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Long Q, Xiang M, Xiao L, Wang J, Guan X, Liu J, Liao C. The Biological Significance Of AFF4: Promoting Transcription Elongation, Osteogenic Differentiation and Tumor Progression. Comb Chem High Throughput Screen 2023:CCHTS-EPUB-134858. [PMID: 37815186 DOI: 10.2174/0113862073241079230920082056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 10/11/2023]
Abstract
As a member of the AF4/FMR2 (AFF) family, AFF4 is a scaffold protein in the superelongation complex (SEC). In this mini-view, we discuss the role of AFF4 as a transcription elongation factor that mediates HIV activation and replication and stem cell osteogenic differentiation. AFF4 also promotes the progression of head and neck squamous cell carcinoma, leukemia, breast cancer, bladder cancer and other malignant tumors. The biological function of AFF4 is largely achieved through SEC assembly, regulates SRY-box transcription factor 2 (SOX2), MYC, estrogen receptor alpha (ESR1), inhibitor of differentiation 1 (ID1), c-Jun and noncanonical nuclear factor-κB (NF-κB) transcription and combines with fusion in sarcoma (FUS), unique regulatory cyclins (CycT1), or mixed lineage leukemia (MLL). We explore the prospects of using AFF4 as a therapeutic in Acquired immunodeficiency syndrome (AIDS) and malignant tumors and its potential as a stemness regulator.
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Affiliation(s)
- Qian Long
- Zunyi Medical University Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University Zunyi China
| | - Mingli Xiang
- Zunyi Medical University Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University Zunyi China
| | - Linlin Xiao
- Zunyi Medical University Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University Zunyi China
| | - Jiajia Wang
- Zunyi Medical University Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University Zunyi China
| | - Xiaoyan Guan
- Zunyi Medical University Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University Zunyi China
| | - Jianguo Liu
- Zunyi Medical University Oral Disease Research Key Laboratory of Guizhou Tertiary Institution Zunyi China
| | - Chengcheng Liao
- Zunyi Medical University Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University Zunyi China
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2
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Yang ZM, Zhang G, Wei G, Jing LL, Yu M. AFF4 globally affects the release of paused RNA polymerase II in HEL cells. Yi Chuan 2023; 45:658-668. [PMID: 37609817 DOI: 10.16288/j.yczz.23-143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
P-TEFb, a heterodimer of the kinase CDK9 and Cyclin T1, is a critical regulator of promoter-proximal pause release of Pol II in metazoans. It is capable of forming three larger complexes, including the super elongation complex (SEC), the BRD4/P-TEFb complex and the 7SK snRNP. In the SEC or the BRD4/P-TEFb complex, P-TEFb is enzymatically active, while in the 7SK snRNP, its activity is inhibited. The SEC consists of AFF1 or 4, ENL or AF9, ELL1, 2 or 3 and EAF1 or 2 in addition to P-TEFb, the only subunit with catalytic activity, and the noncatalytic subunits have been found to be able to regulate pause release through P-TEFb. We and others recently found that AFF1, ENL and AF9 are capable of regulating transcriptional initiation, but it is unknown yet whether AFF4 is also capable of doing so. With respect to the gene regulation selectivity of the SEC and the BRD4/P-TEFb complex, one recent study showed that in human DLD-1 cells, the SEC only regulates pause release of heat shock (HS) genes, whereas the BRD4/P-TEFb complex regulates pause release of the rest of the genes. However, it is unclear whether those mechanisms are general. In this study for the purpose of further understanding the role of AFF4 in transcriptional regulation, we found that AFF4 knockdown by RNA interference in human HEL cells decreased not only cellular level but also global chromatin occupancy of CTD serine 2 phosphorylated Pol II. Direct target genes of AFF4 were identified by RNA-seq and CUT&Tag. Notably, we found by ChIP-seq and PRO-seq that AFF4 loss also increased promoter-proximal pause of Pol II on several hundred HS and thousands of non-HS genes. Mechanistically, AFF4 promotes pause release likely by facilitating the binding of P-TEFb to Pol II. These results suggest that extent of the impact of AFF4 on pause release is likely to be context-dependent or cell-type dependent.
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Affiliation(s)
- Zi-Mei Yang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Li-Li Jing
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200052, China
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Che Z, Liu X, Dai Q, Fang K, Guo C, Yue J, Fang H, Xie P, Luo Z, Lin C. Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation. J Mol Cell Biol 2023:mjad049. [PMID: 37528066 DOI: 10.1093/jmcb/mjad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
The super elongation complex (SEC) containing P-TEFb plays a critical role in regulating transcription elongation. AFF1 and AFF4, members of the AF4/FMR2 family, act as central scaffold proteins of SEC and are associated with various human diseases. However, their precise roles in transcriptional control remain unclear. We here reveal differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites (TSSs). AFF1 mainly binds upstream of the TSSs, while AFF4 is enriched downstream of the TSSs. Notably, disruption of AFF4 results in slow elongation and early termination in a subset of AFF4 bound active genes, whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same gene subset. Additionally, AFF1 knockdown increases AFF4 levels at chromatin, and vice versa. In summary, these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate Pol II transcription.
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Affiliation(s)
- Zhuanzhuan Che
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Xiaoxu Liu
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Qian Dai
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Ke Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Chenghao Guo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Junjie Yue
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Haitong Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Peng Xie
- School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhuojuan Luo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Chengqi Lin
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
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Weiner L, Brissette JL. Finding meaning in chaos: a selection signature for functional interactions and its use in molecular biology. FEBS J 2023; 290:3914-3927. [PMID: 35653424 DOI: 10.1111/febs.16542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
A primary goal of biomedical research is to elucidate molecular mechanisms, particularly those responsible for human traits, either normal or pathological. Yet achieving this goal is difficult if not impossible when the traits of interest lack tractable models and so cannot be dissected through time-honoured approaches like forward genetics or reconstitution. Arguably, no biological problem has hindered scientific progress more than this: the inability to dissect a trait's mechanism without a tractable likeness of the trait. At root, forward genetics and reconstitution are powerful approaches because they assay for specific molecular functions. Here, we discuss an alternative way to uncover important mechanistic interactions, namely, to assay for positive natural selection. If an interaction has been selected for, then it must perform an important function, a function that significantly promotes reproductive success. Accordingly, selection is a consequence and indicator of function, and uncovering multimolecular selection will reveal important functional interactions. We propose a selection signature for interactions and review recent selection-based approaches through which to dissect traits that are not inherently tractable. The review includes proof-of-principle studies in which important interactions were uncovered by screening for selection. In sum, screens for selection appear feasible when screens for specific functions are not. Selection screens thus constitute a novel tool through which to reveal the mechanisms that shape the fates of organisms.
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Affiliation(s)
- Lorin Weiner
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Janice L Brissette
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
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Ni C, Liu W, Zheng K, Guo S, Song B, Jing W, Li G, Li B, Ni C, Shi K, Jin G, Yu G. PI3K/ c-Myc/ AFF4 axis promotes pancreatic tumorigenesis through fueling nucleotide metabolism. Int J Biol Sci 2023; 19:1968-1982. [PMID: 37063434 PMCID: PMC10092763 DOI: 10.7150/ijbs.77150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/01/2023] [Indexed: 04/18/2023] Open
Abstract
MLL-AFF4 fusion gene has been discovered in acute leukemia, whether AFF4 alone plays a role in tumor, especially pancreatic tumorigenesis, is still elusive. Increasing evidence suggests that cancer cells altered nucleotide metabolism during tumorigenesis. In present study, we observed AFF4 overexpression promoted cell proliferation, colony formation and cell cycle progression while loss of AFF4 impairs above phenotypes of pancreatic ductal carcinoma (PDAC) cells. Using RNA-profiling, we revealed that HPRT1 and IMPDH2, two enzymes in the nucleotide metabolism pathway, were upregulated following AFF4 overexpression. Simultaneous expression of HPRT1 and IMPDH2 would mainly rescue the phenotypes of cells lacking AFF4. Additionally, xenograft study proved HPRT1 and IMPDH2 genetically function in the downstream of AFF4, which was recruited by PAX2 when CDK9 mediated AFF4 phosphorylation at S388 and drove HPRT1 and IMPDH2 expression. We further discovered PI3K/c-Myc axis is required for AFF4 expression in PDAC cells. Finally, we obtained the positive correlation between c-Myc and AFF4 or AFF4 and HPRT1/IMPDH2 in clinical PDAC samples. Otherwise, we conducted data-mining and found that the expression levels of AFF4 and HPRT1/IMPDH2 are correlated with patients' prognosis, establishing AFF4 as a potential biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Chenming Ni
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Wenyu Liu
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Kailian Zheng
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Shiwei Guo
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Bin Song
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Wei Jing
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Gang Li
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Bo Li
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Canrong Ni
- Department of Pathology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Keqing Shi
- Precision Medical Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, 325000, China
| | - Gang Jin
- Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- ✉ Corresponding authors: Guanzhen Yu, Precision Medical Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, 325000, China. (). Gang Jin, Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China. ()
| | - Guanzhen Yu
- Precision Medical Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, 325000, China
- ✉ Corresponding authors: Guanzhen Yu, Precision Medical Center Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, 325000, China. (). Gang Jin, Department of Pancreatic Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200433, China. ()
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Abstract
The circular RNA, hsa_circ_0057452, is highly expressed in keloids, but its specific mechanism of action remains unknown. The levels of hsa_circ_0057452, microRNA (miR)-1225-3p, and AF4/FMR2 family member 4 (AFF4) in keloid tissues and keloid fibroblasts (KFs) were determined using quantitative reverse transcription-polymerase chain reaction. Changes in KFs viability, proliferation, apoptosis, and migration were investigated using the cell counting kit-8, bromodeoxyuridine, flow cytometry, and Transwell assays. Luciferase, RNA immunoprecipitation, and RNA pull-down assays were performed to identify the binding relationship among hsa_circ_0057452, miR-1225-3p, and AFF4. We found that hsa_circ_0057452 and AFF4 expression levels were upregulated, whereas miR-1225-3p expression levels were downregulated in keloids. Knockdown of hsa_circ_0057452 or AFF4 suppressed the viability, proliferation, and migration of KFs and induced apoptosis, whereas hsa_circ_0057452 overexpression and miR-1225-3p knockdown showed the opposite trend. Furthermore, hsa_circ_0057452 affected the biological behavior of KFs by releasing AFF4 via sponging of miR-1225-3p. Therefore, our results show that hsa_circ_0057452 promotes keloid progression by targeting miR-1225-3p and regulating AFF4 levels.
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Affiliation(s)
- Hu Gao
- Wound Repair & Rehabilitation Centre, Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, Hubei, China
| | - Zhen Hu
- Department of Dermatology, Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, Hubei, China
| | - Xiangming Zhang
- Wound Repair & Rehabilitation Centre, Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, Hubei, China
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Wu Z, Guo J, Zhang Y, Liu J, Ma H, Tang Y. MiR-425-5p accelerated the proliferation, migration, and invasion of ovarian cancer cells via targeting AFF4. J Ovarian Res 2021; 14:138. [PMID: 34686190 PMCID: PMC8539801 DOI: 10.1186/s13048-021-00894-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background Accumulating data have established that microRNAs (miRNAs) play significant regulatory roles in the carcinogenesis and progression of ovarian cancer (OC). MiR-425-5p was reported to function in various tumors. However, the roles and underlying mechanism of miR-425-5p involvement in OC development and progression are unclear. Methods A comprehensive strategy of data mining, computational biology, and real-time polymerase chain reaction was employed to identify the involvement of miR-425-5p in OC progression. The effect of miR-425-5p on the proliferation, migration, and invasion of OC cells was determined using Cell Counting Kit-8, wound-healing, and Matrigel invasion assays, respectively. Luciferase assay was performed to evaluate the interactions between miR-425-5p and MAGI2-AS3 or AFF4. Results miR-425-5p was significantly up-regulated in OC tissues and cells. The luciferase reporter assay revealed that miR-425-5p was negatively regulated by MAGI2-AS3. Silencing miR-425-5p inhibited the proliferation, migration, and invasion of OC cells in vitro. Bioinformatics analysis and luciferase reporter assay revealed that AFF4 was the target gene of miR-425-5p. Moreover, AFF4 expression was significantly decreased in OC and was closely related to the good prognosis of patients with OC. AFF4 overexpression inhibited the proliferation, migration, and invasion of OC cells in vitro. By contrast, silencing AFF4 promoted the proliferation, migration, and invasion of OC cells in vitro. Finally, AFF4 suppression rescued the inhibitory effect of silencing miR-425-5p on the proliferation, migration, and invasion of OC cells. Conclusion To the best our knowledge, this is the first study to demonstrate that miR-425-5p overexpression in OC is negatively regulated by MAGI2-AS3. Moreover, miR-425-5p promotes the proliferation, migration, and invasion of OC cells by targeting AFF4, suggesting that miR-425-5p/AFF4 signaling pathway represented a novel therapeutic target for patients with OC. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00894-x.
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Affiliation(s)
- Zhihui Wu
- Department of Clinical Laboratory, Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian Province, China
| | - Jianlin Guo
- Department of Laboratory, Second People's Hospital, Kashgar Area, Xinjiang, 844000, China
| | - Ying Zhang
- Department of Clinical Laboratory, Tuoli County People's Hospital, Tacheng, Xinjiang, 834500, Uygur Autonomous Region, China
| | - Jianhua Liu
- Department of Clinical Laboratory, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, 100144, China.
| | - Hongping Ma
- Department of Clinical Laboratory, Children's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830054, Uygur Autonomous Region, China.
| | - Yurong Tang
- Laboratory Department of Shengli Oilfield Central Hospital, Dongying, 257100, China.
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Voisin N, Schnur RE, Douzgou S, Hiatt SM, Rustad CF, Brown NJ, Earl DL, Keren B, Levchenko O, Geuer S, Verheyen S, Johnson D, Zarate YA, Hančárová M, Amor DJ, Bebin EM, Blatterer J, Brusco A, Cappuccio G, Charrow J, Chatron N, Cooper GM, Courtin T, Dadali E, Delafontaine J, Del Giudice E, Doco M, Douglas G, Eisenkölbl A, Funari T, Giannuzzi G, Gruber-Sedlmayr U, Guex N, Heron D, Holla ØL, Hurst ACE, Juusola J, Kronn D, Lavrov A, Lee C, Lorrain S, Merckoll E, Mikhaleva A, Norman J, Pradervand S, Prchalová D, Rhodes L, Sanders VR, Sedláček Z, Seebacher HA, Sellars EA, Sirchia F, Takenouchi T, Tanaka AJ, Taska-Tench H, Tønne E, Tveten K, Vitiello G, Vlčková M, Uehara T, Nava C, Yalcin B, Kosaki K, Donnai D, Mundlos S, Brunetti-Pierri N, Chung WK, Reymond A. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy. Am J Hum Genet 2021; 108:857-873. [PMID: 33961779 DOI: 10.1016/j.ajhg.2021.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3- and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.
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Affiliation(s)
- Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Rhonda E Schnur
- GeneDx, Gaithersburg, MD 20877, USA; Cooper Medical School of Rowan University, Division of Genetics, Camden, NJ 08103, USA
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, UK
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Flemington Road, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | | | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Olga Levchenko
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | - Sinje Geuer
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sarah Verheyen
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield S10 2TQ, UK
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | - Miroslava Hančárová
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - David J Amor
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jasmin Blatterer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino 10126, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino 10126, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Naples 80078, Italy
| | - Joel Charrow
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Nicolas Chatron
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Genetics Department, Lyon University Hospital, Lyon 69007, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Thomas Courtin
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Elena Dadali
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | | | - Ennio Del Giudice
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy
| | - Martine Doco
- Secteur Génétique, CHU Reims, EA3801, SFR CAPSANTE, 51092 Reims, France
| | | | - Astrid Eisenkölbl
- Department of Pediatrics and Adolescent Medicine, Johannes Kepler University, Kepler University Hospital Linz, Krankenhausstraße 26-30, 4020 Linz, Austria
| | | | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Ursula Gruber-Sedlmayr
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Nicolas Guex
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Bioinformatics Competence Center, University of Lausanne, Lausanne 1015, Switzerland
| | - Delphine Heron
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Øystein L Holla
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | - David Kronn
- New York Medical College, Valhalla, NY 10595, USA
| | | | - Crystle Lee
- Victorian Clinical Genetics Services, Flemington Road, Parkville, VIC 3052, Australia
| | - Séverine Lorrain
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Protein Analysis Facility, University of Lausanne, Lausanne 1015, Switzerland
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Anna Mikhaleva
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Sylvain Pradervand
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste 34100, Italy
| | - Darina Prchalová
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | | | - Victoria R Sanders
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Zdeněk Sedláček
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Heidelis A Seebacher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Elizabeth A Sellars
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | - Fabio Sirchia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste 34100, Italy
| | - Toshiki Takenouchi
- Center for Medical Genetics, Department of Pediatrics, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Akemi J Tanaka
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Heidi Taska-Tench
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Elin Tønne
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Giuseppina Vitiello
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy
| | - Markéta Vlčková
- Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Tomoko Uehara
- Center for Medical Genetics, Department of Pediatrics, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Caroline Nava
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique - Hôpitaux de Paris, Groupe de Recherche Clinique Déficience Intellectuelle et Autisme UPMC, Paris 75013, France
| | - Binnaz Yalcin
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Kenjiro Kosaki
- Center for Medical Genetics, Department of Pediatrics, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, UK
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples 80131, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Naples 80078, Italy
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland.
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9
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Li S, Liang X, Liang Y, Li L, Gan J, Cao L, Zou Y. Identification of the transcription factor, AFF4, as a new target of miR-203 in CNS. Int J Biol Macromol 2021; 181:919-927. [PMID: 33878354 DOI: 10.1016/j.ijbiomac.2021.04.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022]
Abstract
MiR-203 was identified as a hub of a potential regulatory miRNA network in central nervous system. Overexpressing of miR-203 in the frontal cortex of C57BL/6J wild type mouse induced neurodegeneration by increasing the apoptotic pathway and neuron death. AFF4, a transcription factor, was identified as a new bona fida protein target of miR-203 in CNS. The miRNA:mRNA interaction of miR-203 and AFF4 was verified using Dural-luciferase assay. Down-regulated expression of AFF4 was induced by overexpressing miR-203 both in vitro and in vivo. Open field test, Y maze and Morris water maze test were conducted for the behavioral assessment of the mice with stereotactic injection of lentiviral vector overexpressing miR-203 in the hippocampus. No anxiety-like behavior or impaired cognition was noticed in these mice. Consistent with the results of the behavioral assessment, the electron micrograph and Nissl staining revealed no significant change in the synaptic density and no neuron injuries in the hippocampus of mice overexpressing miR-203, respectively. Our results indicated that instead of promoting neurodegenerative phenotype, a more profound function should be ascribed to miR-203 in regulating neuron behavioral activities and cognition. Neuron-type specific functions of miR-203 are likely to be executed via its various downstream protein interactors.
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Affiliation(s)
- Shufang Li
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Xiaosheng Liang
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Yaohui Liang
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Linpeng Li
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Jia Gan
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Lin Cao
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Yi Zou
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China.
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10
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Kim SY, Kim MJ, Kim SJ, Lee JE, Chae JH, Ko JM. A case of CHOPS syndrome accompanied with moyamoya disease and systemic vasculopathy. Brain Dev 2021; 43:454-8. [PMID: 33248856 DOI: 10.1016/j.braindev.2020.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/29/2020] [Accepted: 11/06/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND CHOPS syndrome, caused by a mutation in the AFF4 gene, is a recently established and extremely rare genetic disorder, which has moderate phenotypic overlap with Cornelia de Lange syndrome. The main phenotypes include characteristic facial features, short stature, obesity, skeletal and pulmonary involvement, and neurodevelopmental impairment. CASE REPORT We report on a Korean girl with CHOPS syndrome presenting with an atypical manifestation. The patient was referred to the out-patient clinic to evaluate the underlying etiology of short stature, obesity, developmental delay, and Moyamoya disease. The patient showed characteristic facial features including a round face, thick eyebrows, and synophrys. Her developmental milestones had been delayed since infancy and a moderate degree of intellectual disability persisted. She was also diagnosed with Moyamoya disease at 6 years of age and had undergone synangiosis surgery thrice. Her renal arteries and infrarenal aorta were diffusely narrowed. A novel de novo missense variant, c.758C > T (p.Pro253Leu) in AFF4 was identified by whole exome sequencing. No additional candidate variants for her vascular manifestation were found except a susceptibility variant, c.14429G > A (p.Arg4810Lys) in RNF213, inherited from asymptomatic mother. CONCLUSION This is the first case of CHOPS syndrome accompanied by systemic vasculopathy. More clinical observations and functional studies are required to clarify this association.
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11
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Hu H, Zhang Y, Zhao L, Zhao W, Wang X, Ye E, Dong Y, Zhang L, Ran F, Zhou Y, Huang Y. AFF4 facilitates melanoma cell progression by regulating c-Jun activity. Exp Cell Res 2021; 399:112445. [PMID: 33417923 DOI: 10.1016/j.yexcr.2020.112445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 01/15/2023]
Abstract
Melanoma is characterized by high mortality and poor prognosis due to metastasis. AFF4 (AF4/FMR2 family member 4), as a scaffold protein, is a component of the super elongation complex (SEC), and is involved in the progression of tumors, e.g., leukemia, head and neck squamous cell carcinoma (HNSCC). However, few studies on AFF4 have focused on melanoma. Here, AFF4 expression levels and clinicopathological features were evaluated in melanoma tissue samples. Then, we performed cell proliferation, migration and invasion assays in A375 and A2058 cells lines in vitro to evaluate the role of AFF4 in melanoma. The effects of AFF4 knockdown in vivo were characterized via a xenograft mouse model. Finally, the correlation between c-Jun and AFF4 protein levels in melanoma was analyzed by rescue assay and immunohistochemistry (IHC). We found that AFF4 expression was upregulated in melanoma tumor tissues and that AFF4 protein expression was also closely related to the prognosis of patients with cutaneous melanoma. Moreover, AFF4 could promote the invasion and migration of melanoma cells by mediating epithelial to mesenchymal transition (EMT). AFF4 might regulate c-Jun activity to promote the invasion and migration of melanoma cells. Importantly, c-Jun was regulated by the AFF4 promoted melanoma tumorigenesis in vivo. Taken together, AFF4 may be a novel oncogene that promotes melanoma progression through regulation of c-Jun activity.
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Affiliation(s)
- Hongyan Hu
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Yi Zhang
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Liufang Zhao
- Department of Head and Neck Cancer, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Wentao Zhao
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Xiaoxiong Wang
- International Joint Laboratory on High Altitude Regional Cancer, Kunming, China; Yunnan Key Laboratory of Lung Cancer Research, Kunming, China
| | - En Ye
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Yan Dong
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Lijuan Zhang
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Fengming Ran
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Center), Kunming, China
| | - Yongchun Zhou
- International Joint Laboratory on High Altitude Regional Cancer, Kunming, China; Yunnan Key Laboratory of Lung Cancer Research, Kunming, China
| | - Yunchao Huang
- Yunnan Key Laboratory of Lung Cancer Research, Kunming, China.
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12
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Alfonso-Dunn R, Arbuckle JH, Vogel JL, Kristie TM. Inhibition of the Super Elongation Complex Suppresses Herpes Simplex Virus Immediate Early Gene Expression, Lytic Infection, and Reactivation from Latency. mBio 2020; 11:e01216-20. [PMID: 32518191 DOI: 10.1128/mBio.01216-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
HSV infections can cause pathologies ranging from recurrent lesions to significant ocular disease. Initiation of lytic infection and reactivation from latency in sensory neurons are dependent on the induced expression of the viral immediate early genes. Transcription of these genes is controlled at multiple levels, including modulation of the chromatin state of the viral genome and appropriate recruitment of transcription factors and coactivators. Following initiation of transcription, IE genes are subject to a key regulatory stage in which transcriptional elongation rates are controlled by the activity of the super elongation complex. Inhibition of the SEC blocks both lytic infection and reactivation from latency in sensory neurons. In addition to providing insights into the mechanisms controlling viral infection and reactivation, inhibitors of critical components such as the SEC may represent novel antivirals. Induction of herpes simplex virus (HSV) immediate early (IE) gene transcription promotes the initiation of lytic infection and reactivation from latency in sensory neurons. IE genes are transcribed by the cellular RNA polymerase II (RNAPII) and regulated by multiple transcription factors and coactivators. The HCF-1 cellular coactivator plays a central role in driving IE expression at multiple stages through interactions with transcription factors, chromatin modulation complexes, and transcription elongation components, including the active super elongation complex/P-TEFb (SEC-P-TEFb). Here, we demonstrate that the SEC occupies the promoters of HSV IE genes during the initiation of lytic infection and during reactivation from latency. Specific inhibitors of the SEC suppress viral IE expression and block the spread of HSV infection. Significantly, these inhibitors also block the initiation of viral reactivation from latency in sensory ganglia. The potent suppression of IE gene expression by SEC inhibitors indicates that transcriptional elongation represents a determining rate-limiting stage in HSV IE gene transcription and that the SEC plays a critical role in driving productive elongation during both phases of the viral life cycle. Most importantly, this supports the model that signal-mediated induction of SEC-P-TEFb levels can promote reactivation of a population of poised latent genomes.
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13
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Dahl NA, Danis E, Balakrishnan I, Wang D, Pierce A, Walker FM, Gilani A, Serkova NJ, Madhavan K, Fosmire S, Green AL, Foreman NK, Venkataraman S, Vibhakar R. Super Elongation Complex as a Targetable Dependency in Diffuse Midline Glioma. Cell Rep 2020; 31:107485. [PMID: 32268092 DOI: 10.1016/j.celrep.2020.03.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 02/03/2020] [Accepted: 03/16/2020] [Indexed: 12/27/2022] Open
Abstract
Histone 3 gene mutations are the eponymous drivers in diffuse midline gliomas (DMGs), aggressive pediatric brain cancers for which no curative therapy currently exists. These recurrent oncohistones induce a global loss of repressive H3K27me3 residues and broad epigenetic dysregulation. In order to identify therapeutically targetable dependencies within this disease context, we performed an RNAi screen targeting epigenetic/chromatin-associated genes in patient-derived DMG cultures. This identified AFF4, the scaffold protein of the super elongation complex (SEC), as a molecular dependency in DMG. Interrogation of SEC function demonstrates a key role for maintaining clonogenic potential while promoting self-renewal of tumor stem cells. Small-molecule inhibition of SEC using clinically relevant CDK9 inhibitors restores regulatory RNA polymerase II pausing, promotes cellular differentiation, and leads to potent anti-tumor effect both in vitro and in patient-derived xenograft models. These studies present a rationale for further exploration of SEC inhibition as a promising therapeutic approach to this intractable disease.
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Affiliation(s)
- Nathan A Dahl
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA; Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA.
| | - Etienne Danis
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ilango Balakrishnan
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dong Wang
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Angela Pierce
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Faye M Walker
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Natalie J Serkova
- Department of Radiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Krishna Madhavan
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Susan Fosmire
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA; Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA; Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA; Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sujatha Venkataraman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA; Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA; Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA.
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14
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Zhang Y, Xiao Q, Wu Z, Xu R, Zou S, Zhou C. AFF4 enhances odontogenic differentiation of human dental pulp cells. Biochem Biophys Res Commun 2020; 525:687-692. [PMID: 32139123 DOI: 10.1016/j.bbrc.2020.02.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/20/2020] [Indexed: 02/08/2023]
Abstract
AFF4 is a component of super elongation complex (SECs) and functions as a scaffold protein to bridge the transcription elongation factors. It is associated with leukemia, HIV transcription, and head neck cancer. However, its role in odontogenic differentiation of dental pulp cells (DPCs) is unclear. Here, we show the expression of AFF4 is increased during odontogenesis. Depletion of AFF4 in human DPCs leads to a decrease of alkaline phosphatase (ALP) activity, calcium mineralization and odontogenic-related genes expression. On the contrary, Lentivirus-mediated overexpression of AFF4 induces the odontogenic potential of DPCs. Mechanistically, we found AFF4 regulates the transcription of NFIC, a key factor for tooth root formation. Overexpression of NFIC successfully rescues the restricted differentiation of AFF4-depleted cells. Our data demonstrate that AFF4 serves as a previously unknown regulator of odontogenesis.
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Affiliation(s)
- Yuning Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qingyue Xiao
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Zuping Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Ruoshi Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Shujuan Zou
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China; Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Chenchen Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China; Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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15
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Li J, Ge J, Yang Y, Liu B, Zheng M, Shi R. Long noncoding RNA ZFPM2-AS1 is involved in lung adenocarcinoma via miR-511-3p/ AFF4 pathway. J Cell Biochem 2019; 121:2534-2542. [PMID: 31692047 DOI: 10.1002/jcb.29476] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/10/2019] [Indexed: 02/05/2023]
Abstract
Lung cancer is the dominating cause of cancer-induced death and can be classified into small cell lung cancer and non-small cell lung cancer (NSCLC). Lung adenocarcinoma (LUAD) is the most common histological subtype of NSCLC and its pathology remains unclear. Mounting reports have revealed that lncRNAs could regulate cellular activities in cancers. Yet the role of ZFPM2 antisense RNA 1 (ZFPM2-AS1) in LUAD has not been elucidated. Using GEPIA online dataset, we identified the amplification of ZFPM2-AS1 in LUAD tissues. Through quantitative real-time reverse transcription-polymerase chain reaction analysis, we observed an upregulation of ZFPM2-AS1 in LUAD cell lines. Conducting loss-of-function assays, we found that ZFPM2-AS1 depletion impaired cell viability, suppressed cell migration, and reversed epithelial-mesenchymal transition progress in LUAD cells. Mechanism investigation manifested that ZFPM2-AS1 was distributed in the cytoplasm of LUAD cells. Moreover, ZFPM2-AS1 functioned as a molecular sponge of miR-511-3p, which was a suppressor in LUAD. Moreover, ZFPM2-AS1 sponged miR-511-3p and thereby deregulated AF4/FMR2 family member 4 (AFF4), a target of miR-511-3p. At length, rescue assays indicated that AFF4 overexpression revived the inhibiting effects of ZFPM2-AS1 knockdown on the biological processes in LUAD. All in all, this study uncovered the function and the mechanism of ZFPM2-AS1 in LUAD.
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Affiliation(s)
- Juan Li
- Standard Treatment Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Medicine School of University of Electronic Science and Technology, Chengdu, China
| | - Jun Ge
- Standard Treatment Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Medicine School of University of Electronic Science and Technology, Chengdu, China
| | - Ye Yang
- Standard Treatment Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Medicine School of University of Electronic Science and Technology, Chengdu, China
| | - Bin Liu
- Standard Treatment Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Medicine School of University of Electronic Science and Technology, Chengdu, China
| | - Min Zheng
- Standard Treatment Department of Medical Oncology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Medicine School of University of Electronic Science and Technology, Chengdu, China
| | - Rui Shi
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, China
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16
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Raible SE, Mehta D, Bettale C, Fiordaliso S, Kaur M, Medne L, Rio M, Haan E, White SM, Cusmano-Ozog K, Nishi E, Guo Y, Wu H, Shi X, Zhao Q, Zhang X, Lei Q, Lu A, He X, Okamoto N, Miyake N, Piccione J, Allen J, Matsumoto N, Pipan M, Krantz ID, Izumi K. Clinical and molecular spectrum of CHOPS syndrome. Am J Med Genet A 2019; 179:1126-1138. [PMID: 31058441 DOI: 10.1002/ajmg.a.61174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/24/2019] [Accepted: 03/30/2019] [Indexed: 11/07/2022]
Abstract
CHOPS syndrome is a multisystem disorder caused by missense mutations in AFF4. Previously, we reported three individuals whose primary phenotype included cognitive impairment and coarse facies, heart defects, obesity, pulmonary involvement, and short stature. This syndrome overlaps phenotypically with Cornelia de Lange syndrome, but presents distinct differences including facial features, pulmonary involvement, and obesity. Here, we provide clinical descriptions of an additional eight individuals with CHOPS syndrome, as well as neurocognitive analysis of three individuals. All 11 individuals presented with features reminiscent of Cornelia de Lange syndrome such as synophrys, upturned nasal tip, arched eyebrows, and long eyelashes. All 11 individuals had short stature and obesity. Congenital heart disease and pulmonary involvement were common, and those were seen in about 70% of individuals with CHOPS syndrome. Skeletal abnormalities are also common, and those include abnormal shape of vertebral bodies, hypoplastic long bones, and low bone mineral density. Our observation indicates that obesity, pulmonary involvement, skeletal findings are the most notable features distinguishing CHOPS syndrome from Cornelia de Lange syndrome. In fact, two out of eight of our newly identified patients were found to have AFF4 mutations by targeted AFF4 mutational analysis rather than exome sequencing. These phenotypic findings establish CHOPS syndrome as a distinct, clinically recognizable disorder. Additionally, we report three novel missense mutations causative for CHOPS syndrome that lie within the highly conserved, 14 amino acid sequence of the ALF homology domain of the AFF4 gene, emphasizing the critical functional role of this region in human development.
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Affiliation(s)
- Sarah E Raible
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Roberts Individualized Medical Genetics Center (RIMGC), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Devanshi Mehta
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chiara Bettale
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah Fiordaliso
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Maninder Kaur
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Roberts Individualized Medical Genetics Center (RIMGC), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Livija Medne
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Roberts Individualized Medical Genetics Center (RIMGC), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Marlene Rio
- Department of Genetics, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Eric Haan
- Australia and Faculty of Health and Medical Sciences, Adult Genetics Unit, Royal Adelaide Hospital, University of Adelaide, Adelaide, South Australia, Australia
| | - Susan M White
- Department of Paediatrics, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Australia
| | - Kristina Cusmano-Ozog
- Rare Disease Institute, Children's National Health System, Washington, District of Columbia
| | - Eriko Nishi
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yiran Guo
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Honglin Wu
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Xiaoqing Shi
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Qingjie Zhao
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Xueqin Zhang
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Qi Lei
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Aimei Lu
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Xiyu He
- Department of Pediatrics, The 307 Hospital, Beijing, China
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Joseph Piccione
- Division of Pulmonary Medicine and Center for Pediatric Airway Disorders, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Julian Allen
- Division of Pulmonary Medicine and Center for Pediatric Airway Disorders, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Naomichi Matsumoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Mary Pipan
- Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Developmental Behavioral Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Roberts Individualized Medical Genetics Center (RIMGC), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kosuke Izumi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Roberts Individualized Medical Genetics Center (RIMGC), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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17
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Yang H, Basquin D, Pauli D, Oliver B. Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. BMC Genomics 2017; 18:384. [PMID: 28521739 PMCID: PMC5436443 DOI: 10.1186/s12864-017-3755-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 11/22/2022] Open
Abstract
Background Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then rapidly elongate following recruitment of positive elongation factors. Multiple elongation complexes exist, but the role of specific components in adult Drosophila is underexplored. Results We conducted RNA-seq experiments to analyze the effect of RNAi knockdown of Suppressor of Triplolethal and lilliputian. We similarly analyzed the effect of expressing a dominant negative Cyclin-dependent kinase 9 allele. We observed that almost half of the genes expressed in adults showed reduced expression, supporting a broad role for the three tested genes in steady-state transcript abundance. Expression profiles following lilliputian and Suppressor of Triplolethal RNAi were nearly identical raising the possibility that they are obligatory co-factors. Genes showing reduced expression due to these RNAi treatments were short and enriched for genes encoding metabolic or enzymatic functions. The dominant-negative Cyclin-dependent kinase 9 profiles showed both overlapping and specific differential expression, suggesting involvement in multiple complexes. We also observed hundreds of genes with sex-biased differential expression following treatment. Conclusion Transcriptional profiles suggest that Lilliputian and Suppressor of Triplolethal are obligatory cofactors in the adult and that they can also function with Cyclin-dependent kinase 9 at a subset of loci. Our results suggest that transcriptional elongation control is especially important for rapidly expressed genes to support digestion and metabolism, many of which have sex-biased function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3755-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haiwang Yang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA.
| | - Denis Basquin
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Daniel Pauli
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA
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Dorsett D. The Drosophila melanogaster model for Cornelia de Lange syndrome: Implications for etiology and therapeutics. Am J Med Genet C Semin Med Genet 2016; 172:129-37. [PMID: 27097273 DOI: 10.1002/ajmg.c.31490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Discovery of genetic alterations that cause human birth defects provide key opportunities to improve the diagnosis, treatment, and family counseling. Frequently, however, these opportunities are limited by the lack of knowledge about the normal functions of the affected genes. In many cases, there is more information about the gene's orthologs in model organisms, including Drosophila melanogaster. Despite almost a billion years of evolutionary divergence, over three-quarters of genes linked to human diseases have Drosophila homologs. With a short generation time, a twenty-fold smaller genome, and unique genetic tools, the conserved functions of genes are often more easily elucidated in Drosophila than in other organisms. Here we present how this applies to Cornelia de Lange syndrome, as a model for how Drosophila can be used to increase understanding of genetic syndromes caused by mutations with broad effects on gene transcription and exploited to develop novel therapies. © 2016 Wiley Periodicals, Inc.
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Gu J, Babayeva ND, Suwa Y, Baranovskiy AG, Price DH, Tahirov TH. Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4. Cell Cycle 2014; 13:1788-97. [PMID: 24727379 DOI: 10.4161/cc.28756] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Developing anti-viral therapies targeting HIV-1 transcription has been hampered by the limited structural knowledge of the proteins involved. HIV-1 hijacks the cellular machinery that controls RNA polymerase II elongation through an interaction of HIV-1 Tat with the positive transcription elongation factor P-TEFb, which interacts with an AF4 family member (AFF1/2/3/4) in the super elongation complex (SEC). Because inclusion of Tat•P-TEFb into the SEC is critical for HIV transcription, we have determined the crystal structure of the Tat•AFF4•P-TEFb complex containing HIV-1 Tat (residues 1-48), human Cyclin T1 (1-266), human Cdk9 (7-332), and human AFF4 (27-69). Tat binding to AFF4•P-TEFb causes concerted structural changes in AFF4 via a shift of helix H5' of Cyclin T1 and the α-3 10 helix of AFF4. The interaction between Tat and AFF4 provides structural constraints that explain tolerated Tat mutations. Analysis of the Tat-binding surface of AFF4 coupled with modeling of all other AF4 family members suggests that AFF1 and AFF4 would be preferred over AFF2 or AFF3 for interaction with Tat•P-TEFb. The structure establishes that the Tat-TAR recognition motif (TRM) in Cyclin T1 interacts with both Tat and AFF4, leading to the exposure of arginine side chains for binding to TAR RNA. Furthermore, modeling of Tat Lys28 acetylation suggests that the acetyl group would be in a favorable position for H-bond formation with Asn257 of TRM, thereby stabilizing the TRM in Cyclin T1, and provides a structural basis for the modulation of TAR RNA binding by acetylation of Tat Lys28.
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Affiliation(s)
- Jianyou Gu
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE USA
| | - Yoshiaki Suwa
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE USA
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE USA
| | - David H Price
- Biochemistry Department; University of Iowa; Iowa City, IA USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE USA
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