Changes in Nuclear Gene Expression Related to Mitochondrial Function Affect Extracellular Matrix, Collagens, and Focal Adhesion in Keratoconus

Abstract

Purpose Mitochondrial DNA (mtDNA) abnormalities were previously found to be causative in the pathogenesis of various diseases. Here, comprehensive mitochondrial and nuclear sequence and transcript analyses, along with analyses of the methylation aspects of nuclear genes related to mitochondrial function, were performed in patients with keratoconus (KTCN) to evaluate their contribution to the KTCN pathogenesis. Methods Blood mtDNA of 42 KTCN and 51 non-KTCN individuals was Sanger sequenced and analyzed along with the previously obtained corneal RNA-sequencing data of 20 KTCN and 21 non-KTCN individuals. In addition, the expression and methylation of mtDNA genes and 1223 mitochondria-related nuclear genes were evaluated. Results The mtDNA sequence alterations detected in blood coincided with variants identified in transcripts of the matched corneal tissues. In KTCN corneas, 97 mitochondria-related genes were deregulated, including TGFB1 , P4HB , and BCL2 , which are involved in the extracellular matrix (ECM) organization, collagen formation, and focal adhesion pathways. No changes in the expression of mtDNA transcripts and no differentially methylated genes among the assessed mitochondrial–nuclear gene sets were found. Conclusions The absence of corneal-specific mtDNA variants indicates that there is no direct relationship between mitochondrial sequence variability and KTCN phenotype in the studied individuals. However, the identified KTCN-specific transcriptomic alterations of the nuclear genes directly related to the mitochondria functioning point to their possible involvement in the ECM organization, collagen formation, and focal adhesion. Translational Relevance The identification of abnormalities within nuclear genes regulating ECM formation, collagen synthesis, and/or focal adhesion may form the basis of future treatment strategies or predict the progression of corneal changes in KTCN.

Differentially expressed microRNAs targeting genes in key pathways in keratoconus

“…Also, GO terms enrichment analysis indicated mainly molecular processes associated with the regulation of transcription processes and DNA binding were revealed in the GO assessment. This is in line with our previous studies on KTCN corneas as we had identified differentially expressed genes that were involved in ECM organization, and signal transduction, including Wnt signaling pathways, disrupted in KTCN, assessing transcriptomic (Kabza et al, 2017b;Karolak et al, 2020b), genomic (Karolak et al, 2020a), and mitochondrial features (Nowak-Malczewska et al, 2021). Moreover, in our continuous study on additional corneal samples derived again from unrelated Polish patients with KTCN, we have identified both coding and noncoding sequence variation in genes that are involved, among others, in ECM and Wnt signaling (Jaskiewicz et al, 2023a).…”

Methylation in cornea and corneal diseases: a systematic review

“…No differences were found in the mtDNA methylation sequencing, suggesting that the role of mtDNA methylation modifications in KTCN was not responsible for expression differences. The deeper mechanisms are worth exploring [ 202 ].…”