Profiling circulating microRNA and regulatory pathways in transfusion-dependent thalassemia and thalassemia trait compared to healthy controls: a preliminary study

Lantip Rujito; Tirta Wardana; Joko Mulyanto; Ita Margaretha Nainggolan; Teguh Haryo Sasongko

doi:10.55092/exrna20240011

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Profiling circulating microRNA and regulatory pathways in transfusion-dependent thalassemia and thalassemia trait compared to healthy controls: a preliminary study

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Lantip Rujito¹^,∗, Tirta Wardana¹, Joko Mulyanto², Ita Margaretha Nainggolan³, Teguh Haryo Sasongko⁴

¹ Departemen of Genetics and Molecular Medicine, Faculty of Medicine, Jenderal Soedirman University, Purwokerto, Indonesia

² Department of Community Medicine, Faculty of Medicine, Jenderal Soedirman University, Purwokerto, Indonesia

³ Department of Clinical Pathology, School of Medicine and Health Sciences, Atma Jaya Catholic University, Jakarta, Indonesia

⁴ School of Medicine and Institute of Research, Development, and Innovations, International Medical University, Kuala Lumpur, Malaysia

* l.rujito@unsoed.ac.id

Volume
Volume 6 Issue 3, 2024
Citation
Rujito L, Wardana T, Mulyanto J, Nainggolan IM, Sasongko TH. Profiling circulating microRNA and regulatory pathways in transfusion-dependent thalassemia and thalassemia trait compared to healthy controls: a preliminary study. ExRNA 2024(3):0011, https://doi.org/10.55092/exrna20240011.
DOI
10.55092/exrna20240011
Copyright
Copyright2024 by the authors. Published by ELSP.

Abstract

Background: Thalassemia is a genetic blood disorder characterized by abnormal hemoglobin production. MicroRNAs (miRNAs) regulate gene expression and are implicated in thalassemia pathogenesis. This study aimed to profile circulating miRNAs in transfusion-dependent (TD), Thalassemia trait (TT), and non-thalassemic individuals, and elucidate their functional pathways. Methods: Serum samples were collected from TD thalassemia patients (n = 4), thalassemia trait (n = 4), and healthy controls (n = 4). Total RNA was extracted and miRNA expression analyzed using NanoString nCounter assays. The nCounter Human v3 miRNA panel consisting of 800 miRNAs was used to scan and quantify miRNA levels. Differentially expressed miRNAs between the three groups were identified through statistical analysis. Bioinformatics analysis using DIANA-miRPath was then conducted on the top differentially expressed miRNAs to identify associated molecular pathways and gene targets. Results: Three miRNAs (miR-4435, miR-566, miR-219a) were upregulated while miR-485-5p was downregulated in both TD and TT groups versus controls. miRNA profiles were also compared between TD and TT groups. Initial pathway analysis revealed involvement of upregulated miRNAs in hematopoietic, erythroid differentiation, and AMPK signaling pathways. Conclusion: Distinct circulating miRNA profiles exist between TD, TT, and healthy controls. miR-4435, miR-566, and miR-219a are consistently upregulated while miR-485-5p is downregulated, suggesting their functional significance.

Keywords

thalassemia; miRNA; therapeutic; transfusion

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References

[1] Williams TN, Weatherall DJ. World Distribution, Population Genetics, and Health Burden of the Hemoglobinopathies. CSH. Perspect. Med. 2012, 2(9):a011692.
[2] Kattamis A, Kwiatkowski JL, Aydinok Y. Thalassaemia. Lancet 2022, 399(10343):2310–2324.
[3] Wang H, Chen M, Xu S, Pan Y, Zhang Y, et al. Abnormal regulation of microRNAs and related genes in pediatric β‐thalassemia. J. Clin. Lab. Anal. 2021, 35(9):e23945.
[4] Li B, Zhu X, Ward CM, Starlard-Davenport A, Takezaki M, et al. MIR-144-mediated NRF2 gene silencing inhibits fetal hemoglobin expression in sickle cell disease. Exp. Hematol. 2019, 70:85–96.e5.
[5] Zakaria NA, Islam A, Abdullah WZ, Bahar R, Mohamed Yusoff AA, et al. Epigenetic Insights and Potential Modifiers as Therapeutic Targets in Β–Thalassemia. Biomolecules 2021, 11(5):75
[6] Li Y, Zhang H, Hu B, Wang P, Wang W, et al. Post-Transcriptional Regulation of Erythropoiesis. Blood Sci. 2023, 5(3):150–159.
[7] Guo C, Li X, Liu S, Sun M. MicroRNAs as Potential Markers Involved in Erythroid Differentiation: A Systematic Literature Review. Sci. J. Clin. Med. 2021, 10(2), 16–29.
[8] Betts M, Flight PA, Paramore LC, Tian L, Milenković D, et al. Systematic Literature Review of the Burden of Disease and Treatment for Transfusion-dependent β-Thalassemia. Clin. Ther. 2020, 42(2):322–337.
[9] Hasanshahi F, Khanjani N. Investigating the reasons for marriage among couples with thalassemia minor, in Iran. J. Community Genet. 2021, 12(4):507–513.
[10] Li L, Yi H, Liu Z, Long P, Pan T, et al. Genetic correction of concurrent α- and β-thalassemia patient-derived pluripotent stem cells by the CRISPR-Cas9 technology. Stem Cell Res. Ther. 2022, 13(1):102.
[11] Rujito L, Basalamah M, Mulatsih S, Sofro ASM. Molecular Scanning of β-Thalassemia in the Southern Region of Central Java, Indonesia; a Step Towards a Local Prevention Program. Hemoglobin 2015, 39(5):330–333.
[12] Susanto ZA, Siswandari W, Rujito L. Cd60 (GTG > GAG)/Hb Cagliari mutation was found in scanning of β-thalassemia alleles from patients of East Kalimantan, Indonesia. Mol. Genet. Metab. Rep. 2020, 22:100550.
[13] Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, et al. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res. 2015, 43(D1):D153–D159.
[14] Hsu JBK, Chiu CM, Da Hsu S, Huang WY, Chien CH, et al. MiRTar: An integrated system for identifying miRNA-target interactions in human, BMC Bioinf. 2011, 12:1–12.
[15] Wan Z, Zhang X, Luo Y, Zhao B. Identification of Hepatocellular Carcinoma-Related Potential Genes and Pathways through Bioinformatic-Based Analyses. Genet. Test. Mol. Biomarkers 2019, 23(11):766–777.
[16] Aoki S. BIORENDER. Available: https://app.biorender.com. (accessed on 14 December 2023).
[17] Kozomara A, Birgaoanu M, Griffiths-Jones S. MiRBase: From microRNA sequences to function. Nucleic Acids Res. 2019, 47(D1):D155–D162.
[18] Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ. miRBase: Tools for microRNA genomics. Nucleic Acids Res. 2007, 36(suppl_1):D154–D158
[19] Kalaigar SS, Rajashekar RB, Nataraj SM, Vishwanath P, Prashant A. Bioinformatic Tools for the Identification of MicroRNAs Regulating the Transcription Factors in Patients with β-Thalassemia. Bioinf. Biol. Insights 2022, 16:11779322221115536.
[20] Huang HY, Lin YCD, Li J, Huang KY, Shrestha S, et al. MiRTarBase 2020: Updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Res. 2020, 48(D1):D148–D154.
[21] Bravo Vázquez LA, Moreno Becerril MY, Mora Hernández EO, de León Carmona GG, Aguirre Padilla ME, et al. The Emerging Role of MicroRNAs in Bone Diseases and Their Therapeutic Potential. Molecules 2021, 27(1):211.
[22] Papadopoulos KI, Sutheesophon W, Manipalviratn S, Aw TC. A Southeast Asian Perspective on the COVID-19 Pandemic: Hemoglobin E (HbE)-Trait Confers Resistance Against COVID-19. Med. Sci. Monit. Basic Res. 2021, 27:e929207–1.
[23] Eltaweel NH, ElKamah GY, Khairat R, Atia HAE, Amr KS. Epigenetic effects toward new insights as potential therapeutic target in B-thalassemia. J. Genet. Eng. Biotechnol. 2021, 19(1):51.
[24] Zhu X, Hao M, Yu X, Lin W, Ma X, et al. Dissecting the Pathogenesis of Diabetic Retinopathy Based on the Biological ceRNA Network and Genome Variation Disturbance. Comput. Math. Methods Med. 2021, 2021(1):9833142.
[25] Hong JW, Kim JM, Kim JE, Cho H, Kim D, et al. MiR-4435 Is an UQCRB-related Circulating miRNA in Human Colorectal Cancer. Sci. Rep. 2020, 10(1):2833.
[26] Yu H, Li S. Role of LINC00152 in Non-Small Cell Lung Cancer. J. Zhejiang Univ. Sci. B 2020, 21(3):179–191.
[27] Vashukova ES, Kozyulina PY, Illarionov RA, Yurkina NO, Pachuliia OV, et al. High-Throughput Sequencing of Circulating MicroRNAs in Plasma and Serum During Pregnancy Progression. Life 2021, 11(10):1055.
[28] Yin J, Xie X, Ye Y, Wang L, Che F. BCL11A: A Potential Diagnostic Biomarker and Therapeutic Target in Human Diseases. Biosci. Rep. 2019, 39(11):BSR20190604.
[29] Basak A, Munschauer M, Lareau CA, Montbleau KE, Ulirsch JC, et al. Control of Human Hemoglobin Switching by LIN28B-mediated Regulation of BCL11A Translation. Nat. Genet. 2020, 52(2):138–145.
[30] Wong JJ, Ritchie W, Gao D, Lau KA, Gonzalez M, et al. Identification of nuclear-enriched miRNAs during mouse granulopoiesis. J. Hematol. Oncol. 2014, 7:1–15.
[31] Pacifici R. Osteoimmunology and Its Implications for Transplantation. Am. J. Transplant. 2013, 13(9):2245–2254.
[32] Yan J, Bu X, Li Z, Wu J, Wang C, et al. Screening the expression of several miRNAs from TaqMan Low Density Array in traumatic brain injury: miR‐219a‐5p regulates neuronal apoptosis by modulating CCNA2 and CACUL1. J. Neurochem. 2019, 150(2):202–217.
[33] Yang C, Zhang S, Chang X, Huang Y, Cui D, et al. MicroRNA‑219a‑2‑3p modulates the proliferation of thyroid cancer cells via the HPSE/cyclin D1 pathway. Exp. Ther. Med. 2021, 21(6):1–8.
[34] Xu K, Shi J, Mo D, Yang Y, Fu Q, et al. miR-219a-1 inhibits colon cancer cells proliferation and invasion by targeting MEMO1. Cancer Biol. Ther. 2020, 21(12):1163–1170.
[35] Zhang D, Nie Q, Liu Y, Li Z, Xie W, et al. Mir-485-5p on the Morphology and Function of Cardiovascular System, Cell. Mol. Biol. 2022, 68(1):117–123.
[36] Sun ZP, Tan ZG, Peng C. Long noncoding RNA LINC01419 promotes hepatocellular carcinoma malignancy by mediating miR‐485‐5p/LSM4 axis. Kaohsiung J. Med. Sci. 2022, 38(9):826–838.
[37] Gao F, Wu H, Wang R, Guo Y, Zhang Z, et al. MicroRNA-485-5p suppresses the proliferation, migration and invasion of small cell lung cancer cells by targeting flotillin-2. Bioengineered 2019, 10(1):1–12.
[38] Wan H, Wang Y, Pan Q, Chen X, Chen S, et al. Quercetin attenuates the proliferation, inflammation, and oxidative stress of high glucose-induced human mesangial cells by regulating the miR-485-5p/YAP1 pathway. Int. J. Immunopathol. Pharmacol. 2022, 36:20587384211066440.
[39] Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, et al. DIANA-miRPath v3.0: Deciphering microRNA function with experimental support. Nucleic Acids Res. 2015, 43(W1):W460–W466.
[40] Zhang Z, Yao L, Yang J, Wang Z, Du G. PI3K/Akt and HIF-1 signaling pathway in hypoxia-ischemia (Review). Mol. Med. Rep. 2018, 18(4):3547–3554.
[41] Norbitt CF, Kimita W, Ko J, Bharmal SH, Petrov MS. Associations of Habitual Mineral Intake with New-Onset Prediabetes/Diabetes after Acute Pancreatitis. Nutrients 2021, 13(11):3978.
[42] Zhou J, Schmid T, Frank R, Brüne B. PI3K/Akt Is Required for Heat Shock Proteins to Protect Hypoxia-inducible Factor 1α from pVHL-independent Degradation. J. Biol. Chem. 2004, 279(14):13506–13513.
[43] Ferro E, Visalli G, Currò M, La Rosa MA, Piraino B, et al. HIF1α and Glut1 receptor in transfused and untransfused thalassemic patients. Br. J. Haematol. 2016, 174(5):824–826.
[44] Kontoghiorghes G, Kontoghiorghe C. Iron and Chelation in Biochemistry and Medicine: New Approaches to Controlling Iron Metabolism and Treating Related Diseases. Cells 2020, 9(6):1456.
[45] Qiang Y.W, Kopantzev E, Rudikoff S. Insulinlike growth factor-I signaling in multiple myeloma: Downstream elements, functional correlates, and pathway cross-talk. Blood 2002, 99(11):4138–4146.
[46] Wang L, Lin N, Li Y. The PI3K/AKT signaling pathway regulates ABCG2 expression and confers resistance to chemotherapy in human multiple myeloma. Oncol. Rep. 2019, 41(3):1678–1690.
[47] Chen M, Wang X, Wang H, Zhang M, Chen L, et al. Down-Regulated hsa-miR-190b-5p is Correlated With BCL11A Expression in Pediatric β -Thalassemia. Res. Pre-Print 2021, 1–12.
[48] Kim J, Barsoum IB, Loh H, ParéJ, Siemens DR, et al. Inhibition of hypoxia-inducible factor 1α accumulation by glyceryl trinitrate and cyclic guanosine monophosphate. Biosci. Rep. 2020, 40(1):BSR20192345.
[49] Parisi S, Finelli C, Fazio A, De Stefano A, Mongiorgi S, et al. Clinical and Molecular Insights in Erythropoiesis Regulation of Signal Transduction Pathways in Myelodysplastic Syndromes and β-Thalassemia. Int. J. Mol. Sci. 2021, 22(2):827.
[50] Manolova V, Nyffenegger N, Flace A, Altermatt P, Varol A, et al. Oral ferroportin inhibitor ameliorates ineffective erythropoiesis in a model of β-thalassemia. J. Clin. Invest. 2020, 130(1):491–506.
[51] Garcia JA, Chen R, Xu M, Comerford SA, Hammer RE, et al. Acss2/HIF-2 signaling facilitates colon cancer growth and metastasis. PLoS One 2023, 18(3):e0282223.
[52] Li H, He T, Zha YJ, Du F, Liu J, et al. HIF-1α rs11549465 C>T polymorphism contributes to increased cancer susceptibility: Evidence from 49 studies. J. Cancer 2019, 10(24):5955.
[53] Saad HKM, Abd Rahman AA, Ab Ghani AS, Taib WRW, Ismail I, et al. Activation of STAT and SMAD Signaling Induces Hepcidin Re-Expression as a Therapeutic Target for β-Thalassemia Patients. Biomedicines 2022, 10(1):189.
[54] Li Z, Rana TM. Therapeutic targeting of microRNAs: current status and future challenges. Nat. Rev. Drug Discov. 2014, 13(8):622–638.
[55] Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. Jurga S, Erdmann (Deceased) V, Barciszewski J, Eds. In Modified Nucleic Acids in Biology and Medicine. Cham: Springer, 2016, pp. 299–317.