1
|
Mu M, Lu Y, Tu K, Tu L, Guo C, Li Z, Zhang X, Chen Y, Liu X, Xu Q, Huang D, Li X. FAM188B promotes the growth, metastasis, and invasion of hepatocellular carcinoma by targeting the hnRNPA1/PKM2 axis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119773. [PMID: 38844182 DOI: 10.1016/j.bbamcr.2024.119773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
Hepatocellular carcinoma (HCC), the leading cause of cancer-related deaths worldwide, is characterised by rapid growth and marked invasiveness. Accumulating evidence suggests that deubiquitinases play a pivotal role in HCC growth and metastasis. However, the expression of the deubiquitinase FAM188B and its biological functions in HCC remain unknown. The aim of our study was to investigate the potential role of FAM188B in HCC. The expression of FAM188B was significantly upregulated in liver cancer cells compared to normal liver cells, both at the transcriptional and translational levels. Similarly, FAM188B expression was higher in liver cancer tissues than in normal liver tissues. Bioinformatic analysis revealed that high FAM188B expression was associated with poor prognosis in patients with HCC. We further demonstrated that FAM188B knockdown inhibited cell proliferation, epithelial-mesenchymal transition, migration and invasion both in vitro and in vivo. Mechanistically, FAM188B knockdown significantly inhibited the hnRNPA1/PKM2 pathway in HCC cells. FAM188B may inhibit ubiquitin-mediated degradation of hnRNPA1 through deubiquitination. Notably, we observed that the inhibitory effects of FAM188B knockdown on HCC cell proliferation, migration and invasion were reversed when hnRNPA1 expression was restored. In conclusion, FAM188B promotes HCC progression by enhancing the deubiquitination of hnRNPA1 and subsequently activating the hnRNPA1/PKM2 pathway. Therefore, targeting FAM188B is a potential strategy for HCC therapy.
Collapse
Affiliation(s)
- Mingshan Mu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China
| | - Yisong Lu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Linglan Tu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310053, Zhejiang, China
| | - Chaoqin Guo
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China
| | - Zilin Li
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China
| | - Xu Zhang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China
| | - Yihong Chen
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China
| | - Xin Liu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Qiuran Xu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China; Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, Zhejiang, China.
| | - Dongsheng Huang
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, Zhejiang, China.
| | - Xiaoyan Li
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou 310053, Zhejiang, China; Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, Zhejiang, China.
| |
Collapse
|
2
|
Yazdani K, Seshadri S, Tillo D, Yang M, Sibley CD, Vinson C, Schneekloth JS. Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays. Nucleic Acids Res 2023; 51:12020-12030. [PMID: 37962331 PMCID: PMC10711443 DOI: 10.1093/nar/gkad981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.
Collapse
Affiliation(s)
- Kamyar Yazdani
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Srinath Seshadri
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Desiree Tillo
- Genome Analysis Unit, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20892, USA
| | - Mo Yang
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Christopher D Sibley
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20892, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| |
Collapse
|
3
|
Linscott ML, Yildiz Y, Flury S, Newby ML, Pak TR. Age and 17β-Estradiol (E 2) Facilitate Nuclear Export and Argonaute Loading of microRNAs in the Female Brain. Noncoding RNA 2023; 9:74. [PMID: 38133208 PMCID: PMC10745551 DOI: 10.3390/ncrna9060074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Aging in women is accompanied by a dramatic change in circulating sex steroid hormones. Specifically, the primary circulating estrogen, 17β-estradiol (E2), is nearly undetectable in post-menopausal women. This decline is associated with a variety of cognitive and mood disorders, yet hormone replacement therapy is only effective within a narrow window of time surrounding the menopausal transition. Our previous work identified microRNAs as a potential molecular substrate underlying the change in E2 efficacy associated with menopause in advanced age. Specifically, we showed that E2 regulated a small subset of mature miRNAs in the aging female brain. In this study, we hypothesized that E2 regulates the stability of mature miRNAs by altering their subcellular localization and their association with argonaute proteins. We also tested the hypothesis that the RNA binding protein, hnRNP A1, was an important regulator of mature miR-9-5p expression in neuronal cells. Our results demonstrated that E2 treatment affected miRNA subcellular localization and its association with argonaute proteins differently, depending on the length of time following E2 deprivation (i.e., ovariectomy). We also provide strong evidence that hnRNP A1 regulates the transcription of pri-miR-9 and likely plays a posttranscriptional role in mature miR-9-5p turnover. Taken together, these data have important implications for considering the optimal timing for hormone replacement therapy, which might be less dependent on age and more related to how long treatment is delayed following menopause.
Collapse
Affiliation(s)
| | | | | | | | - Toni R. Pak
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (M.L.L.); (Y.Y.); (S.F.); (M.L.N.)
| |
Collapse
|
4
|
Romano F, Di Porzio A, Iaccarino N, Riccardi G, Di Lorenzo R, Laneri S, Pagano B, Amato J, Randazzo A. G-quadruplexes in cancer-related gene promoters: from identification to therapeutic targeting. Expert Opin Ther Pat 2023; 33:745-773. [PMID: 37855085 DOI: 10.1080/13543776.2023.2271168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Guanine-rich DNA sequences can fold into four-stranded noncanonical secondary structures called G-quadruplexes (G4s) which are widely distributed in functional regions of the human genome, such as telomeres and gene promoter regions. Compelling evidence suggests their involvement in key genome functions such as gene expression and genome stability. Notably, the abundance of G4-forming sequences near transcription start sites suggests their potential involvement in regulating oncogenes. AREAS COVERED This review provides an overview of current knowledge on G4s in human oncogene promoters. The most representative G4-binding ligands have also been documented. The objective of this work is to present a comprehensive overview of the most promising targets for the development of novel and highly specific anticancer drugs capable of selectively impacting the expression of individual or a limited number of genes. EXPERT OPINION Modulation of G4 formation by specific ligands has been proposed as a powerful new tool to treat cancer through the control of oncogene expression. Actually, most of G4-binding small molecules seem to simultaneously target a range of gene promoter G4s, potentially influencing several critical driver genes in cancer, thus producing significant therapeutic benefits.
Collapse
Affiliation(s)
- Francesca Romano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| |
Collapse
|
5
|
Zheng Y, Zhong G, He C, Li M. Targeted splicing therapy: new strategies for colorectal cancer. Front Oncol 2023; 13:1222932. [PMID: 37664052 PMCID: PMC10470845 DOI: 10.3389/fonc.2023.1222932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
RNA splicing is the process of forming mature mRNA, which is an essential phase necessary for gene expression and controls many aspects of cell proliferation, survival, and differentiation. Abnormal gene-splicing events are closely related to the development of tumors, and the generation of oncogenic isoform in splicing can promote tumor progression. As a main process of tumor-specific splicing variants, alternative splicing (AS) can promote tumor progression by increasing the production of oncogenic splicing isoforms and/or reducing the production of normal splicing isoforms. This is the focus of current research on the regulation of aberrant tumor splicing. So far, AS has been found to be associated with various aspects of tumor biology, including cell proliferation and invasion, resistance to apoptosis, and sensitivity to different chemotherapeutic drugs. This article will review the abnormal splicing events in colorectal cancer (CRC), especially the tumor-associated splicing variants arising from AS, aiming to offer an insight into CRC-targeted splicing therapy.
Collapse
Affiliation(s)
| | | | - Chengcheng He
- Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | | |
Collapse
|
6
|
Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
Collapse
Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| |
Collapse
|
7
|
Chen Y, Wu Y, Li J, Chen K, Wang W, Ye Z, Feng K, Yang Y, Xu Y, Kang J, Guo X. Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation. Cell Death Discov 2023; 9:244. [PMID: 37452012 PMCID: PMC10349095 DOI: 10.1038/s41420-023-01548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The zinc finger proteins (ZNFs) mediated transcriptional regulation is critical for cell fate transition. However, it is still unclear how the ZNFs realize their specific regulatory roles in the stage-specific determination of cardiomyocyte differentiation. Here, we reported that the zinc fingers and homeoboxes 1 (Zhx1) protein, transiently expressed during the cell fate transition from mesoderm to cardiac progenitors, was indispensable for the proper cardiomyocyte differentiation of mouse and human embryonic stem cells. Moreover, Zhx1 majorly promoted the specification of cardiac progenitors via interacting with hnRNPA1 and co-activated the transcription of a wide range of genes. In-depth mechanistic studies showed that Zhx1 was bound with hnRNPA1 by the amino acid residues (Thr111-His120) of the second Znf domain, thus participating in the formation of cardiac progenitors. Together, our study highlights the unrevealed interaction of Zhx1/hnRNPA1 for activating gene transcription during cardiac progenitor specification and also provides new evidence for the specificity of cell fate determination in cardiomyocyte differentiation.
Collapse
Affiliation(s)
- Yang Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianguo Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Kai Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Wuchan Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zihui Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Ke Feng
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yiwei Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Institute for Advanced Study, Tongji University, Shanghai, 200092, China.
| |
Collapse
|
8
|
Pavlova I, Iudin M, Surdina A, Severov V, Varizhuk A. G-Quadruplexes in Nuclear Biomolecular Condensates. Genes (Basel) 2023; 14:genes14051076. [PMID: 37239436 DOI: 10.3390/genes14051076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates.
Collapse
Affiliation(s)
- Iuliia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Mikhail Iudin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anastasiya Surdina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| |
Collapse
|
9
|
Yazdani K, Seshadri S, Tillo D, Vinson C, Schneekloth JS. DECODING COMPLEXITY IN BIOMOLECULAR RECOGNITION OF DNA I-MOTIFS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537548. [PMID: 37131644 PMCID: PMC10153190 DOI: 10.1101/2023.04.19.537548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10,976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone, and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.
Collapse
Affiliation(s)
- Kamyar Yazdani
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702
| | - Srinath Seshadri
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702
| | - Desiree Tillo
- Genome Analysis Unit, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20892
| | - Charles Vinson
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, 37 Convent Dr., Bethesda MD 20892
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702
| |
Collapse
|
10
|
Cao Z, Guan L, Yu R, Yang F, Chen J. High Expression of Heterogeneous Nuclear Ribonucleoprotein A1 Facilitates Hepatocellular Carcinoma Growth. J Hepatocell Carcinoma 2023; 10:517-530. [PMID: 37034304 PMCID: PMC10075271 DOI: 10.2147/jhc.s402247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) represents one of the most common tumors in the world. Our study aims to explore new markers and therapeutic targets for HCC. Heterogeneous Nuclear ribonucleoprotein A1 (hnRNPA1) has recently been found to be involved in the progression of several types of cancer, but its role in HCC remains uncovered. Methods We performed bioinformatic analysis to preliminarily show the relationship between hnRNPA1 and liver cancer. Then the correlation of the hnRNPA1 gene expression with clinicopathological characteristics of HCC patients was verified by human liver cancer tissue microarrays. The functional role of this gene was evaluated by in vivo and vitro experiments. Results Results showed that the expression of hnRNPA1 was upregulated in HCC tissues and was associated with pathological stage of HCC patients. Knockdown of hnRNPA1 gene markedly inhibited tumor growth in vivo, and reversed the effects on proliferation, migration and invasion and promoted apoptosis in vitro. Furthermore, down-regulation of hnRNPA1 gene expression can inhibit the activity of the MEK/ERK pathway. Conclusion In our work, we combined bioinformatic analysis with in vivo and in vitro experiments to initially elucidate the function of hnRNPA1 in liver cancer, which may help to explore biomarkers and therapeutic targets for HCC patients.
Collapse
Affiliation(s)
- Ziyi Cao
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
| | - Li Guan
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
| | - Runzhi Yu
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
| | - Fan Yang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, 200040, People’s Republic of China
| | - Jie Chen
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, People’s Republic of China
- Correspondence: Jie Chen; Fan Yang, Email ;
| |
Collapse
|
11
|
Role of Heterogeneous Nuclear Ribonucleoproteins in the Cancer-Immune Landscape. Int J Mol Sci 2023; 24:ijms24065086. [PMID: 36982162 PMCID: PMC10049280 DOI: 10.3390/ijms24065086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Cancer remains the second leading cause of death, accounting for approximately 20% of all fatalities. Evolving cancer cells and a dysregulated immune system create complex tumor environments that fuel tumor growth, metastasis, and resistance. Over the past decades, significant progress in deciphering cancer cell behavior and recognizing the immune system as a hallmark of tumorigenesis has been achieved. However, the underlying mechanisms controlling the evolving cancer-immune landscape remain mostly unexplored. Heterogeneous nuclear ribonuclear proteins (hnRNP), a highly conserved family of RNA-binding proteins, have vital roles in critical cellular processes, including transcription, post-transcriptional modifications, and translation. Dysregulation of hnRNP is a critical contributor to cancer development and resistance. HnRNP contribute to the diversity of tumor and immune-associated aberrant proteomes by controlling alternative splicing and translation. They can also promote cancer-associated gene expression by regulating transcription factors, binding to DNA directly, or promoting chromatin remodeling. HnRNP are emerging as newly recognized mRNA readers. Here, we review the roles of hnRNP as regulators of the cancer-immune landscape. Dissecting the molecular functions of hnRNP will provide a better understanding of cancer-immune biology and will impact the development of new approaches to control and treat cancer.
Collapse
|
12
|
Ma Y, Yang Y, Xin J, He L, Hu Z, Gao T, Pan F, Guo Z. RNA G-Quadruplex within the 5'-UTR of FEN1 Regulates mRNA Stability under Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12020276. [PMID: 36829835 PMCID: PMC9952066 DOI: 10.3390/antiox12020276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Reactive oxygen species (ROS) are a group of highly oxidative molecules that induce DNA damage, affecting DNA damage response (DDR) and gene expression. It is now recognized that DNA base excision repair (BER) is one of the important pathways responsible for sensing oxidative stress to eliminate DNA damage, in which FEN1 plays an important role in this process. However, the regulation of FEN1 under oxidative stress is still unclear. Here, we identified a novel RNA G-quadruplex (rG4) sequence in the 5'untranslated region (5'UTR) of FEN1 mRNA. Under oxidative stress, the G bases in the G4-forming sequence can be oxidized by ROS, resulting in structural disruption of the G-quadruplex. ROS or TMPyP4, a G4-structural ligand, disrupted the formation of G4 structure and affected the expression of FEN1. Furthermore, pull-down experiments identified a novel FEN1 rG4-binding protein, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), and cellular studies have shown that hnRNPA1 plays an important role in regulating FEN1 expression. This work demonstrates that rG4 acts as a ROS sensor in the 5'UTR of FEN1 mRNA. Taken together, these results suggest a novel role for rG4 in translational control under oxidative stress.
Collapse
Affiliation(s)
- Ying Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jingyu Xin
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
| |
Collapse
|
13
|
Feng J, Zhou J, Lin Y, Huang W. hnRNP A1 in RNA metabolism regulation and as a potential therapeutic target. Front Pharmacol 2022; 13:986409. [PMID: 36339596 PMCID: PMC9634572 DOI: 10.3389/fphar.2022.986409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/10/2022] [Indexed: 11/22/2022] Open
Abstract
Abnormal RNA metabolism, regulated by various RNA binding proteins, can have functional consequences for multiple diseases. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an important RNA binding protein, that regulates various RNA metabolic processes, including transcription, alternative splicing of pre-mRNA, translation, miRNA processing and mRNA stability. As a potent splicing factor, hnRNP A1 can regulate multiple splicing events, including itself, collaborating with other cooperative or antagonistical splicing factors by binding to splicing sites and regulatory elements in exons or introns. hnRNP A1 can modulate gene transcription by directly interacting with promoters or indirectly impacting Pol II activities. Moreover, by interacting with the internal ribosome entry site (IRES) or 3′-UTR of mRNAs, hnRNP A1 can affect mRNA translation. hnRNP A1 can alter the stability of mRNAs by binding to specific locations of 3′-UTR, miRNAs biogenesis and Nonsense-mediated mRNA decay (NMD) pathway. In this review, we conclude the selective sites where hnRNP A1 binds to RNA and DNA, and the co-regulatory factors that interact with hnRNP A1. Given the dysregulation of hnRNP A1 in diverse diseases, especially in cancers and neurodegeneration diseases, targeting hnRNP A1 for therapeutic treatment is extremely promising. Therefore, this review also provides the small-molecule drugs, biomedicines and novel strategies targeting hnRNP A1 for therapeutic purposes.
Collapse
|
14
|
Zhao B, Lv X, Zhao X, Maimaitiaili S, Zhang Y, Su K, Yu H, Liu C, Qiao T. Tumor-Promoting Actions of HNRNP A1 in HCC Are Associated with Cell Cycle, Mitochondrial Dynamics, and Necroptosis. Int J Mol Sci 2022; 23:ijms231810209. [PMID: 36142139 PMCID: PMC9499416 DOI: 10.3390/ijms231810209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent malignancies in the world. Although increasing evidence supports the role of heterogeneous ribonucleoprotein particle A1 (HNRNP A1) in tumor progression, the function of HNRNP A1 in HCC remains unclear. Here, we focused on the role of HNRNP A1 in the development of HCC. In this study, we found HNRNP A1 participates in many aspects of HCC, such as progression and prognosis. Our results showed that HNRNP A1 is upregulated in human HCC tissues and cell lines. High expression of HNRNP A1 can promote the proliferation, migration, and invasion in HCC cells and accelerate tumor progression in mice. Moreover, we found that HNRNP A1 prevents the senescence process of HCC cells. Knocking down of HNRNP A1 promotes the expression of P16INK4, which arrests the cell cycle and then induces the senescence phenotype in HCC cells. Furthermore, we found that HNRNP A1 regulated necroptosis and mitochondrial dynamics. In summary, our study indicates that HNRNP A1 promotes the development of HCC, which suggests a potential therapeutic target for HCC.
Collapse
Affiliation(s)
- Biao Zhao
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Xiaochen Lv
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Xiaoqi Zhao
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Subinuer Maimaitiaili
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yuheng Zhang
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Ke Su
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Hang Yu
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
- Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210008, China
| | - Cheng Liu
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
- Correspondence: (C.L.); (T.Q.)
| | - Tong Qiao
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
- Correspondence: (C.L.); (T.Q.)
| |
Collapse
|
15
|
Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
Collapse
Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
| |
Collapse
|
16
|
Heterogeneous nuclear ribonucleoprotein A/B: an emerging group of cancer biomarkers and therapeutic targets. Cell Death Dis 2022; 8:337. [PMID: 35879279 PMCID: PMC9314375 DOI: 10.1038/s41420-022-01129-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein A/B (hnRNPA/B) is one of the core members of the RNA binding protein (RBP) hnRNPs family, including four main subtypes, A0, A1, A2/B1 and A3, which share the similar structure and functions. With the advance in understanding the molecular biology of hnRNPA/B, it has been gradually revealed that hnRNPA/B plays a critical role in almost the entire steps of RNA life cycle and its aberrant expression and mutation have important effects on the occurrence and progression of various cancers. This review focuses on the clinical significance of hnRNPA/B in various cancers and systematically summarizes its biological function and molecular mechanisms.
Collapse
|
17
|
Cao W, Lei S, Zeng Z, Xiao C, Sun B, Xie P, Li Y, Luo D, Yu W. Transformer 2 alpha homolog is a downstream gene of hypoxia-inducible factor 1 subunit alpha and is involved in the progression of pancreatic cancer. Bioengineered 2022; 13:13238-13251. [PMID: 35635094 PMCID: PMC9275993 DOI: 10.1080/21655979.2022.2079243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/06/2022] Open
Abstract
Intratumoral hypoxia is a common feature of pancreatic cancer (PC) and also plays a role in its progression. However, hypoxia-regulated signatures in PC are still not completely understood. This study aimed to identify core hypoxia-associated genes and determine their underlying molecular mechanisms in PC cells. Transformer 2 alpha homolog (TRA2A) was found to be an important hypoxia-associated gene, which was upregulated in PC tissues and in PC cells cultured under hypoxia. High TRA2A expression was associated with advanced stage, poor differentiation, and lymph node metastasis. Under normoxic and hypoxic conditions, knockdown of TRA2A both markedly suppressed PC cell proliferation and motility in vitro and in vivo, as well as activation of the AKT pathway. Hypoxia-inducible factor 1 subunit alpha (HIF1α) upregulated the transcription of TRA2A by directly binding to its promoter. TRA2A showed a co-expression relationship with HIF1α in PC tissues. Overexpression of TRA2A alleviated the pro-inhibitive functions of HIF1α-inhibition on PC cell proliferation and motility under hypoxia. In conclusion, TRA2A is a crucial downstream gene of HIF1α that accelerates the proliferation and motility of PC cells. TRA2A may be a novel and practical molecular target for investigating the hypoxic response of PC cells.Abbreviations: TRA2A, transformer 2A protein; PC, pancreatic cancer; HIF1α, hypoxia-inducible factor 1-alpha; GEO, Gene Expression Omnibus; IHC, immunohistochemical staining.
Collapse
Affiliation(s)
- Wenpeng Cao
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Shan Lei
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhirui Zeng
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Chaolun Xiao
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Baofei Sun
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Peng Xie
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, School of Basic Medical, Guizhou Medical University, Guiyang, Guizhou, China
- Key Laboratory of Medical Molecular Biology, School of Basic Medical, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yumei Li
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daopeng Luo
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wenfeng Yu
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, School of Basic Medical, Guizhou Medical University, Guiyang, Guizhou, China
- Key Laboratory of Medical Molecular Biology, School of Basic Medical, Guizhou Medical University, Guiyang, Guizhou, China
| |
Collapse
|
18
|
Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
Collapse
Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
| |
Collapse
|
19
|
Ferino A, Marquevielle J, Choudhary H, Cinque G, Robert C, Bourdoncle A, Picco R, Mergny JL, Salgado GF, Xodo LE. hnRNPA1/UP1 Unfolds KRAS G-Quadruplexes and Feeds a Regulatory Axis Controlling Gene Expression. ACS OMEGA 2021; 6:34092-34106. [PMID: 34926957 PMCID: PMC8675163 DOI: 10.1021/acsomega.1c05538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/12/2021] [Indexed: 05/20/2023]
Abstract
Recent studies have proven that the genetic landscape of pancreatic cancer is dominated by the KRAS oncogene. Its transcription is controlled by a G-rich motif (called 32R) located immediately upstream of the TSS. 32R may fold into a G-quadruplex (G4) in equilibrium between two G4 conformers: G9T (T M = 61.2 °C) and G25T (T M = 54.7 °C). We found that both G4s bind to hnRNPA1 and its proteolytic fragment UP1, promoting several contacts with the RRM protein domains. 1D NMR analysis of DNA imino protons shows that, upon binding to UP1, G25T is readily unfolded at both 5' and 3' tetrads, while G9T is only partially unfolded. The impact of hnRNPA1 on KRAS expression was determined by comparing Panc-1 cells with two Panc-1 knockout cell lines in which hnRNPA1 was deleted by the CRISPR/Cas9 technology. The results showed that the expression of KRAS is inhibited in the knockout cell lines, indicating that hnRNPA1 is essential for the transcription of KRAS. In addition, the knockout cell lines, compared to normal Panc-1 cells, show a dramatic decrease in cell growth and capacity of colony formation. Pull-down and Western blot experiments indicate that conformer G25T is a better platform than conformer G9T for the assembly of the transcription preinitiation complex with PARP1, Ku70, MAZ, and hnRNPA1. Together, our data prove that hnRNPA1, being a key transcription factor for the activation of KRAS, can be a new therapeutic target for the rational design of anticancer strategies.
Collapse
Affiliation(s)
- Annalisa Ferino
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Julien Marquevielle
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Himanshi Choudhary
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Giorgio Cinque
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Coralie Robert
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Anne Bourdoncle
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Raffaella Picco
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Jean-Louis Mergny
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
- Laboratoire
d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Route de Saclay, Palaiseau Cedex 91128, France
| | - Gilmar F. Salgado
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Luigi E. Xodo
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
- luigi.xodo@uniud.it
| |
Collapse
|
20
|
Longley MJ, Lee J, Jung J, Lohoff FW. Epigenetics of alcohol use disorder-A review of recent advances in DNA methylation profiling. Addict Biol 2021; 26:e13006. [PMID: 33538087 PMCID: PMC8596445 DOI: 10.1111/adb.13006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) is a major contributor to morbidity and mortality worldwide. Although there is a heritable component, the etiology of AUD is complex and can involve environmental exposures like trauma and can be associated with many different patterns of alcohol consumption. Epigenetic modifications, which can mediate the influence of genetic variants and environmental variables on gene expression, have emerged as an important area of AUD research. Over the past decade, the number of studies investigating AUD and DNA methylation, a form of epigenetic modification, has grown rapidly. Yet we are still far from understanding how DNA methylation contributes to or reflects aspects of AUD. In this paper, we reviewed studies of DNA methylation and AUD and discussed how the field has evolved. We found that global DNA and candidate DNA methylation studies did not produce replicable results. To assess whether findings of epigenome-wide association studies (EWAS) were replicated, we aggregated significant findings across studies and identified 184 genes and 15 gene ontological pathways that were differentially methylated in at least two studies and four genes and three gene ontological pathways that were differentially methylated in three studies. These genes and pathways repeatedly found enrichment of immune processes, which is in line with recent developments suggesting that the immune system may be altered in AUD. Finally, we assess the current limitations of studies of DNA methylation and AUD and make recommendations on how to design future studies to resolve outstanding questions.
Collapse
Affiliation(s)
- Martha J. Longley
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Falk W. Lohoff
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| |
Collapse
|
21
|
Jiang R, Su G, Chen X, Chen S, Li Q, Xie B, Zhao Y. Esculetin inhibits endometrial cancer proliferation and promotes apoptosis via hnRNPA1 to downregulate BCLXL and XIAP. Cancer Lett 2021; 521:308-321. [PMID: 34480971 DOI: 10.1016/j.canlet.2021.08.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/10/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022]
Abstract
Endometrial cancer represents one of the most common gynecological tumors in the world. Advanced and relapsed patients rely on drug therapy. Therefore, it is extremely important to seek more effective targeted drugs. This study found that esculetin has an anti-tumor effect on endometrial cancer through cellular proliferation and apoptosis. At the same time, its anti-tumor effect has also been verified in human endometrial cancer xenograft models in nude mice. Western blot results showed that BCLXL, XIAP, and pAKT protein expression level were down-regulated. A pulldown experiment and LC-MS/MS analysis technology revealed that esculetin targets the hnRNPA1 protein. Cellular proliferation experiments following si-hnRNPA1 transfection verified the tumor-promoting effect of hnRNPA1 in endometrial cancer cells. Nuclear and cytoplasmic separation experiment demonstrated esculetin affecting the export of the hnRNPA1/mRNA complex from the nucleus into the cytoplasm. Thus, esculetin targets hnRNPA1, thereby downregulates BCLXL and XIAP mRNA transcription and translation, resulting in apoptosis and an arrest in proliferation.
Collapse
Affiliation(s)
- Ruqi Jiang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Guifeng Su
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Qianhui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| |
Collapse
|
22
|
Thibault PA, Ganesan A, Kalyaanamoorthy S, Clarke JPWE, Salapa HE, Levin MC. hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease. BIOLOGY 2021; 10:biology10080712. [PMID: 34439945 PMCID: PMC8389229 DOI: 10.3390/biology10080712] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022]
Abstract
The hnRNP A/B family of proteins is canonically central to cellular RNA metabolism, but due to their highly conserved nature, the functional differences between hnRNP A1, A2/B1, A0, and A3 are often overlooked. In this review, we explore and identify the shared and disparate homeostatic and disease-related functions of the hnRNP A/B family proteins, highlighting areas where the proteins have not been clearly differentiated. Herein, we provide a comprehensive assembly of the literature on these proteins. We find that there are critical gaps in our grasp of A/B proteins' alternative splice isoforms, structures, regulation, and tissue and cell-type-specific functions, and propose that future mechanistic research integrating multiple A/B proteins will significantly improve our understanding of how this essential protein family contributes to cell homeostasis and disease.
Collapse
Affiliation(s)
- Patricia A. Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Aravindhan Ganesan
- ArGan’s Lab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Joseph-Patrick W. E. Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Hannah E. Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Michael C. Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Correspondence:
| |
Collapse
|
23
|
Jeong KY, Park M. Poly adenosine diphosphate-ribosylation, a promising target for colorectal cancer treatment. World J Gastrointest Oncol 2021. [PMID: 34163574 DOI: 10.4251/wjgo.v13.i6.574.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of colorectal cancer (CRC) can result from changes in a variety of cellular systems within the tumor microenvironment. Particularly, it is primarily associated with genomic instability that is the gradual accumulation of genetic and epigenetic changes consisting of a characteristic set of mutations crucial for pathways in CRC progression. Based on this background, the potential to focus on poly [adenosine diphosphate (ADP)-ribose] polymerase (PARP)-1 and poly-ADP ribosylation (PARylation) as the main causes of malignant formation of CRC may be considered. One of the important functions of PARP-1 and PARylation is its deoxyribonucleic acid (DNA) repair function, which plays a pivotal role in the DNA damage response and prevention of DNA damage maintaining the redox homeostasis involved in the regulation of oxidation and superoxide. PARP-1 and PARylation can also alter epigenetic markers and chromatin structure involved in transcriptional regulation for the oncogenes or tumor suppressor genes by remodeling histone and chromatin enzymes. Given the high importance of these processes in CRC, it can be considered that PARP-1 and PARylation are at the forefront of the pathological changes required for CRC progression. Therefore, this review addresses the current molecular biological features for understanding the multifactorial function of PARP-1 and PARylation in CRC related to the aforementioned roles; furthermore, it presents a summary of recent approaches with PARP-1 inhibition in non-clinical and clinical studies targeting CRC. This understanding could help embrace the importance of targeting PARP-1 and PARylation in the treatment of CRC, which may present the potential to identify various research topics that can be challenged both non-clinically and clinically.
Collapse
Affiliation(s)
- Keun-Yeong Jeong
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea.
| | - Minhee Park
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea
| |
Collapse
|
24
|
Jeong KY, Park M. Poly adenosine diphosphate-ribosylation, a promising target for colorectal cancer treatment. World J Gastrointest Oncol 2021; 13:574-588. [PMID: 34163574 PMCID: PMC8204356 DOI: 10.4251/wjgo.v13.i6.574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/22/2021] [Accepted: 05/08/2021] [Indexed: 02/06/2023] Open
Abstract
The development of colorectal cancer (CRC) can result from changes in a variety of cellular systems within the tumor microenvironment. Particularly, it is primarily associated with genomic instability that is the gradual accumulation of genetic and epigenetic changes consisting of a characteristic set of mutations crucial for pathways in CRC progression. Based on this background, the potential to focus on poly [adenosine diphosphate (ADP)-ribose] polymerase (PARP)-1 and poly-ADP ribosylation (PARylation) as the main causes of malignant formation of CRC may be considered. One of the important functions of PARP-1 and PARylation is its deoxyribonucleic acid (DNA) repair function, which plays a pivotal role in the DNA damage response and prevention of DNA damage maintaining the redox homeostasis involved in the regulation of oxidation and superoxide. PARP-1 and PARylation can also alter epigenetic markers and chromatin structure involved in transcriptional regulation for the oncogenes or tumor suppressor genes by remodeling histone and chromatin enzymes. Given the high importance of these processes in CRC, it can be considered that PARP-1 and PARylation are at the forefront of the pathological changes required for CRC progression. Therefore, this review addresses the current molecular biological features for understanding the multifactorial function of PARP-1 and PARylation in CRC related to the aforementioned roles; furthermore, it presents a summary of recent approaches with PARP-1 inhibition in non-clinical and clinical studies targeting CRC. This understanding could help embrace the importance of targeting PARP-1 and PARylation in the treatment of CRC, which may present the potential to identify various research topics that can be challenged both non-clinically and clinically.
Collapse
Affiliation(s)
- Keun-Yeong Jeong
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea
| | - Minhee Park
- Research and Development, Metimedi Pharmaceuticals, Incheon 22006, South Korea
| |
Collapse
|
25
|
Clarke JP, Thibault PA, Salapa HE, Levin MC. A Comprehensive Analysis of the Role of hnRNP A1 Function and Dysfunction in the Pathogenesis of Neurodegenerative Disease. Front Mol Biosci 2021; 8:659610. [PMID: 33912591 PMCID: PMC8072284 DOI: 10.3389/fmolb.2021.659610] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a member of the hnRNP family of conserved proteins that is involved in RNA transcription, pre-mRNA splicing, mRNA transport, protein translation, microRNA processing, telomere maintenance and the regulation of transcription factor activity. HnRNP A1 is ubiquitously, yet differentially, expressed in many cell types, and due to post-translational modifications, can vary in its molecular function. While a plethora of knowledge is known about the function and dysfunction of hnRNP A1 in diseases other than neurodegenerative disease (e.g., cancer), numerous studies in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, multiple sclerosis, spinal muscular atrophy, Alzheimer’s disease, and Huntington’s disease have found that the dysregulation of hnRNP A1 may contribute to disease pathogenesis. How hnRNP A1 mechanistically contributes to these diseases, and whether mutations and/or altered post-translational modifications contribute to pathogenesis, however, is currently under investigation. The aim of this comprehensive review is to first describe the background of hnRNP A1, including its structure, biological functions in RNA metabolism and the post-translational modifications known to modify its function. With this knowledge, the review then describes the influence of hnRNP A1 in neurodegenerative disease, and how its dysfunction may contribute the pathogenesis.
Collapse
Affiliation(s)
- Joseph P Clarke
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael C Levin
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
26
|
Huang YS, Lu KC, Chao HW, Chen A, Chao TK, Guo CY, Hsieh HY, Shih HM, Sytwu HK, Wu CC. The MTNR1A mRNA is stabilized by the cytoplasmic hnRNPL in renal tubular cells. J Cell Physiol 2021; 236:2023-2035. [PMID: 32730662 DOI: 10.1002/jcp.29988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022]
Abstract
The downregulation of melatonin receptor 1A (MTNR1A) is associated with a range of pathological conditions, including membranous nephropathy. Knowledge of the mechanism underlying MTNR1A expression has been limited to the transcriptional regulation level. Here, RNA interference screening in human kidney cells revealed that heterogeneous nuclear ribonucleoprotein L (hnRNPL) upregulated MTNR1A RNA post-transcriptionally. hnRNPL knockdown or overexpression led to increased or decreased levels of cyclic adenosine monophosphate-responsive element-binding protein phosphorylation, respectively. Molecular studies showed that cytoplasmic hnRNPL exerts a stabilizing effect on the MTNR1A transcript through CA-repeat elements in its coding region. Further studies revealed that the interaction between hnRNPL and MTNR1A serves to protect MNTR1A RNA degradation by the exosome component 10 protein. MTNR1A, but not hnRNPL, displays a diurnal rhythm in mouse kidneys. Enhanced levels of MTNR1A recorded at midnight correlated with robust binding activity between cytoplasmic hnRNPL and the MTNR1A transcript. Both hnRNPL and MTNR1A were decreased in the cytoplasm of tubular epithelial cells from experimental membranous nephropathy kidneys, supporting their clinical relevance. Collectively, our data identified cytoplasmic hnRNPL as a novel player in the upregulation of MTNR1A expression in renal tubular epithelial cells, and as a potential therapeutic target.
Collapse
MESH Headings
- Animals
- Cell Line
- Circadian Rhythm/genetics
- Cyclic AMP Response Element-Binding Protein/metabolism
- Cytoplasm/metabolism
- Epithelial Cells/metabolism
- Exoribonucleases/metabolism
- Exosome Multienzyme Ribonuclease Complex/metabolism
- Glomerulonephritis, Membranous/genetics
- Glomerulonephritis, Membranous/pathology
- Heterogeneous-Nuclear Ribonucleoprotein L/metabolism
- Humans
- Kidney Tubules/metabolism
- Kidney Tubules/pathology
- Mice, Inbred BALB C
- Models, Biological
- Open Reading Frames/genetics
- Phosphorylation
- RNA Stability/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, Melatonin, MT1/genetics
- Receptor, Melatonin, MT1/metabolism
- Repetitive Sequences, Nucleic Acid/genetics
- Up-Regulation/genetics
- Mice
Collapse
Affiliation(s)
- Yen-Sung Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Hsu-Wen Chao
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ann Chen
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Yi Guo
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hsin-Yi Hsieh
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Chao Wu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| |
Collapse
|
27
|
Pan Y, Xie Z, Cen S, Li M, Liu W, Tang S, Ye G, Li J, Zheng G, Li Z, Yu W, Wang P, Wu Y, Shen H. Long noncoding RNA repressor of adipogenesis negatively regulates the adipogenic differentiation of mesenchymal stem cells through the hnRNP A1-PTX3-ERK axis. Clin Transl Med 2020; 10:e227. [PMID: 33252864 PMCID: PMC7648959 DOI: 10.1002/ctm2.227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) are pluripotent stem cells that can differentiate via osteogenesis and adipogenesis. The mechanism underlying MSC lineage commitment still remains incompletely elucidated. Understanding the regulatory mechanism of MSC differentiation will help researchers induce MSCs toward specific lineages for clinical use. In this research, we intended to figure out the long noncoding RNA (lncRNA) that plays a central role in MSC fate determination and explore its application value in tissue engineering. METHODS The expression pattern of lncRNAs during MSC osteogenesis/adipogenesis was detected by microarray and qRT-PCR. Lentivirus and siRNAs were constructed to regulate the expression of lncRNA repressor of adipogenesis (ROA). MSC osteogenesis/adipogenesis was evaluated by western blot and alizarin red/oil red staining. An adipokine array was used to select the paracrine/autocrine factor PTX3, followed by RNA interference or recombinant human protein stimulation to confirm its function. The activation of signaling pathways was also detected by western blot, and a small molecule inhibitor, SCH772984, was used to inhibit the activation of the ERK pathway. The interaction between ROA and hnRNP A1 was detected by RNA pull-down and RIP assays. Luciferase reporter and chromatin immunoprecipitation assays were used to confirm the binding of hnRNP A1 to the PTX3 promotor. Additionally, an in vivo adipogenesis experiment was conducted to evaluate the regulatory value of ROA in tissue engineering. RESULTS In this study, we demonstrated that MSC adipogenesis is regulated by lncRNA ROA both in vitro and in vivo. Mechanistically, ROA inhibits MSC adipogenesis by downregulating the expression of the key autocrine/paracrine factor PTX3 and the downstream ERK pathway. This downregulation was achieved through transcription inhibition by impeding hnRNP A1 from binding to the promoter of PTX3. CONCLUSIONS ROA negatively regulates MSC adipogenesis through the hnRNP A1-PTX3-ERK axis. ROA may be an effective target for modulating MSCs in tissue engineering.
Collapse
Affiliation(s)
- Yiqian Pan
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Zhongyu Xie
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
| | - Shuizhong Cen
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
- Department of OrthopedicsZhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Ming Li
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Wenjie Liu
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
| | - Su'an Tang
- Clinical Research CenterZhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Guiwen Ye
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Jinteng Li
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
| | - Guan Zheng
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
| | - Zhaofeng Li
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Wenhui Yu
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Peng Wang
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
| | - Yanfeng Wu
- Center for BiotherapySun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Huiyong Shen
- Department of OrthopedicsThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenChina
- Department of OrthopedicsSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouChina
| |
Collapse
|
28
|
Wang YP, Zhao YJ, Kong XL. A metalloproteinase of the disintegrin and metalloproteinases and the ThromboSpondin Motifs 6 as a novel marker for colon cancer: functional experiments. Genet Mol Biol 2020; 43:e20190266. [PMID: 33063817 PMCID: PMC7564043 DOI: 10.1590/1678-4685-gmb-2019-0266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 05/05/2020] [Indexed: 12/28/2022] Open
Abstract
Herein, we aimed to investigate the functions of ADAMTS6 in colon cancer and its potential mechanism. Based on the data acquired from TCGA database, we revealed that ADAMTS6 was highly expressed in colon cancer tissues, and high expression of ADAMTS6 predicted worse prognosis in patients with colon cancer. Moreover, qRT-PCR demonstrated that the levels of ADAMTS6 were higher in colon cancer cell lines (NCI-H508, Caco-2, CW-2 and HCT 116) than that in normal control cell line CCD-18Co. Functional experiments displayed that depletion of ADAMTS6 repressed NCI-H508 cell growth, invasion and migration whilst overexpression of ADAMTS6 facilitated Caco-2 cell growth, invasion and migration. Moreover, ADAMTS6 silencing enhanced the protein expression of E-cadherin and reduced the levels of N-cadherin, Vimentin and Snail in NCI-H508 cells, whereas ADAMTS6 overexpression showed the counter effects in Caco-2 cells. The protein levels of p-AKT and p-p65 were decreased by depletion of ADAMTS6 in NCI-H508 cells, while their levels were enhanced by overexpression of ADAMTS6 in Caco-2 cells. These consequences indicated that the accelerating effect of ADAMTS6 on colon cancer cell growth, migration and invasion might be achieved by modulating EMT and AKT/NF-κB signaling pathway, offering important foundations for colon cancer treatment.
Collapse
Affiliation(s)
- Yun-Peng Wang
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Digestive Endoscopy, Jinan, Shandong, P.R. China
| | - Yu-Jie Zhao
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Digestive Endoscopy, Jinan, Shandong, P.R. China
| | - Xiang-Liang Kong
- The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Digestive Endoscopy, Jinan, Shandong, P.R. China
| |
Collapse
|
29
|
Luo Y, Liu F, Ma J, Fu Y, Gui R. A novel epigenetic regulation of circFoxp1 on Foxp1 in colon cancer cells. Cell Death Dis 2020; 11:782. [PMID: 32951006 PMCID: PMC7502072 DOI: 10.1038/s41419-020-03007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 01/17/2023]
Abstract
Foxp1 is a tumor suppressor in colon cancer. However, circFoxp1 derived from Foxp1 is an oncogene. In this study, we aim to investigate the role of circFoxp1 in colon cancer and the regulatory mechanism between circFoxp1 and Foxp1. 78 human colon tumor tissues and the matched paracancerous tissues were collected. Quantitative polymerase chain reaction, immunohistochemistry, quantitative methylation-specific PCR, chromatin immunoprecipitation assay, CCK-8 assay, and Tumor xenograft in nude mice were performed. The expression of circFoxp1 was increased and Foxp1 was reduced in colon cancer tissues, which were associated with a poor overall survival rate of the patients with colon cancer. CircFoxp1 recruited DNMT1 to the promoter of Foxp1, leading to promotor hypermethylation, thereby inhibiting Foxp1 transcription. Interfering circFoxp1 by siRNA in SW620 cells significantly inhibited cell viability, while knockdown Foxp1 expression partially restored SW620 cell viability. In addition, knockdown of circFoxp1 significantly sensitized colon cancer cells to Capecitabine in vitro and vivo through regulating Foxp1. We discovered a novel epigenetic pathway that circFoxp1 regulated Foxp1 in colon cancer cells. CircFoxp1 may regulate DNA methylation and demethylation to coordinate colon cancer cell proliferation and participate in chemotherapy drug responses. Therefore, circFoxp1 may be a potential therapeutic target for colon cancer.
Collapse
Affiliation(s)
- Yanwei Luo
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China
| | - Fengxia Liu
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China
| | - Jinqi Ma
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China
| | - Yunfeng Fu
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China.
| | - Rong Gui
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China.
| |
Collapse
|
30
|
Singh M, Wang S, Joo H, Ye Z, Christison KM, Hekman R, Vierra C, Xue L. Use of neomycin as a structured amino-containing side chain motif for phenanthroline-based G-quadruplex ligands and telomerase inhibitors. Chem Biol Drug Des 2020; 96:1292-1304. [PMID: 32516846 DOI: 10.1111/cbdd.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/31/2020] [Indexed: 01/05/2023]
Abstract
In this paper, we report the synthesis of a phenanthroline and neomycin conjugate (7). Compound 7 binds to a human telomeric G-quadruplex (G1) with a higher affinity compared with its parent compounds (phenanthroline and neomycin), which is determined by several biophysical studies. Compound 7 shows good selectivity for G-quadruplex (G4) DNA over duplex DNA. The binding of 7 with G1 is predominantly enthalpy-driven, and the binding stoichiometry of 7 with G1 is one for the tight-binding event as determined by ESI mass spectrometry. A plausible binding mode is a synergistic effect of end-stacking and groove interactions, as indicated by docking studies. Compound 7 can inhibit human telomerase activity at low micromolar concentrations, which is more potent than previously reported 5-substituted phenanthroline derivatives.
Collapse
Affiliation(s)
- Mandeep Singh
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Siwen Wang
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Zhihan Ye
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | | | - Ryan Hekman
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Craig Vierra
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| |
Collapse
|
31
|
Bone marrow mesenchymal stem cell-derived exosomal miR-206 inhibits osteosarcoma progression by targeting TRA2B. Cancer Lett 2020; 490:54-65. [PMID: 32682951 DOI: 10.1016/j.canlet.2020.07.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023]
Abstract
Osteosarcoma is the most common primary malignant bone tumor in young people. Recently, extracellular vesicles, especially exosomes, have been reported to play an increasingly important role in the development of many types of tumors. In this research, we found that overexpression of transformer 2β (TRA2B) was associated with tumor progression in osteosarcoma, and TRA2B was the target gene of miR-206, which was downregulated in osteosarcoma tissues. Furthermore, we observed that bone marrow mesenchymal stem cell (BMSC)-derived exosomes could carry and transport miR-206 to osteosarcoma cells. Both in vitro and in vivo results showed that BMSC-derived exosomal miR-206 could inhibit the proliferation, migration and invasion of osteosarcoma cells and induce their apoptosis. Taken together, our study demonstrates that BMSC-derived exosomal miR-206 can be transferred into osteosarcoma cells and inhibit tumor progression by targeting TRA2B, which provides new insight into the molecular mechanism of osteosarcoma and highlights the potential of miR-206 and TRA2B as new therapeutic targets.
Collapse
|
32
|
Vordenbäumen S, Brinks R, Schriek P, Lueking A, Richter JG, Budde P, Schulz-Knappe P, Zucht HD, Callhoff J, Schneider M. Profiling of IgG antibodies targeting unmodified and corresponding citrullinated autoantigens in a multicenter national cohort of early arthritis in Germany. Arthritis Res Ther 2020; 22:167. [PMID: 32631453 PMCID: PMC7336616 DOI: 10.1186/s13075-020-02252-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To assess the diagnostic potential of IgG antibodies to citrullinated and corresponding native autoantigens in early arthritis. METHODS IgG autoantibodies to 390 distinct unmodified and corresponding in vitro citrullinated recombinant proteins were measured by a multiplex assay in baseline blood samples from a German multicenter national cohort of 411 early arthritis patients (56.5 ± 14.6 years, 62.8% female). The cohort was randomly split into a training cohort (n = 329, 28.6% ACPA positive) and a validation cohort (n = 82, 32.9% ACPA pos.). The diagnostic properties of candidate antibodies to predict a subsequent diagnosis of rheumatoid arthritis (RA) as opposed to a non-RA diagnosis were assessed by receiver operating characteristics analysis and generalized linear modeling (GLM) with Bonferroni correction in comparison to clinically determined IgM rheumatoid factor (RF) and citrullinated peptide antibody (ACPA) status. RESULTS Of 411 patients, 309 (75.2%) were classified as RA. Detection rates of antibody responses to citrullinated and uncitrullinated forms of the proteins were weakly correlated (Spearman's r = 0.13 (95% CI 0.029-0.22), p = 0.01). The concentration of 34 autoantibodies (32 to citrullinated and 2 to uncitrullinated antigens) was increased at least 2-fold in RA patients and further assessed. In the training cohort, a significant association of citrullinated "transformer 2 beta homolog" (cTRA2B)-IgG with RA was observed (OR 5.3 × 103, 95% CI 0.8 × 103-3.0 × 106, p = 0.047). Sensitivity and specificity of cTRA2B-IgG (51.0%/82.9%) were comparable to RF (30.8%/91.6%) or ACPA (32.1%/94.7%). Similar results were obtained in the validation cohort. The addition of cTRA2B-IgG to ACPA improved the diagnostic performance over ACPA alone (p = 0.026 by likelihood ratio test). CONCLUSIONS cTRA2B-IgG has the potential to improve RA diagnosis in conjunction with RF and ACPA in early arthritis.
Collapse
Affiliation(s)
- Stefan Vordenbäumen
- Department Rheumatology & Hiller Research Unit, UKD, Heinrich-Heine-University Düsseldorf, Merowingerplatz 1a, 40225, Düsseldorf, Germany.
| | - Ralph Brinks
- Department Rheumatology & Hiller Research Unit, UKD, Heinrich-Heine-University Düsseldorf, Merowingerplatz 1a, 40225, Düsseldorf, Germany
| | - Patrick Schriek
- Protagen AG (now Oncimmune Germany GmbH), Otto-Hahn-Str. 15, 44227, Dortmund, Germany
- Bio21 Molecular Science & Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Angelika Lueking
- Protagen AG (now Oncimmune Germany GmbH), Otto-Hahn-Str. 15, 44227, Dortmund, Germany
- SensID GmbH, Schillingallee 68, 18057, Rostock, Germany
| | - Jutta G Richter
- Department Rheumatology & Hiller Research Unit, UKD, Heinrich-Heine-University Düsseldorf, Merowingerplatz 1a, 40225, Düsseldorf, Germany
| | - Petra Budde
- Oncimmune Germany GmbH, Otto-Hahn-Str. 15, 44227, Dortmund, Germany
| | - Peter Schulz-Knappe
- Protagen AG (now Oncimmune Germany GmbH), Otto-Hahn-Str. 15, 44227, Dortmund, Germany
- Immunovia AB, Medicon Village, Scheelevägen, 22381, Lund, Sweden
| | | | - Johanna Callhoff
- Department of Epidemiology, German Rheumatism Research Center DRFZ, Charitéplatz 1, 10117, Berlin, Germany
| | - Matthias Schneider
- Department Rheumatology & Hiller Research Unit, UKD, Heinrich-Heine-University Düsseldorf, Merowingerplatz 1a, 40225, Düsseldorf, Germany
| |
Collapse
|
33
|
Bartas M, Brázda V, Bohálová N, Cantara A, Volná A, Stachurová T, Malachová K, Jagelská EB, Porubiaková O, Červeň J, Pečinka P. In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles. Front Microbiol 2020; 11:1583. [PMID: 32719673 PMCID: PMC7347907 DOI: 10.3389/fmicb.2020.01583] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Non-canonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain non-canonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5'UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3'UTR, inside 5'UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Non-canonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.
Collapse
Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Alessio Cantara
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Tereza Stachurová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Kateřina Malachová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Eva B. Jagelská
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Otília Porubiaková
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| |
Collapse
|
34
|
Lan Z, Yao X, Sun K, Li A, Liu S, Wang X. The Interaction Between lncRNA SNHG6 and hnRNPA1 Contributes to the Growth of Colorectal Cancer by Enhancing Aerobic Glycolysis Through the Regulation of Alternative Splicing of PKM. Front Oncol 2020; 10:363. [PMID: 32296635 PMCID: PMC7136466 DOI: 10.3389/fonc.2020.00363] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Small nucleolar RNA host gene 6 (SNHG6) acts as a carcinogenic gene in colorectal cancer (CRC). However, previous studies on the mechanism by which long non-coding RNA (lncRNA) SNHG6 exerts its carcinogenic effect in CRC have not involved the direct interaction between SNHG6 and proteins, which is a very important carcinogenic mechanism of lncRNAs. Hence, our study conducted a comprehensive RNA-binding proteins-mass spectrometry (ChIRP-MS) analysis on SNHG6 to further explore its carcinogenic mechanism in CRC. Methods: Proteins that interact with SNHG6 were found using ChIRP-MS analysis and were used to construct the protein-protein interactive (PPI) network using STRING, while the core module of the PPI network was identified using the MCODE plugin in Cytoscape. Pathway enrichment analyses, using WebGestalt, were performed on proteins and RNAs that were found to be associated with the expression of SNHG6 or which directly interacted with SNHG6. Finally, CatRAPID, miRbase, and TargetScanHuman were used to identify the sites of interaction between SNHG6, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), and pyruvate kinase M (PKM) mRNA. Results: The expression of SNHG6 in CRC was found to be higher than that of normal tissues and was positively correlated with a poor prognosis (p < 0.05). A total of 467 proteins that are able to interact with SNHG6 in CRC cells were identified using ChIRP-MS analysis and were used to create a PPI network, within which a core module composed of 44 proteins that performed the function of splicing mRNA, including hnRNPA1, was found to be positively correlated with SNHG6 (p < 0.05). The results of the pathway enrichment analyses suggested that SNHG6 played an important role in the metabolism of CRC by affecting the expression of PKM and SNHG6. The increase in the ratio of PKM2/PKM1 was proven using quantitative real-time polymerase chain reaction analysis. Further exploration suggested that SNHG6 could bind to hnRNPA1 and PKM. Conclusion: SNHG6 was found to be able to target the mRNA of PKM as well as induce hnRNPA1 to specifically splice PKM mRNA, which increased the proportion of PKM2/PKM1, which may be an important carcinogenic mechanism in CRC that proceeds through the enhancement of aerobic glycolysis in CRC cells.
Collapse
Affiliation(s)
- Zhixian Lan
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiang Yao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kangyue Sun
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinke Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|