1
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Melnick AF, Mullin C, Lin K, McCarter AC, Liang S, Liu YE, Wang Q, Jerome NA, Choe E, Kunnath N, Bodanapu G, Akter F, Magnuson B, Kumar S, Lombard DB, Muntean AG, Ljungman M, Sekiguchi J, Ryan RJH, Chiang MY. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. Blood 2023; 142:2159-2174. [PMID: 37616559 PMCID: PMC10733839 DOI: 10.1182/blood.2023020144] [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: 02/16/2023] [Revised: 07/13/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
ABSTRACT Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL), but pan-Notch inhibitors showed excessive toxicity in clinical trials. To find alternative ways to target Notch signals, we investigated cell division cycle 73 (Cdc73), which is a Notch cofactor and key component of the RNA polymerase-associated transcriptional machinery, an emerging target in T-ALL. Although we confirmed previous work that CDC73 interacts with NOTCH1, we also found that the interaction in T-ALL was context-dependent and facilitated by the transcription factor ETS1. Using mouse models, we showed that Cdc73 is important for Notch-induced T-cell development and T-ALL maintenance. Mechanistically, chromatin and nascent gene expression profiling showed that Cdc73 intersects with Ets1 and Notch at chromatin within enhancers to activate expression of known T-ALL oncogenes through its enhancer functions. Cdc73 also intersects with these factors within promoters to activate transcription of genes that are important for DNA repair and oxidative phosphorylation through its gene body functions. Consistently, Cdc73 deletion induced DNA damage and apoptosis and impaired mitochondrial function. The CDC73-induced DNA repair expression program co-opted by NOTCH1 is more highly expressed in T-ALL than in any other cancer. These data suggest that Cdc73 might induce a gene expression program that was eventually intersected and hijacked by oncogenic Notch to augment proliferation and mitigate the genotoxic and metabolic stresses of elevated Notch signaling. Our report supports studying factors such as CDC73 that intersect with Notch to derive a basic scientific understanding on how to combat Notch-dependent cancers without directly targeting the Notch complex.
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Affiliation(s)
- Ashley F. Melnick
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Carea Mullin
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Karena Lin
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Anna C. McCarter
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Shannon Liang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Yiran E. Liu
- Cancer Biology Program, Stanford University, Stanford, CA
| | - Qing Wang
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Nicole A. Jerome
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Elizabeth Choe
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Nicholas Kunnath
- Center for Healthcare Outcomes and Policy, University of Michigan School of Medicine, Ann Arbor, MI
| | - Geethika Bodanapu
- School of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Fatema Akter
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Brian Magnuson
- Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI
| | - Surinder Kumar
- Department of Pathology and Laboratory Medicine and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL
| | - David B. Lombard
- Department of Pathology and Laboratory Medicine and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL
| | - Andrew G. Muntean
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Mats Ljungman
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Radiology Oncology, University of Michigan School of Medicine, Ann Arbor, MI
| | - JoAnn Sekiguchi
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI
| | - Russell J. H. Ryan
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Mark Y. Chiang
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
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2
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Eldem V, Zararsız G, Erkan M. Global expression pattern of genes containing positively selected sites in European anchovy (Engraulis encrasicolus L.) may shed light on teleost reproduction. PLoS One 2023; 18:e0289940. [PMID: 37566603 PMCID: PMC10420382 DOI: 10.1371/journal.pone.0289940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
European anchovy is a multiple-spawning and highly fecundate pelagic fish with high economic and ecological significance. Although fecundity is influenced by nutrition, temperature and weight of spawners, high reproductive capacity is related to molecular processes in the ovary. The ovary is an essential and complex reproductive organ composed of various somatic and germ cells, which interact to facilitate the development of the ovary and functional oocytes. Revealing the ovarian transcriptome profile of highly fecundate fishes provides insights into oocyte production in teleosts. Here we use a comprehensive tissue-specific RNA sequencing which yielded 102.3 billion clean bases to analyze the transcriptional profiles of the ovary compared with other organs (liver, kidney, ovary, testis, fin, cauda and gill) and juvenile tissues of European anchovy. We conducted a comparative transcriptome and positive selection analysis of seven teleost species with varying fecundity rates to identify genes potentially involved in oogenesis and oocyte development. Of the 2,272 single copies of orthologous genes found, up to 535 genes were under positive selection in European anchovy and these genes are associated with a wide spectrum of cellular and molecular functions, with enrichments such as RNA methylation and modification, ribosome biogenesis, DNA repair, cell cycle processing and peptide/amide biosynthesis. Of the 535 positively selected genes, 55 were upregulated, and 45 were downregulated in the ovary, most of which were related to RNA and DNA transferase, developmental transcription factors, protein kinases and replication factors. Overall, our analysis of the transcriptome level in the ovarian tissue of a teleost will provide further insights into molecular processes and deepen our genetic understanding of egg production in highly fecund fish.
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Affiliation(s)
- Vahap Eldem
- Faculty of Sciences, Department of Biology, Istanbul University, Istanbul, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
| | - Melike Erkan
- Faculty of Sciences, Department of Biology, Istanbul University, Istanbul, Turkey
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3
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Liu Z, Luo P, Cao K, Hu Q, Hu B, Cui L, Wang X, Shi H, Zhang B, Wang R. SIAH1/CTR9 axis promotes the epithelial-mesenchymal transition of hepatocellular carcinoma. Carcinogenesis 2023; 44:304-316. [PMID: 37038329 DOI: 10.1093/carcin/bgad021] [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: 03/08/2023] [Revised: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 04/12/2023] Open
Abstract
SIAH1 has been reported to participate in several human cancers, including hepatocellular carcinoma (HCC). However, the effect of SIAH1 on the epithelial-mesenchymal transition (EMT) has not been reported in HCC cells. Here, we discovered the inhibitory effect of SIAH1 on HCC cell migration and invasion, which was related with regulating EMT. Molecularly, a yeast two-hybrid experiment indicated that Cln Three Requiring 9 (CTR9) was a potential interacting protein of SIAH1, which was further verified by co-immunoprecipitation assays. Furthermore, SIAH1 inhibited the EMT of HCC cells through negatively regulating CTR9. Importantly, CTR9 was ubiquitinated and degraded by SIAH1 via the proteasome pathway in HCC cells. Additionally, it was showed that SIAH1 mainly mediated the K48-linked polyubiquitination on CTR9. Finally, the protein level of CTR9 was found to be inversely correlated with SIAH1 in human HCC tissues. Summed up all together, these findings reveal that SIAH1/CTR9 axis promotes the EMT of HCC cells and is a promising therapeutic target for HCC therapy.
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Affiliation(s)
- Zhiyi Liu
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Pengchao Luo
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Kuan Cao
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qinghe Hu
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Bin Hu
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Licheng Cui
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaotian Wang
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hengliang Shi
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Central Laboratory, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Bin Zhang
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Renhao Wang
- Research Center of Digestive Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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4
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Melnick A, Liang S, Liu Y, Wang Q, Dean N, Choe E, Kunnath N, Bodanapu G, Mullin C, Akter F, Lin K, Magnuson B, Kumar S, Lombard DB, Muntean AG, Ljungman M, Sekiguchi J, Ryan RJH, Chiang MY. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525059. [PMID: 36711472 PMCID: PMC9882378 DOI: 10.1101/2023.01.22.525059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL) but pan-Notch inhibitors were toxic in clinical trials. To find alternative ways to target Notch signals, we investigated Cell division cycle 73 (Cdc73), which is a Notch cofactor and component of transcriptional machinery, a potential target in T-ALL. While we confirmed previous work that CDC73 interacts with NOTCH1, we also found that the interaction in T-ALL was context-dependent and facilitated by the lymphoid transcription factor ETS1. Using mouse models, we showed that Cdc73 is important for Notch-induced T-cell development and T-ALL maintenance. Mechanistically, Cdc73, Ets1, and Notch intersect chromatin at promoters and enhancers to activate oncogenes and genes that are important for DNA repair and oxidative phosphorylation. Consistently, Cdc73 deletion in T-ALL cells induced DNA damage and impaired mitochondrial function. Our data suggests that Cdc73 might promote a gene expression program that was eventually intersected by Notch to mitigate the genotoxic and metabolic stresses of elevated Notch signaling. We also provide mechanistic support for testing inhibitors of DNA repair, oxidative phosphorylation, and transcriptional machinery. Inhibiting pathways like Cdc73 that intersect with Notch at chromatin might constitute a strategy to weaken Notch signals without directly targeting the Notch complex.
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5
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A male germ-cell-specific ribosome controls male fertility. Nature 2022; 612:725-731. [PMID: 36517592 DOI: 10.1038/s41586-022-05508-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/01/2022] [Indexed: 12/23/2022]
Abstract
Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis1,2. Male germ cell development involves complex translational regulation during sperm formation3. However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, RibosomeST, that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (RibosomeCore) protein RPL39. Deletion of RibosomeST in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that RibosomeST features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with RibosomeCore. RibosomeST predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of RibosomeST were not replaceable by RibosomeCore. Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals.
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Kenaston MW, Pham OH, Petit MJ, Shah PS. Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks. BMC Genomics 2022; 23:787. [PMID: 36451099 PMCID: PMC9713194 DOI: 10.1186/s12864-022-09013-6] [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: 05/20/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Sitting at the interface of gene expression and host-pathogen interaction, polymerase associated factor 1 complex (PAF1C) is a rising player in the innate immune response. The complex localizes to the nucleus and associates with chromatin to modulate RNA polymerase II (RNAPII) elongation of gene transcripts. Performing this function at both proximal and distal regulatory elements, PAF1C interacts with many host factors across such sites, along with several microbial proteins during infection. Therefore, translating the ubiquity of PAF1C into specific impacts on immune gene expression remains especially relevant. RESULTS Advancing past work, we treat PAF1 knockout cells with a slate of immune stimuli to identify key trends in PAF1-dependent gene expression with broad analytical depth. From our transcriptomic data, we confirm PAF1 is an activator of traditional immune response pathways as well as other cellular pathways correlated with pathogen defense. With this model, we employ computational approaches to refine how PAF1 may contribute to both gene activation and suppression. Specifically focusing on transcriptional motifs and regulons, we predict gene regulatory elements strongly associated with PAF1, including those implicated in an immune response. Overall, our results suggest PAF1 is involved in innate immunity at several distinct axes of regulation. CONCLUSIONS By identifying PAF1-dependent gene expression across several pathogenic contexts, we confirm PAF1C to be a key mediator of innate immunity. Combining these transcriptomic profiles with potential regulatory networks corroborates the previously identified functions of PAF1C. With this, we foster new avenues for its study as a regulator of innate immunity, and our results will serve as a basis for targeted study of PAF1C in future validation studies.
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Affiliation(s)
- Matthew W. Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Oanh H. Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Marine J. Petit
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA ,grid.301713.70000 0004 0393 3981MRC-University of Glasgow, Centre for Virus Research, G61 1HQ, Glasgow, UK
| | - Priya S. Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA ,Department of Chemical Engineering, University of California, Davis, Davis, California, USA
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Chan N, Huang J, Ma G, Zeng H, Donahue K, Wang Y, Li L, Xu W. The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium. Nucleic Acids Res 2022; 50:1969-1992. [PMID: 35137163 PMCID: PMC8887485 DOI: 10.1093/nar/gkac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
CTR9 is the scaffold subunit in polymerase-associated factor complex (PAFc), a multifunctional complex employed in multiple steps of RNA Polymerase II (RNAPII)-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor that regulates gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the H3K27me3 levels are strictly controlled by CTR9. Quantitative profiling of histone modifications revealed a striking increase of H3K27me3 levels upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Further, CTR9 depletion triggers a PRC2 subtype switch from the less active PRC2.2, to the more active PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism that explains the transition from transcriptionally active chromatin states to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.
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Affiliation(s)
- Ngai Ting Chan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gui Ma
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hao Zeng
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kristine Donahue
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yidan Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- To whom correspondence should be addressed. Tel: +1 608 265 5540; Fax: +1 608 262 2824; Email :
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8
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Li Q, Zhang J, Liu S, Zhang F, Zhuang J, Chen Y. MicroRNA-17-3p is upregulated in psoriasis and regulates keratinocyte hyperproliferation and pro-inflammatory cytokine secretion by targeting <em>CTR9</em>. Eur J Histochem 2022; 66. [PMID: 35016493 PMCID: PMC8764465 DOI: 10.4081/ejh.2022.3275] [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: 05/18/2021] [Accepted: 12/31/2021] [Indexed: 11/23/2022] Open
Abstract
Psoriasis is a chronic inflammatory skin disease. Although miRNAs are reported to be associated with the pathogenesis of psoriasis, the contribution of individual microRNAs toward psoriasis remains unclear. The miR-17-92 cluster regulates cell growth and immune functions that are associated with psoriasis. miR-17-3p is a member of miR-17-92 cluster; however, its role in dermatological diseases remains unclear. Our study aims at investigating the effects of miR-17-3p and its potential target gene on keratinocytes proliferation and secretion of pro-inflammatory cytokine and their involvement in psoriasis. Initially, we found that miR-17-3p was upregulated in psoriatic skin lesions, and bioinformatic analyses suggested that CTR9 is likely to be a target gene of miR-17-3p. Quantitative reverse-transcriptase PCR and immunohistochemical analysis revealed that CTR9 expression was downregulated in psoriatic lesions. Using dual-luciferase reporter assays, we identified CTR9 as a direct target of miR-17-3p. Further functional experiments demonstrated that miR-17-3p promoted the proliferation and pro-inflammatory cytokine secretion of keratinocytes, whereas CTR9 exerted the opposite effects. Gain-of-function studies confirmed that CTR9 suppression partially accounted for the effects of miR- 17-3p in keratinocytes. Furthermore, Western blot revealed that miR-17-3p activates the downstream STAT3 signaling pathway while CTR9 inactivates the STAT3 signaling pathway. Together, these findings indicate that miR-17-3p regulates keratinocyte proliferation and pro-inflammatory cytokine secretion partially by targeting the CTR9, which inactivates the downstream STAT3 protein, implying that miR-17-3p might be a novel therapeutic target for psoriasis.
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Affiliation(s)
- Qingwen Li
- Dermatology Hospital, Southern Medical University, Guangzhou.
| | - Jiao Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou.
| | - Shougang Liu
- Dermatology Hospital, Southern Medical University, Guangzhou.
| | - Fangfei Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou.
| | - Jiayi Zhuang
- Dermatology Hospital, Southern Medical University, Guangzhou.
| | - Yongfeng Chen
- Dermatology Hospital, Southern Medical University, Guangzhou.
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Zhang B, Liu ZY, Wu R, Zhang CM, Cao K, Shan WG, Liu Z, Ji M, Tian ZL, Sethi G, Shi HL, Wang RH. Transcriptional regulator CTR9 promotes hepatocellular carcinoma progression and metastasis via increasing PEG10 transcriptional activity. Acta Pharmacol Sin 2021; 43:2109-2118. [PMID: 34876700 PMCID: PMC9343652 DOI: 10.1038/s41401-021-00812-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/31/2021] [Indexed: 11/09/2022] Open
Abstract
Cln Three Requiring 9 (CTR9), a scaffold protein of the polymerase-associated factor-1 (PAF1) complex (PAF1c), is primarily localized in the nucleus of cells. Recent studies show that CTR9 plays essential roles in the development of various human cancers and their occurrence; however, its regulatory roles and precise mechanisms in hepatocellular carcinoma (HCC) remain unclear. In this study, we investigated the roles of CTR9 using in vitro assays and a xenograft mouse model. We found that CTR9 protein is upregulated in tumor tissues from HCC patients. Knockdown of CTR9 substantially reduced HCC cell proliferation, invasion, and migration, whereas its overexpression promoted these activities. In addition, in vitro results revealed that CTR9 silencing dramatically increased cell cycle regulators, p21 and p27, but markedly decreased matrix metalloproteinases, MMP2 and MMP9, with these outcomes reversed upon CTR9 overexpression. Furthermore, the underlying molecular mechanism suggests that CTR9 promoted the oncogene paternally expressed gene 10 (PEG10) transcription via its promoter region. Finally, the oncogenic roles of CTR9 were confirmed in a xenograft mouse model. This study confirms that CTR9, an oncoprotein that promotes HCC cell proliferation, invasion, and migration, increases tumor growth in a xenograft mouse model. CTR9 could be a novel therapeutic target. Further investigation is warranted to verify CTR9 potential in novel therapies for HCC.
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Chen F, Liu B, Zeng J, Guo L, Ge X, Feng W, Li DF, Zhou H, Long J. Crystal Structure of the Core Module of the Yeast Paf1 Complex. J Mol Biol 2021; 434:167369. [PMID: 34852272 DOI: 10.1016/j.jmb.2021.167369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/31/2022]
Abstract
The highly conserved multifunctional polymerase-associated factor 1 (Paf1) complex (PAF1C), which consists of five core subunits: Ctr9, Paf1, Leo1, Cdc73, and Rtf1, acts as a diverse hub that regulates all stages of RNA polymerase II-mediated transcription and various other cellular functions. However, the underlying mechanisms remain unclear. Here, we report the crystal structure of the core module derived from a quaternary Ctr9/Paf1/Cdc73/Rtf1 complex of S. cerevisiae PAF1C, which reveals interfaces between the tetratricopeptide repeat module in Ctr9 and Cdc73 or Rtf1, and find that the Ctr9/Paf1 subcomplex is the key scaffold for PAF1C assembly. Our study demonstrates that Cdc73 binds Ctr9/Paf1 subcomplex with a very similar conformation within thermophilic fungi or human PAF1C, and that the binding of Cdc73 to PAF1C is important for yeast growth. Importantly, our structure reveals for the first time that the extreme C-terminus of Rtf1 adopts an "L"-shaped structure, which interacts with Ctr9 specifically. In addition, disruption of the binding of either Cdc73 or Rtf1 to PAF1C greatly affects the normal level of histone H2B K123 monoubiquitination in vivo. Collectively, our results provide a structural insight into the architecture of the quaternary Ctr9/Paf1/Cdc73/Rtf1 complex and PAF1C functional regulation.
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Affiliation(s)
- Feilong Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Beibei Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jianwei Zeng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuan Ge
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hao Zhou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Jiafu Long
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; Nankai International Advanced Research Institute (Shenzhen Futian), Shenzhen, Guangdong 518045, China.
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Liu F, Ma M, Gao A, Ma F, Ma G, Liu P, Jia C, Wang Y, Donahue K, Zhang S, Ong IM, Keles S, Li L, Xu W. PKM2-TMEM33 axis regulates lipid homeostasis in cancer cells by controlling SCAP stability. EMBO J 2021; 40:e108065. [PMID: 34487377 PMCID: PMC8591543 DOI: 10.15252/embj.2021108065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 02/01/2023] Open
Abstract
The pyruvate kinase M2 isoform (PKM2) is preferentially expressed in cancer cells to regulate anabolic metabolism. Although PKM2 was recently reported to regulate lipid homeostasis, the molecular mechanism remains unclear. Herein, we discovered an ER transmembrane protein 33 (TMEM33) as a downstream effector of PKM2 that regulates activation of SREBPs and lipid metabolism. Loss of PKM2 leads to up-regulation of TMEM33, which recruits RNF5, an E3 ligase, to promote SREBP-cleavage activating protein (SCAP) degradation. TMEM33 is transcriptionally regulated by nuclear factor erythroid 2-like 1 (NRF1), whose cleavage and activation are controlled by PKM2 levels. Total plasma cholesterol levels are elevated by either treatment with PKM2 tetramer-promoting agent TEPP-46 or by global PKM2 knockout in mice, highlighting the essential function of PKM2 in lipid metabolism. Although depletion of PKM2 decreases cancer cell growth, global PKM2 knockout accelerates allografted tumor growth. Together, our findings reveal the cell-autonomous and systemic effects of PKM2 in lipid homeostasis and carcinogenesis, as well as TMEM33 as a bona fide regulator of lipid metabolism.
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Affiliation(s)
- Fabao Liu
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Min Ma
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Ang Gao
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Fengfei Ma
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Protein Sciences, Discovery BiologicsMerck & Co., Inc.South San FranciscoCAUSA
| | - Gui Ma
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Peng Liu
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin‐MadisonMadisonWIUSA
- UW Carbone Cancer CenterSchool of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Chenxi Jia
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
State Key Laboratory of ProteomicsNational Center for Protein Sciences‐BeijingBeijing Proteome Research CenterBeijing Institute of Radiation MedicineBeijingChina
| | - Yidan Wang
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Kristine Donahue
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Shengjie Zhang
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Irene M Ong
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin‐MadisonMadisonWIUSA
- UW Carbone Cancer CenterSchool of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Sunduz Keles
- Department of StatisticsUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Lingjun Li
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Wei Xu
- McArdle Laboratory for Cancer ResearchUniversity of Wisconsin‐MadisonMadisonWIUSA
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12
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Xu Y, Chen J, He G, Zhang Y. CTR9-mediated JAK2/STAT3 pathway promotes the proliferation, migration, and invasion of human glioma cells. J Clin Lab Anal 2021; 35:e23943. [PMID: 34369006 PMCID: PMC8418497 DOI: 10.1002/jcla.23943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/17/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Background CTR9 (Cln three requiring 9) has been reported to be implicated in protein modification and oncogenesis of several human cancers. However, the protein expression and mechanism of CTR9 in glioma progression remain unclear. Methods We analyzed mRNA expression of CTR9 and CTR9‐related survival curves in the public database. Then, we detected CTR9 expression in glioma tissues and constructed U251 and U87 cells with stable silencing or overexpression of CTR9. Cell function tests and Western blot were conducted to explore the effects of CTR9 on glioma proliferation, invasion and migration, and the specific mechanism. All the date was presented as means ± SEM. Two‐sample t test and one‐way analysis of variance (ANOVA) were used to identify whether there was a significant difference between each group of data. Results We found that CTR9 was overexpressed in glioma and inversely associated with glioma patient survival. The results manifested that knockdown of CTR9 suppressed the proliferation, migration, and invasion of glioma cells, while overexpression facilitated them. The underlying molecular mechanism may involve the regulation of JAK2/STAT3 pathway by CTR9. Conclusion Our present study indicates that CTR9 is highly expressed in glioma and related to glioma grading and prognosis. CTR9 regulates malignant behaviors of glioma cells by activating JAK2/STAT3 pathway. Therefore, CTR9 may be a promising biomarker for the targeted therapy and prognosis evaluation of glioma.
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Affiliation(s)
- Yang Xu
- Department of neurosurgery, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Jiaguo Chen
- Department of neurosurgery, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Gao He
- Breast Disease Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Yuhai Zhang
- Department of neurosurgery, the Affiliated Brain Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
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13
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Francette AM, Tripplehorn SA, Arndt KM. The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin. J Mol Biol 2021; 433:166979. [PMID: 33811920 PMCID: PMC8184591 DOI: 10.1016/j.jmb.2021.166979] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
The regulation of transcription by RNA polymerase II is closely intertwined with the regulation of chromatin structure. A host of proteins required for the disassembly, reassembly, and modification of nucleosomes interacts with Pol II to aid its movement and counteract its disruptive effects on chromatin. The highly conserved Polymerase Associated Factor 1 Complex, Paf1C, travels with Pol II and exerts control over transcription elongation and chromatin structure, while broadly impacting the transcriptome in both single cell and multicellular eukaryotes. Recent studies have yielded exciting new insights into the mechanisms by which Paf1C regulates transcription elongation, epigenetic modifications, and post-transcriptional steps in eukaryotic gene expression. Importantly, these functional studies are now supported by an extensive foundation of high-resolution structural information, providing intimate views of Paf1C and its integration into the larger Pol II elongation complex. As a global regulatory factor operating at the interface between chromatin and transcription, the impact of Paf1C is broad and its influence reverberates into other domains of nuclear regulation, including genome stability, telomere maintenance, and DNA replication.
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Affiliation(s)
- Alex M Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Sarah A Tripplehorn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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14
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Cao Z, Sloper DT, Nakamura N. Identification of Altered Proteins in the Plasma of Rats With Chronic Prostatic Inflammation Induced by Estradiol Benzoate and Sex Hormones. ACS OMEGA 2021; 6:14361-14370. [PMID: 34124458 PMCID: PMC8190918 DOI: 10.1021/acsomega.1c01191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/07/2021] [Indexed: 05/05/2023]
Abstract
The cause of nonbacterial chronic prostatitis is unknown, yet its prevalence accounts for more than 90% of all prostatitis cases. Whole blood, plasma, and serum have been used to identify prostate cancer biomarkers; however, few studies have performed protein profiling to identify prostatitis biomarkers. The purpose of this study was to identify protein biomarkers altered by chronic prostatitis. To perform the study, we chemically induced chronic prostate inflammation in Sprague Dawley rats using estradiol benzoate (EB), testosterone (T), and estradiol (E) and then examined protein levels in their plasma. Plasma was collected on postnatal days (PNDs) 90, 100, 145, and 200; plasma proteins were profiled using liquid chromatography-tandem mass spectrometry. Chronic inflammation was observed in the rat prostate induced with EB on PNDs 1, 3, and 5. Rats then were dosed with T+E during PNDs 90-200 via subcutaneous implants. We identified time-specific expression for several proteins (i.e., CFB, MYH9, AZGP1). Some altered proteins that were expressed in the prostate (i.e., SERPINF1, CTR9) also were identified in the rat plasma in the EB+T+E group on PNDs 145 and 200. These findings suggest that the identified proteins could be used as biomarkers of chronic prostatitis. Further studies are needed to verify the results in human samples.
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15
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Podtelezhnikov AA, Monroe JJ, Aslamkhan AG, Pearson K, Qin C, Tamburino AM, Loboda AP, Glaab WE, Sistare FD, Tanis KQ. Quantitative Transcriptional Biomarkers of Xenobiotic Receptor Activation in Rat Liver for the Early Assessment of Drug Safety Liabilities. Toxicol Sci 2021; 175:98-112. [PMID: 32119089 DOI: 10.1093/toxsci/kfaa026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The robust transcriptional plasticity of liver mediated through xenobiotic receptors underlies its ability to respond rapidly and effectively to diverse chemical stressors. Thus, drug-induced gene expression changes in liver serve not only as biomarkers of liver injury, but also as mechanistic sentinels of adaptation in metabolism, detoxification, and tissue protection from chemicals. Modern RNA sequencing methods offer an unmatched opportunity to quantitatively monitor these processes in parallel and to contextualize the spectrum of dose-dependent stress, adaptation, protection, and injury responses induced in liver by drug treatments. Using this approach, we profiled the transcriptional changes in rat liver following daily oral administration of 120 different compounds, many of which are known to be associated with clinical risk for drug-induced liver injury by diverse mechanisms. Clustering, correlation, and linear modeling analyses were used to identify and optimize coexpressed gene signatures modulated by drug treatment. Here, we specifically focused on prioritizing 9 key signatures for their pragmatic utility for routine monitoring in initial rat tolerability studies just prior to entering drug development. These signatures are associated with 5 canonical xenobiotic nuclear receptors (AHR, CAR, PXR, PPARα, ER), 3 mediators of reactive metabolite-mediated stress responses (NRF2, NRF1, P53), and 1 liver response following activation of the innate immune response. Comparing paradigm chemical inducers of each receptor to the other compounds surveyed enabled us to identify sets of optimized gene expression panels and associated scoring algorithms proposed as quantitative mechanistic biomarkers with high sensitivity, specificity, and quantitative accuracy. These findings were further qualified using public datasets, Open TG-GATEs and DrugMatrix, and internal development compounds. With broader collaboration and additional qualification, the quantitative toxicogenomic framework described here could inform candidate selection prior to committing to drug development, as well as complement and provide a deeper understanding of the conventional toxicology study endpoints used later in drug development.
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Affiliation(s)
| | - James J Monroe
- Safety Assessment and Laboratory Animal Resources, Merck & Co., Inc., West Point, Pennsylvania 19486-0004
| | - Amy G Aslamkhan
- Safety Assessment and Laboratory Animal Resources, Merck & Co., Inc., West Point, Pennsylvania 19486-0004
| | - Kara Pearson
- Safety Assessment and Laboratory Animal Resources, Merck & Co., Inc., West Point, Pennsylvania 19486-0004
| | - Chunhua Qin
- Safety Assessment and Laboratory Animal Resources, Merck & Co., Inc., West Point, Pennsylvania 19486-0004
| | | | | | - Warren E Glaab
- Safety Assessment and Laboratory Animal Resources, Merck & Co., Inc., West Point, Pennsylvania 19486-0004
| | - Frank D Sistare
- Safety Assessment and Laboratory Animal Resources, Merck & Co., Inc., West Point, Pennsylvania 19486-0004
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16
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Karmakar S, Rauth S, Nallasamy P, Perumal N, Nimmakalaya RK, Leon F, Gupta R, Barkeer S, Venkata RC, Raman V, Rachagani S, Ponnusamy MP, Batra SK. RNA Polymerase II-Associated Factor 1 Regulates Stem Cell Features of Pancreatic Cancer Cells, Independently of the PAF1 Complex, via Interactions With PHF5A and DDX3. Gastroenterology 2020; 159:1898-1915.e6. [PMID: 32781084 PMCID: PMC7680365 DOI: 10.1053/j.gastro.2020.07.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/13/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS It is not clear how pancreatic cancer stem cells (CSCs) are regulated, resulting in ineffective treatments for pancreatic cancer. PAF1, a RNA polymerase II-associated factor 1 complex (PAF1C) component, maintains pluripotency of stem cells, by unclear mechanisms, and is a marker of CSCs. We investigated mechanisms by which PAF1 maintains CSCs and contributes to development of pancreatic tumors. METHODS Pancreatic cancer cell lines were engineered to knockdown PAF1 using inducible small hairpin RNAs. These cells were grown as orthotopic tumors in athymic nude mice and PAF1 knockdown was induced by administration of doxycycline in drinking water. Tumor growth and metastasis were monitored via IVIS imaging. CSCs were isolated from pancreatic cancer cell populations using flow cytometry and characterized by tumor sphere formation, tumor formation in nude mice, and expression of CSC markers. Isolated CSCs were depleted of PAF1 using the CRISPR/Cas9 system. PAF1-regulated genes in CSCs were identified via RNA-seq and PCR array analyses of cells with PAF1 knockdown. Proteins that interact with PAF1 in CSCs were identified by immunoprecipitations and mass spectrometry. We performed chromatin immunoprecipitation sequencing of CSCs to confirm the binding of the PAF1 sub-complex to target genes. RESULTS Pancreatic cancer cells depleted of PAF1 formed smaller and fewer tumor spheres in culture and orthotopic tumors and metastases in mice. Isolated CSCs depleted of PAF1 downregulated markers of self-renewal (NANOG, SOX9, and β-CATENIN), of CSCs (CD44v6, and ALDH1), and the metastasis-associated gene signature, compared to CSCs without knockdown of PAF1. The role of PAF1 in CSC maintenance was independent of its RNA polymerase II-associated factor 1 complex component identity. We identified DDX3 and PHF5A as proteins that interact with PAF1 in CSCs and demonstrated that the PAF1-PHF5A-DDX3 sub-complex bound to the promoter region of Nanog, whose product regulates genes that control stemness. Levels of the PAF1-DDX3 and PAF1-PHF5A were increased and co-localized in human pancreatic tumor specimens, human pancreatic tumor-derived organoids, and organoids derived from tumors of KPC mice, compared with controls. Binding of DDX3 and PAF1 to the Nanog promoter, and the self-renewal capacity of CSCs, were decreased in cells incubated with the DDX3 inhibitor RK-33. CSCs depleted of PAF1 downregulated genes that regulate stem cell features (Flot2, Taz, Epcam, Erbb2, Foxp1, Abcc5, Ddr1, Muc1, Pecam1, Notch3, Aldh1a3, Foxa2, Plat, and Lif). CONCLUSIONS In pancreatic CSCs, PAF1 interacts with DDX3 and PHF5A to regulate expression of NANOG and other genes that regulate stemness. Knockdown of PAF1 reduces the ability of orthotopic pancreatic tumors to develop and progress in mice and their numbers of CSCs. Strategies to target the PAF1-PHF5A-DDX3 complex might be developed to slow or inhibit progression of pancreatic cancer.
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Affiliation(s)
- Saswati Karmakar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Sanchita Rauth
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Palanisamy Nallasamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Naveenkumar Perumal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Rama Krishna Nimmakalaya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Frank Leon
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Rohitesh Gupta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Srikanth Barkeer
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | | | - Venu Raman
- Departments of Radiology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, U.S.A
| | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A
| | - Moorthy P. Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A.,Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, U.S.A.,Correspondence: Surinder K. Batra, Ph.D., or Moorthy P. Ponnusamy, Ph.D. Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5870, U.S.A. Phone: 402-559-5455, Fax: 402-559-6650, or
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, U.S.A.,Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, U.S.A.,Correspondence: Surinder K. Batra, Ph.D., or Moorthy P. Ponnusamy, Ph.D. Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5870, U.S.A. Phone: 402-559-5455, Fax: 402-559-6650, or
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17
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Sharma S, Gangenahalli GU, Singh U. Regulation of Hematopoietic Activity Involving New Interacting Partners (RRAGC & PSMC2, CKAP4 & MANF and CTR9 & CNTNAP2). Cell 2020. [DOI: 10.4236/cellbio.2020.93007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Yin J, Wu K, Ma Q, Dong H, Zhu Y, Hu L, Kong X. Revisiting Non-BRCA1/2 Familial Whole Exome Sequencing Datasets Implicates NCK1 as a Cancer Gene. Front Genet 2019; 10:527. [PMID: 31214250 PMCID: PMC6557995 DOI: 10.3389/fgene.2019.00527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
Through linkage and candidate gene screening, many breast cancer (BC) predisposition genes have been identified in the past 20 years. However, the majority of genetic risks that contribute to familial BC remains undetermined. In this study, we revisited whole exome sequencing datasets from non-BRCA1/2 familial BC patients, to search for novel BC predisposition genes. Based on the infinite mutation model, we supposed that rare non-silent variants that cooccurred between familial and TCGA-germline datasets, might play a predisposition contributing role. In our analysis, we not only identified novel potential pathogenic variants from known cancer predisposition genes, such as MRE11, CTR9 but also identified novel candidate predisposition genes, such as NCK1. According to the TCGA mRNA expression dataset of BC, NCK1 was significantly upregulated in basal-like subtypes and downregulated in luminal subtypes. In vitro, NCK1 mutants (D73H and R42Q) transfected MCF7 cell lines, which attributed to the luminal subtype, were much more viable and invasive than the wild type. On the other side, our results also showed that overall survival and disease-free survival of patients with NCK1 variations might be dependent on the genomic context. In conclusion, genetic heterogeneity exists among non-BRCA1/2 BC pedigrees and NCK1 could be a novel BC predisposition gene.
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Affiliation(s)
- Jie Yin
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qingyang Ma
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hang Dong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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The PAF1c Subunit CDC73 Is Required for Mouse Hematopoietic Stem Cell Maintenance but Displays Leukemia-Specific Gene Regulation. Stem Cell Reports 2019; 12:1069-1083. [PMID: 31031188 PMCID: PMC6524170 DOI: 10.1016/j.stemcr.2019.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
The Polymerase Associated Factor 1 complex (PAF1c) functions at the interface of epigenetics and gene transcription. The PAF1c is required for MLL fusion-driven acute myeloid leukemia (AML) through direct regulation of pro-leukemic target genes such as Hoxa9 and Meis1. However, the role of the PAF1c in normal hematopoiesis is unknown. Here, we discovered that the PAF1c subunit, CDC73, is required for both fetal and adult hematopoiesis. Loss of Cdc73 in hematopoietic cells is lethal because of extensive bone marrow failure. Cdc73 has an essential cell-autonomous role for adult hematopoietic stem cell function in vivo, and deletion of Cdc73 results in cell-cycle defects in hematopoietic progenitors. Gene expression profiling indicated a differential regulation of Hoxa9/Meis1 gene programs by CDC73 in progenitors compared with AML cells, suggesting disease-specific functions. Thus, the PAF1c subunit, CDC73 is essential for hematopoietic stem cell function but exhibits leukemia-specific regulation of self-renewal gene programs in AML cells. CDC73 is necessary for embryonic and adult hematopoietic stem cell function Proliferation and survival of cKIT+ hematopoietic progenitors require CDC73 CDC73 regulates unique gene programs in leukemia and hematopoietic progenitor cells
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Nassa G, Salvati A, Tarallo R, Gigantino V, Alexandrova E, Memoli D, Sellitto A, Rizzo F, Malanga D, Mirante T, Morelli E, Nees M, Åkerfelt M, Kangaspeska S, Nyman TA, Milanesi L, Giurato G, Weisz A. Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells. SCIENCE ADVANCES 2019; 5:eaav5590. [PMID: 30775443 PMCID: PMC6365116 DOI: 10.1126/sciadv.aav5590] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 06/01/2023]
Abstract
Breast cancer (BC) resistance to endocrine therapy results from constitutively active or aberrant estrogen receptor α (ERα) signaling, and ways to block ERα pathway in these tumors are sought after. We identified the H3K79 methyltransferase DOT1L as a novel cofactor of ERα in BC cell chromatin, where the two proteins colocalize to regulate estrogen target gene transcription. DOT1L blockade reduces proliferation of hormone-responsive BC cells in vivo and in vitro, consequent to cell cycle arrest and apoptotic cell death, with widespread effects on ER-dependent gene transcription, including ERα and FOXA1 gene silencing. Antiestrogen-resistant BC cells respond to DOT1L inhibition also in mouse xenografts, with reduction in ERα levels, H3K79 methylation, and tumor growth. These results indicate that DOT1L is an exploitable epigenetic target for treatment of endocrine therapy-resistant ERα-positive BCs.
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Affiliation(s)
- Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Valerio Gigantino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
- Genomix4Life Srl, University of Salerno, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
| | - Donatella Malanga
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, Catanzaro (CZ), Italy
| | - Teresa Mirante
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, Catanzaro (CZ), Italy
| | - Eugenio Morelli
- Department of Experimental and Clinical Medicine, University “Magna Graecia”, Catanzaro (CZ), Italy
| | - Matthias Nees
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Malin Åkerfelt
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sara Kangaspeska
- Institute for Molecular Medicine, Biomedicum 2U, Helsinki, Finland
| | - Tuula A. Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Segrate, MI, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
- Genomix4Life Srl, University of Salerno, Baronissi, SA, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi, SA, Italy
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21
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Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation. Nat Commun 2018; 9:3795. [PMID: 30228257 PMCID: PMC6143631 DOI: 10.1038/s41467-018-06237-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 08/15/2018] [Indexed: 11/09/2022] Open
Abstract
The evolutionarily conserved multifunctional polymerase-associated factor 1 (Paf1) complex (Paf1C), which is composed of at least five subunits (Paf1, Leo1, Ctr9, Cdc73, and Rtf1), plays vital roles in gene regulation and has connections to development and human diseases. Here, we report two structures of each of the human and yeast Ctr9/Paf1 subcomplexes, which assemble into heterodimers with very similar conformations, revealing an interface between the tetratricopeptide repeat module in Ctr9 and Paf1. The structure of the Ctr9/Paf1 subcomplex may provide mechanistic explanations for disease-associated mutations in human PAF1 and CTR9. Our study reveals that the formation of the Ctr9/Paf1 heterodimer is required for the assembly of yeast Paf1C, and is essential for yeast viability. In addition, disruption of the interaction between Paf1 and Ctr9 greatly affects the level of histone H3 methylation in vivo. Collectively, our results shed light on Paf1C assembly and functional regulation.
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Coriano CG, Liu F, Sievers CK, Liang M, Wang Y, Lim Y, Yu M, Xu W. A Computational-Based Approach to Identify Estrogen Receptor α/ β Heterodimer Selective Ligands. Mol Pharmacol 2018; 93:197-207. [PMID: 29295894 DOI: 10.1124/mol.117.108696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 12/11/2017] [Indexed: 01/28/2023] Open
Abstract
The biologic effects of estrogens are transduced by two estrogen receptors (ERs), ERα and ERβ, which function in dimer forms. The ERα/α homodimer promotes and the ERβ/β inhibits estrogen-dependent growth of mammary epithelial cells; the functions of ERα/β heterodimers remain elusive. Using compounds that promote ERα/β heterodimerization, we have previously shown that ERα/β heterodimers appeared to inhibit tumor cell growth and migration in vitro. Further dissection of ERα/β heterodimer functions was hampered by the lack of ERα/β heterodimer-specific ligands. Herein, we report a multistep workflow to identify the selective ERα/β heterodimer-inducing compound. Phytoestrogenic compounds were first screened for ER transcriptional activity using reporter assays and ER dimerization preference using a bioluminescence resonance energy transfer assay. The top hits were subjected to in silico modeling to identify the pharmacophore that confers ERα/β heterodimer specificity. The pharmacophore encompassing seven features that are potentially important for the formation of the ERα/β heterodimer was retrieved and subsequently used for virtual screening of large chemical libraries. Four chemical compounds were identified that selectively induce ERα/β heterodimers over their respective homodimers. Such ligands will become unique tools to reveal the functional insights of ERα/β heterodimers.
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Affiliation(s)
- Carlos G Coriano
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Fabao Liu
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Chelsie K Sievers
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Muxuan Liang
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Yidan Wang
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Yoongho Lim
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Menggang Yu
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
| | - Wei Xu
- Molecular & Environmental Toxicology Center, Department of Oncology (C.G.C., W.X.), Department of Oncology (C.G.C., F.L., C.K.S., Y.W., W.X.), and Wisconsin Clinical Sciences Center, Department of Biostatistics and Medical Informatics (M.L., M.Y.), University of Wisconsin-Madison, Madison, Wisconsin; and Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul, Republic of Korea (Y.L.)
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The PAF complex regulation of Prmt5 facilitates the progression and maintenance of MLL fusion leukemia. Oncogene 2017; 37:450-460. [PMID: 28945229 PMCID: PMC5785415 DOI: 10.1038/onc.2017.337] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/20/2017] [Accepted: 07/31/2017] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a disease associated with epigenetic dysregulation. 11q23 translocations involving the H3K4 methyltransferase MLL1 (KMT2A) generate oncogenic fusion proteins with deregulated transcriptional potential. The Polymerase Associated Factor complex (PAFc) is an epigenetic co-activator complex that makes direct contact with MLL fusion proteins and is involved in AML, however its functions are not well understood. Here, we explored the transcriptional targets regulated by the PAFc that facilitate leukemia by performing RNA-sequencing after conditional loss of the PAFc subunit Cdc73. We found Cdc73 promotes expression of an early hematopoietic progenitor gene program that prevents differentiation. Among the target genes, we confirmed the protein arginine methyltransferase Prmt5 is a direct target that is positively regulated by a transcriptional unit that includes the PAFc, MLL1, HOXA9 and STAT5 in leukemic cells. We observed reduced PRMT5-mediated H4R3me2s following excision of Cdc73 placing this histone modification downstream of the PAFc and revealing a novel mechanism between the PAFc and Prmt5. Knock down or pharmacologic inhibition of Prmt5 causes a G1 arrest and reduced proliferation resulting in extended leukemic disease latency in vivo. Overall, we demonstrate the PAFc regulates Prmt5 to facilitate leukemic progression and is a potential therapeutic target for AMLs.
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Zeng H, Lu L, Chan NT, Horswill M, Ahlquist P, Zhong X, Xu W. Systematic identification of Ctr9 regulome in ERα-positive breast cancer. BMC Genomics 2016; 17:902. [PMID: 27829357 PMCID: PMC5103509 DOI: 10.1186/s12864-016-3248-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/02/2016] [Indexed: 02/08/2023] Open
Abstract
Background We had previously identified Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), as a key factor regulating a massive ERα target gene expression and ERα-positive breast cancer growth. Furthermore, we have shown that knockdown of Ctr9 reduces ERα protein stability and decreases the occupancy of ERα and RNAPII at a few ERα-target loci. However, it remains to be determined whether Ctr9 controls ERα-target gene expression by regulating the global chromatin occupancy of ERα and RNAPII in the presence of estrogen. Results In this study, we determined the genome-wide ERα and RNAPII occupancy in response to estrogen treatment and/or Ctr9 knockdown by performing chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). We found that loss of Ctr9 dramatically decreases the global occupancy of ERα and RNAPII, highlighting the significance of Ctr9 in regulating estrogen signaling in ERα-positive breast cancer cells. Combining this resource with previously published genomic data sets, we identified a unique subset of ERα and Ctr9 target genes, and further delineated the independent function of Ctr9 from other subunits in PAFc when regulating transcription. Conclusions Our data demonstrated that Ctr9, independent of other PAFc subunits, controls ERα-target gene expression by regulating global chromatin occupancies of ERα and RNAPII. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3248-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Zeng
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Present address: Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Li Lu
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ngai Ting Chan
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mark Horswill
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Wei Xu
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System. G3-GENES GENOMES GENETICS 2016; 6:3229-3239. [PMID: 27520958 PMCID: PMC5068944 DOI: 10.1534/g3.116.034231] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Paf1 protein complex (Paf1C) is increasingly recognized as a highly conserved and broadly utilized regulator of a variety of transcriptional processes. These include the promotion of H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components, including Paf1 and Ctr9, which are critical for overall complex integrity, as well as Rtf1, Leo1, and Cdc73/Parafibromin(Hrpt2)/Hyrax. In spite of a growing appreciation for the importance of Paf1C from yeast and mammalian studies, there has only been limited work in Drosophila. Here, we provide the first detailed phenotypic study of Ctr9 function in Drosophila. We found that Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system reexpression of Ctr9. We observed a number of phenotypes in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as downregulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression revealed upregulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. We also found reduction of H3K4me3 modification in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes, and neuropeptide genes. In addition, we find significant effects on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila.
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PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLoS Genet 2016; 12:e1005794. [PMID: 26765774 PMCID: PMC4713055 DOI: 10.1371/journal.pgen.1005794] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/17/2015] [Indexed: 01/08/2023] Open
Abstract
The PAF complex (Paf1C) has been shown to regulate chromatin modifications, gene transcription, and RNA polymerase II (PolII) elongation. Here, we provide the first genome-wide profiles for the distribution of the entire complex in mammalian cells using chromatin immunoprecipitation and high throughput sequencing. We show that Paf1C is recruited not only to promoters and gene bodies, but also to regions downstream of cleavage/polyadenylation (pA) sites at 3' ends, a profile that sharply contrasted with the yeast complex. Remarkably, we identified novel, subunit-specific links between Paf1C and regulation of alternative cleavage and polyadenylation (APA) and upstream antisense transcription using RNAi coupled with deep sequencing of the 3' ends of transcripts. Moreover, we found that depletion of Paf1C subunits resulted in the accumulation of PolII over gene bodies, which coincided with APA. Depletion of specific Paf1C subunits led to global loss of histone H2B ubiquitylation, although there was little impact of Paf1C depletion on other histone modifications, including tri-methylation of histone H3 on lysines 4 and 36 (H3K4me3 and H3K36me3), previously associated with this complex. Our results provide surprising differences with yeast, while unifying observations that link Paf1C with PolII elongation and RNA processing, and indicate that Paf1C subunits could play roles in controlling transcript length through suppression of PolII accumulation at transcription start site (TSS)-proximal pA sites and regulating pA site choice in 3'UTRs.
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Zeng H, Xu W. Gene expression profiling of Ctr9-regulated transcriptome in ERα-positive breast cancer. GENOMICS DATA 2015; 7:103-4. [PMID: 26981377 PMCID: PMC4778656 DOI: 10.1016/j.gdata.2015.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/15/2015] [Indexed: 11/27/2022]
Abstract
Ctr9, the key scaffold subunit in human RNA polymerase II associated factor complex (PAFc), has diverse functions in cells and has been implicated in human diseases. Recently, our study found that loss of Ctr9 led to apparent morphological change, decrease of proliferation, and reduced colony formation in ERα+ breast cancer cells. Moreover, Ctr9 and ERα show positive correlation at protein levels and the high levels of Ctr9 are associated with poor survival among all women with ERα+ breast cancers, and specifically among those treated with tamoxifen. To gain a molecular understanding of the role of Ctr9 in promoting ERα+ breast cancer, we performed a microarray gene expression profiling of Ctr9-regulated transcriptome. Here we provide the experimental details and analysis of the microarray data, which have been deposited into Gene Expression Omnibus (GEO): GSE73388.
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Affiliation(s)
- Hao Zeng
- Graduate Program in Cellular and Molecular Biology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- Graduate Program in Cellular and Molecular Biology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
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