Biology subjects

Karnok, N.

Publications and source records attributed to Karnok, N..

3 recordsLinked to original sources

bioRxiv2023

RPPA survey of cancer hotspot panel proteins and cell markers in matched tumor-normal human breast and kidney samples reveals a weak correlation between proteins expression and public transcriptome repositories

Despite the tremendous global effort in discovering and cataloguing somatic mutations in cancer-related genes and the impact they exert on human cancers, the effects of these mutations on the levels of protein expression are inadequately addressed. Here, we semi-quantitated the expression of 48 (out of 50) proteins represented by the most widely used cancer hotspot panel, the Ion AmpliSeq Cancer Hotspot Panel v2, and 14 cell markers commonly used as house-keeping proteins, using reverse phase protein array (RPPA) technology in 586 human breast- and 192 kidney matched tumor-normal samples. We further correlated our RPPA data with gene chip data from the Gene Expression Omnibus repository fetched through the TNMplot portal. Nearly half of proteins expression exhibited a negative correlation from their gene expression, while several of the remaining were only moderately correlated. Our data complement the vast information obtained elsewhere by transcriptomic analysis of the respective genes and gene products, potentially assisting in harmonizing proteomic with NGS outputs.

cancer biology↗

bioRxiv2022

Viability of HepG2 and MCF-7 Cells is not Correlated with Mitochondrial Bioenergetics

Alterations in metabolism is a hallmark of cancer. It is unclear, however, if oxidative phosphorylation (OXPHOS) is required for tumor cell survival. We investigated the effect of severe hypoxia, site-specific inhibition of respiratory chain (RC) components, and uncouplers on the survival of HepG2 and MCF-7 2D cultured cells. Comparable respiratory complex activities were observed in both cell lines, but HepG2 cells exhibited much higher oxygen consumption rates (OCR) and respiratory capacity than the MCF-7 cells. Significant non-mitochondrial OCR was found in MCF-7 cells that was insensitive to acute combined inhibition of complexes I and III. However, pre-treatment of either cell line with RC inhibitors for 24-72 hours abolished respective complex activities and OCRs completely, and this was associated with a time-dependent decrease in citrate synthase activity, suggesting mitophagy. HepG2 cells viability was mostly unaffected by any pharmacological treatment or severe hypoxia as temporally recorded from high-content automated microscopy. Conversely, MCF-7 cells viability exhibited strong sensitivity to CIV or CV inhibition, severe hypoxia, and uncoupling, but were only moderately affected by CI, CII and CIII inhibition. CII, CIII and CIV-inhibitor mediated MCF-7 cell death were partially abrogated by aspartate. The data show that OXPHOS activity and viability are uncorrelated in these cell lines indicating that a linkage of OXPHOS to cancer cell survival must be cell- and condition-defined.

cancer biology↗

bioRxiv2022

Residual Complex I activity supports glutamate catabolism and mtSLP via canonical Krebs cycle activity during acute anoxia without OXPHOS

Anoxia halts oxidative phosphorylation (OXPHOS) causing an accumulation of reduced compounds in mitochondrial matrix which impedes dehydrogenases. By simultaneously measuring oxygen concentration, NADH autofluorescence, mitochondrial membrane potential and ubiquinone reduction extent in organello in real-time, we show that Complex I utilized endogenous quinones to oxidize NADH under acute anoxia. Untargeted or [U-13C]glutamate-targeted metabolomic analysis of matrix and effluxed metabolites extracted during anoxia in the presence or absence of site-specific inhibitors of the electron transfer system inferred that NAD+ regenerated by Complex I is reduced by the 2-oxoglutarate dehydrogenase complex yielding succinyl-CoA supporting mitochondrial substrate-level phosphorylation (mtSLP), releasing succinate. Yet, targeted metabolomic analysis using [U-13C]malate also revealed concomitant succinate dehydrogenase reversal during anoxia yielding succinate by reducing fumarate, albeit to a small extent. Our results highlight the importance of quinone availability to Complex I oxidizing NADH, thus maintaining glutamate catabolism and mtSLP in the absence of OXPHOS.

biochemistry↗