Overview of Transcriptomic Research on Type 2 Diabetes: Challenges and Perspectives

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2022 Jul 27

PMID 35885959

Authors

Ziravard N Tonyan

Yulia A Nasykhova

Maria M Danilova

Yury A Barbitoff

Anton I Changalidi

Anastasiia A Mikhailova

Andrey S Glotov

Affiliations

Soon will be listed here.

Abstract

Type 2 diabetes (T2D) is a common chronic disease whose etiology is known to have a strong genetic component. Standard genetic approaches, although allowing for the detection of a number of gene variants associated with the disease as well as differentially expressed genes, cannot fully explain the hereditary factor in T2D. The explosive growth in the genomic sequencing technologies over the last decades provided an exceptional impetus for transcriptomic studies and new approaches to gene expression measurement, such as RNA-sequencing (RNA-seq) and single-cell technologies. The transcriptomic analysis has the potential to find new biomarkers to identify risk groups for developing T2D and its microvascular and macrovascular complications, which will significantly affect the strategies for early diagnosis, treatment, and preventing the development of complications. In this article, we focused on transcriptomic studies conducted using expression arrays, RNA-seq, and single-cell sequencing to highlight recent findings related to T2D and challenges associated with transcriptome experiments.

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References

Jenkinson C, Goring H, Arya R, Blangero J, Duggirala R, DeFronzo R . Transcriptomics in type 2 diabetes: Bridging the gap between genotype and phenotype. Genom Data. 2016; 8:25-36. PMC: 4832048. DOI: 10.1016/j.gdata.2015.12.001. View

Liu L, Kodama K, Wei K, Tolentino L, Choi O, Engleman E . The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue. Diabetologia. 2015; 58(7):1579-86. DOI: 10.1007/s00125-015-3603-y. View

Alkhatatbeh M, Enjeti A, Acharya S, Thorne R, Lincz L . The origin of circulating CD36 in type 2 diabetes. Nutr Diabetes. 2013; 3:e59. PMC: 3584987. DOI: 10.1038/nutd.2013.1. View

Nichols B, Quezada-Calvillo R, Robayo-Torres C, Ao Z, Hamaker B, Butte N . Mucosal maltase-glucoamylase plays a crucial role in starch digestion and prandial glucose homeostasis of mice. J Nutr. 2009; 139(4):684-90. PMC: 2666363. DOI: 10.3945/jn.108.098434. View

Dominguez Gutierrez G, Gromada J, Sussel L . Heterogeneity of the Pancreatic Beta Cell. Front Genet. 2017; 8:22. PMC: 5337801. DOI: 10.3389/fgene.2017.00022. View

Lee H, Yea K, Kim J, Lee B, Chae Y, Kim H . Epidermal growth factor increases insulin secretion and lowers blood glucose in diabetic mice. J Cell Mol Med. 2007; 12(5A):1593-604. PMC: 3918075. DOI: 10.1111/j.1582-4934.2007.00169.x. View

Karolina D, Armugam A, Tavintharan S, Wong M, Lim S, Sum C . MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in type 2 diabetes mellitus. PLoS One. 2011; 6(8):e22839. PMC: 3148231. DOI: 10.1371/journal.pone.0022839. View

Alessandri L, Arigoni M, Calogero R . Differential Expression Analysis in Single-Cell Transcriptomics. Methods Mol Biol. 2019; 1979:425-432. DOI: 10.1007/978-1-4939-9240-9_25. View

Xue A, Wu Y, Zhu Z, Zhang F, Kemper K, Zheng Z . Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes. Nat Commun. 2018; 9(1):2941. PMC: 6063971. DOI: 10.1038/s41467-018-04951-w. View

10.

Jermendy A, Toschi E, Aye T, Koh A, Aguayo-Mazzucato C, Sharma A . Rat neonatal beta cells lack the specialised metabolic phenotype of mature beta cells. Diabetologia. 2011; 54(3):594-604. PMC: 3045081. DOI: 10.1007/s00125-010-2036-x. View

11.

Grayson B, Wang L, Aune T . Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes. Genes Immun. 2011; 12(5):341-51. PMC: 3137736. DOI: 10.1038/gene.2011.13. View

12.

Ninichuk V, Anders H . Chemokine receptor CCR1: a new target for progressive kidney disease. Am J Nephrol. 2005; 25(4):365-72. DOI: 10.1159/000087185. View

13.

He Y, Ding Y, Liang B, Lin J, Kim T, Yu H . A Systematic Study of Dysregulated MicroRNA in Type 2 Diabetes Mellitus. Int J Mol Sci. 2017; 18(3). PMC: 5372489. DOI: 10.3390/ijms18030456. View

14.

. Standards of medical care in diabetes. Diabetes Care. 2003; 27 Suppl 1:S15-35. DOI: 10.2337/diacare.27.2007.s15. View

15.

Trayhurn P . Northern blotting. Proc Nutr Soc. 1996; 55(1B):583-9. DOI: 10.1079/pns19960051. View

16.

Dorrell C, Schug J, Canaday P, Russ H, Tarlow B, Grompe M . Human islets contain four distinct subtypes of β cells. Nat Commun. 2016; 7:11756. PMC: 4942571. DOI: 10.1038/ncomms11756. View

17.

Rojewska E, Zychowska M, Piotrowska A, Kreiner G, Nalepa I, Mika J . Involvement of Macrophage Inflammatory Protein-1 Family Members in the Development of Diabetic Neuropathy and Their Contribution to Effectiveness of Morphine. Front Immunol. 2018; 9:494. PMC: 5857572. DOI: 10.3389/fimmu.2018.00494. View

18.

Zhao C, Mao J, Ai J, Shenwu M, Shi T, Zhang D . Integrated lipidomics and transcriptomic analysis of peripheral blood reveals significantly enriched pathways in type 2 diabetes mellitus. BMC Med Genomics. 2013; 6 Suppl 1:S12. PMC: 3552685. DOI: 10.1186/1755-8794-6-S1-S12. View

19.

Groen N, Leenders F, Mahfouz A, Munoz-Garcia A, Muraro M, de Graaf N . Single-Cell Transcriptomics Links Loss of Human Pancreatic β-Cell Identity to ER Stress. Cells. 2021; 10(12). PMC: 8700697. DOI: 10.3390/cells10123585. View

20.

Cruz Tfaile Corbi S, Bastos A, Nepomuceno R, Cirelli T, Alves Dos Santos R, Takahashi C . Expression Profile of Genes Potentially Associated with Adequate Glycemic Control in Patients with Type 2 Diabetes Mellitus. J Diabetes Res. 2017; 2017:2180819. PMC: 5547755. DOI: 10.1155/2017/2180819. View