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Talebi E, Ghoraeian P, Shams Z, Rahimi H. Molecular insights into the hedgehog signaling pathway correlated non-coding RNAs in acute lymphoblastic leukemia, a bioinformatics study. Ann Hematol 2024:10.1007/s00277-024-05763-3. [PMID: 39223285 DOI: 10.1007/s00277-024-05763-3] [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: 12/16/2023] [Accepted: 04/16/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is a common hematologic cancer with unique incidence and prognosis patterns in people of all ages. Recent molecular biology advances have illuminated ALL's complex molecular pathways, notably the Hedgehog (Hh) signaling system and non-coding RNAs (ncRNAs). This work aimed to unravel the molecular complexities of the link between Hh signaling and ALL by concentrating on long non-coding RNAs (lncRNAs) and their interactions with significant Hh pathway genes. METHODS To analyze differentially expressed lncRNAs and genes in ALL, microarray data from the Gene Expression Omnibus (GEO) was reanalyzed using a systems biology approach. Hh signaling pathway-related genes were identified and their relationship with differentially expressed long non-coding RNAs (DElncRNAs) was analyzed using Pearson's correlation analysis. A regulatory network was built by identifying miRNAs that target Hh signaling pathway-related mRNAs. RESULTS 193 DEGs and 226 DElncRNAs were found between ALL and normal bone marrow samples. Notably, DEGs associated with the Hh signaling pathway were correlated to 26 DElncRNAs. Later studies showed interesting links between DElncRNAs and biological processes and pathways, including drug resistance, immune system control, and carcinogenic characteristics. DEGs associated with the Hh signaling pathway have miRNAs in common with miRNAs already known to be involved in ALL, including miR-155-5p, and miR-211, highlighting the complexity of the regulatory landscape in this disease. CONCLUSION The complex connections between Hh signaling, lncRNAs, and miRNAs in ALL have been unveiled in this study, indicating that DElncRNAs linked to Hh signaling pathway genes could potentially serve as therapeutic targets and diagnostic biomarkers for ALL.
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Affiliation(s)
- Elham Talebi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Pegah Ghoraeian
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Zinat Shams
- Department of Biological Science, Kharazmi University, Tehran, Iran
| | - Hamzeh Rahimi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Cipriano GL, Schepici G, Mazzon E, Anchesi I. Multiple Sclerosis: Roles of miRNA, lcnRNA, and circRNA and Their Implications in Cellular Pathways. Int J Mol Sci 2024; 25:2255. [PMID: 38396932 PMCID: PMC10889752 DOI: 10.3390/ijms25042255] [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: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Multiple sclerosis (MS) is a degenerative condition characterized by axonal damage and demyelination induced by autoreactive immune cells that occur in the Central Nervous System (CNS). The interaction between epigenetic changes and genetic factors can be widely involved in the onset, development, and progression of the disease. Although numerous efforts were made to discover new therapies able to prevent and improve the course of MS, definitive curative treatments have not been found yet. However, in recent years, it has been reported that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), acting as gene expression regulators, could be used as potential therapeutic targets or biomarkers to diagnose and fight MS. In this review, we discussed the role of miRNAs, lncRNAs, and circRNAs, as well as their expression level changes and signaling pathways that are related to preclinical and human MS studies. Hence, the investigation of ncRNAs could be important to provide additional information regarding MS pathogenesis as well as promote the discovery of new therapeutic strategies or biomarkers.
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Affiliation(s)
| | | | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Strada Statale 113, Contrada Casazza, 98124 Messina, Italy; (G.L.C.); (G.S.); (I.A.)
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Sánchez-Sanz A, Muñoz-Viana R, Sabín-Muñoz J, Moreno-Torres I, Brea-Álvarez B, Rodríguez-De la Fuente O, García-Merino A, Sánchez-López AJ. Response to Fingolimod in Multiple Sclerosis Patients Is Associated with a Differential Transcriptomic Regulation. Int J Mol Sci 2024; 25:1372. [PMID: 38338652 PMCID: PMC10855583 DOI: 10.3390/ijms25031372] [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: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Fingolimod is an immunomodulatory sphingosine-1-phosphate (S1P) analogue approved for the treatment of relapsing-remitting multiple sclerosis (RRMS). The identification of biomarkers of clinical responses to fingolimod is a major necessity in MS to identify optimal responders and avoid the risk of disease progression in non-responders. With this aim, we used RNA sequencing to study the transcriptomic changes induced by fingolimod in peripheral blood mononuclear cells of MS-treated patients and their association with clinical response. Samples were obtained from 10 RRMS patients (five responders and five non-responders) at baseline and at 12 months of fingolimod therapy. Fingolimod exerted a vast impact at the transcriptional level, identifying 7155 differentially expressed genes (DEGs) compared to baseline that affected the regulation of numerous signaling pathways. These DEGs were predominantly immune related, including genes associated with S1P metabolism, cytokines, lymphocyte trafficking, master transcription factors of lymphocyte functions and the NF-kB pathway. Responder and non-responder patients exhibited a differential transcriptomic regulation during treatment, with responders presenting a higher number of DEGs (6405) compared to non-responders (2653). The S1P, NF-kB and TCR signaling pathways were differentially modulated in responder and non-responder patients. These transcriptomic differences offer the potential of being exploited as biomarkers of a clinical response to fingolimod.
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Affiliation(s)
- Alicia Sánchez-Sanz
- Neuroimmunology Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
| | - Rafael Muñoz-Viana
- Bioinformatics Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
| | - Julia Sabín-Muñoz
- Department of Neurology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain; (J.S.-M.); (O.R.-D.l.F.)
| | - Irene Moreno-Torres
- Demyelinating Diseases Unit, Hospital Universitario Fundación Jiménez Díaz, 28040 Madrid, Spain;
| | - Beatriz Brea-Álvarez
- Radiodiagnostic Division, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain;
| | - Ofir Rodríguez-De la Fuente
- Department of Neurology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain; (J.S.-M.); (O.R.-D.l.F.)
| | - Antonio García-Merino
- Neuroimmunology Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
- Department of Neurology, Hospital Universitario Puerta de Hierro Majadahonda, 28222 Madrid, Spain; (J.S.-M.); (O.R.-D.l.F.)
- Department of Medicine, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Red Española de Esclerosis Múltiple (REEM), 08028 Barcelona, Spain
| | - Antonio J. Sánchez-López
- Neuroimmunology Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain;
- Red Española de Esclerosis Múltiple (REEM), 08028 Barcelona, Spain
- Biobank, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, 28222 Madrid, Spain
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Harsij A, Gharebaghi A, Ghiasian M, Eslami S, Ghafouri-Fard S, Taheri M, Sayad A. Expression analysis of Treg-related lncRNAs in neuromyelitis optica spectrum disorder. Mult Scler Relat Disord 2024; 81:105350. [PMID: 38091807 DOI: 10.1016/j.msard.2023.105350] [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: 07/27/2023] [Revised: 09/06/2023] [Accepted: 11/26/2023] [Indexed: 01/23/2024]
Abstract
Neuromyelitis Optica Spectrum Disorder (NMOSD) is an autoimmune condition affecting the central nervous system, in which various kinds of immune cells, including T and B cells, and numerous cytokines and chemokines are implicated. LncRNAs modulating the function or differentiation of regulatory T cells (Tregs) may be involved in the pathoetiology of NMO. To assess the involvement of these lncRNAs in this disease, we studied the expression levels of TH2-LCR, MAFTRR, NEST, RMRP, and FLICR in NMO patients and healthy subjects. All of the lncRNAs listed were up-regulated in NMO patients compared with healthy controls. Although the interaction of group and gender factors significantly affected the expression of NEST, RMRP, and TH2-LCR genes, we detected no effect of gender factor on the expression of the examined genes. The highest expression correlation was found between RMRP and TH2-LCR among cases with correlation coefficient 0.73. ROC curve analysis indicated that TH2-LCR, MAFTRR, RMRP, and FLICR had significant prospective diagnostic power (AUC ± SD = 0.99 ± 0.002, 0.97 ± 0.01, 0.91 ± 0.01 and 0.84 ± 0.04, respectively). Best of these genes was TH2-LCR with AUC ± SD = 0.99 ± 0.002, sensitivity= 0.97, specificity= 1, P-value= <0.0001. RMRP and TH2-LCR had a positive correlation with age and age at onset and a negative correlation with EDSS. Cumulatively, TH2-LCR, MAFTRR, RMRP, and FLICR lncRNAs, particularly TH2-LCR, could be considered as potential contributors to the pathogenesis of NMO disease.
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Affiliation(s)
- Atefeh Harsij
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Gharebaghi
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Masoud Ghiasian
- Department of Neurology, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Arezou Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Moallemi-Rad L, Ghorbani A, Dadyar M, Hussen BM, Rasul MF, Eslami S, Taheri M, Jamali E, Ghafouri-Fard S. Expression of Treg-associated lncRNAs in breast cancer. Pathol Res Pract 2023; 241:154270. [PMID: 36535227 DOI: 10.1016/j.prp.2022.154270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Regulatory T cells (Tregs) have important functions in tumor microenvironment, particularly for induction of immune evasion. In order to find the underlying mechanism of dysregulation of Tregs in breast cancer tissues, we designed the current study to appraise expression of five Treg-related long non-coding RNAs (lncRNAs), namely FLICR (FOXP3 Regulating Long Intergenic Non-Coding RNA), NEST (IFNG-AS1), RMRP (RNA Component of Mitochondrial RNA Processing Endoribonuclease), MAFTRR (MAF Transcriptional Regulator RNA) and TH2-LCR (Th2 Cytokine Locus Control Region) in paired breast cancer and nearby noncancerous tissues. Expression levels of RMRP, TH2-LCR, MAFTRR and GATA3-AS1 were significantly higher in breast cancer samples compared with non-tumoral tissues. The calculated AUC values for GATA3-AS1, TH2-LCR, RMRP and MAFTRR were 0.66, 0.63, 0.63 and 0.60, respectively. There were significant positive associations between expression level of RMRP gene in tumor tissues and nuclear grade, tubule formation and tumor sizes. In addition, there was a significant positive association between expression levels of MAFTRR genes in tumor tissues and nuclear grade. Besides, expression levels of FLICR were different among tumors with different levels of HER2/neu receptor. Taken together, Treg-associated lncRNAs might contribute to the pathogenesis of breast cancer.
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Affiliation(s)
- Lina Moallemi-Rad
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Islamic Republic of Iran
| | - Amin Ghorbani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Islamic Republic of Iran
| | - Maryam Dadyar
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Islamic Republic of Iran; Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Islamic Republic of Iran
| | - Mohammad Taheri
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran; Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
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