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Kafida M, Karela M, Giakountis A. RNA-Independent Regulatory Functions of lncRNA in Complex Disease. Cancers (Basel) 2024; 16:2728. [PMID: 39123456 PMCID: PMC11311644 DOI: 10.3390/cancers16152728] [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: 07/06/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of the transcribed genome. During the past decades, the regulatory role of these non-coding transcripts along with their interactions with other molecules have been extensively characterized. However, the study of long non-coding RNAs (lncRNAs), an ncRNA regulatory class with transcript lengths that exceed 200 nucleotides, revealed that certain non-coding transcripts are transcriptional "by-products", while their loci exert their downstream regulatory functions through RNA-independent mechanisms. Such mechanisms include, but are not limited to, chromatin interactions and complex promoter-enhancer competition schemes that involve the underlying ncRNA locus with or without its nascent transcription, mediating significant or even exclusive roles in the regulation of downstream target genes in mammals. Interestingly, such RNA-independent mechanisms often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples of lncRNAs that regulate target genes independently of their produced transcripts.
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Affiliation(s)
| | | | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
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2
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Xie Q, Hu B, Li H. Acetylation- and ubiquitination-regulated SFMBT2 acts as a tumor suppressor in clear cell renal cell carcinoma. Biol Direct 2024; 19:37. [PMID: 38734627 PMCID: PMC11088781 DOI: 10.1186/s13062-024-00480-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (RCC) is the most common kidney tumor. The analysis from medical database showed that Scm-like with four MBT domains protein 2 (SFMBT2) was decreased in advanced clear cell RCC cases, and its downregulation was associated with the poor prognosis. This study aims to investigate the role of SFMBT2 in clear cell RCC. METHODS The expression of SFMBT2 in clear cell RCC specimens were determined by immunohistochemistry staining and western blot. The overexpression and knockdown of SFMBT2 was realized by infection of lentivirus loaded with SFMBT2 coding sequence or silencing fragment in 786-O and 769-P cells, and its effects on proliferation and metastasis were assessed by MTT, colony formation, flow cytometry, wound healing, transwell assay, xenograft and metastasis experiments in nude mice. The interaction of SFMBT2 with histone deacetylase 3 (HDAC3) and seven in absentia homolog 1 (SIAH1) was confirmed by co-immunoprecipitation. RESULTS In our study, SFMBT2 exhibited lower expression in clear cell RCC specimens with advanced stages than those with early stages. Overexpression of SFMBT2 inhibited the growth and metastasis of clear cell RCC cells, 786-O and 769-P, in vitro and in vivo, and its silencing displayed opposites effects. HDAC3 led to deacetylation of SFMBT2, and the HDAC3 inhibitor-induced acetylation prevented SFMBT2 from SIAH1-mediated ubiquitination modification and proteasome degradation. K687 in SFMBT2 protein molecule may be the key site for acetylation and ubiquitination. CONCLUSIONS SFMBT2 exerted an anti-tumor role in clear cell RCC cells, and HDAC3-mediated deacetylation promoted SIAH1-controlled ubiquitination of SFMBT2. SFMBT2 may be considered as a novel clinical diagnostic marker and/or therapeutic target of clear cell RCC, and crosstalk between its post-translational modifications may provide novel insights for agent development.
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Affiliation(s)
- Qingpeng Xie
- Department of Urology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, China
| | - Bin Hu
- Department of Urology, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning, China.
| | - Haosong Li
- Department of Pediatrics, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
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Brandes D, Yasin L, Nebral K, Ebler J, Schinnerl D, Picard D, Bergmann AK, Alam J, Köhrer S, Haas OA, Attarbaschi A, Marschall T, Stanulla M, Borkhardt A, Brozou T, Fischer U, Wagener R. Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e925. [PMID: 37469802 PMCID: PMC10353714 DOI: 10.1097/hs9.0000000000000925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/01/2023] [Indexed: 07/21/2023] Open
Abstract
The mutational landscape of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the most common pediatric cancer, is not fully described partially because commonly applied short-read next generation sequencing has a limited ability to identify structural variations. By combining comprehensive analysis of structural variants (SVs), single-nucleotide variants (SNVs), and small insertions-deletions, new subtype-defining and therapeutic targets may be detected. We analyzed the landscape of somatic alterations in 60 pediatric patients diagnosed with the most common BCP-ALL subtypes, ETV6::RUNX1+ and classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome sequencing (WES), and the novel optical genome mapping (OGM) technique. Ninety-five percent of SVs detected by cytogenetics and SNP-array were verified by OGM. OGM detected an additional 677 SVs not identified using the conventional methods, including (subclonal) IKZF1 deletions. Based on OGM, ETV6::RUNX1+ BCP-ALL harbored 2.7 times more SVs than HD BCP-ALL, mainly focal deletions. Besides SVs in known leukemia development genes (ETV6, PAX5, BTG1, CDKN2A), we identified 19 novel recurrently altered regions (in n ≥ 3) including 9p21.3 (FOCAD/HACD4), 8p11.21 (IKBKB), 1p34.3 (ZMYM1), 4q24 (MANBA), 8p23.1 (MSRA), and 10p14 (SFMBT2), as well as ETV6::RUNX1+ subtype-specific SVs (12p13.1 (GPRC5A), 12q24.21 (MED13L), 18q11.2 (MIB1), 20q11.22 (NCOA6)). We detected 3 novel fusion genes (SFMBT2::DGKD, PDS5B::STAG2, and TDRD5::LPCAT2), for which the sequence and expression were validated by long-read and whole transcriptome sequencing, respectively. OGM and WES identified double hits of SVs and SNVs (ETV6, BTG1, STAG2, MANBA, TBL1XR1, NSD2) in the same patient demonstrating the power of the combined approach to define the landscape of genomic alterations in BCP-ALL.
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Affiliation(s)
- Danielle Brandes
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- Dusseldorf School of Oncology (DSO), Medical Faculty, Heinrich-Heine University, Dusseldorf, Germany
| | - Layal Yasin
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
| | - Karin Nebral
- Labdia Labordiagnostik, Clinical Genetics, Vienna, Austria
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich-Heine University, Dusseldorf, Germany
- Center for Digital Medicine, Heinrich-Heine University, Dusseldorf, Germany
| | - Dagmar Schinnerl
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Daniel Picard
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
| | - Anke K. Bergmann
- Institute of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Jubayer Alam
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
| | - Stefan Köhrer
- Labdia Labordiagnostik, Clinical Genetics, Vienna, Austria
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Oskar A. Haas
- St. Anna Children’s Hospital, Department of Pediatric Hematology/Oncology, Pediatric Clinic, Medical University, Vienna, Austria
| | - Andishe Attarbaschi
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Children’s Hospital, Department of Pediatric Hematology/Oncology, Pediatric Clinic, Medical University, Vienna, Austria
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich-Heine University, Dusseldorf, Germany
- Center for Digital Medicine, Heinrich-Heine University, Dusseldorf, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School (MHH), Hannover, Germany
| | - Arndt Borkhardt
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
| | - Triantafyllia Brozou
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
| | - Ute Fischer
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
| | - Rabea Wagener
- Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University and University Hospital Dusseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Dusseldorf, Germany
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Wu H, Tao Y, Zhang W, Wang G, Zhang Q. circ‑0000212 promotes cell proliferation of colorectal cancer by sponging miR‑491 and modulating FOXP4 expression. Mol Med Rep 2021; 23:300. [PMID: 33649850 PMCID: PMC7930931 DOI: 10.3892/mmr.2021.11939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 02/01/2021] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer (CRC) is a lethal and common malignancy worldwide. Non-coding (nc)RNAs have been shown to modulate tumor progression in several types of cancer. The present study aimed to investigate the role of hsa_circ_0000212 in CRC, as a sponge of microRNA (miR)-491. The expression levels of miR-491 and forkhead box P4 (FOXP4) were analyzed using data from The Cancer Genome Atlas. The association between miR-491 and FOXP4 and the clinicopathological characteristics were also analyzed. A novel circular (circ)RNA, hsa_circ_0000212, was found to sponge miR-491 based on bioinformatics analysis. The potential binding site between miR-491 and FOXP4 or circ-0000212 was validated using luciferase and RNA immunoprecipitation assays. The expression levels and distribution of circ-0000212 was also determined. Cell Counting Kit-8 and colony formation assays were performed to determine the role of miR-491 or circ-0000212 on the proliferation of the CRC cells. Decreased miR-491 or increased FOXP4 expression levels were associated with the pathological stage in patients with CRC. In addition, miR-491 inhibited cell proliferation by targeting FOXP4. circ-0000212 was increased in CRC tissues and was predominantly localized in the cytoplasm. Furthermore, circ-0000212 augmented viability of the CRC cells by sponging miR-491 and modulating FOXP4. In conclusion, circ-0000212 may serve as a novel tumor-promoter and drug target in CRC.
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Affiliation(s)
- Hongyu Wu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Yangbao Tao
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Weiyuan Zhang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Guiyu Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Qian Zhang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
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Li B, Dong J, Yu J, Fan Y, Shang L, Zhou X, Bai Y. Pinpointing miRNA and genes enrichment over trait-relevant tissue network in Genome-Wide Association Studies. BMC Med Genomics 2020; 13:191. [PMID: 33371893 PMCID: PMC7771066 DOI: 10.1186/s12920-020-00830-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Understanding gene regulation is important but difficult. Elucidating tissue-specific gene regulation mechanism is even more challenging and requires gene co-expression network assembled from protein-protein interaction, transcription factor and gene binding, and post-transcriptional regulation (e.g., miRNA targeting) information. The miRNA binding affinity could therefore be changed by SNP(s) located at the 3' untranslated regions (3'UTR) of the target messenger RNA (mRNA) which miRNA(s) interacts with. Genome-wide association study (GWAS) has reported significant numbers of loci hosting SNPs associated with many traits. The goal of this study is to pinpoint GWAS functional variants located in 3'UTRs and elucidate if the genes harboring these variants along with their targeting miRNAs are associated with genetic traits relevant to certain tissues. METHODS By applying MIGWAS, CoCoNet, ANNOVAR, and DAVID bioinformatics software and utilizing the gene expression database (e.g. GTEx data) to study GWAS summary statistics for 43 traits from 28 GWAS studies, we have identified a list of miRNAs and targeted genes harboring 3'UTR variants, which could contribute to trait-relevant tissue over miRNA-target gene network. RESULTS Our result demonstrated that strong association between traits and tissues exists, and in particular, the Primary Biliary Cirrhosis (PBC) trait has the most significant p-value for all 180 tissues among all 43 traits used for this study. We reported SNPs located in 3'UTR regions of genes (SFMBT2, ZC3HAV1, and UGT3A1) targeted by miRNAs for PBC trait and its tissue association network. After employing Gene Ontology (GO) analysis for PBC trait, we have also identified a very important miRNA targeted gene over miRNA-target gene network, PFKL, which encodes the liver subunit of an enzyme. CONCLUSIONS The non-coding variants identified from GWAS studies are casually assumed to be not critical to translated protein product. However, 3' untranslated regions (3'UTRs) of genes harbor variants can often change the binding affinity of targeting miRNAs playing important roles in protein translation degree. Our study has shown that GWAS variants could play important roles on miRNA-target gene networks by contributing the association between traits and tissues. Our analysis expands our knowledge on trait-relevant tissue network and paves way for future human disease studies.
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Affiliation(s)
- Binze Li
- Bellaire High School, 5100 Maple St, Bellaire, TX, 77401, USA
| | - Julian Dong
- Northville High School, 45700 Six Mile Road, Northville, MI, 48168, USA
| | - Jiaqi Yu
- College Preparatory School, 6100 Broadway, Oakland, CA, 94618, USA
| | - Yuqi Fan
- The Master's Academy, 1500 Lukas Ln, Oviedo, FL, 32765, USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.,Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, 48197, USA. .,Next-Gen Intelligent Science Training, Ann Arbor, MI, 48105, USA.
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Gwak J, Jeong H, Lee K, Shin JY, Sim T, Na J, Kim J, Ju BG. SFMBT2-Mediated Infiltration of Preadipocytes and TAMs in Prostate Cancer. Cancers (Basel) 2020; 12:E2718. [PMID: 32971847 PMCID: PMC7565541 DOI: 10.3390/cancers12092718] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/07/2020] [Accepted: 08/16/2020] [Indexed: 12/22/2022] Open
Abstract
Infiltration of diverse cell types into tumor microenvironment plays a critical role in cancer progression including metastasis. We previously reported that SFMBT2 (Scm-like with four mbt domains 2) regulates the expression of matrix metalloproteinases (MMPs) and migration and invasion of cancer cells in prostate cancer. Here we investigated whether the down-regulation of SFMBT2 regulates the infiltration of preadipocytes and tumor-associated macrophages (TAMs) in prostate cancer. We found that the down-regulation of SFMBT2 promotes the infiltration of preadipocytes and TAMs through up-regulation of CXCL8, CCL2, CXCL10, and CCL20 expression in prostate cancer. Expression of CXCL8, CCL2, CXCL10, and CCL20 was also elevated in prostate cancer patients having a higher Gleason score (≥8), which had substantially lower SFMBT2 expression. We also found that the up-regulation of CXCL8, CCL2, CXCL10, and CCL20 expression is dependent on NF-κB activation in prostate cancer cells expressing a low level of SFMBT2. Moreover, increased IL-6 from infiltrated preadipocytes and TAMs promoted migration and invasion of prostate cancer cells expressing a low level of SFMBT2. Our study may suggest that SFMBT2 a critical regulator for the infiltration of preadipocytes and TAMs into the prostate tumor microenvironment. Thus, the regulation of SFMBT2 may provide a new therapeutic strategy to inhibit prostate cancer metastasis, and SFMBT2 could be used as a potential biomarker in prostate cancer metastasis.
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Affiliation(s)
| | | | | | | | | | | | | | - Bong-Gun Ju
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.G.); (H.J.); (K.L.); (J.Y.S.); (T.S.); (J.N.); (J.K.)
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Zhang X, Wan S, Yu Y, Ruan W, Wang H, Xu L, Wang C, Chen S, Cao T, Peng Q, Li S, Hu T, Jiang Z, Chen Z, Fan JB. Identifying potential DNA methylation markers in early-stage colorectal Cancer. Genomics 2020; 112:3365-3373. [PMID: 32531444 DOI: 10.1016/j.ygeno.2020.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 01/20/2023]
Abstract
Colorectal cancer (CRC) is the second leading malignancy worldwide. Accurate screening is pivotal to early CRC detection, yet current screening modality involves invasive colonoscopy while non-invasive FIT tests have limited sensitivity. We applied a DNA methylation assay to identify biomarkers for early-stage CRC detection, risk stratification and precancerous lesion screening at tissue level. A model of biomarkers SFMBT2, ITGA4, THBD and ZNF304 showed 96.1% sensitivity and 87.0% specificity in CRC detection, with 100.0% sensitivity for advanced precancerous lesion and stage I CRC. Performances were further validated with TCGA data set, which showed a consistent AUC of 0.99 and exhibited specificity against other cancer types. KCNJ12, VAV3-AS1 and EVC were further identified for stage stratification (stage 0-I versus stage II-IV), with AUC of 0.87, 83.0% sensitivity and 71.2% specificity. Additionally, dual markers of NEUROD1 and FAM72C showed 83.2% sensitivity and 77.4% specificity in differing non-advanced precancerous lesions from inflammatory bowel diseases.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Shenmei Wan
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Yanqi Yu
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Weimei Ruan
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Hong Wang
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Linhao Xu
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Chanjuan Wang
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Shang Chen
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Tianfeng Cao
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Quanzhou Peng
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Sihui Li
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Tianliang Hu
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Zeyu Jiang
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China
| | - Zhiwei Chen
- AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China; AnchorDx, Inc., 46305 Landing Pkwy, Fremont, CA 94538, United States.
| | - Jian-Bing Fan
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China; AnchorDx Medical Co., Ltd, Unit 502, 3(rd) Luoxuan Road, International Bio-Island, Guangzhou, 510300, China.
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Sarvagalla S, Kolapalli SP, Vallabhapurapu S. The Two Sides of YY1 in Cancer: A Friend and a Foe. Front Oncol 2019; 9:1230. [PMID: 31824839 PMCID: PMC6879672 DOI: 10.3389/fonc.2019.01230] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
Yin Yang 1 (YY1), a dual function transcription factor, is known to regulate transcriptional activation and repression of many genes associated with multiple cellular processes including cellular differentiation, DNA repair, autophagy, cell survival vs. apoptosis, and cell division. Owing to its role in processes that upon deregulation are linked to malignant transformation, YY1 has been implicated as a major driver of many cancers. While a large body of evidence supports the role of YY1 as a tumor promoter, recent reports indicated that YY1 also functions as a tumor suppressor. The mechanism by which YY1 brings out opposing outcome in tumor growth vs. suppression is not completely clear and some of the recent reports have provided significant insight into this. Likewise, the mechanism by which YY1 functions both as a transcriptional activator and repressor is not completely clear. It is likely that the proteins with which YY1 interacts might determine its function as an activator or repressor of transcription as well as its role as a tumor suppressor or promoter. Hence, a collection of YY1-protein interactions in the context of different cancers would help us gain an insight into how YY1 promotes or suppresses cancers. This review focuses on the YY1 interacting partners and its target genes in different cancer models. Finally, we discuss the possibility of therapeutically targeting the YY1 in cancers where it functions as a tumor promoter.
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Affiliation(s)
- Sailu Sarvagalla
- Division of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | | | - Sivakumar Vallabhapurapu
- Division of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
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de Boer S, Baran Y, Garcia-Garcia HM, Eskin I, Lenzen MJ, Kleber ME, Regar E, de Jaegere PJ, Ligthart JM, van Geuns RJ, Lehtimäki T, Laaksonen R, Boersma E, Marz W, Halperin E, Serruys PW, Koenig W. The European Collaborative Project on Inflammation and Vascular Wall Remodeling in Atherosclerosis - Intravascular Ultrasound (ATHEROREMO-IVUS) study. EUROINTERVENTION 2019; 14:194-203. [PMID: 28943493 DOI: 10.4244/eij-d-17-00180] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
AIMS The European Collaborative Project on Inflammation and Vascular Wall Remodeling in Atherosclerosis - Intravascular Ultrasound (ATHEROREMO-IVUS) study was designed as an exploratory clinical study in order to investigate the associations between genetic variation, coronary atherosclerosis phenotypes, and plaque vulnerability as determined by IVUS. METHODS AND RESULTS The ATHEROREMO-IVUS study was a prospective, observational study of 581 patients with stable angina pectoris or acute coronary syndrome (ACS) who were referred for coronary angiography to the Thoraxcenter, Rotterdam, enriched with 265 IBIS-2 participants (total population, n=846). Prior to catheterisation, blood samples were drawn for genetic analyses. During the catheterisation procedure, IVUS was performed in a non-culprit coronary artery. The primary endpoint was the presence of vulnerable plaque as determined by IVUS virtual histology (VH). In addition, we performed a genome-wide association study of plaque morphology. We observed strong signals associated with plaque morphology in several chromosomal regions: twelve SNPs (rs17300022, rs6904106, rs17177818, rs2248165, rs2477539, rs16865681, rs2396058, rs4753663, rs4082252, rs6932, rs12862206, rs6780676) in or near eight different genes (GNA12, NMBR, SFMBT2, CUL3, SESN3, SLC22A25, EFBN2, SEC62) were most significant. CONCLUSIONS In conclusion, we found twelve SNPs in or in the proximity of eight genes, which were possibly associated with markers of vulnerable plaque. ClinicalTrials.gov Identifier: NCT01789411.
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Hussain S, Sun M, Guo Y, Mushtaq N, Zhao Y, Yuan Y, Hussain N, Osoro E, Suleiman A, Sadiq M, Zhang F, Han Y, Sun J, Lu S. SFMBT2 positively regulates SOX9 and chondrocyte proliferation. Int J Mol Med 2018; 42:3503-3512. [PMID: 30272322 DOI: 10.3892/ijmm.2018.3894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/19/2018] [Indexed: 11/06/2022] Open
Abstract
SRY‑box 9 (SOX9) is the master regulator of the chondrocyte phenotype, which is essential for differentiating chondrogenic mesenchymal condensations into chondrocytes, and is involved in regulating every stage of chondrocyte differentiation. SOX9 deletion in chondrocytes at the late stages of cartilage development results in decreased chondrocyte proliferation; inhibited expression of cartilage matrix genes, including Indian hedgehog and the downstream parathyroid hormone‑related protein; and premature conversion of proliferating chondrocytes into hypertrophic chondrocytes, which mineralize their matrix prematurely. Therefore, SOX9 is considered vital for the majority of phases of chondrocyte lineage, from early condensations to the differentiation of proliferating chondrocytes, leading to chondrocyte hypertrophy. It has been reported that SOX9 expression is decreased in osteoarthritis (OA) cartilage. Regeneration or repair of cartilage degradation in OA remains a challenge. Previous studies have indicated that overexpression of SOX9 can promote cartilage repair and can be used as a potential therapeutic agent at the early stages of human OA. The present study identified Scm‑like with four malignant brain tumor domains 2 (SFMBT2) as a novel regulator of SOX9 expression in human chondrocytes. Our previous study revealed that SFMBT2 is negatively regulated in OA cartilage, and decreased levels of SFMBT2 contribute to the catabolic phenotype of chondrocytes. The present study detected increased expression levels of SFMBT2 in early cartilage development and during the early phases of chondrogenesis. Overexpression of SFMBT2 in C28/I2 cells upregulated SOX9 expression in a dose‑dependent manner. Furthermore, SFMBT2 positively regulated C28/I2 cell proliferation and restored the decreased levels of SOX9 in chondrocytes following tumor necrosis factor‑α treatment. Additional studies may reveal novel insights into the molecular mechanism involved and the potential role of SFMBT2 in cartilage repair and OA management.
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Affiliation(s)
- Safdar Hussain
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Mengyao Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Yuanxu Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Nosheen Mushtaq
- Department of Microbiology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Yitong Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Ying Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Nazim Hussain
- Centre for Applied Molecular Biology (CAMB), University of The Punjab, Lahore 53700, Pakistan
| | - Ezra Osoro
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Abubakar Suleiman
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Muhammad Sadiq
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Fujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Yan Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Jian Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Shemin Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi 710061, P.R. China
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11
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Hussain S, Sun M, Min Z, Guo Y, Xu J, Mushtaq N, Heng L, Huang H, Zhao Y, Yuan Y, Hussain N, Zhang F, Han Y, Xu P, Sun J, Lu S. Down-regulated in OA cartilage, SFMBT2 contributes to NF-κB-mediated ECM degradation. J Cell Mol Med 2018; 22:5753-5758. [PMID: 30133133 PMCID: PMC6201222 DOI: 10.1111/jcmm.13826] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/05/2018] [Indexed: 12/24/2022] Open
Abstract
The interplay between anabolic and catabolic factors regulates cartilage matrix homoeostasis. In OA, this balance is disrupted which results in cartilage degradation involving a plethora of inflammatory factors. Here, we identify a novel gene "Scm-like with four MBT domains protein 2" (SFMBT2) negatively regulated in OA cartilage. Articular cartilage from human OA patients undergoing knee arthroplasty surgery exhibited significantly decreased levels of SFMBT2 compared to the normal controls. Down-regulation of SFMBT2 by specific siRNA disturbed the metabolic homoeostasis and led to decreased expression of anabolic genes (SOX9, COL2A1) while increasing the expression of catabolic genes (MMP13 and ADAMTS4), in human chondrocytes. Finally, we revealed that SFMBT2 intervention by siRNA contributed to the catabolic phenotype of human chondrocytes mediated by NF-kB pathway.
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Affiliation(s)
- Safdar Hussain
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Mengyao Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Zixin Min
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yuanxu Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jing Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Nosheen Mushtaq
- Department of Microbiology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Lisong Heng
- Department of Orthopedics and Traumatology, Honghui Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Huang Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yitong Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Ying Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Nazim Hussain
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Fujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Peng Xu
- Department of Orthopedics and Traumatology, Honghui Hospital, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jian Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, China
| | - Shemin Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, China
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12
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Lin R, Wang Y, Chen Q, Liu Z, Xiao S, Wang B, Shi B. TRPM2 promotes the proliferation and invasion of pancreatic ductal adenocarcinoma. Mol Med Rep 2018; 17:7537-7544. [PMID: 29620272 PMCID: PMC5983953 DOI: 10.3892/mmr.2018.8816] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/29/2018] [Indexed: 01/05/2023] Open
Abstract
The aim of the present study was to investigate transient receptor potential cation channel subfamily M member 2 (TRPM2), a promising therapeutic target and biomarker for pancreatic ductal adenocarcinoma (PDAC) prognosis, in addition to determining its effects regarding tumor progression and invasion. PDAC is a fatal disease with a poor prognosis, and its associated pathogenic molecular mechanisms remain to be determined. In the present study, combined analysis using genomic and transcriptomic data from two PDAC studies was performed to discover a survival‑associated biomarker of PDAC. Survival analysis for genes mutated in ≥10 patients was performed using a Kaplan‑Meier curve and tested for significance using a log‑rank test. Furthermore, gene‑expression correlation analysis was performed to determine the genes with the strongest correlations to TRPM2. In addition, a Cell Counting Kit‑8 assay, a scratch wound‑healing assay and a Transwell assay were performed in the present study to investigate the proliferative, invasive and metastatic ability of PANC‑1 cells in TRPM2‑overexpressing and downregulated groups. The mutated TRPM2 gene had a strong negative correlation with patient survival probability compared with the normal control group (P=1.06x10‑4). Expression of TRPM2 was strongly correlated with expression of probable phospholipid‑transporting ATPase IM, γ‑parvin, tudor domain containing 9, Toll‑like receptor 7 and Scm‑like with four MBT domains protein 2 according to the criterion of a correlation coefficient >0.5. Furthermore, the results of the present study demonstrated that the TRPM2 overexpression in a PDAC cell line (PANC‑1) promoted cell proliferation, invasion and metastatic ability. TRPM2 represents a potential therapeutic target and prognostic marker for patients with PDAC. TRPM2 regulates cell proliferation, invasion and migration; however, the underlying mechanism requires further investigation in future studies.
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Affiliation(s)
- Rui Lin
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Yufeng Wang
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Quanning Chen
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Zhongyan Liu
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Shuai Xiao
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Bingyi Wang
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Baomin Shi
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
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13
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Gwak J, Shin JY, Lee K, Hong SK, Oh S, Goh SH, Kim WS, Ju BG. SFMBT2 (Scm-like with four mbt domains 2) negatively regulates cell migration and invasion in prostate cancer cells. Oncotarget 2018; 7:48250-48264. [PMID: 27340776 PMCID: PMC5217015 DOI: 10.18632/oncotarget.10198] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 06/04/2016] [Indexed: 12/12/2022] Open
Abstract
Metastatic prostate cancer is the leading cause of morbidity and mortality in men. In this study, we found that expression level of SFMBT2 is altered during prostate cancer progression and has been associated with the migration and invasion of prostate cancer cells. The expression level of SFMBT2 is high in poorly metastatic prostate cancer cells compared to highly metastatic prostate cancer cells. We also found that SFMBT2 knockdown elevates MMP-2, MMP-3, MMP-9, and MMP-26 expression, leading to increased cell migration and invasion in LNCaP and VCaP cells. SFMBT2 interacts with YY1, RNF2, N-CoR and HDAC1/3, as well as repressive histone marks such as H3K9me2, H4K20me2, and H2AK119Ub which are associated with transcriptional repression. In addition, SFMBT2 knockdown decreased KAI1 gene expression through up-regulation of N-CoR gene expression. Expression of SFMBT2 in prostate cancer was strongly associated with clinicopathological features. Patients having higher Gleason score (≥ 8) had substantially lower SFMBT2 expression than patients with lower Gleason score. Moreover, tail vein or intraprostatic injection of SFMBT2 knockdown LNCaP cells induced metastasis. Taken together, our findings suggest that regulation of SFMBT2 may provide a new therapeutic strategy to control prostate cancer metastasis as well as being a potential biomarker of metastatic prostate cancer.
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Affiliation(s)
- Jungsug Gwak
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Jee Yoon Shin
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Kwanghyun Lee
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Soon Ki Hong
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Sangtaek Oh
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 136-702, Republic of Korea
| | - Sung-Ho Goh
- Research Institute, National Cancer Center, Goyang, Gyeonggi-do 410-769, Republic of Korea
| | - Won Sun Kim
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Bong Gun Ju
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
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14
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Dawes M, Kochan KJ, Riggs PK, Timothy Lightfoot J. Differential miRNA expression in inherently high- and low-active inbred mice. Physiol Rep 2015; 3:3/7/e12469. [PMID: 26229004 PMCID: PMC4552544 DOI: 10.14814/phy2.12469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/26/2015] [Indexed: 01/12/2023] Open
Abstract
Despite established health benefits of regular exercise, the majority of Americans do not meet the recommended levels of physical activity. While it is known that voluntary activity levels are largely heritable, the genetic mechanisms that regulate activity are not well understood. MicroRNAs (miRNAs) are small non-coding RNAs that inhibit transcription by binding to a target gene, inhibiting protein production. The purpose of this study was to investigate differential miRNA expression between inherently high- (C57L/J) and low- (C3H/HeJ) active inbred mice in soleus, extensor digitorum longus (EDL), and nucleus accumbens tissues. Expression was initially determined by miRNA microarray analysis, and selected miRNAs were validated by qRT-PCR. Expression of 13 miRNAs varied between strains in the nucleus accumbens, 20 in soleus, and eight in EDL, by microarray analysis. Two miRNAs were validated by qRT-PCR in the nucleus accumbens; miR-466 was downregulated (∼4 fold; P < 0.0004), and miR-342-5p was upregulated (∼115 fold; P < 0.0001) in high-active mice. MiR-466 was downregulated (∼5 fold; P < 0.0001) in the soleus of high-active mice as well. Interestingly, miR-466 is one of several miRNA families with sequence located in intron 10 of Sfmbt2; miRNAs at this locus are thought to drive imprinting of this gene. “Pathways in cancer” and “TGFβ signaling” were the most significant pathways of putative target genes in both the soleus and nucleus accumbens. Our results are the first to consider differential miRNA expression between high- and low-active mice, and suggest that miRNAs may play a role in regulation of physical activity.
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Affiliation(s)
- Michelle Dawes
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas, USA
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - Penny K Riggs
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - J Timothy Lightfoot
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas, USA
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15
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Poletaeva I, Surina N, Ashapkin V, Fedotova I, Merzalov I, Perepelkina O, Pavlova G. Maternal methyl-enriched diet in rat reduced the audiogenic seizure proneness in progeny. Pharmacol Biochem Behav 2014; 127:21-6. [DOI: 10.1016/j.pbb.2014.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 12/18/2022]
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16
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Surina NM, Ashapkin VV, Merzalov IB, Perepelkina OV, Fedotova IB, Pavlova GV, Poletaeva II. Audiogenic seizure proneness after methyl-enriched diet in ontogeny. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2014; 454:62-4. [PMID: 24659292 DOI: 10.1134/s0012496614010219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Indexed: 11/23/2022]
Affiliation(s)
- N M Surina
- Biology Faculty, Moscow State University, Moscow, 199992, Russia
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