SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Targeting mitochondrial glycerol 3-phosphate dehydrogenase and mitochondrial complex III in PC-3 prostate cancer cells

Cancer is the second main cause of death worldwide. Reactive oxygen species (ROS) play a special role in tumor development and growth. The mitochondrial glycerol 3-phosphate dehydrogenase (mG3PDH) and the mitochondrial complex III (CIII) have a high proportion of cellular ROS production. Due to inadequate blood supply tumors very often are characterized by low oxygen pressure. ROS as well as the oxygen supply regulate the stability of the hypoxic inducing factor (HIF) which induces the expression of key glycolytic (iso)enzymes (i.e. lactate dehydrogenase A (LDHA), pyruvate kinase type M2 (M2-PK)) required for energy production, synthesis of building blocks and cancer cell proliferation. ROS have been shown to induce a dimerization as well as a reduction of M2-PK activity thereby diverting glucose flux towards the synthesis of cell building blocks. In tumor cells besides glycolysis, glutaminolysis is an important pathway to provide energy and metabolic precursors for cell building blocks which are both important in cells with high proliferation rate such as tumor cells. The aim of this study was to investigate the impact of targeting mG3PDH and mitochondrial CIII on cell proliferation and metabolism of PC-3 prostate cancer cells which are characterized by high mG3PDH activity. The impact of mG3PDH and CIII inhibition on cell proliferation was investigated in presence of 21% O2 which corresponds to the oxygen concentrations in the air and is used in most of the published cell culture studies as well as in presence of 1.5% O2 which corresponds to the mean oxygen concentration in a variety of solid tumors. In order to simulate therapy over several days long-term incubation periods (96 hours) of PC-3 cells with the corresponding inhibitors were performed. In the first part of the study two substances published as inhibitors of mG3PDH (iGP-1 and RH02211) were investigated. mG3PDH together with cytosolic glycerol 3-P dehydrogenase (cG3PDH) is involved in the transfer of hydrogen from cytosolic NADH + H+ produced within the cytosolic glyceraldehyde 3-P dehydrogenase (GAPDH) reaction into the mitochondrial electron transport chain in order to restore the cytosolic NAD+ for glycolysis. Both iGP-1 and RH02211 induced an inhibition of PC-3 cell proliferation. The RH02211-induced inhibition of cell proliferation was independent upon oxygen supply. The inhibitory effect of both inhibitors on PC-3 cell proliferation was weakened when pyruvate was supplemented into the cultivation medium of the cells suggesting that extracellular pyruvate is an escape mechanism for the inhibition of cell proliferation by both RH02211 and iGP-1. Pyruvate is the substrate via which the LDH oxidizes NADH + H+ to NAD+. A nutrient medium without supplementation of pyruvate is closer to the physiological pyruvate concentrations in the blood. When cultivated in pyruvate supplemented medium PC-3 control cells shifted from production of pyruvate to consumption of extracellular pyruvate and glycolytic as well as glutaminolytic conversion rates decreased which points to a severe impact of extracellular pyruvate on the metabolism of the cells. In contrast to the first published description which showed a decrease of H2O2 production in pyruvate supplemented PC-3 cells treated for 15 minutes with 1-30 µM RH02211 in our experiments 16 µM RH02211 induced an increase of H2O2 production as well as an increase of oxygen consumption independent upon the pyruvate concentration in the medium. Although the H2O2 production rates increased together with the glycolytic conversion rates in pyruvate starved RH02211 treated PC-3 cells the tetramer : dimer ration of M2-PK, the LDH isoenzyme equipment as well as the composition of the glycolytic enzymes were not impaired. In pyruvate supplemented cultivation medium RH02211 did not impair the glycolytic conversion rates. iGP-1 induced an increase of glycolysis and glutaminolysis in pyruvate starved PC-3 cells. In the second part of the study three different commercially available CIII inhibitors (Antimycin A, Myxothiazol and S3QEL-2) that target CIII by different mode of actions were investigated. All three inhibitors induced a dose dependent inhibition of PC-3 cells proliferation in pyruvate starved medium. The inhibition of cell proliferation by CIII inhibition was weakened by hypoxia when Qi site was inhibited (AA) but not when CIII Qo was inhibited (Myx and S3QEL-2). Measurements of metabolic nutrients and products in the cell cultivation supernatants of the cells point to an activation of glycolysis by AA, Myx and S3QEL-2 independently upon oxygen supply. Glutaminolysis was downregulated in AA and Myx treated cells at both 21% and 1.5% O2 as well as in S3QEL-2 treated cells at 1.5% O2 but not at 21% O2. These results indicate that glucose became the main energetic source for PC-3 cell proliferation when CIII was inhibited. The increase in glycolysis in AA, Myx and S3QEL-2 treated cells was not linked with changes in the activity of the glycolytic enzymes as well as with changes in H2O2 production. Both AA and Myx strongly decreased PC-3 cell respiration. In contrast to the first published description which showed no impact of S3QEL-2 on respiration of HEK 293 cells treated for 3 hours with 34 µM S3QEL-2 in our experiments a slight but significant decrease in oxygen consumption was found in presence of 12 µM S3QEL-2. The weaker effect of S3QEL-2 on mitochondrial respiration compared to Myx may be an explanation for the significantly higher IC50 values of S3QEL-2 in comparison to Myx for the inhibition of PC-3 cell proliferation

Comparative Analysis of Commercial and Home-Made Media on RSPO1/S6R Axis in Organoids with Different Wnt Backgrounds: A Methodological Guide for the Selection of Intestinal Patient-Derived Organoids Culture Media

WNT3A is an intestinal ligand triggering the Wnt/β-catenin (Wnt) pathway, which can be enhanced by R-spondin 1 (RSPO1) through the RSPO1–LGR axis or antagonized by the adenomatous polyposis coli (APC) protein supporting β-catenin-degradation. Wnt interplays with several pathways including PI3K/mTOR (mTOR). In this study, we evaluated the influence of WNT3A-commercial and home-made culture media and RSPO1 protein on the Wnt and mTOR interplay in non-APC and APC-mutated intestinal patient-derived organoids (PDOs). Normal mucosa (NM) of sporadic CRC and FAP PDOs were cultured with: WNT3A-lacking/containing commercial (A/A+B) or home-made (BASAL/WNT3A-conditioned medium (CM)±RSPO1) media. In non-APC-mutated-PDOs (CRC-NM), WNT3A-CM, over commercial A+B, strongly activated Wnt-target-genes CCND1 and c-MYC. Most importantly, the addition of RSPO1 to home-made WNT3A-CM or A+B led to the downregulation of the mTOR-downstream-effector phospho-S6 ribosomal protein (p-S6R), highlighting the activation of the RSPO1–pS6R in both non-APC (CRC-NM) and APC-mutated (FAP-NM) PDOs, independently from LGR5 gene expression modulation. Our work demonstrates that home-made WNT3A-CM strongly impacts the crosstalk between Wnt and mTOR over commercial media, and proposes RSPO1 as a key regulator of the RSPO1–p-S6R axis in both non-APC and APC-mutated PDOs. Together, these findings represent an important methodological guide for scientists working in these fields to select the most appropriate intestinal PDO media

Patient-Derived Organoid Biobanks for Translational Research and Precision Medicine: Challenges and Future Perspectives

Over the past decade, patient-derived organoids (PDOs) have emerged as powerful in vitro models that closely recapitulate the histological, genetic, and functional features of their parental primary tissues, representing a ground-breaking tool for cancer research and precision medicine. This advancement has led to the development of living PDO biobanks, collections of organoids derived from a wide range of tumor types and patient populations, which serve as essential platforms for drug screening, biomarker discovery, and functional genomics. The classification and global distribution of these biobanks reflect a growing international effort to standardize protocols and broaden accessibility, supporting both basic and translational research. While their relevance to personalized medicine is increasingly recognized, the establishment and maintenance of PDO biobanks remain technically demanding, particularly in terms of optimizing long-term culture conditions, preserving sample viability, and mimicking the tumor microenvironment. In this context, this review provides an overview of the classification and worldwide distribution of tumor and paired healthy tissue-specific PDO biobanks, explores their translational applications, highlights recent advances in culture systems and media formulations, and discusses current challenges and future perspectives for their integration into clinical practice

Impact of mtG3PDH inhibitors on proliferation and metabolism of androgen receptor-negative prostate cancer cells: Role of extracellular pyruvate.

Mitochondrial glycerol 3-P dehydrogenase (mtG3PDH) plays a significant role in cellular bioenergetics by serving as a rate-limiting element in the glycerophosphate shuttle, which connects cytosolic glycolysis to mitochondrial oxidative metabolism. mtG3PDH was identified as an important site of electron leakage leading to ROS production to the mitochondrial matrix and intermembrane space. Our research focused on the role of two published mtG3PDH inhibitors (RH02211 and iGP-1) on the proliferation and metabolism of PC-3 and DU145 prostate cancer cells characterized by different mtG3PDH activities. Since pyruvate as a substrate of lactate dehydrogenase (LDH) may represent an escape mechanism for the recycling of cytosolic NAD+ via the glycerophosphate shuttle, we investigated the effect of pyruvate on the mode of action of the mtG3PDH inhibitors. Extracellular pyruvate weakened the growth-inhibitory effects of RH02211 and iGP-1 in PC-3 cells but not in DU145 cells, which correlated with higher H-type LDH and lower mitochondrial glutamate-oxaloacetate transaminase in DU145 cells. In the pyruvate-low medium, the strength of inhibition was more pronounced in PC-3 cells, characterized by higher mtG3PDH activities compared to DU145 cells. Pyruvate conversion rates (production in pyruvate-low and consumption in pyruvate-high PC-3 cells) were not impaired by RH02211 and iGP-1, suggesting that the conversion of extracellular pyruvate to lactate was not the primary factor responsible for the weakening effect of extracellular pyruvate on the RH02211-induced inhibition of PC-3 proliferation. In pyruvate-high PC-3 cells, the intracellular glycerol-3-P and dihydroxyacetone-P concentrations were consistent with an inhibition of mtG3PDH. In contrast, in pyruvate-low cells, the concentrations of these metabolites suggested an activation of mtG3PDH in parallel with an impairment of cytosolic G3PDH by RH02211. Of all metabolic characterizations recorded in this study (fluxes, intracellular intermediates, O2 consumption and H2O2 production), the decrease in glutaminolysis correlated best with the RH02211-induced inhibition of proliferation in pyruvate-low and pyruvate-high PC-3 cells