1
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Chaudhary U, Banerjee S. Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration. ACS Pharmacol Transl Sci 2024; 7:1901-1915. [PMID: 39022352 PMCID: PMC11249652 DOI: 10.1021/acsptsci.3c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
Non-coding RNAs are pivotal regulators of gene and protein expression, exerting crucial influences on diverse biological processes. Their dysregulation is frequently implicated in the onset and progression of diseases, notably cancer. A profound comprehension of the intricate mechanisms governing ncRNAs is imperative for devising innovative therapeutic interventions against these debilitating conditions. Significantly, nearly 80% of our genome comprises ncRNAs, underscoring their centrality in cellular processes. The elucidation of ncRNA functions is pivotal for grasping the complexities of gene regulation and its implications for human health. Modern genome sequencing techniques yield vast datasets, stored in specialized databases. To harness this wealth of information and to understand the crosstalk of non-coding RNAs, knowledge of available databases is required, and many new sophisticated computational tools have emerged. These tools play a pivotal role in the identification, prediction, and annotation of ncRNAs, thereby facilitating their experimental validation. This Review succinctly outlines the current understanding of ncRNAs, emphasizing their involvement in disease development. It also highlights the databases and tools instrumental in classifying, annotating, and evaluating ncRNAs. By extracting meaningful biological insights from seemingly "junk" data, these tools empower scientists to unravel the intricate roles of ncRNAs in shaping human health.
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Affiliation(s)
- Uma Chaudhary
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
| | - Satarupa Banerjee
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
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2
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Mohammed OA, Alghamdi M, Alfaifi J, Alamri MMS, Al-Shahrani AM, Alharthi MH, Alshahrani AM, Alhalafi AH, Adam MIE, Bahashwan E, Jarallah AlQahtani AA, BinAfif WF, Abdel-Reheim MA, Abdel Mageed SS, Doghish AS. The emerging role of miRNAs in myocardial infarction: From molecular signatures to therapeutic targets. Pathol Res Pract 2024; 253:155087. [PMID: 38183820 DOI: 10.1016/j.prp.2023.155087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024]
Abstract
Globally, myocardial infarction (MI) and other cardiovascular illnesses have long been considered the top killers. Heart failure and mortality are the results of myocardial apoptosis, cardiomyocyte fibrosis, and cardiomyocyte hypertrophy, all of which are caused by MI. MicroRNAs (miRNAs) play a crucial regulatory function in the progression and advancement of heart disease following an MI. By consolidating the existing data on miRNAs, our aim is to gain a more comprehensive understanding of their role in the pathological progression of myocardial injury after MI and to identify potential crucial target pathways. Also included are the primary treatment modalities and their most recent developments. miRNAs have the ability to regulate both normal and pathological activity, including the key signaling pathways. As a result, they may exert medicinal benefits. This review presents a comprehensive analysis of the role of miRNAs in MI with a specific emphasis on their impact on the regeneration of cardiomyocytes and other forms of cell death, such as apoptosis, necrosis, and autophagy. Furthermore, the targets of pro- and anti-MI miRNAs are comparatively elucidated.
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Affiliation(s)
- Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia.
| | - Mushabab Alghamdi
- Department of Internal Medicine, Division of Rheumatology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Jaber Alfaifi
- Department of Child Health, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Mohannad Mohammad S Alamri
- Department of Family and Community Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Abdullah M Al-Shahrani
- Department of Family and Community Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Muffarah Hamid Alharthi
- Department of Family and Community Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Abdullah M Alshahrani
- Department of Family and Community Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Abdullah Hassan Alhalafi
- Department of Family and Community Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Masoud I E Adam
- Department of Medical Education and Internal Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Emad Bahashwan
- Department of Internal Medicine, Division of Dermatology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - AbdulElah Al Jarallah AlQahtani
- Department of Internal Medicine, Division of Dermatology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Waad Fuad BinAfif
- Department of Internal Medicine, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef 62521, Egypt.
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
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3
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Elsakka EGE, Abulsoud AI, El-Mahdy HA, Ismail A, Elballal MS, Mageed SSA, Khidr EG, Mohammed OA, Sarhan OM, Elkhawaga SY, El-Husseiny AA, Abdelmaksoud NM, El-Demerdash AA, Shahin RK, Midan HM, Elrebehy MA, Doghish AA, Doghish AS. miRNAs orchestration of cardiovascular diseases - Particular emphasis on diagnosis, and progression. Pathol Res Pract 2023; 248:154613. [PMID: 37327567 DOI: 10.1016/j.prp.2023.154613] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
MicroRNAs (miRNAs; miRs) are small non-coding ribonucleic acids sequences vital in regulating gene expression. They are significant in many biological and pathological processes and are even detectable in various body fluids such as serum, plasma, and urine. Research has demonstrated that the irregularity of miRNA in multiplying cardiac cells is linked to developmental deformities in the heart's structure. It has also shown that miRNAs are crucial in diagnosing and progressing several cardiovascular diseases (CVDs). The review covers the function of miRNAs in the pathophysiology of CVD. Additionally, the review provides an overview of the potential role of miRNAs as disease-specific diagnostic and prognostic biomarkers for human CVD, as well as their biological implications in CVD.
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Affiliation(s)
- Elsayed G E Elsakka
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt.
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt
| | - Osama A Mohammed
- Department of Clinical Pharmacology, Faculty of Medicine, Bisha University, Bisha 61922, Saudi Arabia; Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Omnia M Sarhan
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, 11829 Cairo, Egypt
| | | | - Aya A El-Demerdash
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Reem K Shahin
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Heba M Midan
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ayman A Doghish
- Department of Cardiovascular & Thoracic Surgery, Ain-Shams University Hospital, Faculty of Medicine, Cairo, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt.
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4
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Ryabykh GK, Kuznetsov SV, Korostelev YD, Sigorskikh AI, Zharikova AA, Mironov AA. RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome. Database (Oxford) 2023; 2023:baad025. [PMID: 37221043 PMCID: PMC10205464 DOI: 10.1093/database/baad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/12/2023] [Accepted: 04/01/2023] [Indexed: 05/25/2023]
Abstract
Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser. Database URL https://genome.ucsc.edu/.
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Affiliation(s)
- G K Ryabykh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - S V Kuznetsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Y D Korostelev
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - A I Sigorskikh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - A A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky per., Moscow, 101000, Russia
| | - A A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
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Kansakar U, Varzideh F, Mone P, Jankauskas SS, Santulli G. Functional Role of microRNAs in Regulating Cardiomyocyte Death. Cells 2022; 11:983. [PMID: 35326433 PMCID: PMC8946783 DOI: 10.3390/cells11060983] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/08/2023] Open
Abstract
microRNAs (miRNA, miRs) play crucial roles in cardiovascular disease regulating numerous processes, including inflammation, cell proliferation, angiogenesis, and cell death. Herein, we present an updated and comprehensive overview of the functional involvement of miRs in the regulation of cardiomyocyte death, a central event in acute myocardial infarction, ischemia/reperfusion, and heart failure. Specifically, in this systematic review we are focusing on necrosis, apoptosis, and autophagy.
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Affiliation(s)
- Urna Kansakar
- Department of Medicine (Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA; (U.K.); (F.V.); (P.M.); (S.S.J.)
| | - Fahimeh Varzideh
- Department of Medicine (Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA; (U.K.); (F.V.); (P.M.); (S.S.J.)
| | - Pasquale Mone
- Department of Medicine (Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA; (U.K.); (F.V.); (P.M.); (S.S.J.)
| | - Stanislovas S. Jankauskas
- Department of Medicine (Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA; (U.K.); (F.V.); (P.M.); (S.S.J.)
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Gaetano Santulli
- Department of Medicine (Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA; (U.K.); (F.V.); (P.M.); (S.S.J.)
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
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6
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Gao F, Wang X, Fan T, Luo Z, Ma M, Hu G, Li Y, Liang Y, Lin X, Xu B. LncRNA LINC00461 exacerbates myocardial ischemia-reperfusion injury via microRNA-185-3p/Myd88. Mol Med 2022; 28:33. [PMID: 35272621 PMCID: PMC8908691 DOI: 10.1186/s10020-022-00452-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/26/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE Long non-coding RNAs (lncRNAs) play critically in the pathogenesis of myocardial ischemia-reperfusion (I/R) injury. Thus, it was proposed to investigate the mechanism of LINC00461 in the disease through mediating microRNA-185-3p (miR-185-3p)/myeloid differentiation primary response gene 88 (Myd88) axis. METHODS miR-185-3p, LINC00461 and Myd88 expression in mice with I/R injury was measured. Mice with I/R injury were injected with the gene expression-modified vectors, after which cardiac function, hemodynamics, myocardial enzyme, oxidative stress, and cardiomyocyte apoptosis were analyzed. RESULTS I/R mice showed LINC00461 and Myd88 up-regulation and miR-185-3p down-regulation. Down-regulating LINC00461 or up-regulating miR-185-3p recovered cardiac function, reduced myocardial enzyme levels, and attenuated oxidative stress and cardiomyocyte apoptosis in mice with I/R. miR-185-3p overexpression rescued the promoting effect of LINC00461 upregulation on myocardial injury in I/R mice. CONCLUSION LINC00461 knockdown attenuates myocardial I/R injury via elevating miR-185-3p expression to suppress Myd88 expression.
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Affiliation(s)
- Feng Gao
- Department of Cardiology, Economic Development District, Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road, Hefei, 230601, Anhui, China
| | - Xiaochen Wang
- Department of Cardiology, Economic Development District, Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road, Hefei, 230601, Anhui, China
| | - Tingting Fan
- Department of Cardiology, Economic Development District, Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road, Hefei, 230601, Anhui, China
| | - Zhidan Luo
- Department of Geriatrics, Chongqing People's Hospital, Chongqing, 400013, China
| | - Mengqing Ma
- Department of Cardiology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei, 230022, Anhui, China
| | - Guangquan Hu
- Department of Cardiology, Economic Development District, Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road, Hefei, 230601, Anhui, China
| | - Yue Li
- Department of Cardiology, Economic Development District, Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road, Hefei, 230601, Anhui, China
| | - Yi Liang
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA
| | - Xianhe Lin
- Department of Cardiology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei, 230022, Anhui, China.
| | - Banglong Xu
- Department of Cardiology, Economic Development District, Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road, Hefei, 230601, Anhui, China
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Mubarak G, Zahir FR. Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine. J Pers Med 2022; 12:199. [PMID: 35207687 PMCID: PMC8877836 DOI: 10.3390/jpm12020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/07/2022] Open
Abstract
With the advent of genome-wide screening methods-beginning with microarray technologies and moving onto next generation sequencing methods-the era of precision and personalized medicine was born. Genomics led the way, and its contributions are well recognized. However, "other-omics" fields have rapidly emerged and are becoming as important toward defining disease causes and exploring therapeutic benefits. In this review, we focus on the impacts of transcriptomics, and its extension-epitranscriptomics-on personalized and precision medicine efforts. There has been an explosion of transcriptomic studies particularly in the last decade, along with a growing number of recent epitranscriptomic studies in several disease areas. Here, we summarize and overview major efforts for cancer, cardiovascular disease, and neurodevelopmental disorders (including autism spectrum disorder and intellectual disability) for transcriptomics/epitranscriptomics in precision and personalized medicine. We show that leading advances are being made in both diagnostics, and in investigative and landscaping disease pathophysiological studies. As transcriptomics/epitranscriptomics screens become more widespread, it is certain that they will yield vital and transformative precision and personalized medicine contributions in ways that will significantly further genomics gains.
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Affiliation(s)
| | - Farah R. Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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8
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Chen K, Gan JX, Huang ZP, Liu J, Liu HP. Clinical significance of long noncoding RNA MNX1-AS1 in human cancers: a meta-analysis of cohort studies and bioinformatics analysis based on TCGA datasets. Bioengineered 2021; 12:875-885. [PMID: 33685348 PMCID: PMC8291812 DOI: 10.1080/21655979.2021.1888596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/11/2023] Open
Abstract
MNX1-AS1 expression has been proposed to be abnormally upregulated in multiple human malignancies and be linked with the survival outcome of patients. However, relevant conclusions were yielded based on the limited samples. Therefore, we herein implemented a meta-analysis of the published cohort studies to further decipher the relationship of MNX1-AS1 level to prognosis and clinicopathological features in various cancers. Additionally, using The Cancer Genome Atlas (TCGA) datasets we carried out a bioinformatics analysis to make a further evaluation on the prognostic value of MNX1-AS1 expression. The results of meta-analysis indicated elevated MNX1-AS1 level closely correlated with poorer overall survival (OS) (HR = 1.97, 95% CI, 1.73-2.24; P < 0.00001), and disease-free survival (DFS) (HR = 2.24, 95% CI, 1.48-3.38; P = 0.0001) in cancers, which was confirmed by the bioinformatics analysis. Besides, it was observed the upregulated MNX1-AS1 level was significantly related to invasion depth, disease stage, tumor metastasis, and differentiation. Collectively, high MNX1-AS1 level correlated with poor survival outcome and aggressive clinicopathological characteristics in various cancers, suggesting that MNX1-AS1 may be applied as a prognostic marker and even a therapeutic target. Nevertheless, more high-quality studies designed with a large sample size should be conducted to further determine the clinical role of MNX1-AS1 in specific cancer types.
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Affiliation(s)
- Kang Chen
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Jian-Xin Gan
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Ze-Ping Huang
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Jun Liu
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hai-Peng Liu
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
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9
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Gandhi S, Witten A, De Majo F, Gilbers M, Maessen J, Schotten U, de Windt LJ, Stoll M. Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology. Genomics 2021; 113:3782-3792. [PMID: 34506887 DOI: 10.1016/j.ygeno.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/17/2021] [Accepted: 09/05/2021] [Indexed: 12/14/2022]
Abstract
Cardiovascular disease (CVD) remains the leading cause of death worldwide. A deeper characterization of regional transcription patterns within different heart chambers may aid to improve our understanding of the molecular mechanisms involved in myocardial function and further, our ability to develop novel therapeutic strategies. Here, we used RNA sequencing to determine differentially expressed protein coding (PC) and long non-coding (lncRNA) transcripts within the heart chambers across seven vertebrate species and identified evolutionarily conserved chamber specific genes, lncRNAs and pathways. We investigated lncRNA homologs based on sequence, secondary structure, synteny and expressional conservation and found most lncRNAs to be conserved by synteny. Regional co-expression patterns of transcripts are modulated by multiple factors, including genomic overlap, strandedness and transcript biotype. Finally, we provide a community resource designated EvoACTG, which informs researchers on the conserved yet intertwined nature of the coding and non-coding cardiac transcriptome across popular model organisms in CVD research.
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Affiliation(s)
- Shrey Gandhi
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Anika Witten
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Federica De Majo
- Department of Molecular Genetics, Maastricht University, Maastricht, the Netherlands
| | - Martijn Gilbers
- Department of Cardiothoracic Surgery, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | - Jos Maessen
- Department of Cardiothoracic Surgery, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | - Ulrich Schotten
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - Leon J de Windt
- Department of Molecular Genetics, Maastricht University, Maastricht, the Netherlands
| | - Monika Stoll
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany; Department of Biochemistry, Genetic Epidemiology and Statistical Genetics, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands.
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10
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Boric MP, Durán WN, Figueroa XF. Editorial: Cell Communication in Vascular Biology. Front Physiol 2021; 12:656959. [PMID: 33746785 PMCID: PMC7965979 DOI: 10.3389/fphys.2021.656959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/09/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mauricio P Boric
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Walter N Durán
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Xavier F Figueroa
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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