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Chodur GM, Steinberg FM. Human MicroRNAs Modulated by Diet: A Scoping Review. Adv Nutr 2024; 15:100241. [PMID: 38734078 DOI: 10.1016/j.advnut.2024.100241] [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: 02/28/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024] Open
Abstract
Because of their role in regulating and fine-tuning gene expression in the posttranscriptional period, microRNA (miRNA) may represent a mediating factor that connects diet and metabolic regulation. Given the vast number of miRNAs and that modulations in miRNA happen in response to a variety of stimuli, a comprehensive registry of miRNAs impacted by diet and the food items that modulate them, would have utility in the identification of miRNA complements for analysis of diet interventions and in helping to establish linkages between the specific impacts of diet components. A scoping literature search of online databases (PubMed, SCOPUS, EMBASE, and Web of Science) was performed. Only studies in human populations, those that used a diet intervention or meal challenge, and those that measured miRNA profiles in the same subject at multiple time points were included. Of the 6167 studies screened, only 25 met the study criteria and were included in the review. Seven studies examined miRNA following a meal challenge, whereas 18 investigated miRNA following a sustained diet intervention. The results demonstrated that miRNA are modulated following a variety of diet interventions and that intensity of miRNA response is greater in metabolically healthy subjects. Heterogeneity in the intensity and length of the diet intervention, the study populations being observed, and the methodology through which target miRNA are identified contribute to a lack of comparability across studies. The findings of this review highlight the need for more study of miRNA responsiveness to intake and provide recommendations for future research.
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Affiliation(s)
- Gwen M Chodur
- Department of Nutrition, University of California-Davis, Davis, CA, United States
| | - Francene M Steinberg
- Department of Nutrition, University of California-Davis, Davis, CA, United States.
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2
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Lee YJ, Kim WR, Park EG, Lee DH, Kim JM, Shin HJ, Jeong HS, Roh HY, Kim HS. Exploring the Key Signaling Pathways and ncRNAs in Colorectal Cancer. Int J Mol Sci 2024; 25:4548. [PMID: 38674135 PMCID: PMC11050203 DOI: 10.3390/ijms25084548] [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: 03/29/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer to be diagnosed, and it has a substantial mortality rate. Despite numerous studies being conducted on CRC, it remains a significant health concern. The disease-free survival rates notably decrease as CRC progresses, emphasizing the urgency for effective diagnostic and therapeutic approaches. CRC development is caused by environmental factors, which mostly lead to the disruption of signaling pathways. Among these pathways, the Wingless/Integrated (Wnt) signaling pathway, Phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway, Mitogen-Activated Protein Kinase (MAPK) signaling pathway, Transforming Growth Factor-β (TGF-β) signaling pathway, and p53 signaling pathway are considered to be important. These signaling pathways are also regulated by non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). They have emerged as crucial regulators of gene expression in CRC by changing their expression levels. The altered expression patterns of these ncRNAs have been implicated in CRC progression and development, suggesting their potential as diagnostic and therapeutic targets. This review provides an overview of the five key signaling pathways and regulation of ncRNAs involved in CRC pathogenesis that are studied to identify promising avenues for diagnosis and treatment strategies.
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Affiliation(s)
- Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyeon-su Jeong
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyun-Young Roh
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
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3
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Doghish AS, Radwan AF, Zaki MB, Elfar N, Moussa R, Walash Z, Alhamshry NAA, Mohammed OA, Abdel-Reheim MA, Elimam H. Decoding the role of long non-coding RNAs in gallbladder cancer pathogenesis: A review focus on signaling pathways interplay. Int J Biol Macromol 2024; 264:130426. [PMID: 38428766 DOI: 10.1016/j.ijbiomac.2024.130426] [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: 12/26/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Gallbladder cancer (GBC) is one of the most aggressive types of biliary tree cancers and the commonest despite its rarity. It is infrequently diagnosed at an early stage, further contributing to its poor prognosis and low survival rate. The lethal nature of the disease has underlined a crucial need to discern the underlying mechanisms of GBC carcinogenesis which are still largely unknown. However, with the continual evolution in the research of cancer biology and molecular genetics, studies have found that non-coding RNAs (ncRNAs) play an active role in the molecular pathophysiology of GBC development. Dysregulated long non-coding RNAs (lncRNAs) and their interaction with intracellular signaling pathways contribute to malignancy and disease development. LncRNAs, a subclass of ncRNAs with over 200 nucleotides, regulate gene expression at transcriptional, translational, and post-translational levels and especially as epigenetic modulators. Thus, their expression abnormalities have been linked to malignancy and therapeutic resistance. lnsRNAs have also been found in GBC patients' serum and tumor tissue biopsies, highlighting their potential as novel biomarkers and for targeted therapy. This review will examine the growing involvement of lncRNAs in GBC pathophysiology, including related signaling pathways and their wider clinical use.
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Affiliation(s)
- 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.
| | - Abdullah F Radwan
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Nourhan Elfar
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital 11578, Cairo, Egypt; Egyptian Drug Authority (EDA), Ministry of Health and Population, Cairo 11567, Egypt
| | - Rewan Moussa
- Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Zahraa Walash
- Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Nora A A Alhamshry
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Osama A Mohammed
- Department of Pharmacology, 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.
| | - Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt.
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4
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Chen Z, Zhang J, Pan Y, Hao Z, Li S. Extracellular vesicles as carriers for noncoding RNA-based regulation of macrophage/microglia polarization: an emerging candidate regulator for lung and traumatic brain injuries. Front Immunol 2024; 15:1343364. [PMID: 38558799 PMCID: PMC10978530 DOI: 10.3389/fimmu.2024.1343364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Macrophage/microglia function as immune defense and homeostatic cells that originate from bone marrow progenitor cells. Macrophage/microglia activation is historically divided into proinflammatory M1 or anti-inflammatory M2 states based on intracellular dynamics and protein production. The polarization of macrophages/microglia involves a pivotal impact in modulating the development of inflammatory disorders, namely lung and traumatic brain injuries. Recent evidence indicates shared signaling pathways in lung and traumatic brain injuries, regulated through non-coding RNAs (ncRNAs) loaded into extracellular vesicles (EVs). This packaging protects ncRNAs from degradation. These vesicles are subcellular components released through a paracellular mechanism, constituting a group of nanoparticles that involve exosomes, microvesicles, and apoptotic bodies. EVs are characterized by a double-layered membrane and are abound with proteins, nucleic acids, and other bioactive compounds. ncRNAs are RNA molecules with functional roles, despite their absence of coding capacity. They actively participate in the regulation of mRNA expression and function through various mechanisms. Recent studies pointed out that selective packaging of ncRNAs into EVs plays a role in modulating distinct facets of macrophage/microglia polarization, under conditions of lung and traumatic brain injuries. This study will explore the latest findings regarding the role of EVs in the progression of lung and traumatic brain injuries, with a specific focus on the involvement of ncRNAs within these vesicles. The conclusion of this review will emphasize the clinical opportunities presented by EV-ncRNAs, underscoring their potential functions as both biomarkers and targets for therapeutic interventions.
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Affiliation(s)
- Zhihong Chen
- Department of Respiratory Medicine, The Third People’s Hospital of Longgang District, Shenzhen, China
| | - Jingang Zhang
- Department of Orthopedic, The Third People’s Hospital of Longgang District, Shenzhen, China
| | - Yongli Pan
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Zhongnan Hao
- Department of Neurology, University Medical Center of Göttingen, Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
| | - Shuang Li
- Department of Respiratory Medicine, The Third People’s Hospital of Longgang District, Shenzhen, China
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5
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Yazarlou F, Alizadeh F, Lipovich L, Giordo R, Ghafouri-Fard S. Tracing vitamins on the long non-coding lane of the transcriptome: vitamin regulation of LncRNAs. GENES & NUTRITION 2024; 19:5. [PMID: 38475720 DOI: 10.1186/s12263-024-00739-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
A major revelation of genome-scale biological studies in the post-genomic era has been that two-thirds of human genes do not encode proteins. The majority of non-coding RNA transcripts in humans are long non-coding RNA (lncRNA) molecules, non-protein-coding regulatory transcripts with sizes greater than 500 nucleotides. LncRNAs are involved in nearly every aspect of cellular physiology, playing fundamental regulatory roles both in normal cells and in disease. As result, they are functionally linked to multiple human diseases, from cancer to autoimmune, inflammatory, and neurological disorders. Numerous human conditions and diseases stem from gene-environment interactions; in this regard, a wealth of reports demonstrate that the intake of specific and essential nutrients, including vitamins, shapes our transcriptome, with corresponding impacts on health. Vitamins command a vast array of biological activities, acting as coenzymes, antioxidants, hormones, and regulating cellular proliferation and coagulation. Emerging evidence suggests that vitamins and lncRNAs are interconnected through several regulatory axes. This type of interaction is expected, since lncRNA has been implicated in sensing the environment in eukaryotes, conceptually similar to riboswitches and other RNAs that act as molecular sensors in prokaryotes. In this review, we summarize the peer-reviewed literature to date that has reported specific functional linkages between vitamins and lncRNAs, with an emphasis on mammalian models and humans, while providing a brief overview of the source, metabolism, and function of the vitamins most frequently investigated within the context of lncRNA molecular mechanisms, and discussing the published research findings that document specific connections between vitamins and lncRNAs.
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Affiliation(s)
- Fatemeh Yazarlou
- Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Box 505055, Dubai, United Arab Emirates
| | - Fatemeh Alizadeh
- Department of Genomic Psychiatry and Behavioral Genomics (DGPBG), Roozbeh Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co. Ltd., 601 Building C1, Guangming Science Park, Fenghuang Street, 518000, Shenzhen, Guangdong, People's Republic of China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 3222 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Roberta Giordo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Box 505055, Dubai, United Arab Emirates.
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro, Sassari, 07100, Italy.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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6
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Kiel K, Król SK, Bronisz A, Godlewski J. MiR-128-3p - a gray eminence of the human central nervous system. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102141. [PMID: 38419943 PMCID: PMC10899074 DOI: 10.1016/j.omtn.2024.102141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
MicroRNA-128-3p (miR-128-3p) is a versatile molecule with multiple functions in the physiopathology of the human central nervous system. Perturbations of miR-128-3p, which is enriched in the brain, contribute to a plethora of neurodegenerative disorders, brain injuries, and malignancies, as this miRNA is a crucial regulator of gene expression in the brain, playing an essential role in the maintenance and function of cells stemming from neuronal lineage. However, the differential expression of miR-128-3p in pathologies underscores the importance of the balance between its high and low levels. Significantly, numerous reports pointed to miR-128-3p as one of the most depleted in glioblastoma, implying it is a critical player in the disease's pathogenesis and thus may serve as a therapeutic agent for this most aggressive form of brain tumor. In this review, we summarize the current knowledge of the diverse roles of miR-128-3p. We focus on its involvement in the neurogenesis and pathophysiology of malignant and neurodegenerative diseases. We also highlight the promising potential of miR-128-3p as an antitumor agent for the future therapy of human cancers, including glioblastoma, and as the linchpin of brain development and function, potentially leading to the development of new therapies for neurological conditions.
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Affiliation(s)
- Klaudia Kiel
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Sylwia Katarzyna Król
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Agnieszka Bronisz
- Tumor Microenvironment Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
| | - Jakub Godlewski
- Department of Neurooncology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Street, Warsaw, Poland
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7
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Chen Y, Mateski J, Gerace L, Wheeler J, Burl J, Prakash B, Svedin C, Amrick R, Adams BD. Non-coding RNAs and neuroinflammation: implications for neurological disorders. Exp Biol Med (Maywood) 2024; 249:10120. [PMID: 38463392 PMCID: PMC10911137 DOI: 10.3389/ebm.2024.10120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
Neuroinflammation is considered a balanced inflammatory response important in the intrinsic repair process after injury or infection. Under chronic states of disease, injury, or infection, persistent neuroinflammation results in a heightened presence of cytokines, chemokines, and reactive oxygen species that result in tissue damage. In the CNS, the surrounding microglia normally contain macrophages and other innate immune cells that perform active immune surveillance. The resulting cytokines produced by these macrophages affect the growth, development, and responsiveness of the microglia present in both white and gray matter regions of the CNS. Controlling the levels of these cytokines ultimately improves neurocognitive function and results in the repair of lesions associated with neurologic disease. MicroRNAs (miRNAs) are master regulators of the genome and subsequently control the activity of inflammatory responses crucial in sustaining a robust and acute immunological response towards an acute infection while dampening pathways that result in heightened levels of cytokines and chemokines associated with chronic neuroinflammation. Numerous reports have directly implicated miRNAs in controlling the abundance and activity of interleukins, TGF-B, NF-kB, and toll-like receptor-signaling intrinsically linked with the development of neurological disorders such as Parkinson's, ALS, epilepsy, Alzheimer's, and neuromuscular degeneration. This review is focused on discussing the role miRNAs play in regulating or initiating these chronic neurological states, many of which maintain the level and/or activity of neuron-specific secondary messengers. Dysregulated miRNAs present in the microglia, astrocytes, oligodendrocytes, and epididymal cells, contribute to an overall glial-specific inflammatory niche that impacts the activity of neuronal conductivity, signaling action potentials, neurotransmitter robustness, neuron-neuron specific communication, and neuron-muscular connections. Understanding which miRNAs regulate microglial activation is a crucial step forward in developing non-coding RNA-based therapeutics to treat and potentially correct the behavioral and cognitive deficits typically found in patients suffering from chronic neuroinflammation.
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Affiliation(s)
- Yvonne Chen
- Department of Biology, Brandeis University, Waltham, MA, United States
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
| | - Julia Mateski
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Biological Sciences, Gustavus Adolphus College, St. Peter, MN, United States
| | - Linda Gerace
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Missouri State University, Springfield, MO, United States
| | - Jonathan Wheeler
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Electrical and Computer Engineering Tech, New York Institute of Tech, Old Westbury, NY, United States
| | - Jan Burl
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Southern New Hampshire University, Manchester, NH, United States
| | - Bhavna Prakash
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Medicine, Tufts Medical Center, Medford, MA, United States
| | - Cherie Svedin
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Biology, Utah Tech University, St. George, UT, United States
| | - Rebecca Amrick
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Villanova University, Villanova, PA, United States
| | - Brian D Adams
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
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8
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Munguía-Ramírez B, Giménez-Lirola L, Zimmerman J. Assessment of Strategies for Preserving Swine Viral RNA Targets in Diagnostic Specimens. Microorganisms 2024; 12:410. [PMID: 38399814 PMCID: PMC10892022 DOI: 10.3390/microorganisms12020410] [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: 01/29/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Successful downstream molecular analyses of viral ribonucleic acid (RNA) in diagnostic laboratories, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or next-generation sequencing, are dependent on the quality of the RNA in the specimen. In swine specimens, preserving the integrity of RNA requires proper sample handling at the time the sample is collected on the farm, during transport, and in the laboratory until RNA extraction is performed. Options for proper handling are limited to maintaining the cold chain or using commercial specimen storage matrices. Herein, we reviewed the refereed literature for evidence that commercial specimen storage matrices can play a role in preserving swine viral RNA in clinical specimens. Refereed publications were included if they compared RNA detection in matrix-treated vs. untreated samples. At present, the small number of refereed studies and the inconsistency in reported results preclude the routine use of commercial specimen storage matrices. For example, specimen storage matrices may be useful under specific circumstances, e.g., where it is mandatory to render the virus inactive. In a broader view, statistically sound side-by-side comparisons between specimens, viral RNA targets, and storage conditions are needed to establish if, when, and how commercial specimen storage matrices could be used in diagnostic medicine.
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Affiliation(s)
- Berenice Munguía-Ramírez
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (L.G.-L.); (J.Z.)
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9
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Zhang Y, Xie J. Ferroptosis-related exosomal non-coding RNAs: promising targets in pathogenesis and treatment of non-malignant diseases. Front Cell Dev Biol 2024; 12:1344060. [PMID: 38385027 PMCID: PMC10879574 DOI: 10.3389/fcell.2024.1344060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
Ferroptosis, an iron-dependent form of programmed cell death, introduces a novel perspective on cellular demise. This study investigates the regulatory network of exosomal non-coding RNAs (ncRNAs), including miRNAs, circRNAs, and lncRNAs, in ferroptosis modulation. The primary goal is to examine the pathological roles of ferroptosis-related exosomal ncRNAs, particularly in ischemic reperfusion injuries. The research reveals intricate molecular interactions governing the regulatory interplay between exosomal ncRNAs and ferroptosis, elucidating their diverse roles in different non-malignant pathological contexts. Attention is given to their impact on diseases, including cardiac, cerebral, liver, and kidney ischemic injuries, as well as lung, wound, and neuronal injuries. Beyond theoretical exploration, the study provides insights into potential therapeutic applications, emphasizing the significance of mesenchymal stem cells (MSCs)-derived exosomes. Findings underscore the pivotal role of MSC-derived exosomal ncRNAs in modulating cellular responses related to ferroptosis regulation, introducing a cutting-edge dimension. This recognition emphasizes the importance of MSC-derived exosomes as crucial mediators with broad therapeutic implications. Insights unveil promising avenues for targeted interventions, capitalizing on the diverse roles of exosomal ncRNAs, providing a comprehensive foundation for future therapeutic strategies.
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Affiliation(s)
- Yiping Zhang
- School of Life Science, Fudan University, Shanghai, China
- Wanchuanhui (Shanghai) Medical Technology Co., Ltd., Shanghai, China
| | - Jun Xie
- School of Life Science, Fudan University, Shanghai, China
- Wanchuanhui (Shanghai) Medical Technology Co., Ltd., Shanghai, China
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10
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Amalric A, Attina A, Bastide A, Buffard M, Mateus S, Planque C, Rivals E, Hirtz C, David A. Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation. Anal Chem 2024; 96:1825-1833. [PMID: 38275837 PMCID: PMC10851184 DOI: 10.1021/acs.analchem.3c02635] [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: 06/16/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
Cancer onset and progression are known to be regulated by genetic and epigenetic events, including RNA modifications (a.k.a. epitranscriptomics). So far, more than 150 chemical modifications have been described in all RNA subtypes, including messenger, ribosomal, and transfer RNAs. RNA modifications and their regulators are known to be implicated in all steps of post-transcriptional regulation. The dysregulation of this complex yet delicate balance can contribute to disease evolution, particularly in the context of carcinogenesis, where cells are subjected to various stresses. We sought to discover RNA modifications involved in cancer cell adaptation to inhospitable environments, a peculiar feature of cancer stem cells (CSCs). We were particularly interested in the RNA marks that help the adaptation of cancer cells to suspension culture, which is often used as a surrogate to evaluate the tumorigenic potential. For this purpose, we designed an experimental pipeline consisting of four steps: (1) cell culture in different growth conditions to favor CSC survival; (2) simultaneous RNA subtype (mRNA, rRNA, tRNA) enrichment and RNA hydrolysis; (3) the multiplex analysis of nucleosides by LC-MS/MS followed by statistical/bioinformatic analysis; and (4) the functional validation of identified RNA marks. This study demonstrates that the RNA modification landscape evolves along with the cancer cell phenotype under growth constraints. Remarkably, we discovered a short epitranscriptomic signature, conserved across colorectal cancer cell lines and associated with enrichment in CSCs. Functional tests confirmed the importance of selected marks in the process of adaptation to suspension culture, confirming the validity of our approach and opening up interesting prospects in the field.
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Affiliation(s)
- Amandine Amalric
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Aurore Attina
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Amandine Bastide
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Marion Buffard
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- LIRMM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Stéphanie Mateus
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Chris Planque
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Eric Rivals
- LIRMM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Christophe Hirtz
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Alexandre David
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
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11
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Shivakumar KM, Mahendran G, Brown JA. Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels. Int J Mol Sci 2024; 25:1630. [PMID: 38338910 PMCID: PMC10855403 DOI: 10.3390/ijms25031630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.
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Affiliation(s)
| | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.M.S.); (G.M.)
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12
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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13
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Suleiman AA, Al-Chalabi R, Shaban SA. Integrative role of small non-coding RNAs in viral immune response: a systematic review. Mol Biol Rep 2024; 51:107. [PMID: 38227137 DOI: 10.1007/s11033-023-09141-6] [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: 07/06/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Various viruses cause viral infection, and these viruses have different microscopic sizes, genetic material, and morphological forms. Due to a viral infection, the host body induces defense mechanisms that activate the innate and adaptive immune system. sncRNAs are involved in various biological processes and play an essential role in antiviral response in viruses including ZIKV, HCV, DENV, SARS-CoV, and West Nile virus, and regulate the complex interactions between the viruses and host cells. This review discusses the role of miRNAs, siRNAs, piRNAs, and tiRNAs in antiviral response. Cellular miRNAs bind with virus mRNA and perform their antiviral response in multiple viruses. However, the chemical modifications of miRNA necessary to avoid nuclease attack, which is then involved with intracellular processing, have proven challenging for therapeutic replacement of miRNAs. siRNAs have significant antiviral responses by targeting any gene of interest along the correct nucleotide of targeting mRNA. Due to this ability, siRNAs have valuable characteristics in antiviral response for therapeutic purposes. Additionally, the researchers noted the involvement of piRNAs and tiRNAs in the antiviral response, yet their findings were deemed insignificant.
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Affiliation(s)
| | | | - Semaa A Shaban
- Biology Department, College of Sciences, Tikrit University, Tikrit, Iraq
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14
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Yadav V, Jena MK, Parashar G, Parashar NC, Joshi H, Ramniwas S, Tuli HS. Emerging role of microRNAs as regulators of protein kinase C substrate MARCKS and MARCKSL1 in cancer. Exp Cell Res 2024; 434:113891. [PMID: 38104645 DOI: 10.1016/j.yexcr.2023.113891] [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: 09/24/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
MicroRNAs (miRNAs) have emerged as pivotal regulators of gene expression, playing essential roles in diverse cellular processes, including the development and progression of cancer. Among the numerous proteins influenced by miRNAs, the MARCKS/MARCKSL1 protein, a key regulator of cellular cytoskeletal dynamics and membrane-cytosol communication, has garnered significant attention due to its multifaceted involvement in various cancer-related processes, including cell migration, invasion, metastasis, and drug resistance. Motivated by the encouraging early clinical success of peptides targeting MARCKS in several pathological conditions, this review article delves into the intricate interplay between miRNAs and the MARCKS protein in cancer. Herein, we have highlighted the latest findings on specific miRNAs that modulate MARCKS/MARCKSL1 expression, providing a comprehensive overview of their roles in different cancer types. We have underscored the need for in-depth investigations into the therapeutic feasibility of targeting the miRNA-MARCKS axis in cancer, taking cues from the successes witnessed in related fields. Unlocking the full potential of miRNA-mediated MARCKS regulation could pave the way for innovative and effective therapeutic interventions against various cancer types.
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Affiliation(s)
- Vikas Yadav
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, 4000, Liège, Belgium; Department of Translational Medicine, Clinical Research Centre, Skåne University Hospital, Lund University, SE 20213, Malmö, Sweden.
| | - Manoj Kumar Jena
- Department of Biotechnology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Gaurav Parashar
- Division of Biomedical & Life Sciences, School of Science, Navrachana University, Vadodara, Gujarat, 391410, India
| | - Nidarshana Chaturvedi Parashar
- Department of Biosciences & Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Hemant Joshi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Seema Ramniwas
- University Centre for Research & Development, University Institute of Pharmaceutical Sciences, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Hardeep Singh Tuli
- Department of Biosciences & Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
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15
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Mahato RK, Bhattacharya S, Khullar N, Sidhu IS, Reddy PH, Bhatti GK, Bhatti JS. Targeting long non-coding RNAs in cancer therapy using CRISPR-Cas9 technology: A novel paradigm for precision oncology. J Biotechnol 2024; 379:98-119. [PMID: 38065367 DOI: 10.1016/j.jbiotec.2023.12.003] [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: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Cancer is the second leading cause of death worldwide, despite recent advances in its identification and management. To improve cancer patient diagnosis and care, it is necessary to identify new biomarkers and molecular targets. In recent years, long non-coding RNAs (lncRNAs) have surfaced as important contributors to various cellular activities, with growing proof indicating their substantial role in the genesis, development, and spread of cancer. Their unique expression profiles within specific tissues and their wide-ranging functionalities make lncRNAs excellent candidates for potential therapeutic intervention in cancer management. They are implicated in multiple hallmarks of cancer, such as uncontrolled proliferation, angiogenesis, and immune evasion. This review article explores the innovative application of CRISPR-Cas9 technology in targeting lncRNAs as a cancer therapeutic strategy. The CRISPR-Cas9 system has been widely applied in functional genomics, gene therapy, and cancer research, offering a versatile platform for lncRNA targeting. CRISPR-Cas9-mediated targeting of lncRNAs can be achieved through CRISPR interference, activation or the complete knockout of lncRNA loci. Combining CRISPR-Cas9 technology with high-throughput functional genomics makes it possible to identify lncRNAs critical for the survival of specific cancer subtypes, opening the door for tailored treatments and personalised cancer therapies. CRISPR-Cas9-mediated lncRNA targeting with other cutting-edge cancer therapies, such as immunotherapy and targeted molecular therapeutics can be used to overcome the drug resistance in cancer. The synergy of lncRNA research and CRISPR-Cas9 technology presents immense potential for individualized cancer treatment, offering renewed hope in the battle against this disease.
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Affiliation(s)
- Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Inderpal Singh Sidhu
- Department of Zoology, Sri Guru Gobind Singh College, Sector 26, Chandigarh, India
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Pharmacology & Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
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16
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Chen C, Wang N, Huang T, Cheng G, Hu Y, Wang B, Zhang Y, Wang C. Chloroprocaine antagonizes progression of breast cancer by regulating LINC00494/miR-3619-5p/MED19 axis. J Biochem Mol Toxicol 2024; 38:e23524. [PMID: 37650745 DOI: 10.1002/jbt.23524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/03/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Breast cancer, as the most prevalent female malignancy, leads the cancer-related death in women worldwide. Local anesthetic chloroprocaine exhibits antitumor potential, but its specific functions and underlying molecular mechanisms in breast cancer remain unclear. Here, we demonstrated chloroprocaine significantly inhibited proliferation, invasion and induced apoptosis of breast cancer cells in vitro. Tumor growth and pulmonary metastasis were also suppressed in BABL/c nude mice model with chloroprocaine treatment. LINC00494 was identified as one of the most downregulated long noncoding RNAs in chloroprocaine-treated breast cancer cells by high-throughput sequencing. Futhermore, high level of LINC00494 was positively associated with poor outcome of breast cancer patients. LINC00494 acted as a "miRNAs sponge" to compete with MED19 for the biding of miR-3619-5p, led to the upregulation of MED19. LINC00494/miR-3619-5p/MED19 axis participated in chloroprocaine-mediated inhibition of proliferation, invasion and promotion of apoptosis of breast cancer cells. Consequently, our finding suggested local anesthetic chloroprocaine attenuated breast cancer aggressiveness through LINC00494-mediated signaling pathway, which detailly revealed the clinical value of chloroprocaine during breast cancer treatment.
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Affiliation(s)
- Chen Chen
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Anesthesiology and Perioperative Medicine of Anhui Higher Education Institutes, Anhui Medical University, Hefei, Anhui, China
| | - Ning Wang
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Tingting Huang
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Gao Cheng
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Yuexia Hu
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Bingjie Wang
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Ye Zhang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Anesthesiology and Perioperative Medicine of Anhui Higher Education Institutes, Anhui Medical University, Hefei, Anhui, China
| | - Chunhui Wang
- Department of Anesthesiology, The First Affifiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
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17
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Santana-da-Silva MN, Sena-dos-Santos C, Cáceres-Durán MÁ, de Souza FG, Gobbo AR, Pinto P, Salgado CG, dos Santos SEB. ncRNAs: an unexplored cellular defense mechanism in leprosy. Front Genet 2023; 14:1295586. [PMID: 38116294 PMCID: PMC10729009 DOI: 10.3389/fgene.2023.1295586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Leprosy is an infectious disease primarily caused by the obligate intracellular parasite Mycobacterium leprae. Although it has been considered eradicated in many countries, leprosy continues to be a health issue in developing nations. Besides the social stigma associated with it, individuals affected by leprosy may experience nerve damage leading to physical disabilities if the disease is not properly treated or early diagnosed. Leprosy is recognized as a complex disease wherein socioenvironmental factors, immune response, and host genetics interact to contribute to its development. Recently, a new field of study called epigenetics has emerged, revealing that the immune response and other mechanisms related to infectious diseases can be influenced by noncoding RNAs. This review aims to summarize the significant advancements concerning non-coding RNAs in leprosy, discussing the key perspectives on this novel approach to comprehending the pathophysiology of the disease and identifying molecular markers. In our view, investigations on non-coding RNAs in leprosy hold promise and warrant increased attention from researches in this field.
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Affiliation(s)
- Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Imunologia, Seção de Virologia (SAVIR), Instituto Evandro Chagas, Ananindeua, Brazil
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Angelica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Sidney Emanuel Batista dos Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
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18
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Biswas A, Kumari A, Gaikwad DS, Pandey DK. Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:550-569. [PMID: 38100404 DOI: 10.1089/omi.2023.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.
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Affiliation(s)
- Aakanksha Biswas
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
| | - Aditi Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
| | - D S Gaikwad
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Dhananjay K Pandey
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
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19
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Ramazi S, Daddzadi M, Sahafnejad Z, Allahverdi A. Epigenetic regulation in lung cancer. MedComm (Beijing) 2023; 4:e401. [PMID: 37901797 PMCID: PMC10600507 DOI: 10.1002/mco2.401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/31/2023] Open
Abstract
Lung cancer is indeed a major cause of cancer-related deaths worldwide. The development of tumors involves a complex interplay of genetic, epigenetic, and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, and microRNA expression, play a crucial role in this process. Changes in DNAm patterns can lead to the silencing of important genes involved in cellular functions, contributing to the development and progression of lung cancer. MicroRNAs and exosomes have also emerged as reliable biomarkers for lung cancer. They can provide valuable information about early diagnosis and treatment assessment. In particular, abnormal hypermethylation of gene promoters and its effects on tumorigenesis, as well as its roles in the Wnt signaling pathway, have been extensively studied. Epigenetic drugs have shown promise in the treatment of lung cancer. These drugs target the aberrant epigenetic modifications that are involved in the development and progression of the disease. Several factors have been identified as drug targets in non-small cell lung cancer. Recently, combination therapy has been discussed as a successful strategy for overcoming drug resistance. Overall, understanding the role of epigenetic mechanisms and their targeting through drugs is an important area of research in lung cancer treatment.
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Affiliation(s)
- Shahin Ramazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Meadeh Daddzadi
- Department of BiotechnologyFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Zahra Sahafnejad
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Abdollah Allahverdi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
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20
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Laputková G, Talian I, Schwartzová V. Medication-Related Osteonecrosis of the Jaw: A Systematic Review and a Bioinformatic Analysis. Int J Mol Sci 2023; 24:16745. [PMID: 38069068 PMCID: PMC10706386 DOI: 10.3390/ijms242316745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The objective was to evaluate the current evidence regarding the etiology of medication-related osteonecrosis of the jaw (MRONJ). This study systematically reviewed the literature by searching PubMed, Web of Science, and ProQuest databases for genes, proteins, and microRNAs associated with MRONJ from the earliest records through April 2023. Conference abstracts, letters, review articles, non-human studies, and non-English publications were excluded. Twelve studies meeting the inclusion criteria involving exposure of human oral mucosa, blood, serum, saliva, or adjacent bone or periodontium to anti-resorptive or anti-angiogenic agents were analyzed. The Cochrane Collaboration risk assessment tool was used to assess the quality of the studies. A total of 824 differentially expressed genes/proteins (DEGs) and 22 microRNAs were extracted for further bioinformatic analysis using Cytoscape, STRING, BiNGO, cytoHubba, MCODE, and ReactomeFI software packages and web-based platforms: DIANA mirPath, OmicsNet, and miRNet tools. The analysis yielded an interactome consisting of 17 hub genes and hsa-mir-16-1, hsa-mir-21, hsa-mir-23a, hsa-mir-145, hsa-mir-186, hsa-mir-221, and hsa-mir-424. A dominance of cytokine pathways was observed in both the cluster of hub DEGs and the interactome of hub genes with dysregulated miRNAs. In conclusion, a panel of genes, miRNAs, and related pathways were found, which is a step toward understanding the complexity of the disease.
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Affiliation(s)
- Galina Laputková
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik, Trieda SNP 1, 040 11 Košice, Slovakia;
| | - Ivan Talian
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik, Trieda SNP 1, 040 11 Košice, Slovakia;
| | - Vladimíra Schwartzová
- Clinic of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of P. J. Šafárik and Louis Pasteur University Hospital, 041 90 Košice, Slovakia;
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21
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Stacey VM, Kõks S. Genome-Wide Differential Transcription of Long Noncoding RNAs in Psoriatic Skin. Int J Mol Sci 2023; 24:16344. [PMID: 38003532 PMCID: PMC10671291 DOI: 10.3390/ijms242216344] [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: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) may contribute to the formation of psoriatic lesions. The present study's objective was to identify long lncRNA genes that are differentially expressed in patient samples of psoriasis through computational analysis techniques. By using previously published RNA sequencing data from psoriatic and healthy patients (n = 324), we analysed the differential expression of lncRNAs to determine transcripts of heightened expression. We computationally screened lncRNA transcripts as annotated by GENCODE across the human genome and compared transcription in psoriatic and healthy samples from two separate studies. We observed 54 differentially expressed genes as seen in two independent datasets collected from psoriasis and healthy patients. We also identified the differential expression of LINC01215 and LINC1206 associated with the cell cycle pathway and psoriasis pathogenesis. SH3PXD2A-AS1 was identified as a participant in the STAT3/SH3PXD2A-AS1/miR-125b/STAT3 positive feedback loop. Both the SH3PXD2A-AS1 and CERNA2 genes have already been recognised as part of the IFN-γ signalling pathway regulation. Additionally, EPHA1-AS1, CYP4Z2P and SNHG12 gene upregulation have all been previously linked to inflammatory skin diseases. Differential expression of various lncRNAs affects the pathogenesis of psoriasis. Further characterisation of lncRNAs and their functions are important for developing our understanding of psoriasis.
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Affiliation(s)
- Valerie M. Stacey
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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22
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Giorgia Q, Gomez Garcia de la Banda M, Smeriglio P. Role of circulating biomarkers in spinal muscular atrophy: insights from a new treatment era. Front Neurol 2023; 14:1226969. [PMID: 38020652 PMCID: PMC10679720 DOI: 10.3389/fneur.2023.1226969] [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: 05/23/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a lower motor neuron disease due to biallelic mutations in the SMN1 gene on chromosome 5. It is characterized by progressive muscle weakness of limbs, bulbar and respiratory muscles. The disease is usually classified in four different phenotypes (1-4) according to age at symptoms onset and maximal motor milestones achieved. Recently, three disease modifying treatments have received approval from the Food and Drug Administration (FDA) and the European Medicines Agency (EMA), while several other innovative drugs are under study. New therapies have been game changing, improving survival and life quality for SMA patients. However, they have also intensified the need for accurate biomarkers to monitor disease progression and treatment efficacy. While clinical and neurophysiological biomarkers are well established and helpful in describing disease progression, there is a great need to develop more robust and sensitive circulating biomarkers, such as proteins, nucleic acids, and other small molecules. Used alone or in combination with clinical biomarkers, they will play a critical role in enhancing patients' stratification for clinical trials and access to approved treatments, as well as in tracking response to therapy, paving the way to the development of individualized therapeutic approaches. In this comprehensive review, we describe the foremost circulating biomarkers of current significance, analyzing existing literature on non-treated and treated patients with a special focus on neurofilaments and circulating miRNA, aiming to identify and examine their role in the follow-up of patients treated with innovative treatments, including gene therapy.
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Affiliation(s)
- Querin Giorgia
- APHP, Service de Neuromyologie, Hôpital Pitié-Salpêtrière, Centre Référent pour les Maladies Neuromusculaires Nord/Est/Ile de France, Paris, France
- Institut de Myologie, I-Motion Clinical Trials Platform, Paris, France
- European Reference Center Network (Euro-NMD ERN), Paris, France
| | - Marta Gomez Garcia de la Banda
- Institut de Myologie, I-Motion Clinical Trials Platform, Paris, France
- APHP, Pediatric Neurology Department, Hôpital Armand Trousseau, Centre Référent pour les Maladies Neuromusculaires Nord/Est/Ile de France, Paris, France
- APHP, Pediatric Neurology and ICU Department, Université Paris Saclay, DMU Santé de l'Enfant et de l'Adolescent, Hôpital Raymond Poincaré, Garches, France
| | - Piera Smeriglio
- Centre of Research in Myology, Institute of Myology, Sorbonne Université, INSERM, Paris, France
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Osei GY, Adu-Amankwaah J, Koomson S, Beletaa S, Ahmad MK, Asiamah EA, Smith-Togobo C, Abdul Razak SR. Revolutionizing colorectal cancer treatment: unleashing the potential of miRNAs in targeting cancer stem cells. Future Oncol 2023; 19:2369-2382. [PMID: 37970643 DOI: 10.2217/fon-2023-0426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023] Open
Abstract
Colorectal cancer (CRC) is a significant contributor to cancer mortality worldwide, and the presence of cancer stem cells (CSC) represents a major challenge for achieving effective treatment. miRNAs have emerged as critical regulators of gene expression, and recent studies have highlighted their role in regulating stemness and therapeutic resistance in CRC stem cells. This review highlights the mechanisms of CSC development, therapy resistance and the potential of miRNAs as therapeutic targets for CRC. It emphasizes the promise of miRNAs as a novel approach to CRC treatment and calls for further research to explore effective miRNA-based therapies and strategies for delivering miRNAs to CSCs in vivo.
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Affiliation(s)
- George Yiadom Osei
- Department of Biomedical Sciences, Advanced Medical & Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang, Malaysia
- Department of Medical Laboratory Sciences, University of Health & Allied Sciences, PMB 31, Ho, Ghana
| | - Joseph Adu-Amankwaah
- Department of Physiology, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Selina Koomson
- Department of Medical Laboratory Sciences, University of Health & Allied Sciences, PMB 31, Ho, Ghana
| | - Solomon Beletaa
- Department of Medical Laboratory Sciences, University of Health & Allied Sciences, PMB 31, Ho, Ghana
| | - Muhammad Khairi Ahmad
- Department of Biomedical Sciences, Advanced Medical & Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - Emmanuel Akomanin Asiamah
- Department of Medical Laboratory Sciences, University of Health & Allied Sciences, PMB 31, Ho, Ghana
- Discipline of Public Health Medicine, School of Nursing & Public Health, University of KwaZulu-Natal, Durban, 4001, South Africa
- Cancer & Infectious Diseases Epidemiology Research Unit (CIDERU), College of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Cecilia Smith-Togobo
- Department of Medical Laboratory Sciences, University of Health & Allied Sciences, PMB 31, Ho, Ghana
| | - Siti Razila Abdul Razak
- Department of Biomedical Sciences, Advanced Medical & Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang, Malaysia
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Xiong L, Tang M, Xing S, Yang X. The role of noncoding RNA and its diagnostic potential in intrahepatic cholestasis of pregnancy: a research update. Front Genet 2023; 14:1239693. [PMID: 37900174 PMCID: PMC10611463 DOI: 10.3389/fgene.2023.1239693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
Intrahepatic cholestasis of pregnancy (ICP) is a common liver disorder that generally occurs during the second or third trimester of pregnancy. It rarely causes any harm to the mother; however, it can result in short- and long-term complications in the offspring. Therefore, it is crucial to diagnose and treat this condition to avoid poor pregnancy outcomes. The identification of novel markers with potential diagnostic, prognostic, and therapeutic utility in ICP has gained attention. Noncoding RNAs (ncRNAs), including microRNA, long noncoding RNA, and circular RNA, are a type of transcripts that are not translated into proteins. They possess vital biological functions, including transcriptional and translational regulation and DNA, RNA, and protein interactions. The pathogenesis of ICP is related to the aberrant expression of several circulating or placenta-related ncRNAs. In this review, we summarized all recent findings on ncRNAs and ICP and outlined the concepts that form the basis for the early diagnosis and targeted treatment of ICP.
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Affiliation(s)
- Liling Xiong
- Obstetrics Department, Chengdu Women’s and Children’s Center Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Mi Tang
- GCP Institution, Chengdu Women’s and Children’s Center Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shasha Xing
- GCP Institution, Chengdu Women’s and Children’s Center Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao Yang
- Obstetrics Department, Chengdu Women’s and Children’s Center Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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25
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Kyrgiafini MA, Giannoulis T, Chatziparasidou A, Christoforidis N, Mamuris Z. Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility. Int J Mol Sci 2023; 24:15002. [PMID: 37834450 PMCID: PMC10573971 DOI: 10.3390/ijms241915002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Male infertility is a global health issue, affecting over 20 million men worldwide. Genetic factors are crucial in various male infertility forms, including teratozoospermia. Nonetheless, the genetic causes of male infertility remain largely unexplored. In this study, we employed whole-genome sequencing and RNA expression analysis to detect differentially expressed (DE) long-noncoding RNAs (lncRNAs) in teratozoospermia, along with mutations that are exclusive to teratozoospermic individuals within these DE lncRNAs regions. Bioinformatic tools were used to assess variants' impact on lncRNA structure, function, and lncRNA-miRNA interactions. Our analysis identified 1166 unique mutations in teratozoospermic men within DE lncRNAs, distinguishing them from normozoospermic men. Among these, 64 variants in 23 lncRNAs showed potential regulatory roles, 7 variants affected 4 lncRNA structures, while 37 variants in 17 lncRNAs caused miRNA target loss or gain. Pathway Enrichment and Gene Ontology analyses of the genes targeted by the affected miRNAs revealed dysregulated pathways in teratozoospermia and a link between male infertility and cancer. This study lists novel variants and lncRNAs associated for the first time with teratozoospermia. These findings pave the way for future studies aiming to enhance diagnosis and therapy in the field of male infertility.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Alexia Chatziparasidou
- Embryolab IVF Unit, St. 173-175 Ethnikis Antistaseos, Kalamaria, 55134 Thessaloniki, Greece
| | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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26
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Gentile AM, Lhamyani S, Mengual Mesa M, Pavón-Morón FJ, Pearson JR, Salas J, Clemente-Postigo M, Pérez Costillas L, Fuster GO, El Bekay Rizky R. A Network Comprised of miR-15b and miR-29a Is Involved in Vascular Endothelial Growth Factor Pathway Regulation in Thymus Adipose Tissue from Elderly Ischemic Cardiomyopathy Subjects. Int J Mol Sci 2023; 24:14456. [PMID: 37833902 PMCID: PMC10572810 DOI: 10.3390/ijms241914456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/09/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
As the human thymus ages, it undergoes a transformation into adipose tissue known as TAT. Interestingly, in previous research, we observed elevated levels of vascular endothelial growth factor A (VEGFA) in TAT from patients with ischemic cardiomyopathy (IC), particularly in those over 70 years old. Moreover, in contrast to subcutaneous adipose tissue (SAT), TAT in elderly individuals exhibits enhanced angiogenic properties and the ability to stimulate tube formation. This makes TAT a promising candidate for angiogenic therapies and the regeneration of ischemic tissues following coronary surgery. MicroRNAs (miRNAs) have emerged as attractive therapeutic targets, especially those that regulate angiogenic processes. The study's purpose is to determine the miRNA network associated with both the VEGFA pathway regulation and the enrichment of age-linked angiogenesis in the TAT. RT-PCR was used to analyze angiogenic miRNAs and the expression levels of their predicted target genes in both TAT and SAT from elderly and middle-aged patients treated with coronary artery bypass graft surgery. miRTargetLink Human was used to search for miRNAs and their target genes. PANTHER was used to annotate the biological processes of the predicted targets. The expression of miR-15b-5p and miR-29a-3p was significantly upregulated in the TAT of elderly compared with middle-aged patients. Interestingly, VEGFA and other angiogenic targets were significantly upregulated in the TAT of elderly patients. Specifically: JAG1, PDGFC, VEGFA, FGF2, KDR, NOTCH2, FOS, PDGFRA, PDGFRB, and RHOB were upregulated, while PIK3CG and WNT7A were downregulated. Our results provide strong evidence of a miRNA/mRNA interaction network linked with age-associated TAT angiogenic enrichment in patients with IC.
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Affiliation(s)
- Adriana Mariel Gentile
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Clinical Unit of Endocrinology and Nutrition, University Regional Hospital of Malaga, 29009 Malaga, Spain
- Andalucía Tech, Faculty of Health Sciences, and Department of Systems and Automation Engineering, School of Industrial Engineering, Universidad de Málaga, Teatinos Campus, s/n, 29071 Málaga, Spain
| | - Said Lhamyani
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Clinical Unit of Endocrinology and Nutrition, University Regional Hospital of Malaga, 29009 Malaga, Spain
| | - María Mengual Mesa
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Clinical Unit of Endocrinology and Nutrition, University Regional Hospital of Malaga, 29009 Malaga, Spain
- Andalucía Tech, Faculty of Health Sciences, and Department of Systems and Automation Engineering, School of Industrial Engineering, Universidad de Málaga, Teatinos Campus, s/n, 29071 Málaga, Spain
| | - Francisco Javier Pavón-Morón
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Clinical Unit of the Cardiology Area, University Hospital Virgen de la Victoria, 29009 Málaga, Spain
- Spain Biomedical Research Networking Center on Cardiovascular Diseases (CIBERCV), Health Institute III, 28029 Madrid, Spain
| | - John R. Pearson
- Biomedicine Institute of Seville (IBiS), 41013 Seville, Spain;
| | - Julián Salas
- Department of Cardiovascular Surgery, University Regional Hospital of Malaga, 29009 Malaga, Spain;
| | - Mercedes Clemente-Postigo
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Reina Sofia University Hospital, Department of Cell Biology, Physiology and Immunology, University of Córdoba, 14004 Córdoba, Spain
- Spanish Biomedical Research Center in Physiopathology of Obesity and Nutrition (CIBERObn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lucía Pérez Costillas
- Research Unit, International Institute for Innovation and Care in Neurodevelopment and Language, Department of Psychiatry and Physiotherapy, Faculty of Medicine, University of Malaga, 29010 Malaga, Spain;
| | - Gabriel Olveira Fuster
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Clinical Unit of Endocrinology and Nutrition, University Regional Hospital of Malaga, 29009 Malaga, Spain
- Biomedical Research Networking Center on Diabetes and Associated Metabolic Diseases (CIBERDEM), Carlos III Health Institute, 28029 Madrid, Spain
| | - Rajaa El Bekay Rizky
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29580 Malaga, Spain; (A.M.G.); (S.L.); (M.M.M.); (F.J.P.-M.); (M.C.-P.); (G.O.F.)
- Clinical Unit of Endocrinology and Nutrition, University Regional Hospital of Malaga, 29009 Malaga, Spain
- Spanish Biomedical Research Center in Physiopathology of Obesity and Nutrition (CIBERObn), Instituto de Salud Carlos III, 28029 Madrid, Spain
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27
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He Q, Chen N, Wang X, Li P, Liu L, Rong Z, Liu W, Jiang K, Zhao J. Prognostic value and immunological roles of GPX3 in gastric cancer. Int J Med Sci 2023; 20:1399-1416. [PMID: 37790850 PMCID: PMC10542182 DOI: 10.7150/ijms.85253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/10/2023] [Indexed: 10/05/2023] Open
Abstract
Objective: The prognosis for gastric cancer (GC), a prevalent tumor of the digestive system, is unfavorable. The involvement of glutathione peroxidase 3 (GPX3) in tumorigenesis is significant, yet its specific role in GC remains insufficiently investigated. Thus, the aim of this study was to determine the potential impact of GPX3 on GC and elucidate the underlying mechanism. Methods: The expression and survival of GPX3 in GC were analyzed using TCGA data. Additionally, the GPX3 mRNA and protein levels in GC were also assessed using datasets from GTEx, GEPIA, and HPA. A total of 38 pairs of GC tissues, along with their adjacent normal tissues, were collected from the Tianjin Medical University General Hospital, accompanied by detailed clinical information. The expression levels of GPX3 were subsequently determined for the purpose of validation. Following expression, correlation, and survival analyses, we proceeded to investigate the upstream non-coding RNA (ncRNA) of GPX3 using starBase and miRNet. Additionally, the co-expression networks of GPX3 were examined based on LinkedOmics. Lastly, we explored the correlation between GPX3 and immune cell infiltration, as well as the biomarkers of immune cells and immune checkpoints in GC. Furthermore, the GDSC database offered valuable drug sensitivity information. Results: A lower expression of GPX3 was observed in individuals with GC, while a higher expression of GPX3 was associated with a poorer prognosis. The DUBR/hsa-miR-502-3p/GPX3 pathway was identified as the most promising upstream ncRNA pathway related to GPX3 in GC. GO and KEGG enrichment analysis revealed that GPX3 expression was linked to coagulation cascades and cell locomotion. Furthermore, GPX3 levels in GC were positively correlated with immune cell infiltration, immune cell biomarkers, and immune checkpoint expression. The group with low GPX3 expression also exhibited increased sensitivity to 5-fluorouracil, doxorubicin, and other drugs. Conclusions: Collectively, we hypothesized that the potential involvement of non-coding RNAs in the downregulation of GPX3 could contribute to the inhibition of tumor formation during the malignant transition from gastritis to GC. Nevertheless, it was plausible that GPX3 may also facilitate tumor progression to advanced stages by promoting immune cell infiltration and activating immune checkpoints.
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Affiliation(s)
| | | | | | | | | | | | | | - Kui Jiang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, No. 154 Anshan Road, Tianjin, 300052, China
| | - Jingwen Zhao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, No. 154 Anshan Road, Tianjin, 300052, China
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28
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Zhou Z, Du Z, Wei J, Zhuo L, Pan S, Fu X, Lian X. MHAM-NPI: Predicting ncRNA-protein interactions based on multi-head attention mechanism. Comput Biol Med 2023; 163:107143. [PMID: 37339574 DOI: 10.1016/j.compbiomed.2023.107143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/20/2023] [Accepted: 06/06/2023] [Indexed: 06/22/2023]
Abstract
Non-coding RNA (ncRNA) is a functional RNA molecule that plays a key role in various fundamental biological processes, such as gene regulation. Therefore, studying the connection between ncRNA and proteins holds significant importance in exploring the function of ncRNA. Although many efficient and accurate methods have been developed by modern biological scientists, accurate predictions still pose a major challenge for various issues. In our approach, we utilize a multi-head attention mechanism to merge residual connections, allowing for the automatic learning of ncRNA and protein sequence features. Specifically, the proposed method projects node features into multiple spaces based on multi-head attention mechanism, thereby obtaining different feature interaction patterns in these spaces. By stacking interaction layers, higher-order interaction modes can be derived, while still preserving the initial feature information through the residual connection. This strategy effectively leverages the sequence information of ncRNA and protein, enabling the capture of hidden high-order features. The final experimental results demonstrate the effectiveness of our method, with AUC values of 97.4%, 98.5%, and 94.8% achieved on the NPInter v2.0, RPI807, and RPI488 datasets, respectively. These impressive results solidify our method as a powerful tool for exploring the connection between ncRNAs and proteins. We have uploaded the implementation code on GitHub: https://github.com/ZZCrazy00/MHAM-NPI.
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Affiliation(s)
- Zhecheng Zhou
- Wenzhou University of Technology, Wenzhou, 325000, China
| | - Zhenya Du
- Guangzhou Xinhua University, Guangzhou, 510520, China
| | - Jinhang Wei
- Wenzhou University of Technology, Wenzhou, 325000, China
| | - Linlin Zhuo
- Wenzhou University of Technology, Wenzhou, 325000, China; Hunan University, Changsha, 410000, China.
| | - Shiyao Pan
- Wenzhou University of Technology, Wenzhou, 325000, China
| | | | - Xinze Lian
- Wenzhou University of Technology, Wenzhou, 325000, China.
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29
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Qian N, Distefano R, Ilieva M, Madsen JH, Rennie S, Uchida S. Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages. Noncoding RNA 2023; 9:50. [PMID: 37736896 PMCID: PMC10514883 DOI: 10.3390/ncrna9050050] [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: 08/07/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023] Open
Abstract
The NLRP3 inflammasome plays a pivotal role in regulating inflammation and immune responses. Its activation can lead to an inflammatory response and pyroptotic cell death. This is beneficial in the case of infections, but excessive activation can lead to chronic inflammation and tissue damage. Moreover, while most of the mammalian genome is transcribed as RNAs, only a small fraction codes for proteins. Among non-protein-coding RNAs, long non-coding RNAs (lncRNAs) have been shown to play key roles in regulating gene expression and cellular processes. They interact with DNA, RNAs, and proteins, and their dysregulation can provide insights into disease mechanisms, including NLRP3 inflammasome activation. Here, we systematically analyzed previously published RNA sequencing (RNA-seq) data of NLRP3 inflammasome activation in monocytes/macrophages to uncover inflammasome-regulated lncRNA genes. To uncover the functional importance of inflammasome-regulated lncRNA genes, one inflammasome-regulated lncRNA, ENSG00000273124, was knocked down in an in vitro model of macrophage polarization. The results indicate that silencing of ENSG00000273124 resulted in the up-regulation tumor necrosis factor (TNF), suggesting that this lncRNA might be involved in pro-inflammatory response in macrophages. To make our analyzed data more accessible, we developed the web database InflammasomeDB.
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Affiliation(s)
- Na Qian
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; (N.Q.); (R.D.); (S.R.)
| | - Rebecca Distefano
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; (N.Q.); (R.D.); (S.R.)
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (M.I.); (J.H.M.)
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (M.I.); (J.H.M.)
| | - Sarah Rennie
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; (N.Q.); (R.D.); (S.R.)
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (M.I.); (J.H.M.)
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30
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Basalova N, Illarionova M, Skryabina M, Vigovskiy M, Tolstoluzhinskaya A, Primak A, Chechekhina E, Chechekhin V, Karagyaur M, Efimenko A. Advances and Obstacles in Using CRISPR/Cas9 Technology for Non-Coding RNA Gene Knockout in Human Mesenchymal Stromal Cells. Noncoding RNA 2023; 9:49. [PMID: 37736895 PMCID: PMC10514828 DOI: 10.3390/ncrna9050049] [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: 07/03/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023] Open
Abstract
Non-coding RNA (ncRNAs) genes have attracted increasing attention in recent years due to their widespread involvement in physiological and pathological processes and regulatory networks. The study of the function and molecular partners of ncRNAs opens up opportunities for the early diagnosis and treatment of previously incurable diseases. However, the classical "loss-of-function" approach in ncRNA function analysis is challenged due to some specific issues. Here, we have studied the potency of two CRISPR/Cas9 variants, wild-type (SpCas9wt) and nickase (SpCas9D10A) programmable nucleases, for the editing of extended DNA sequences in human mesenchymal stromal cells (MSCs). Editing the genes of fibrosis-related hsa-miR-21-5p and hsa-miR-29c-3p, we have shown that a pair of SpCas9D10A molecules can effectively disrupt miRNA genes within the genomes of MSCs. This leads not only to a decrease in the level of knockout miRNA in MSCs and MSC-produced extracellular vesicles, but also to a change in cell physiology and the antifibrotic properties of the cell secretome. These changes correlate well with previously published data for the knockdown of certain miRNAs. The proposed approach can be used to knock out ncRNA genes within the genomes of MSCs or similar cell types in order to study their function in biological processes.
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Affiliation(s)
- Nataliya Basalova
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia; (N.B.); (M.V.); (A.T.)
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Maria Illarionova
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Mariya Skryabina
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Maksim Vigovskiy
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia; (N.B.); (M.V.); (A.T.)
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Anastasia Tolstoluzhinskaya
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia; (N.B.); (M.V.); (A.T.)
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Alexandra Primak
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Elizaveta Chechekhina
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Vadim Chechekhin
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Maxim Karagyaur
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia; (N.B.); (M.V.); (A.T.)
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
| | - Anastasia Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia; (N.B.); (M.V.); (A.T.)
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia; (M.I.); (M.S.); (A.P.); (E.C.); (V.C.)
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Veysari SK, Asghari M, Farshad F, Hodjat M. Epigenetic changes underlie the association between diabetes mellitus and oral diseases. Mol Biol Rep 2023; 50:6987-6996. [PMID: 37378745 DOI: 10.1007/s11033-023-08574-3] [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: 11/06/2022] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
Patients with diabetes mellitus (DM) suffer from oral complications related to oral infections, periodontal diseases, and endodontic lesions. Emerging evidence has revealed the contribution of the epigenetic process as the underlying mechanism of DM complications. DNA methylation, histone modifications, and non-coding RNAs are epigenetic regulators that directly affect gene expression. The present review elaborated on the role of epigenetic dysregulation in the etiology of diabetes-related periodontal and endodontic diseases. The narrative review study was prepared using databases such as PubMed, Google Scholar, Science Direct, and Scopus. The formation of glycation products as a result of hyperglycemic condition increases oxidative stress, and elevates chronic inflammatory mediators that could in turn adversely change the cellular environment and alter the epigenetic status. This process contributes to the alteration of regulatory genes expression, leading to the development of diabetes-induced bone complications and impaired odontogenic capacity of pulp. Indeed, epigenetic mechanisms mediate the interaction between gene expression and DM cellular environment. Further investigations on epigenetic factors involved in DM oral complications may provide novel therapeutic targets.
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Affiliation(s)
- Setareh Kazemi Veysari
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences (TUMS), Tehran, 1417614411, Iran
| | - Mona Asghari
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences (TUMS), Tehran, 1417614411, Iran
| | - Fatemeh Farshad
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences (TUMS), Tehran, 1417614411, Iran
| | - Mahshid Hodjat
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences (TUMS), Tehran, 1417614411, Iran.
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Mirzaei S, Ranjbar B, Tackallou SH. Molecular profile of non-coding RNA-mediated glycolysis control in human cancers. Pathol Res Pract 2023; 248:154708. [PMID: 37536019 DOI: 10.1016/j.prp.2023.154708] [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: 06/15/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]
Abstract
The glycolysis is a common characteristic of cancer and it is responsible for providing enough energy to ensure growth. The glycolysis suppression is beneficial in tumor growth reduction. The stimulation/inhibition of glycolysis in cancer is tightly regulated by ncRNAs. The regulation of glycolysis by ncRNAs can influence proliferation and therapy response of tumor. The miRNAs are capable of inactivating enzymes responsible for glycolysis and suppressing signaling networks resulting in glycolysis induction. By regulation of glycolysis, miRNAs can affect therapy response. The lncRNAs and circRNAs follow a same pathway and by targeting glycolysis, they affect progression and therapy response of tumor. Noteworthy, lncRNAs and circRNAs sponge miRNAs in glycolysis mechanism control in tumor cells. Furthermore, ncRNA-mediated regulation of glycolysis mechanism can influence metastasis to organs of body. The ncRNAs regulating glycolysis are reliable biomarkers in cancer patients and more importantly, exosomal ncRNAs due to their presence in body fluids, are minimally-invasive biomarkers.
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Affiliation(s)
- Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran.
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14117-13116, Iran
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Distefano R, Ilieva M, Madsen JH, Ishii H, Aikawa M, Rennie S, Uchida S. T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes. Noncoding RNA 2023; 9:30. [PMID: 37218990 PMCID: PMC10204529 DOI: 10.3390/ncrna9030030] [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: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
Type II diabetes (T2D) is a growing health problem worldwide due to increased levels of obesity and can lead to other life-threatening diseases, such as cardiovascular and kidney diseases. As the number of individuals diagnosed with T2D rises, there is an urgent need to understand the pathogenesis of the disease in order to prevent further harm to the body caused by elevated blood glucose levels. Recent advances in long non-coding RNA (lncRNA) research may provide insights into the pathogenesis of T2D. Although lncRNAs can be readily detected in RNA sequencing (RNA-seq) data, most published datasets of T2D patients compared to healthy donors focus only on protein-coding genes, leaving lncRNAs to be undiscovered and understudied. To address this knowledge gap, we performed a secondary analysis of published RNA-seq data of T2D patients and of patients with related health complications to systematically analyze the expression changes of lncRNA genes in relation to the protein-coding genes. Since immune cells play important roles in T2D, we conducted loss-of-function experiments to provide functional data on the T2D-related lncRNA USP30-AS1, using an in vitro model of pro-inflammatory macrophage activation. To facilitate lncRNA research in T2D, we developed a web application, T2DB, to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in T2D patients compared to healthy donors or subjects without T2D.
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Affiliation(s)
- Rebecca Distefano
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan;
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Excellence in Vascular Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Rennie
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
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Hosseini SA, Haddadi MH, Fathizadeh H, Nemati F, Aznaveh HM, Taraj F, Aghabozorgizadeh A, Gandomkar G, Bazazzadeh E. Long non-coding RNAs and gastric cancer: An update of potential biomarkers and therapeutic applications. Biomed Pharmacother 2023; 163:114407. [PMID: 37100014 DOI: 10.1016/j.biopha.2023.114407] [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: 12/27/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 04/28/2023] Open
Abstract
The frequent metastasis of gastric cancer (GC) complicates the cure and therefore the development of effective diagnostic and therapeutic approaches is urgently necessary. In recent years, lncRNA has emerged as a drug target in the treatment of GC, particularly in the areas of cancer immunity, cancer metabolism, and cancer metastasis. This has led to the demonstration of the importance of these RNAs as prognostic, diagnostic and therapeutic agents. In this review, we provide an overview of the biological activities of lncRNAs in GC development and update the latest pathological activities, prognostic and diagnostic strategies, and therapeutic options for GC-related lncRNAs.
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Affiliation(s)
- Sayedeh Azimeh Hosseini
- Department of Medical Biotechnology, School of Advanced Technology, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran; USERN office, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Hadis Fathizadeh
- Student Research Committee, Sirjan School of Medical Sciences, Sirjan, Iran; Department of Laboratory sciences, Sirjan School of Medical Sciences, Sirjan, Iran
| | - Foroogh Nemati
- Department of Microbiology, Kashan University of Medical Sciences, Kashan, Iran
| | - Hooman Mahmoudi Aznaveh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-154, Tehran, Iran
| | - Farima Taraj
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - AmirArsalan Aghabozorgizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Golmaryam Gandomkar
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Elaheh Bazazzadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-154, Tehran, Iran
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Cimmino G, Conte S, Palumbo D, Sperlongano S, Torella M, Della Corte A, Golino P. The Novel Role of Noncoding RNAs in Modulating Platelet Function: Implications in Activation and Aggregation. Int J Mol Sci 2023; 24:ijms24087650. [PMID: 37108819 PMCID: PMC10144470 DOI: 10.3390/ijms24087650] [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: 03/12/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
It is currently believed that plaque complication, with the consequent superimposed thrombosis, is a key factor in the clinical occurrence of acute coronary syndromes (ACSs). Platelets are major players in this process. Despite the considerable progress made by the new antithrombotic strategies (P2Y12 receptor inhibitors, new oral anticoagulants, thrombin direct inhibitors, etc.) in terms of a reduction in major cardiovascular events, a significant number of patients with previous ACSs treated with these drugs continue to experience events, indicating that the mechanisms of platelet remain largely unknown. In the last decade, our knowledge of platelet pathophysiology has improved. It has been reported that, in response to physiological and pathological stimuli, platelet activation is accompanied by de novo protein synthesis, through a rapid and particularly well-regulated translation of resident mRNAs of megakaryocytic derivation. Although the platelets are anucleate, they indeed contain an important fraction of mRNAs that can be quickly used for protein synthesis following their activation. A better understanding of the pathophysiology of platelet activation and the interaction with the main cellular components of the vascular wall will open up new perspectives in the treatment of the majority of thrombotic disorders, such as ACSs, stroke, and peripheral artery diseases before and after the acute event. In the present review, we will discuss the novel role of noncoding RNAs in modulating platelet function, highlighting the possible implications in activation and aggregation.
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Affiliation(s)
- Giovanni Cimmino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Stefano Conte
- Department of Translational Medical Sciences, Section of Lung Diseases, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Domenico Palumbo
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Simona Sperlongano
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Michele Torella
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Alessandro Della Corte
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Paolo Golino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
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36
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Peedicayil J. Genome-Environment Interactions and Psychiatric Disorders. Biomedicines 2023; 11:biomedicines11041209. [PMID: 37189827 DOI: 10.3390/biomedicines11041209] [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: 03/27/2023] [Revised: 04/08/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Environmental factors are known to interact with the genome by altering epigenetic mechanisms regulating gene expression and contributing to the pathogenesis of psychiatric disorders. This article is a narrative review of how the major environmental factors contribute to the pathogenesis of common psychiatric disorders such as schizophrenia, bipolar disorder, major depressive disorder, and anxiety disorder this way. The cited articles were published between 1 January 2000 and 31 December 2022 and were obtained from PubMed and Google Scholar. The search terms used were as follows: gene or genetic; genome; environment; mental or psychiatric disorder; epigenetic; and interaction. The following environmental factors were found to act epigenetically on the genome to influence the pathogenesis of psychiatric disorders: social determinants of mental health, maternal prenatal psychological stress, poverty, migration, urban dwelling, pregnancy and birth complications, alcohol and substance abuse, microbiota, and prenatal and postnatal infections. The article also discusses the ways by which factors such as drugs, psychotherapy, electroconvulsive therapy, and physical exercise act epigenetically to alleviate the symptoms of psychiatric disorders in affected patients. These data will be useful information for clinical psychiatrists and those researching the pathogenesis and treatment of psychiatric disorders.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology & Clinical Pharmacology, Christian Medical College, Vellore 632 002, India
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37
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Bhatti JS, Khullar N, Vijayvergiya R, Navik U, Bhatti GK, Reddy PH. Mitochondrial miRNA as epigenomic signatures: Visualizing aging-associated heart diseases through a new lens. Ageing Res Rev 2023; 86:101882. [PMID: 36780957 DOI: 10.1016/j.arr.2023.101882] [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: 12/05/2021] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Aging bears many hard knocks, but heart disorders earn a particular allusion, being the most widespread. Cardiovascular diseases (CVDs) are becoming the biggest concern to mankind due to sundry health conditions directly or indirectly related to heart-linked abnormalities. Scientists know that mitochondria play a critical role in the pathophysiology of cardiac diseases. Both environment and genetics play an essential role in modulating and controlling mitochondrial functions. Even a minor abnormality may prove detrimental to heart function. Advanced age combined with an unhealthy lifestyle can cause most cardiomyocytes to be replaced by fibrotic tissue which upsets the conducting system and leads to arrhythmias. An aging heart encounters far more heart-associated comorbidities than a young heart. Many state-of-the-art technologies and procedures are already being used to prevent and treat heart attacks worldwide. However, it remains a mystery when this heart bomb would explode because it lacks an alarm. This calls for a novel and effective strategy for timely diagnosis and a sure-fire treatment. This review article provides a comprehensive overture of prospective potentials of mitochondrial miRNAs that predict complicated and interconnected pathways concerning heart ailments and signature compilations of relevant miRNAs as biomarkers to plot the role of miRNAs in epigenomics. This article suggests that analysis of DNA methylation patterns in age-associated heart diseases may determine age-impelled biomarkers of heart disease.
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Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India.
| | - Rajesh Vijayvergiya
- Department of Cardiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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38
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MiRNAs in Hematopoiesis and Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:ijms24065436. [PMID: 36982511 PMCID: PMC10049736 DOI: 10.3390/ijms24065436] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 03/14/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common kind of pediatric cancer. Although the cure rates in ALL have significantly increased in developed countries, still 15–20% of patients relapse, with even higher rates in developing countries. The role of non-coding RNA genes as microRNAs (miRNAs) has gained interest from researchers in regard to improving our knowledge of the molecular mechanisms underlying ALL development, as well as identifying biomarkers with clinical relevance. Despite the wide heterogeneity reveled in miRNA studies in ALL, consistent findings give us confidence that miRNAs could be useful to discriminate between leukemia linages, immunophenotypes, molecular groups, high-risk-for-relapse groups, and poor/good responders to chemotherapy. For instance, miR-125b has been associated with prognosis and chemoresistance in ALL, miR-21 has an oncogenic role in lymphoid malignancies, and the miR-181 family can act either as a oncomiR or tumor suppressor in several hematological malignancies. However, few of these studies have explored the molecular interplay between miRNAs and their targeted genes. This review aims to state the different ways in which miRNAs could be involved in ALL and their clinical implications.
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Nam D, Kim S, Kim JH, Lee S, Kim D, Son J, Kim D, Cha BS, Lee ES, Park KS. Low-Temperature Loop-Mediated Isothermal Amplification Operating at Physiological Temperature. BIOSENSORS 2023; 13:367. [PMID: 36979579 PMCID: PMC10046060 DOI: 10.3390/bios13030367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 06/16/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is one of the most widely used isothermal amplification technologies in molecular diagnostics. However, LAMP operates at a high temperature of 65 °C; thus, operating LAMP at a lower temperature is desirable to maximize its usefulness for on-site diagnosis. In this study, we propose a new version of LAMP, termed low-temperature LAMP, which operates at the physiological temperature of 37 °C. Low-temperature LAMP differs from conventional LAMP operating at 65 °C in terms of the concentrations of MgSO4 and deoxyribonucleoside triphosphates (dNTPs), as well as the lengths of DNA probes, which are crucial for the execution of low-temperature LAMP. Under the optimal conditions, the amplification efficiency of low-temperature LAMP is comparable to that of conventional LAMP. In addition, the ligation reaction at 37 °C, which is necessary to detect actual target nucleic acids, is combined without altering the temperature, enabling the identification of miR-21, a cancer-promoting oncogenic miRNA, with high sensitivity and selectivity. The method described in this paper does not require expensive DNA modifications or special additives and would facilitate the widespread application of LAMP in facility-limited or point-of-care settings, paving the way to improvements in other isothermal-amplification-based techniques.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ki Soo Park
- Correspondence: ; Tel.: +82-2-450-3742; Fax: +82-2-450-3742
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Luo YM, Yang SD, Wen MY, Wang B, Liu JH, Li ST, Li YY, Cheng H, Zhao LL, Li SM, Jiang JJ. Insights into the mechanisms of triptolide nephrotoxicity through network pharmacology-based analysis and RNA-seq. FRONTIERS IN PLANT SCIENCE 2023; 14:1144583. [PMID: 36959927 PMCID: PMC10027700 DOI: 10.3389/fpls.2023.1144583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Triptolide (TPL) is a promising plant-derived compound for clinical therapy of multiple human diseases; however, its application was limited considering its toxicity. METHODS To explore the underlying molecular mechanism of TPL nephrotoxicity, a network pharmacology based approach was utilized to predict candidate targets related with TPL toxicity, followed by deep RNA-seq analysis to characterize the features of three transcriptional elements include protein coding genes (PCGs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) as well as their associations with nephrotoxicity in rats with TPL treatment. RESULTS & DISCUSSION Although the deeper mechanisms of TPL nephrotoxcity remain further exploration, our results suggested that c-Jun is a potential target of TPL and Per1 related circadian rhythm signaling is involved in TPL induced renal toxicity.
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Affiliation(s)
- Yue-Ming Luo
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Shu-Dong Yang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Miao-Yu Wen
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Bing Wang
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Hui Liu
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Si-Ting Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yu-Yan Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Hong Cheng
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Li-Li Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Graduate school of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Shun-Min Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jian-Jun Jiang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
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Du X, Jiang Y, Zhang Q, Zhu X, Zhang Y, Liu C, Niu Y, Cai J, Kan H, Chen R. Genome-Wide Profiling of Exosomal Long Noncoding RNAs Following Air Pollution Exposure: A Randomized, Crossover Trial. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2856-2863. [PMID: 36757895 DOI: 10.1021/acs.est.2c05956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Changes in human genome-wide long noncoding RNAs (lncRNAs) associated with air pollution are unknown. This study aimed to investigate the effect of air pollution on human exosomal lncRNAs. A randomized, crossover trial was conducted among 35 healthy adults. Participants were allocated to 4 h exposure in road (high air pollution) and park (low air pollution) sessions in random order with a 2 week washout period. RNA sequencing was performed to measure lncRNAs. Differential lncRNAs were identified using a linear mixed-effect model. Mean concentrations of air pollutants such as ultrafine particles (UFP), black carbon (BC), carbon monoxide (CO), and nitrogen dioxide (NO2) were 2-3 times higher in the road than those in the park. Fifty-five lncRNAs [false discovery rate (FDR) < 0.05] including lncRNA NORAD, MALAT1, and H19 were changed in response to air pollution exposure. We found that 54 lncRNAs were associated with CO, 49 lncRNAs with UFP, 49 lncRNAs with BC, 48 lncRNAs with NO2, and 4 lncRNAs with PM2.5 (FDR < 0.05). These differential lncRNAs participated in dozens of pathways including cardiovascular signaling, epithelial cell proliferation, inflammation, and transforming growth factor. This trial for the first time profiled changes of human exosomal lncRNAs following air pollution. Our findings revealed multiple biological processes moderated by lncRNAs and provided epigenetic insights into cardiovascular effects of air pollution.
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Affiliation(s)
- Xihao Du
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yixuan Jiang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Qingli Zhang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Xinlei Zhu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yang Zhang
- Department of Systems Biology for Medicine, Shanghai Medical College, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Cong Liu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yue Niu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Jing Cai
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
- National Center for Children's Health, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
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Azizidoost S, Nasrolahi A, Sheykhi-Sabzehpoush M, Akiash N, Assareh AR, Anbiyaee O, Antosik P, Dzięgiel P, Farzaneh M, Kempisty B. Potential roles of endothelial cells-related non-coding RNAs in cardiovascular diseases. Pathol Res Pract 2023; 242:154330. [PMID: 36696805 DOI: 10.1016/j.prp.2023.154330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Endothelial dysfunction is identified by a conversion of the endothelium toward decreased vasodilation and prothrombic features and is known as a primary pathogenic incident in cardiovascular diseases. An insight based on particular and promising biomarkers of endothelial dysfunction may possess vital clinical significances. Currently, non-coding RNAs due to their participation in critical cardiovascular processes like initiation and progression have gained much attention as possible diagnostic as well as prognostic biomarkers in cardiovascular diseases. Emerging line of proof has demonstrated that abnormal expression of non-coding RNAs is nearly correlated with the pathogenesis of cardiovascular diseases. In the present review, we focus on the expression and functional effects of various kinds of non-coding RNAs in cardiovascular diseases and negotiate their possible clinical implications as diagnostic or prognostic biomarkers and curative targets.
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Affiliation(s)
- Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Nehzat Akiash
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ahmad Reza Assareh
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Nemazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Paweł Antosik
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Bartosz Kempisty
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland; Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wrocław, Poland; North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC 27695, USA.
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43
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Henry S, Kokity L, Pirity MK. Polycomb protein RYBP activates transcription factor Plagl1 during in vitro cardiac differentiation of mouse embryonic stem cells. Open Biol 2023; 13:220305. [PMID: 36751888 PMCID: PMC9905990 DOI: 10.1098/rsob.220305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
RING1 and YY1 binding protein (RYBP) is primarily known to function as a repressor being a core component of the non-canonical polycomb repressive complexes 1 (ncPRC1s). However, several ncPRC1-independent functions of RYBP have also been described. We previously reported that RYBP is essential for mouse embryonic development and that Rybp null mutant embryonic stem cells cannot form contractile cardiomyocytes (CMCs) in vitro. We also showed that PLAGL1, a cardiac transcription factor, which is often mutated in congenital heart diseases (CHDs), is not expressed in Rybp-null mutant CMCs. However, the underlying mechanism of how RYBP regulates Plagl1 expression was not revealed. Here, we demonstrate that RYBP cooperated with NKX2-5 to transcriptionally activate the P1 and P3 promoters of the Plagl1 gene and that this activation is ncPRC1-independent. We also show that two non-coding RNAs residing in the Plagl1 locus can also regulate the Plagl1 promoters. Finally, PLAGL1 was able to activate Tnnt2, a gene important for contractility of CMCs in transfected HEK293 cells. Our study shows that the activation of Plagl1 by RYBP is important for sarcomere development and contractility, and suggests that RYBP, via its regulatory functions, may contribute to the development of CHDs.
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Affiliation(s)
- Surya Henry
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Lilla Kokity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Melinda Katalin Pirity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary
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44
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Koffler-Brill T, Noy Y, Avraham KB. The long and short: Non-coding RNAs in the mammalian inner ear. Hear Res 2023; 428:108666. [PMID: 36566643 PMCID: PMC9883734 DOI: 10.1016/j.heares.2022.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 10/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Non-coding RNAs (ncRNAs) play a critical role in the entire body, and their mis-regulation is often associated with disease. In parallel with the advances in high-throughput sequencing technologies, there is a great deal of focus on this broad class of RNAs. Although these molecules are not translated into proteins, they are now well established as significant regulatory components in many biological pathways and pathological conditions. ncRNAs can be roughly divided into two main sub-groups based on the length of the transcript, with both the small and long non-coding RNAs having diverse regulatory functions. The smaller length group includes ribosomal RNAs (rRNA), transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), microRNAs (miRNA), small interfering RNAs (siRNA), and PIWI-associated RNAs (piRNA). The longer length group includes linear long non-coding RNAs (lncRNA) and circular RNAs (circRNA). This review is designed to present the different classes of small and long ncRNA molecules and describe some of their known roles in physiological and pathological conditions, as well as methods used to assess the validity and function of miRNAs and lncRNAs, with a focus on their role and functions in the inner ear, hearing and deafness.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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45
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Circular RNAs and tuberculosis infection. Int J Biol Macromol 2023; 226:1218-1225. [PMID: 36442574 DOI: 10.1016/j.ijbiomac.2022.11.235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/13/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is a deadly infectious disease caused by Mycobacterium tuberculosis (Mtb) that affects the immune system chronically. Therefore, effective control and treatment of tuberculosis requires rapid and accurate diagnostic strategies. Tuberculosis has always been a global burden on health, social and economic systems due to the lack of standard curative and diagnostic (bio)markers. Accordingly, the management and monitoring of patients with active TB at the primary care level may be possible through new, rapid and cost-effective non-sputum-based diagnostic procedures. Biomarkers can help diagnose various diseases, including circular RNA (circRNA), which has recently been introduced as an endogenous, abundant and stable RNA in the cytoplasm with unique tissue specificity. There are frequent reports of circRNA involvement in many pathological and physiological processes in human beings. Recent studies have highlighted the presence of circRNAs in serum and their role as promising biomarkers in the diagnosis of the disease, potentially due to the continuous, stable, closed covalent circular structures and lack of easy degradation by nucleases. The purpose of this review article is to scrutinize the behavior of circulating plasma RNAs in relation to the pathogenesis and diagnosis of tuberculosis.
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Cánovas-Cervera I, Nacher-Sendra E, Osca-Verdegal R, Dolz-Andrés E, Beltrán-García J, Rodríguez-Gimillo M, Ferrando-Sánchez C, Carbonell N, García-Giménez JL. The Intricate Role of Non-Coding RNAs in Sepsis-Associated Disseminated Intravascular Coagulation. Int J Mol Sci 2023; 24:ijms24032582. [PMID: 36768905 PMCID: PMC9916911 DOI: 10.3390/ijms24032582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Disseminated Intravascular Coagulation (DIC) is a type of tissue and organ dysregulation in sepsis, due mainly to the effect of the inflammation on the coagulation system. Unfortunately, the underlying molecular mechanisms that lead to this disorder are not fully understood. Moreover, current biomarkers for DIC, including biological and clinical parameters, generally provide a poor diagnosis and prognosis. In recent years, non-coding RNAs have been studied as promising and robust biomarkers for a variety of diseases. Thus, their potential in the diagnosis and prognosis of DIC should be further studied. Specifically, the relationship between the coagulation cascade and non-coding RNAs should be established. In this review, microRNAs, long non-coding RNAs, and circular RNAs are studied in relation to DIC. Specifically, the axis between these non-coding RNAs and the corresponding affected pathway has been identified, including inflammation, alteration of the coagulation cascade, and endothelial damage. The main affected pathway identified is PI3K/AKT/mTOR axis, where several ncRNAs participate in its regulation, including miR-122-5p which is sponged by circ_0005963, ciRS-122, and circPTN, and miR-19a-3p which is modulated by circ_0000096 and circ_0063425. Additionally, both miR-223 and miR-24 were found to affect the PI3K/AKT pathway and were regulated by lncGAS5 and lncKCNQ1OT1, respectively. Thus, this work provides a useful pipeline of inter-connected ncRNAs that future research on their impact on DIC can further explore.
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Affiliation(s)
- Irene Cánovas-Cervera
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Health Research Institute INCLIVA, 46010 Valencia, Spain
| | - Elena Nacher-Sendra
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Health Research Institute INCLIVA, 46010 Valencia, Spain
| | - Rebeca Osca-Verdegal
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain
| | - Enric Dolz-Andrés
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Jesús Beltrán-García
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, CA 92093, USA
| | - María Rodríguez-Gimillo
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Intensive Care Unit, Clinical University Hospital of Valencia, 46010 Valencia, Spain
| | - Carolina Ferrando-Sánchez
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Intensive Care Unit, Clinical University Hospital of Valencia, 46010 Valencia, Spain
| | - Nieves Carbonell
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Intensive Care Unit, Clinical University Hospital of Valencia, 46010 Valencia, Spain
| | - José Luis García-Giménez
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- Health Research Institute INCLIVA, 46010 Valencia, Spain
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain
- Correspondence: ; Tel.: +34-963-864-646
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Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 PMCID: PMC9838419 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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Guo X, Zhu W. Arsenic Trioxide Affects the Proliferation of Gastric Cancer Cells through MiR-885-5p/CDC73 Axis. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:128-137. [PMID: 36824234 PMCID: PMC9941427 DOI: 10.18502/ijph.v52i1.11674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/09/2022] [Indexed: 01/18/2023]
Abstract
Background To explore Arsenic trioxide (As2O3) and its regulated miR-885-5p/CDC73 signaling pathway involved in the development of gastric cancer. Methods Fifty-two healthy patients and patients with gastric cancer were enrolled 2019-2020 in He Xian Memorial Hospital, Guangzhou, China. The patients with gastric cancer were divided into control group and As2O3 administration group. After 2 courses of treatment, their peripheral blood was collected to analyze the therapeutic effect. miR-885-5p expression in peripheral blood was analyzed by qRT-PCR. As2O3 was added into MGC-803 gastric cancer cell line at 0, 10, 20, 40 and 80 μmol/L. The proliferation rate and 48h IC50 value of gastric cancer cells were investigated by CCK-8, and the effect of As2O3 on miR-885-5p expression in the cells was analyzed. Results After 4 weeks of treatment, the objective efficiency of control group and As2O3 administration group was 17.3% and 13.4%, respectively, without significant statistical difference. The overall benefit rate of As2O3 administration group was significantly higher than that of the normal treatment group (P=0.049). qRT-PCR experiment results found that miR-885-5p significantly highly expressed in peripheral blood in the As2O3 administration group, while miR-885-5p in gastric cancer was lower compared with normal people. Adding As2O3 to the gastric cancer cells could significantly inhibit miR-885-5p expression, while miR-885-5p in gastric cancer cells affected cell expression by targeted regulation, affecting cell proliferation. Conclusion As2O3 may be used as a drug treatment program for gastric cancer, and mainly regulates the proliferation of gastric cancer cells by affecting the miR-885-5p/CDC73 target axis to participate in the development of gastric cancer.
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Affiliation(s)
- Xiongbo Guo
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, P.R. China
| | - Wenbiao Zhu
- Department of Laboratory Medicine, Guangzhou Panyu Maternal Child Health Hospital (Guangzhou Panyu District He Xian Memorial Hospital), Guangzhou 511402, P.R. China,Corresponding Author:
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Activation of MYO1G by lncRNA MNX1-AS1 Drives the Progression in Lung Cancer. Mol Biotechnol 2023; 65:72-83. [PMID: 35819746 DOI: 10.1007/s12033-022-00531-y] [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: 10/18/2021] [Accepted: 06/27/2022] [Indexed: 01/25/2023]
Abstract
Lung cancer represents the most prevalent cancer worldwide and causes the death of many patients. Cancer stem cells (CSCs), a subpopulation of cancer cells, have the capacities of self-renewal, unlimited proliferation, and multiple differentiation potential. The purpose of this study was to explore the potential role of long noncoding RNA (lncRNA) MNX1-AS1 on maintaining the stemness of CSC in lung cancer. CSCs were firstly sorted by flow cytometry. After the determination of the target of the present study using Gene Expression Omnibus dataset, MNX1-AS1was found to be highly expressed in lung cancer tissues and cells. Deletion of MNX1-AS1 inhibited proliferation, migration, invasion and sphere-forming abilities of CSC. Furthermore, subcellular fractionation, fluorescence in situ hybridization, RNA immunoprecipitation, and dual-luciferase experiments demonstrated that MNX1-AS1 recruited the transcription factor POU domain class 2 transcription factor 2 (POU2F2) to the nucleus and activated the myosin IG (MYO1G) expression. MYO1G overexpression partially reversed the si-MNX1-AS1-decreased stemness of CSCs. Finally, MNX1-AS1 suppression significantly repressed the growth of xenografts in vivo. Our study highlights the importance of the MNX1-AS1/POU2F2/MYO1G axis in stem cell-like properties of lung cancer cells.
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PCSK9 pathway-noncoding RNAs crosstalk: Emerging opportunities for novel therapeutic approaches in inflammatory atherosclerosis. Int Immunopharmacol 2022; 113:109318. [DOI: 10.1016/j.intimp.2022.109318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
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