human vascular smooth muscle (VSM). WNT16 genotypes that convey risk for bone frailty also convey risk for cardiovascular events in the Dallas Heart Study. Murine Wnt16 deficiency, which causes postnatal bone loss, also reduced systolic blood pressure. Electron microscopy demonstrated abnormal VSM mitochondrial morphology in Wnt16-null mice, with reductions in mitochondrial respiration. Following angiotensin-II (AngII) infusion, thoracic ascending aorta (TAA) dilatation was greater in Wnt16-/- vs Wnt16+/+ mice (LDLR-/- background). Acta2 (vascular smooth muscle alpha actin) deficiency has been shown to impair contractile phenotype and worsen TAA aneurysm with concomitant reductions in blood pressure. Wnt16 deficiency reduced expression of Acta2, SM22 (transgelin), and other contractile genes, and reduced VSM contraction induced by TGFβ. Acta2 and SM22 proteins were reduced in Wnt16-/- VSM as was Ankrd1, a prototypic contractile target of Yap1 and Taz activation via TEA domain (TEAD)-directed transcription. Wnt16-/- VSM exhibited reduced nuclear Taz and Yap1 protein accumulation. SiRNA targeting Wnt16 or Taz, but not Yap1, phenocopied Wnt16 deficiency, and Taz siRNA inhibited contractile gene upregulation by Wnt16. Wnt16 incubation stimulated mitochondrial respiration and contraction (reversed by verteporfin, a Yap/Taz inhibitor). SiRNA targeting Taz inhibitors Ccm2 and Lats1/2 mimicked Wnt16 treatment. Wnt16 stimulated Taz binding to Acta2 chromatin and H3K4me3 methylation. TEAD cognates in the Acta2 promoter conveyed transcriptional responses to Wnt16 and Taz. Wnt16 regulates cardiovascular physiology and VSM contractile phenotype, mediated via Taz signaling.
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Affiliation(s)
- Abraham Behrmann
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dalian Zhong
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Li Li
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shangkui Xie
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Megan Mead
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Parastoo Sabaeifard
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Andrew Lemoff
- Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Julia Kozlitina
- McDermott Center for Human Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dwight A Towler
- Internal Medicine—Endocrine Division and the Pak Center for Mineral Metabolism and Clinical Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
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16
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Yan P, Du Q, Chen H, Guo Z, Wang Z, Tang J, Li WX. Biofortification of iron content by regulating a NAC transcription factor in maize. Science 2023; 382:1159-1165. [PMID: 38060668 DOI: 10.1126/science.adf3256] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Iron (Fe) deficiency remains widespread among people in developing countries. To help solve this problem, breeders have been attempting to develop maize cultivars with high yields and high Fe concentrations in the kernels. We conducted a genome-wide association study and identified a gene, ZmNAC78 (NAM/ATAF/CUC DOMAIN TRANSCRIPTION FACTOR 78), that regulates Fe concentrations in maize kernels. We cultivated maize varieties with both high yield and high Fe concentrations in their kernels by using a molecular marker developed from a 42-base pair insertion or deletion (indel) in the promoter of ZmNAC78. ZmNAC78 expression is enriched in the basal endosperm transfer layer of kernels, and the ZmNAC78 protein directly regulates messenger RNA abundance of Fe transporters. Our results thus provide an approach to develop maize varieties with Fe-enriched kernels.
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Affiliation(s)
- Pengshuai Yan
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Qingguo Du
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Chen
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zifeng Guo
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Shennong Laboratory, Zhengzhou 450002, China
| | - Wen-Xue Li
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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17
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Zhang J, Chen F, Tian Y, Xu W, Zhu Q, Li Z, Qiu L, Lu X, Peng B, Liu X, Gan H, Liu B, Xu X, Zhu WG. PARylated PDHE1α generates acetyl-CoA for local chromatin acetylation and DNA damage repair. Nat Struct Mol Biol 2023; 30:1719-1734. [PMID: 37735618 DOI: 10.1038/s41594-023-01107-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Chromatin relaxation is a prerequisite for the DNA repair machinery to access double-strand breaks (DSBs). Local histones around the DSBs then undergo prompt changes in acetylation status, but how the large demands of acetyl-CoA are met is unclear. Here, we report that pyruvate dehydrogenase 1α (PDHE1α) catalyzes pyruvate metabolism to rapidly provide acetyl-CoA in response to DNA damage. We show that PDHE1α is quickly recruited to chromatin in a polyADP-ribosylation-dependent manner, which drives acetyl-CoA generation to support local chromatin acetylation around DSBs. This process increases the formation of relaxed chromatin to facilitate repair-factor loading, genome stability and cancer cell resistance to DNA-damaging treatments in vitro and in vivo. Indeed, we demonstrate that blocking polyADP-ribosylation-based PDHE1α chromatin recruitment attenuates chromatin relaxation and DSB repair efficiency, resulting in genome instability and restored radiosensitivity. These findings support a mechanism in which chromatin-associated PDHE1α locally generates acetyl-CoA to remodel the chromatin environment adjacent to DSBs and promote their repair.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Zhenhai Li
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Lingyu Qiu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Bin Peng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Haiyun Gan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Baohua Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University Medical School, Shenzhen, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, China
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China.
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18
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Genetta T, Hurwitz J, Clark E, Herold B, Khalil S, Abbas T, Larner J. ZEB1 promotes non-homologous end joining double-strand break repair. Nucleic Acids Res 2023; 51:9863-9879. [PMID: 37665026 PMCID: PMC10570029 DOI: 10.1093/nar/gkad723] [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: 07/20/2022] [Revised: 07/31/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Repair of DSB induced by IR is primarily carried out by Non-Homologous End Joining (NHEJ), a pathway in which 53BP1 plays a key role. We have discovered that the EMT-inducing transcriptional repressor ZEB1 (i) interacts with 53BP1 and that this interaction occurs rapidly and is significantly amplified following exposure of cells to IR; (ii) is required for the localization of 53BP1 to a subset of double-stranded breaks, and for physiological DSB repair; (iii) co-localizes with 53BP1 at IR-induced foci (IRIF); (iv) promotes NHEJ and inhibits Homologous Recombination (HR); (v) depletion increases resection at DSBs and (vi) confers PARP inhibitor (PARPi) sensitivity on BRCA1-deficient cells. Lastly, ZEB1's effects on repair pathway choice, resection, and PARPi sensitivity all rely on its homeodomain. In contrast to the well-characterized therapeutic resistance of high ZEB1-expressing cancer cells, the novel ZEB1-53BP1-shieldin resection axis described here exposes a therapeutic vulnerability: ZEB1 levels in BRCA1-deficient tumors may serve as a predictive biomarker of response to PARPis.
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Affiliation(s)
- Thomas L Genetta
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
| | - Joshua C Hurwitz
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
| | - Evan A Clark
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
| | - Benjamin T Herold
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
| | - Shadi Khalil
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
| | - Tarek Abbas
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
- Dept. of Biochemistry and Molecular Genetics University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - James M Larner
- Dept. of Radiation Oncology, University of Virginia School of Medicine, PO Box 800383, Charlottesville, VA 22908, USA
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19
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Gilan O, Talarmain L, Bell CC, Neville D, Knezevic K, Ferguson DT, Boudes M, Chan YC, Davidovich C, Lam EYN, Dawson MA. CRISPR-ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia. Nat Struct Mol Biol 2023; 30:1592-1606. [PMID: 37679565 DOI: 10.1038/s41594-023-01087-4] [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: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
Chromatin regulation involves the selective recruitment of chromatin factors to facilitate DNA repair, replication and transcription. Here we demonstrate the utility of coupling unbiased functional genomics with chromatin immunoprecipitation (CRISPR-ChIP) to identify the factors associated with active chromatin modifications in mammalian cells. Specifically, an integrated reporter containing a cis-regulatory element of interest and a single guide RNA provide a chromatinized template for a direct readout for regulators of histone modifications associated with actively transcribed genes such as H3K4me3 and H3K79me2. With CRISPR-ChIP, we identify all the nonredundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukemia cells driven by MLL translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units: an oncogenic DOT1L complex directed by the MLL fusion protein in a Menin-dependent manner and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia.
| | - Laure Talarmain
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Neville
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel T Ferguson
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- EMBL-Australia, Clayton, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Clinical Haematology, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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20
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Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
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Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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21
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Broucke E, Dang TTV, Li Y, Hulsmans S, Van Leene J, De Jaeger G, Hwang I, Wim VDE, Rolland F. SnRK1 inhibits anthocyanin biosynthesis through both transcriptional regulation and direct phosphorylation and dissociation of the MYB/bHLH/TTG1 MBW complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1193-1213. [PMID: 37219821 DOI: 10.1111/tpj.16312] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/21/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Plants have evolved an extensive specialized secondary metabolism. The colorful flavonoid anthocyanins, for example, not only stimulate flower pollination and seed dispersal, but also protect different tissues against high light, UV and oxidative stress. Their biosynthesis is highly regulated by environmental and developmental cues and induced by high sucrose levels. Expression of the biosynthetic enzymes involved is controlled by a transcriptional MBW complex, comprising (R2R3) MYB- and bHLH-type transcription factors and the WD40 repeat protein TTG1. Anthocyanin biosynthesis is not only useful, but also carbon- and energy-intensive and non-vital. Consistently, the SnRK1 protein kinase, a metabolic sensor activated in carbon- and energy-depleting stress conditions, represses anthocyanin biosynthesis. Here we show that Arabidopsis SnRK1 represses MBW complex activity both at the transcriptional and post-translational level. In addition to repressing expression of the key transcription factor MYB75/PAP1, SnRK1 activity triggers MBW complex dissociation, associated with loss of target promoter binding, MYB75 protein degradation and nuclear export of TTG1. We also provide evidence for direct interaction with and phosphorylation of multiple MBW complex proteins. These results indicate that repression of expensive anthocyanin biosynthesis is an important strategy to save energy and redirect carbon flow to more essential processes for survival in metabolic stress conditions.
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Affiliation(s)
- Ellen Broucke
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Thi Tuong Vi Dang
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Yi Li
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Sander Hulsmans
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Van den Ende Wim
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Kasteelpark Arenberg 31, 3001 Heverlee, Leuven, Belgium
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22
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Guan S, Zou Q, Wu H, Ding Y. Protein-DNA Binding Residues Prediction Using a Deep Learning Model With Hierarchical Feature Extraction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2619-2628. [PMID: 35834447 DOI: 10.1109/tcbb.2022.3190933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biologically important effects occur when proteins bind to other substances, of which binding to DNA is a crucial one. Therefore, accurate identification of protein-DNA binding residues is important for further understanding of the protein-DNA interaction mechanism. Although wet-lab methods can accurately obtain the location of bound residues, it requires significant human, financial and time costs. There is thus an urgent need to develop efficient computational-based methods. Most current state-of-the-art methods are two-step approaches: the first step uses a sliding window technique to extract residue features; the second step uses each residue as an input to the model for prediction. This has a negative impact on the efficiency of prediction and ease of use. In this study, we propose a sequence-to-sequence (seq2seq) model that can input the entire protein sequence of variable length and use two modules, Transformer Encoder Block and Feature Extracting Block, for hierarchical feature extraction, where Transformer Encoder Block is used to extract global features, and then Feature Extracting Block is used to extract local features to further improve the recognition capability of the model. The comparison results on two benchmark datasets, namely PDNA-543 and PDNA-41, prove the effectiveness of our method in identifying protein-DNA binding residues.
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23
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Qu C, Zhu M, Hu R, Niu Y, Chen S, Zhao H, Li C, Wang Z, Yin N, Sun F, Chen Z, Shen S, Shang G, Zhou Y, Yan X, Wei L, Liu L, Yi B, Lian J, Li J, Tang Z, Liang Y, Xu X, Wang R, Yin J, Wan H, Du H, Qian W, Chai Y, Zhou Q, He Y, Zhong S, Qiu X, Yu H, Lam HM, Lu K, Fu F, Li J. Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus. Nat Commun 2023; 14:5194. [PMID: 37626056 PMCID: PMC10457299 DOI: 10.1038/s41467-023-40838-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Yellow-seed trait is a desirable breeding characteristic of rapeseed (Brassica napus) that could greatly improve seed oil yield and quality. However, the underlying mechanisms controlling this phenotype in B. napus plants are difficult to discern because of their complexity. Here, we assemble high-quality genomes of yellow-seeded (GH06) and black-seeded (ZY821). Combining in-depth fine mapping of a quantitative trait locus (QTL) for seed color with other omics data reveal BnA09MYB47a, encoding an R2R3-MYB-type transcription factor, as the causal gene of a major QTL controlling the yellow-seed trait. Functional studies show that sequence variation of BnA09MYB47a underlies the functional divergence between the yellow- and black-seeded B. napus. The black-seed allele BnA09MYB47aZY821, but not the yellow-seed allele BnA09MYB47aGH06, promotes flavonoid biosynthesis by directly activating the expression of BnTT18. Our discovery suggests a possible approach to breeding B. napus for improved commercial value and facilitates flavonoid biosynthesis studies in Brassica crops.
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Affiliation(s)
- Cunmin Qu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meichen Zhu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ran Hu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yongchao Niu
- The State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Si Chen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Huiyan Zhao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Chengxiang Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Zhen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Nengwen Yin
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Fujun Sun
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhiyou Chen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Shulin Shen
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guoxia Shang
- National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Yan Zhou
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xingying Yan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Lijuan Wei
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Liezhao Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | | | - Jiang Li
- Biozeron Shenzhen, Inc, Shenzhen, China
| | - Zhanglin Tang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ying Liang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xinfu Xu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Rui Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiaming Yin
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Huafang Wan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hai Du
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Qian
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yourong Chai
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qingyuan Zhou
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yajun He
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Silin Zhong
- The State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao Qiu
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Hao Yu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Hon-Ming Lam
- The State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kun Lu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Fuyou Fu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Canada.
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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24
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Du F, Wang Y, Wang J, Li Y, Zhang Y, Zhao X, Xu J, Li Z, Zhao T, Wang W, Fu B. The basic helix-loop-helix transcription factor gene, OsbHLH38, plays a key role in controlling rice salt tolerance. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1859-1873. [PMID: 36988217 DOI: 10.1111/jipb.13489] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination. The considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian (indica) and Geng (japonica) subspecies and between the upland-Geng and lowland-Geng ecotypes. The upland-Geng accessions were most sensitive to ABA. Genome-wide association analyses identified four major quantitative trait loci containing 21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene, OsbHLH38, was the most important for ABA sensitivity. Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses. Overexpression of OsbHLH38 increased seedling salt tolerance, while knockout of OsbHLH38 increased sensitivity to salt stress. A salt-responsive transcription factor, OsDREB2A, interacted with OsbHLH38 and was directly regulated by OsbHLH38. Moreover, OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones, transcription factor genes, and many downstream genes with diverse functions, including photosynthesis, redox homeostasis, and abiotic stress responsiveness. These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.
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Affiliation(s)
- Fengping Du
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yinxiao Wang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Juan Wang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yingbo Li
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yue Zhang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianlong Xu
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhikang Li
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Anhui Agricultural University, Hefei, 230036, China
| | - Tianyong Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Wensheng Wang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Anhui Agricultural University, Hefei, 230036, China
- Hainan Yazhou Bay Seed Lab/National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Binying Fu
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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25
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Zhang W, Qi L, Liu Z, He S, Wang C, Wu Y, Han L, Liu Z, Fu Z, Tu C, Li Z. Integrated multiomic analysis and high-throughput screening reveal potential gene targets and synergetic drug combinations for osteosarcoma therapy. MedComm (Beijing) 2023; 4:e317. [PMID: 37457661 PMCID: PMC10338795 DOI: 10.1002/mco2.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
Although great advances have been made over the past decades, therapeutics for osteosarcoma are quite limited. We performed long-read RNA sequencing and tandem mass tag (TMT)-based quantitative proteome on osteosarcoma and the adjacent normal tissues, next-generation sequencing (NGS) on paired osteosarcoma samples before and after neoadjuvant chemotherapy (NACT), and high-throughput drug combination screen on osteosarcoma cell lines. Single-cell RNA sequencing data were analyzed to reveal the heterogeneity of potential therapeutic target genes. Additionally, we clarified the synergistic mechanisms of doxorubicin (DOX) and HDACs inhibitors for osteosarcoma treatment. Consequently, we identified 2535 osteosarcoma-specific genes and several alternative splicing (AS) events with osteosarcoma specificity and/or patient heterogeneity. Hundreds of potential therapeutic targets were identified among them, which showed the core regulatory roles in osteosarcoma. We also identified 215 inhibitory drugs and 236 synergistic drug combinations for osteosarcoma treatment. More interestingly, the multiomic analysis pointed out the pivotal role of HDAC1 and TOP2A in osteosarcoma. HDAC inhibitors synergized with DOX to suppress osteosarcoma both in vitro and in vivo. Mechanistically, HDAC inhibitors synergized with DOX by downregulating SP1 to transcriptionally modulate TOP2A expression. This study provided a comprehensive view of molecular features, therapeutic targets, and synergistic drug combinations for osteosarcoma.
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Affiliation(s)
- Wenchao Zhang
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Lin Qi
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Zhongyue Liu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Shasha He
- Department of OncologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | | | - Ying Wu
- MegaRobo Technologies Co., LtdSuzhouChina
| | | | | | - Zheng Fu
- MegaRobo Technologies Co., LtdSuzhouChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Zhihong Li
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
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26
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Berber M, Leng S, Wengi A, Winter DV, Odermatt A, Beuschlein F, Loffing J, Breault DT, Penton D. Calcineurin regulates aldosterone production via dephosphorylation of NFATC4. JCI Insight 2023; 8:e157027. [PMID: 37310791 PMCID: PMC10443813 DOI: 10.1172/jci.insight.157027] [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: 01/18/2022] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
The mineralocorticoid aldosterone, secreted by the adrenal zona glomerulosa (ZG), is critical for life, maintaining ion homeostasis and blood pressure. Therapeutic inhibition of protein phosphatase 3 (calcineurin, Cn) results in inappropriately low plasma aldosterone levels despite concomitant hyperkalemia and hyperreninemia. We tested the hypothesis that Cn participates in the signal transduction pathway regulating aldosterone synthesis. Inhibition of Cn with tacrolimus abolished the potassium-stimulated (K+-stimulated) expression of aldosterone synthase, encoded by CYP11B2, in the NCI-H295R human adrenocortical cell line as well as ex vivo in mouse and human adrenal tissue. ZG-specific deletion of the regulatory Cn subunit CnB1 diminished Cyp11b2 expression in vivo and disrupted K+-mediated aldosterone synthesis. Phosphoproteomics analysis identified nuclear factor of activated T cells, cytoplasmic 4 (NFATC4), as a target for Cn-mediated dephosphorylation. Deletion of NFATC4 impaired K+-dependent stimulation of CYP11B2 expression and aldosterone production while expression of a constitutively active form of NFATC4 increased expression of CYP11B2 in NCI-H295R cells. Chromatin immunoprecipitation revealed NFATC4 directly regulated CYP11B2 expression. Thus, Cn controls aldosterone production via the Cn/NFATC4 pathway. Inhibition of Cn/NFATC4 signaling may explain low plasma aldosterone levels and hyperkalemia in patients treated with tacrolimus, and the Cn/NFATC4 pathway may provide novel molecular targets to treat primary aldosteronism.
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Affiliation(s)
- Mesut Berber
- Institute of Anatomy, University of Zurich, Switzerland
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
| | - Sining Leng
- Department of Pediatrics, Harvard Medical School, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | - Denise V. Winter
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Alex Odermatt
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Felix Beuschlein
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | - Johannes Loffing
- Institute of Anatomy, University of Zurich, Switzerland
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
| | - David T. Breault
- Department of Pediatrics, Harvard Medical School, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - David Penton
- Institute of Anatomy, University of Zurich, Switzerland
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
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27
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Liao J, Wang J, Xu Y, Wu Y, Wang M, Zhao Q, Tan X, Meng Y, Wei L, Huang A. LAPTM4B-YAP loop feedback amplification enhances the stemness of hepatocellular carcinoma. iScience 2023; 26:106754. [PMID: 37213231 PMCID: PMC10197148 DOI: 10.1016/j.isci.2023.106754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/10/2023] [Accepted: 04/23/2023] [Indexed: 05/23/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is highly heterogeneous, and stemness signatures are frequently elevated in HCC tumor cells to generate heterogeneous subtypes via multidirectional differentiation. However, the mechanisms affecting the regulation of stemness in HCC remain unclear. In this study, we identified that lysosome-associated protein transmembrane-4β (LAPTM4B) was significantly overexpressed in stem-like tumor cell populations with multidirectional differentiation potential at the single cell level, and verified that LAPTM4B was closely related to stemness of HCC using in vitro and in vivo experiments. Mechanistically, elevated LAPTM4B suppresses Yes-associated protein (YAP) phosphorylation and ubiquitination degradation. In turn, stabilized YAP localizes to the nucleus and binds to cAMP responsive element binding protein-1 (CREB1), which promotes transcription of LAPTM4B. Overall, our findings suggest that LAPTM4B forms a positive feedback loop with YAP, which maintains the stemness of HCC tumor cells and leads to an unfavorable prognosis for HCC patients.
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Affiliation(s)
- Jianping Liao
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
| | - Jiahong Wang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yu Xu
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yong Wu
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Meifeng Wang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Qiudong Zhao
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
| | - Xiaodan Tan
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yan Meng
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
- Department of Medical Ultrasound, Shanghai Tenth People’s Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai 200072, China
- Corresponding author
| | - Lixin Wei
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
- Corresponding author
| | - Aimin Huang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
- Corresponding author
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28
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Xu T, Tao X, He H, Kempher ML, Zhang S, Liu X, Wang J, Wang D, Ning D, Pan C, Ge H, Zhang N, He YX, Zhou J. Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia. THE ISME JOURNAL 2023; 17:823-835. [PMID: 36899058 PMCID: PMC10203250 DOI: 10.1038/s41396-023-01392-2] [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: 09/22/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 05/24/2023]
Abstract
Carbohydrate utilization is critical to microbial survival. The phosphotransferase system (PTS) is a well-documented microbial system with a prominent role in carbohydrate metabolism, which can transport carbohydrates through forming a phosphorylation cascade and regulate metabolism by protein phosphorylation or interactions in model strains. However, those PTS-mediated regulated mechanisms have been underexplored in non-model prokaryotes. Here, we performed massive genome mining for PTS components in nearly 15,000 prokaryotic genomes from 4,293 species and revealed a high prevalence of incomplete PTSs in prokaryotes with no association to microbial phylogeny. Among these incomplete PTS carriers, a group of lignocellulose degrading clostridia was identified to have lost PTS sugar transporters and carry a substitution of the conserved histidine residue in the core PTS component, HPr (histidine-phosphorylatable phosphocarrier). Ruminiclostridium cellulolyticum was then selected as a representative to interrogate the function of incomplete PTS components in carbohydrate metabolism. Inactivation of the HPr homolog reduced rather than increased carbohydrate utilization as previously indicated. In addition to regulating distinct transcriptional profiles, PTS associated CcpA (Catabolite Control Protein A) homologs diverged from previously described CcpA with varied metabolic relevance and distinct DNA binding motifs. Furthermore, the DNA binding of CcpA homologs is independent of HPr homolog, which is determined by structural changes at the interface of CcpA homologs, rather than in HPr homolog. These data concordantly support functional and structural diversification of PTS components in metabolic regulation and bring novel understanding of regulatory mechanisms of incomplete PTSs in cellulose-degrading clostridia.
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Affiliation(s)
- Tao Xu
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Xuanyu Tao
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Hongxi He
- School of Life Sciences, Anhui University, Hefei, 230601, PR China
- Institutes of Material Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Megan L Kempher
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Siping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, PR China
| | - Xiaochun Liu
- School of Life Sciences, Anhui University, Hefei, 230601, PR China
- Institutes of Material Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Jun Wang
- School of Life Sciences, Anhui University, Hefei, 230601, PR China
- Institutes of Material Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Dongyu Wang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Daliang Ning
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Chongle Pan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- School of computer science, University of Oklahoma, Norman, OK, USA
| | - Honghua Ge
- School of Life Sciences, Anhui University, Hefei, 230601, PR China
- Institutes of Material Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Nannan Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, PR China.
- Institutes of Material Science and Information Technology, Anhui University, Hefei, 230601, PR China.
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, PR China.
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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29
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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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Spens AE, Sutliff NA, Bennett SR, Campbell AE, Tapscott SJ. Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction. eLife 2023; 12:e82057. [PMID: 37092726 PMCID: PMC10195082 DOI: 10.7554/elife.82057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 04/21/2023] [Indexed: 04/25/2023] Open
Abstract
DUX4 activates the first wave of zygotic gene expression in the early embryo. Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral dystrophy (FSHD), whereas expression in cancers suppresses IFNγ induction of major histocompatibility complex class I (MHC class I) and contributes to immune evasion. We show that the DUX4 protein interacts with STAT1 and broadly suppresses expression of IFNγ-stimulated genes by decreasing bound STAT1 and Pol-II recruitment. Transcriptional suppression of interferon-stimulated genes (ISGs) requires conserved (L)LxxL(L) motifs in the carboxyterminal region of DUX4 and phosphorylation of STAT1 Y701 enhances interaction with DUX4. Consistent with these findings, expression of endogenous DUX4 in FSHD muscle cells and the CIC-DUX4 fusion containing the DUX4 CTD in a sarcoma cell line inhibit IFNγ induction of ISGs. Mouse Dux similarly interacted with STAT1 and suppressed IFNγ induction of ISGs. These findings identify an evolved role of the DUXC family in modulating immune signaling pathways with implications for development, cancers, and FSHD.
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Affiliation(s)
- Amy E Spens
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Nicholas A Sutliff
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sean R Bennett
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Amy E Campbell
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusDenverUnited States
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Clinical Research Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Neurology, University of WashingtonSeattleUnited States
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31
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Caratti G, Stifel U, Caratti B, Jamil AJM, Chung KJ, Kiehntopf M, Gräler MH, Blüher M, Rauch A, Tuckermann JP. Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance. Nat Commun 2023; 14:2271. [PMID: 37080971 PMCID: PMC10119112 DOI: 10.1038/s41467-023-37831-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/01/2023] [Indexed: 04/22/2023] Open
Abstract
Insulin resistance (IR) during obesity is linked to adipose tissue macrophage (ATM)-driven inflammation of adipose tissue. Whether anti-inflammatory glucocorticoids (GCs) at physiological levels modulate IR is unclear. Here, we report that deletion of the GC receptor (GR) in myeloid cells, including macrophages in mice, aggravates obesity-related IR by enhancing adipose tissue inflammation due to decreased anti-inflammatory ATM leading to exaggerated adipose tissue lipolysis and severe hepatic steatosis. In contrast, GR deletion in Kupffer cells alone does not alter IR. Co-culture experiments show that the absence of GR in macrophages directly causes reduced phospho-AKT and glucose uptake in adipocytes, suggesting an important function of GR in ATM. GR-deficient macrophages are refractory to alternative ATM-inducing IL-4 signaling, due to reduced STAT6 chromatin loading and diminished anti-inflammatory enhancer activation. We demonstrate that GR has an important function in macrophages during obesity by limiting adipose tissue inflammation and lipolysis to promote insulin sensitivity.
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Affiliation(s)
- Giorgio Caratti
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ulrich Stifel
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Bozhena Caratti
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Ali J M Jamil
- Molecular Endocrinology & Stem Cell Research Unit, Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kyoung-Jin Chung
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Michael Kiehntopf
- SG Sepsis Research Clinic for Anesthesiology and Intensive Care, Jena University Hospital, Jena, Germany
| | - Markus H Gräler
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
- Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Matthias Blüher
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Alexander Rauch
- Molecular Endocrinology & Stem Cell Research Unit, Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark.
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
- Steno Diabetes Center Odense, Odense, Denmark.
| | - Jan P Tuckermann
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany.
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Chakraborty A, Roy G, Fatima F, Swami B, Bhaskar S. Mycobacterium indicus pranii therapy suppresses systemic dissemination of tumor cells in B16F10 murine model of melanoma. Biomed Pharmacother 2023; 160:114307. [PMID: 36739765 DOI: 10.1016/j.biopha.2023.114307] [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: 11/23/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Cancer associated morbidity is mostly attributed to the dissemination of tumor cells from their primary niche into the circulation known as "metastasis". Mycobacterium indicus pranii (MIP) an approved immunotherapeutic agent against lung cancer (NSCLC) has shown potent anti-tumor activity in prior studies. While evaluating anti-tumor activity of MIP in mouse model, MIP treated animals typically exhibited less metastatic lesions in their pulmonary compartment. To study the role of MIP in metastasis closely, B16F10 melanoma cells were implanted subcutaneously in the mice, and the dissemination of tumor cells from the solid tumor was evaluated over a period of time. When B16F10 melanoma cells were treated with MIP in vitro, downregulation of epithelial mesenchymal transition markers was observed in these cells, which in turn suppressed the invasion, migration and adhesion of tumor cells. Notably, MIP therapy was found to be effectively reducing the metastatic burden in murine model of melanoma. Molecular characterization of MIP treated tumor cells substantiated that MIP upregulates the PPARγ expression within the tumor cells, which attenuates the NFκB/p65 levels within the nucleus, resulting in the suppression of Mmp9 expression in tumor cells. Besides that, MIP also downregulated the surface expression of chemokine receptor CXCR4 in murine melanoma cells, where chromatin immunoprecipitation confirmed the impeded recruitment of p50 and c-Rel factors to the Cxcr4 promoter, resulting in its downregulation transcriptionally. Taken together, MIP suppressed the dissemination of tumor cells in vivo, by regulating the expression of MMP9 and CXCR4 on these cells.
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Affiliation(s)
- Anush Chakraborty
- Product Development Cell-I, National Institute of Immunology, New Delhi, India
| | - Gargi Roy
- Product Development Cell-I, National Institute of Immunology, New Delhi, India
| | - Farheen Fatima
- Product Development Cell-I, National Institute of Immunology, New Delhi, India
| | - Bharati Swami
- Product Development Cell-I, National Institute of Immunology, New Delhi, India
| | - Sangeeta Bhaskar
- Product Development Cell-I, National Institute of Immunology, New Delhi, India.
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33
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Ueda S, Mizuta H, Uji T. Development of Chromatin Immunoprecipitation for the Analysis of Histone Modifications in Red Macroalga Neopyropia yezoensis (Rhodophyta). Mol Biotechnol 2023; 65:590-597. [PMID: 36098867 DOI: 10.1007/s12033-022-00562-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Epigenetic regulation by histone modification can activate or repress transcription through changes in chromatin dynamics and regulates development and the response to environmental signals in both animals and plants. Chromatin immunoprecipitation (ChIP) is an indispensable tool to identify histones with specific post-translational modifications. The lack of a ChIP technique for macroalgae has hindered understanding of the role of histone modification in the expression of genes in this organism. In this study, a ChIP method with several modifications, based on existing protocols for plant cells, has been developed for the red macroalga, Neopyropia yezoensis, that consists of a heterogeneous alternation of macroscopic leaf-like gametophytes and microscopic filamentous sporophytes. ChIP method coupled with qPCR enables the identification of a histone mark in generation-specific genes from N. yezoensis. The results indicate that acetylation of histone H3 at lysine 9 in the 5' flanking and coding regions from generation-specific genes was maintained at relatively high levels, even in generation-repressed gene expression. The use of this ChIP method will contribute significantly to identify the epigenetic regulatory mechanisms through histone modifications that control a variety of biological processes in red macroalgae.
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Affiliation(s)
- Shinnosuke Ueda
- Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan
| | - Hiroyuki Mizuta
- Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan
| | - Toshiki Uji
- Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan.
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Nguyen BD, Stevens BL, Elson DJ, Finlay D, Gamble J, Kopparapu P, Tanguay RL, Buermeyer AB, Kerkvliet NI, Kolluri SK. 11-Cl-BBQ, a select modulator of AhR-regulated transcription, suppresses lung cancer cell growth via activation of p53 and p27 Kip1. FEBS J 2023; 290:2064-2084. [PMID: 36401795 PMCID: PMC10807707 DOI: 10.1111/febs.16683] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/01/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor and functions as a tumour suppressor in different cancer models. In the present study, we report detailed characterization of 11-chloro-7H-benzimidazo[2,1-a]benzo[de]iso-quinolin-7-one (11-Cl-BBQ) as a select modulator of AhR-regulated transcription (SMAhRT) with anti-cancer actions. Treatment of lung cancer cells with 11-Cl-BBQ induced potent and sustained AhR-dependent anti-proliferative effects by promoting G1 phase cell cycle arrest. Investigation of 11-Cl-BBQ-induced transcription in H460 cells with or without the AhR expression by RNA-sequencing revealed activation of p53 signalling. In addition, 11-Cl-BBQ suppressed multiple pathways involved in DNA replication and increased expression of cyclin-dependent kinase inhibitors, including p27Kip1 , in an AhR-dependent manner. CRISPR/Cas9 knockout of individual genes revealed the requirement for both p53 and p27Kip1 for the AhR-mediated anti-proliferative effects. Our results identify 11-Cl-BBQ as a potential lung cancer therapeutic, highlight the feasibility of targeting AhR and provide important mechanistic insights into AhR-mediated-anticancer actions.
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Affiliation(s)
- Bach D. Nguyen
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Brenna L. Stevens
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Daniel J. Elson
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John Gamble
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Prasad Kopparapu
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Robyn L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- The Pacific Northwest Center for Translational Environmental Health Research, Oregon State University, Corvallis, OR, 97331, USA
| | - Andrew B. Buermeyer
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Nancy I. Kerkvliet
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Siva K. Kolluri
- Cancer Research Laboratory, Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- The Pacific Northwest Center for Translational Environmental Health Research, Oregon State University, Corvallis, OR, 97331, USA
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Gleneadie HJ, Fernandez-Ruiz B, Sardini A, Van de Pette M, Dimond A, Prinjha RK, McGinty J, French PMW, Bagci H, Merkenschlager M, Fisher AG. Endogenous bioluminescent reporters reveal a sustained increase in utrophin gene expression upon EZH2 and ERK1/2 inhibition. Commun Biol 2023; 6:318. [PMID: 36966198 PMCID: PMC10039851 DOI: 10.1038/s42003-023-04666-9] [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: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked disorder caused by loss of function mutations in the dystrophin gene (Dmd), resulting in progressive muscle weakening. Here we modelled the longitudinal expression of endogenous Dmd, and its paralogue Utrn, in mice and in myoblasts by generating bespoke bioluminescent gene reporters. As utrophin can partially compensate for Dmd-deficiency, these reporters were used as tools to ask whether chromatin-modifying drugs can enhance Utrn expression in developing muscle. Myoblasts treated with different PRC2 inhibitors showed significant increases in Utrn transcripts and bioluminescent signals, and these responses were independently verified by conditional Ezh2 deletion. Inhibition of ERK1/2 signalling provoked an additional increase in Utrn expression that was also seen in Dmd-mutant cells, and maintained as myoblasts differentiate. These data reveal PRC2 and ERK1/2 to be negative regulators of Utrn expression and provide specialised molecular imaging tools to monitor utrophin expression as a therapeutic strategy for DMD.
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Affiliation(s)
- Hannah J Gleneadie
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Beatriz Fernandez-Ruiz
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging Facility, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Mathew Van de Pette
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Rab K Prinjha
- Immunology and Epigenetics Research Unit, Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - James McGinty
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ, UK
| | - Hakan Bagci
- Lymphocyte Development Group, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK.
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36
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Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533031. [PMID: 36993219 PMCID: PMC10055122 DOI: 10.1101/2023.03.16.533031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or "omes," measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen repositories. However, these biospecimens have been underutilized for multi-omic analysis due to the low throughput of current analytical technologies that impede large-scale studies. Methods Tissue sampling, preparation, and downstream analysis were integrated into a 96-well format multi-omics workflow, MultiomicsTracks96. Frozen mouse organs were sampled using the CryoGrid system, and matched FFPE samples were processed using a microtome. The 96-well format sonicator, PIXUL, was adapted to extract DNA, RNA, chromatin, and protein from tissues. The 96-well format analytical platform, Matrix, was used for chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), methylated RNA immunoprecipitation (MeRIP), and RNA reverse transcription (RT) assays followed by qPCR and sequencing. LC-MS/MS was used for protein analysis. The Segway genome segmentation algorithm was used to identify functional genomic regions, and linear regressors based on the multi-omics data were trained to predict protein expression. Results MultiomicsTracks96 was used to generate 8-dimensional datasets including RNA-seq measurements of mRNA expression; MeRIP-seq measurements of m6A and m5C; ChIP-seq measurements of H3K27Ac, H3K4m3, and Pol II; MeDIP-seq measurements of 5mC; and LC-MS/MS measurements of proteins. We observed high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles (ChIP-seq: H3K27Ac, H3K4m3, Pol II; MeDIP-seq: 5mC) was able to recapitulate and predict organ-specific super-enhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic expression profiles can be more accurately predicted by the full suite of multi-omics data, compared to using epigenomic, transcriptomic, or epitranscriptomic measurements individually. Conclusions The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies - for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.
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Fedorova V, Amruz Cerna K, Oppelt J, Pospisilova V, Barta T, Mraz M, Bohaciakova D. MicroRNA Profiling of Self-Renewing Human Neural Stem Cells Reveals Novel Sets of Differentially Expressed microRNAs During Neural Differentiation In Vitro. Stem Cell Rev Rep 2023:10.1007/s12015-023-10524-2. [PMID: 36918496 PMCID: PMC10366325 DOI: 10.1007/s12015-023-10524-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
The involvement of microRNAs (miRNAs) in orchestrating self-renewal and differentiation of stem cells has been revealed in a number of recent studies. And while in human pluripotent stem cells, miRNAs have been directly linked to the core pluripotency network, including the cell cycle regulation and the maintenance of the self-renewing capacity, their role in the onset of differentiation in other contexts, such as determination of neural cell fate, remains poorly described. To bridge this gap, we used three model cell types to study miRNA expression patterns: human embryonic stem cells (hESCs), hESCs-derived self-renewing neural stem cells (NSCs), and differentiating NSCs. The comprehensive miRNA profiling presented here reveals novel sets of miRNAs differentially expressed during human neural cell fate determination in vitro. Furthermore, we report a miRNA expression profile of self-renewing human NSCs, which has been lacking to this date. Our data also indicates that miRNA clusters enriched in NSCs share the target-determining seed sequence with cell cycle regulatory miRNAs expressed in pluripotent hESCs. Lastly, our mechanistic experiments confirmed that cluster miR-17-92, one of the NSCs-enriched clusters, is directly transcriptionally regulated by transcription factor c-MYC.
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Affiliation(s)
- Veronika Fedorova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Amruz Cerna
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Veronika Pospisilova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic.
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Zhang Z, Wang X, Hamdan FH, Likhobabina A, Patil S, Aperdannier L, Sen M, Traub J, Neesse A, Fischer A, Papantonis A, Singh SK, Ellenrieder V, Johnsen SA, Hessmann E. NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming. Cell Mol Gastroenterol Hepatol 2023; 15:1219-1246. [PMID: 36758798 PMCID: PMC10064440 DOI: 10.1016/j.jcmgh.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND & AIMS Loss of AT-rich interactive domain-containing protein 1A (ARID1A) fosters acinar-to-ductal metaplasia (ADM) and pancreatic carcinogenesis by down-regulating transcription programs controlling acinar cell identity. However, how ARID1A reacts to metaplasia-triggering environmental cues remains elusive. Here, we aimed to elucidate the role of ARID1A in controlling ductal pancreatic gene signatures and deciphering hierarchical signaling cues determining ARID1A-dependent chromatin regulation during acinar cell reprogramming. METHODS Acinar cell explants with differential ARID1A status were subjected to genome-wide expression analyses. The impact of epidermal growth factor receptor (EGFR) signaling, NFATc1 activity, and ARID1A status on acinar reprogramming processes were characterized by ex vivo ADM assays and transgenic mouse models. EGFR-dependent ARID1A chromatin binding was studied by chromatin immunoprecipitation sequencing analysis and cellular fractionation. RESULTS EGFR signaling interferes with ARID1A-dependent transcription by inducing genome-wide ARID1A displacement, thereby phenocopying ARID1A loss-of-function mutations and inducing a shift toward ADM permissive ductal transcription programs. Moreover, we show that EGFR signaling is required to push ARID1A-deficient acinar cells toward a metaplastic phenotype. Mechanistically, we identified the transcription factor nuclear factor of activated T cells 1 (NFATc1) as the central regulatory hub mediating both EGFR signaling-induced genomic ARID1A displacement and the induction of ADM-promoting gene signatures in the absence of ARID1A. Consequently, pharmacologic inhibition of NFATc1 or its depletion in transgenic mice not only preserves genome-wide ARID1A occupancy, but also attenuates acinar metaplasia led by ARID1A loss. CONCLUSIONS Our data describe an intimate relationship between environmental signaling and chromatin remodeling in orchestrating cell fate decisions in the pancreas, and illustrate how ARID1A loss influences transcriptional regulation in acinar cell reprogramming.
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Affiliation(s)
- Zhe Zhang
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany
| | - Xin Wang
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Feda H Hamdan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany; Gene Regulatory Mechanisms and Molecular Epigenetics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Anna Likhobabina
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany
| | - Shilpa Patil
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany
| | - Lena Aperdannier
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany
| | - Madhobi Sen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jacobe Traub
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Albrecht Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany; Clinical Research Unit 5002, University Medical Center Göttingen, Göttingen, Germany
| | - André Fischer
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases, Göttingen, Germany; Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Argyris Papantonis
- Clinical Research Unit 5002, University Medical Center Göttingen, Göttingen, Germany; Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Shiv K Singh
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany; Clinical Research Unit 5002, University Medical Center Göttingen, Göttingen, Germany
| | - Volker Ellenrieder
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany; Clinical Research Unit 5002, University Medical Center Göttingen, Göttingen, Germany; Comprehensive Cancer Center Lower Saxony, Hannover Medical School, Hannover, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany; Gene Regulatory Mechanisms and Molecular Epigenetics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Elisabeth Hessmann
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany; Clinical Research Unit 5002, University Medical Center Göttingen, Göttingen, Germany; Comprehensive Cancer Center Lower Saxony, Hannover Medical School, Hannover, Germany.
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Caratti G, Desgeorges T, Juban G, Stifel U, Fessard A, Koenen M, Caratti B, Théret M, Skurk C, Chazaud B, Tuckermann JP, Mounier R. Macrophagic AMPKα1 orchestrates regenerative inflammation induced by glucocorticoids. EMBO Rep 2023; 24:e55363. [PMID: 36520372 PMCID: PMC9900347 DOI: 10.15252/embr.202255363] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Macrophages are key cells after tissue damage since they mediate both acute inflammatory phase and regenerative inflammation by shifting from pro-inflammatory to restorative cells. Glucocorticoids (GCs) are the most potent anti-inflammatory hormone in clinical use, still their actions on macrophages are not fully understood. We show that the metabolic sensor AMP-activated protein kinase (AMPK) is required for GCs to induce restorative macrophages. GC Dexamethasone activates AMPK in macrophages and GC receptor (GR) phosphorylation is decreased in AMPK-deficient macrophages. Loss of AMPK in macrophages abrogates the GC-induced acquisition of their repair phenotype and impairs GC-induced resolution of inflammation in vivo during post-injury muscle regeneration and acute lung injury. Mechanistically, two categories of genes are impacted by GC treatment in macrophages. Firstly, canonical cytokine regulation by GCs is not affected by AMPK loss. Secondly, AMPK-dependent GC-induced genes required for the phenotypic transition of macrophages are co-regulated by the transcription factor FOXO3, an AMPK substrate. Thus, beyond cytokine regulation, GR requires AMPK-FOXO3 for immunomodulatory actions in macrophages, linking their metabolic status to transcriptional control in regenerative inflammation.
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Affiliation(s)
- Giorgio Caratti
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Thibaut Desgeorges
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Gaëtan Juban
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Ulrich Stifel
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Aurélie Fessard
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Mascha Koenen
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
- Present address:
Laboratory of Molecular MetabolismThe Rockefeller UniversityNew YorkNYUSA
| | - Bozhena Caratti
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Marine Théret
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
- Present address:
Department of Medical GeneticsSchool of Biomedical Engineering and the Biomedical Research CentreVancouverBCCanada
| | - Carsten Skurk
- Department of CardiologyCharité Universitätsmedizin BerlinBerlinGermany
- Franklin/German Centre for Cardiovascular Research (DZHK), Partner Site Berlin/Institute of Health (BIH)BerlinGermany
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Jan P Tuckermann
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Rémi Mounier
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
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40
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Chen K, Dai M, Luo Q, Wang Y, Shen W, Liao Y, Zhou Y, Cheng W. PARP1 controls the transcription of CD24 by ADP-ribosylating the RNA helicase DDX5 in pancreatic cancer. Int J Biochem Cell Biol 2023; 155:106358. [PMID: 36584909 DOI: 10.1016/j.biocel.2022.106358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/11/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
The PARP1 protein plays a key role in DNA damage repair and ADP-ribosylation to regulate gene expression. Strategies to target PARP1 have rapidly been developed for cancer treatment. However, the role of the innate immune response in targeted anti-PARP1 therapy remains poorly understood. In this work, we aimed to elucidate the regulatory mechanism underlying the immunogenicity of PARP1 and explore efficient therapeutic strategies to enhance the antitumor effect of PARP inhibitors. The relationships between PARP1 expression and immunosuppressive factors were examined by qRTPCR and immunoblot analysis. DNA pull-down, chromatin immunoprecipitation-quantitative PCR (ChIPqPCR) and luciferase reporter assays were employed to reveal the mechanism by which the expression of the immune checkpoint regulator CD24 is regulated by PARP1. Phagocytosis assays and pancreatic cancer animal models were applied to evaluate the therapeutic effect of simultaneous disruption of PARP1 and the antiphagocytic factor CD24. Upregulation of the innate immunosuppressive factor CD24 was observed in pancreatic cancer during PARP1 inhibition. The activating effect of targeting CD24 on macrophage phagocytosis was verified. Then, we showed that PARP1 attenuated the transcription of CD24 by ADP-ribosylating the transcription factor DDX5 in pancreatic cancer. Combined blockade of PARP1 and the antiphagocytic factor CD24 elicited a synergetic antitumor effect in pancreatic cancer. Our research provided evidence that combination treatment with PARP inhibitors and CD24 blocking monoclonal antibodies (mAbs) could be an effective strategy to improve the clinical therapeutic response in pancreatic cancer.
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Affiliation(s)
- Kang Chen
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China; Translational Medicine Laboratory of Pancreas Disease of Hunan Normal University, Changsha 410005, Hunan Province, China
| | - Manxiong Dai
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China; Translational Medicine Laboratory of Pancreas Disease of Hunan Normal University, Changsha 410005, Hunan Province, China
| | - Quanneng Luo
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China; Translational Medicine Laboratory of Pancreas Disease of Hunan Normal University, Changsha 410005, Hunan Province, China
| | - Yi Wang
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China; Translational Medicine Laboratory of Pancreas Disease of Hunan Normal University, Changsha 410005, Hunan Province, China
| | - Weitao Shen
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yan Liao
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China; Translational Medicine Laboratory of Pancreas Disease of Hunan Normal University, Changsha 410005, Hunan Province, China
| | - Yiying Zhou
- Department of Clinical Pathology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China
| | - Wei Cheng
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha 410005, Hunan Province, China; Xiangyue Hospital Affiliated to Hunan Institute of Parasitic Diseases, National Clinical Center for Schistosomiasis Treatment, Yueyang 414000, Hunan Province, China; Translational Medicine Laboratory of Pancreas Disease of Hunan Normal University, Changsha 410005, Hunan Province, China.
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41
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Weber LM, Jia Y, Stielow B, Gisselbrecht S, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forné I, Nist A, Stiewe T, Bulyk M, Wang Z, Liefke R. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Res 2023; 51:574-594. [PMID: 36537216 PMCID: PMC9881136 DOI: 10.1093/nar/gkac1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.
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Affiliation(s)
- Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Yulin Jia
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yinghua Cao
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Jessica King
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Martinsried 82152, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
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42
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Liu B, Liu R, Li W, Mao X, Li Y, Huang T, Wang H, Chen H, Zhong J, Yang B, Chai R, Cao Q, Jin J, Li Y. XAF1 prevents hyperproduction of type I interferon upon viral infection by targeting IRF7. EMBO Rep 2023; 24:e55387. [PMID: 36394357 PMCID: PMC9827551 DOI: 10.15252/embr.202255387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/18/2022] Open
Abstract
Interferon regulatory factor (IRF) 3 and IRF7 are master regulators of type I interferon (IFN-I)-dependent antiviral innate immunity. Upon viral infection, a positive feedback loop is formed, wherein IRF7 promotes further induction of IFN-I in the later stage. Thus, it is critical to maintain a suitably low level of IRF7 to avoid the hyperproduction of IFN-I. In this study, we find that early expression of IFN-I-dependent STAT1 promotes the expression of XAF1 and that XAF1 is associated specifically with IRF7 and inhibits the activity of XIAP. XAF1-knockout and XIAP-transgenic mice display resistance to viral infection, and this resistance is accompanied by increases in IFN-I production and IRF7 stability. Mechanistically, we find that the XAF1-XIAP axis controls the activity of KLHL22, an adaptor of the BTB-CUL3-RBX1 E3 ligase complex through a ubiquitin-dependent pathway. CUL3-KLHL22 directly targets IRF7 and catalyzes its K48-linked ubiquitination and proteasomal degradation. These findings reveal unexpected functions of the XAF1-XIAP axis and KLHL22 in the regulation of IRF7 stability and highlight an important target for antiviral innate immunity.
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Affiliation(s)
- Bao‐qin Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Rong‐bei Liu
- Sir Run Run Shaw HospitalCollege of Medicine Zhejiang UniversityHangzhouChina
| | - Wen‐ping Li
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Xin‐tao Mao
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Yi‐ning Li
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Tao Huang
- Sir Run Run Shaw HospitalCollege of Medicine Zhejiang UniversityHangzhouChina
| | - Hao‐li Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Hao‐tian Chen
- Sir Run Run Shaw HospitalCollege of Medicine Zhejiang UniversityHangzhouChina
| | - Jiang‐yan Zhong
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Bing Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
| | - Ren‐jie Chai
- State Key Laboratory of BioelectronicsDepartment of Otolaryngology Head and Neck SurgeryZhongda Hospital, School of Life Sciences and TechnologyAdvanced Institute for Life and HealthJiangsu Province High‐Tech Key Laboratory for Bio‐Medical ResearchSoutheast UniversityNanjingChina
| | - Qian Cao
- Sir Run Run Shaw HospitalCollege of Medicine Zhejiang UniversityHangzhouChina
| | - Jin Jin
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
- Sir Run Run Shaw HospitalCollege of Medicine Zhejiang UniversityHangzhouChina
| | - Yi‐yuan Li
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences InstituteZhejiang UniversityHangzhouChina
- State Key Laboratory of BioelectronicsDepartment of Otolaryngology Head and Neck SurgeryZhongda Hospital, School of Life Sciences and TechnologyAdvanced Institute for Life and HealthJiangsu Province High‐Tech Key Laboratory for Bio‐Medical ResearchSoutheast UniversityNanjingChina
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Wang Z, Tao T, Tao Y. ChIP and ChIRP Assays in Ferroptosis. Methods Mol Biol 2023; 2712:19-27. [PMID: 37578693 DOI: 10.1007/978-1-0716-3433-2_3] [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] [Indexed: 08/15/2023]
Abstract
Ferroptosis is characterized by the accumulation of lipid peroxidation driven by iron. As a regulated cell death, ferroptosis plays a critical role in various diseases and exhibits great therapeutic potentials. However, the mechanisms underlying ferroptosis, including its occurrence, execution, and regulation, remain poorly understood, which is necessary for developing effective therapeutic strategies. In this chapter, we summarize chromatin immunoprecipitation (ChIP) assay for the research of proteins-chromatin interactions. Moreover, Chromatin Isolation by RNA Purification (ChIRP) trial is introduced to investigate the interactions between lncRNA and chromatin. The application of ChIP and ChIRP is expected to explore the transcription and epigenetic regulation of ferroptosis deeply for therapeutic benefits.
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Affiliation(s)
- Zuli Wang
- Center for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, Guizhou, China
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tania Tao
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Yongguang Tao
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China.
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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44
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Feng R, Kan K, Sticht C, Li Y, Wang S, Liu H, Shao C, Munker S, Niess H, Wang S, Meyer C, Liebe R, Ebert MP, Dooley S, Ding H, Weng H. A hierarchical regulatory network ensures stable albumin transcription under various pathophysiological conditions. Hepatology 2022; 76:1673-1689. [PMID: 35257388 DOI: 10.1002/hep.32414] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/04/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS It remains unknown how patients with liver failure maintain essential albumin levels. Here, we delineate a hierarchical transcription regulatory network that ensures albumin expression under different disease conditions. APPROACH AND RESULTS We examined albumin levels in liver tissues and serum in 157 patients, including 84 with HCC, 38 decompensated cirrhosis, and 35 acute liver failure. Even in patients with liver failure, the average serum albumin concentrations were 30.55 g/L. In healthy subjects and patients with chronic liver diseases, albumin was expressed in hepatocytes. In patients with massive hepatocyte loss, albumin was expressed in liver progenitor cells (LPCs). The albumin gene (ALB) core promoter possesses a TATA box and nucleosome-free area, which allows constitutive RNA polymerase II binding and transcription initiation. Chromatin immunoprecipitation assays revealed that hepatocyte nuclear factor 4 alpha (HNF4α), CCAAT/enhancer-binding protein alpha (C/EBPα), and forkhead box A2 (FOXA2) bound to the ALB enhancer. Knockdown of either of these factors reduced albumin expression in hepatocytes. FOXA2 acts as a pioneer factor to support HNF4α and C/EBPα. In hepatocytes lacking HNF4α and C/EBPα expression, FOXA2 synergized with retinoic acid receptor (RAR) to maintain albumin transcription. RAR nuclear translocation was induced by retinoic acids released by activated HSCs. In patients with massive hepatocyte loss, LPCs expressed HNF4α and FOXA2. RNA sequencing and quantitative PCR analyses revealed that lack of HNF4α and C/EBPα in hepatocytes increased hedgehog ligand biosynthesis. Hedgehog up-regulates FOXA2 expression through glioblastoma family zinc finger 2 binding to the FOXA2 promoter in both hepatocytes and LPCs. CONCLUSIONS A hierarchical regulatory network formed by master and pioneer transcription factors ensures essential albumin expression in various pathophysiological conditions.
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Affiliation(s)
- Rilu Feng
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Kejia Kan
- Department of SurgeryMedical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Carsten Sticht
- NGS Core FacilityMedical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Yujia Li
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Shanshan Wang
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany.,Beijing Institute of HepatologyBeijing You'an HospitalCapital Medical UniversityBeijingChina
| | - Hui Liu
- Department of PathologyBeijing You'an HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Chen Shao
- Department of PathologyBeijing You'an HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Stefan Munker
- Department of Medicine IIUniversity HospitalLudwig-Maximilians-University MunichMunichGermany.,Liver Centre MunichUniversity HospitalLudwig-Maximilians-UniversityMunichGermany
| | - Hanno Niess
- Department of General, Visceral, and Transplant SurgeryLudwig-Maximilians-University MunichMunichGermany.,Biobank of the Department of GeneralVisceral and Transplant SurgeryLudwig-Maximilians-UniversityMunichGermany
| | - Sai Wang
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Christoph Meyer
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Roman Liebe
- Clinic of Gastroenterology, Hepatology and Infectious DiseasesHeinrich Heine UniversityDüsseldorfGermany.,Department of Medicine IISaarland University Medical CenterSaarland UniversityHomburgGermany
| | - Matthias P Ebert
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty MannheimHeidelberg UniversityMannheimGermany.,Clinical Cooperation Unit Healthy MetabolismCenter of Preventive Medicine and Digital HealthMedical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Steven Dooley
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Huiguo Ding
- Department of Gastroenterology and HepatologyBeijing You'an HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Honglei Weng
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
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45
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Histone deacetylase inhibitors improve antisense-mediated exon-skipping efficacy in mdx mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:606-620. [PMID: 36514350 PMCID: PMC9722397 DOI: 10.1016/j.omtn.2022.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Antisense-mediated exon skipping is one of the most promising therapeutic strategies for Duchenne muscular dystrophy (DMD), and some antisense oligonucleotide (ASO) drugs have already been approved by the US FDA despite their low efficacy. The potential of this therapy is still limited by several challenges, including the reduced expression of the dystrophin transcript and the strong 5'-3' imbalance in mutated transcripts. We therefore hypothesize that increasing histone acetylation using histone deacetylase inhibitors (HDACi) could correct the transcript imbalance, offering more available pre-mRNA target and ultimately increasing dystrophin rescue. Here, we evaluated the impact of such a combined therapy on the Dmd transcript imbalance phenomenon and on dystrophin restoration levels in mdx mice. Analysis of the Dmd transcript levels at different exon-exon junctions revealed a tendency to correct the 5'-3' imbalance phenomenon following treatment with HDACi. Significantly higher levels of dystrophin restoration (up to 74% increase) were obtained with givinostat and valproic acid compared with mice treated with ASO alone. Additionally, we demonstrate an increase in H3K9 acetylation in human myocytes after treatment with valproic acid. These findings indicate that HDACi can improve the therapeutic potential of exon-skipping approaches, offering promising perspectives for the treatment of DMD.
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Zhang Y, Sun C, Li Y, Qin J, Amancherla K, Jing Y, Hu Q, Liang K, Zhang Z, Ye Y, Huang LA, Nguyen TK, Egranov SD, Zhao Z, Wu A, Xi Y, Yao J, Hung MC, Calin GA, Cheng J, Lim B, Lehmann LH, Salem JE, Johnson DB, Curran MA, Yu D, Han L, Darabi R, Yang L, Moslehi JJ, Lin C. Hormonal therapies up-regulate MANF and overcome female susceptibility to immune checkpoint inhibitor myocarditis. Sci Transl Med 2022; 14:eabo1981. [PMID: 36322628 PMCID: PMC9809130 DOI: 10.1126/scitranslmed.abo1981] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Immune checkpoint inhibitors (ICIs) have been increasingly used in combination for cancer treatment but are associated with myocarditis. Here, we report that tumor-bearing mice exhibited response to treatment with combinatorial anti-programmed cell death 1 and anti-cytotoxic T lymphocyte antigen-4 antibodies but also presented with cardiovascular toxicities observed clinically with ICI therapy, including myocarditis and arrhythmia. Female mice were preferentially affected with myocarditis compared to male mice, consistent with a previously described genetic model of ICI myocarditis and emerging clinical data. Mechanistically, myocardial tissue from ICI-treated mice, the genetic mouse model, and human heart tissue from affected patients with ICI myocarditis all exhibited down-regulation of MANF (mesencephalic astrocyte-derived neurotrophic factor) and HSPA5 (heat shock 70-kDa protein 5) in the heart; this down-regulation was particularly notable in female mice. ICI myocarditis was amplified by heart-specific genetic deletion of mouse Manf and was attenuated by administration of recombinant MANF protein, suggesting a causal role. Ironically, both MANF and HSPA5 were transcriptionally induced by liganded estrogen receptor β and inhibited by androgen receptor. However, ICI treatment reduced serum estradiol concentration to a greater extent in female compared to male mice. Treatment with an estrogen receptor β-specific agonist and androgen depletion therapy attenuated ICI-associated cardiac effects. Together, our data suggest that ICI treatment inhibits estradiol-dependent expression of MANF/HSPA5 in the heart, curtailing the cardiomyocyte response to immune injury. This endocrine-cardiac-immune pathway offers new insights into the mechanisms of sex differences in cardiac disease and may offer treatment strategies for ICI myocarditis.
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Affiliation(s)
- Yaohua Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, 10069, China.,Corresponding author. (Y.Z.); (L.Y.); (J.J.M.); and (C.L.)
| | - Chengcao Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Current address: Incyte Corporation, Wilmington, DE 19803, USA
| | - Juan Qin
- Section of Cardio-Oncology & Immunology, Division of Cardiology and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kaushik Amancherla
- Department of Medicine, Vanderbilt University of Medical Center, Nashville, TN 37232
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Current address: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China
| | - Ke Liang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Lisa A. Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tina K. Nguyen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sergey D. Egranov
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zilong Zhao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andrew Wu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yutao Xi
- Texas Heart Institute, St. Luke’s Hospital, Houston, TX 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan.,Department of Biotechnology, Asia University, Taichung 413, Taiwan
| | - George A. Calin
- Department of Experimental Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jie Cheng
- Texas Heart Institute, St. Luke’s Hospital, Houston, TX 77030, USA
| | - Bora Lim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lorenz H. Lehmann
- Department of Cardiology, Heidelberg University Hospital, Heidelberg, Germany; Cardio-Oncology Unit, Heidelberg University Hospital, Heidelberg, Germany; German Cardiovascular Research Center (DZHK), partner site Heidelberg/Mannheim, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joe-Elie Salem
- Deprtment of Pharmacology, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, INSERM, CIC-1901, UNICO-GRECO Cardiooncology Program, Paris, France
| | - Douglas B. Johnson
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Michael A. Curran
- Department of Immunology and Scientific Director of the Oncology Research for Biologics and Immunotherapy Translation (ORBIT), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dihua Yu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Corresponding author. (Y.Z.); (L.Y.); (J.J.M.); and (C.L.)
| | - Javid J. Moslehi
- Section of Cardio-Oncology & Immunology, Division of Cardiology and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94143, USA,Corresponding author. (Y.Z.); (L.Y.); (J.J.M.); and (C.L.)
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Corresponding author. (Y.Z.); (L.Y.); (J.J.M.); and (C.L.)
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Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P. Tra1 controls the transcriptional landscape of the aging cell. G3 (BETHESDA, MD.) 2022; 13:6782959. [PMID: 36315064 PMCID: PMC9836359 DOI: 10.1093/g3journal/jkac287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
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Affiliation(s)
- Khaleda Afrin Bari
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Present address for Matthew D Berg: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada,Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Corresponding author: Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada.
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48
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Li S, Mirlekar B, Johnson BM, Brickey WJ, Wrobel JA, Yang N, Song D, Entwistle S, Tan X, Deng M, Cui Y, Li W, Vincent BG, Gale M, Pylayeva-Gupta Y, Ting JPY. STING-induced regulatory B cells compromise NK function in cancer immunity. Nature 2022; 610:373-380. [PMID: 36198789 PMCID: PMC9875944 DOI: 10.1038/s41586-022-05254-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
An immunosuppressive tumour microenvironment is a major obstacle in the control of pancreatic and other solid cancers1-3. Agonists of the stimulator of interferon genes (STING) protein trigger inflammatory innate immune responses to potentially overcome tumour immunosuppression4. Although these agonists hold promise as potential cancer therapies5, tumour resistance to STING monotherapy has emerged in clinical trials and the mechanism(s) is unclear5-7. Here we show that the administration of five distinct STING agonists, including cGAMP, results in an expansion of human and mouse interleukin (IL)-35+ regulatory B cells in pancreatic cancer. Mechanistically, cGAMP drives expression of IL-35 by B cells in an IRF3-dependent but type I interferon-independent manner. In several preclinical cancer models, the loss of STING signalling in B cells increases tumour control. Furthermore, anti-IL-35 blockade or genetic ablation of IL-35 in B cells also reduces tumour growth. Unexpectedly, the STING-IL-35 axis in B cells reduces proliferation of natural killer (NK) cells and attenuates the NK-driven anti-tumour response. These findings reveal an intrinsic barrier to systemic STING agonist monotherapy and provide a combinatorial strategy to overcome immunosuppression in tumours.
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Affiliation(s)
- Sirui Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bhalchandra Mirlekar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brandon M Johnson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W June Brickey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John A Wrobel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Na Yang
- Functional Epigenomics Unit (HNN-2G5), National Institute on Aging, Bethesda, MD, USA
| | - Dingka Song
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meng Deng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA
| | - Yuliya Pylayeva-Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jenny P-Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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49
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Balance between immunoregulatory B cells and plasma cells drives pancreatic tumor immunity. Cell Rep Med 2022; 3:100744. [PMID: 36099917 PMCID: PMC9512696 DOI: 10.1016/j.xcrm.2022.100744] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 06/30/2022] [Accepted: 08/23/2022] [Indexed: 12/15/2022]
Abstract
Plasma cell responses are associated with anti-tumor immunity and favorable response to immunotherapy. B cells can amplify anti-tumor immune responses through antibody production; yet B cells in patients and tumor-bearing mice often fail to support this effector function. We identify dysregulated transcriptional program in B cells that disrupts differentiation of naive B cells into anti-tumor plasma cells. The signaling network contributing to this dysfunction is driven by interleukin (IL) 35 stimulation of a STAT3-PAX5 complex that upregulates the transcriptional regulator BCL6 in naive B cells. Transient inhibition of BCL6 in tumor-educated naive B cells is sufficient to reverse the dysfunction in B cell differentiation, stimulating the intra-tumoral accumulation of plasma cells and effector T cells and rendering pancreatic tumors sensitive to anti-programmed cell death protein 1 (PD-1) blockade. Our findings argue that B cell effector dysfunction in cancer can be due to an active systemic suppression program that can be targeted to synergize with T cell-directed immunotherapy. Balance between regulatory B cells and plasma cells shapes pancreatic tumor growth Cancer primes naive B cells toward regulatory B cell differentiation IL-35 drives B cell reprogramming via formation of a pSTAT3-Pax5 complex IL-35/BCL6 blockade in naive B cells enhances αPD1 efficacy
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50
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Wiegreffe C, Wahl T, Joos NS, Bonnefont J, Liu P, Britsch S. Developmental cell death of cortical projection neurons is controlled by a Bcl11a/Bcl6‐dependent pathway. EMBO Rep 2022; 23:e54104. [PMID: 35766181 PMCID: PMC9346488 DOI: 10.15252/embr.202154104] [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: 10/06/2021] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 12/05/2022] Open
Abstract
Developmental neuron death plays a pivotal role in refining organization and wiring during neocortex formation. Aberrant regulation of this process results in neurodevelopmental disorders including impaired learning and memory. Underlying molecular pathways are incompletely determined. Loss of Bcl11a in cortical projection neurons induces pronounced cell death in upper‐layer cortical projection neurons during postnatal corticogenesis. We use this genetic model to explore genetic mechanisms by which developmental neuron death is controlled. Unexpectedly, we find Bcl6, previously shown to be involved in the transition of cortical neurons from progenitor to postmitotic differentiation state to provide a major checkpoint regulating neuron survival during late cortical development. We show that Bcl11a is a direct transcriptional regulator of Bcl6. Deletion of Bcl6 exerts death of cortical projection neurons. In turn, reintroduction of Bcl6 into Bcl11a mutants prevents induction of cell death in these neurons. Together, our data identify a novel Bcl11a/Bcl6‐dependent molecular pathway in regulation of developmental cell death during corticogenesis.
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Affiliation(s)
| | - Tobias Wahl
- Institute of Molecular and Cellular Anatomy Ulm University Ulm Germany
| | | | - Jerome Bonnefont
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI) Université Libre de Bruxelles (ULB) Brussels Belgium
- VIB‐KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neuroscience Leuven Brain Institute Leuven Belgium
| | - Pentao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine The University of Hong Kong Hong Kong China
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy Ulm University Ulm Germany
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