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Singh, A.

Publications and source records attributed to Singh, A..

At least 271 records · Page 15Linked to original sources

Diurnal variation in skeletal muscle mitochondrial function dictates time of day-dependent differences in exercise capacity

Exercise impinges on almost all physiological processes at an organismal level and is a potent intervention to treat various diseases. Exercise performance is well established to display diurnal rhythm, peaking during the late active phase. However, the underlying molecular/metabolic factors and mitochondrial energetics that possibly dictate time-of-day exercise capacity remain unknown. Here, we have unraveled the importance of diurnal variation in mitochondrial functions as a determinant of skeletal muscle exercise performance. Our results show that exercise-induced muscle metabolome and energetics are distinct at ZT3 and ZT15. Importantly, we have elucidated key diurnal differences in mitochondrial functions that are well correlated with disparate time-of-day dependent exercise capacity. Providing causal evidence, we illustrate that loss of Sirtuin4 (SIRT4), a well-known mitochondrial regulator, abrogates diurnal variation in mitochondrial functions and consequently abolishes time-of-day dependent exercise performance. Therefore, our findings unequivocally demonstrate the pivotal role of baseline skeletal-muscle mitochondrial functions in dictating diurnal exercise capacity.

physiology↗

Consumption of human-relevant levels of sucrose-water rewires macronutrient uptake and utilization mechanisms in a tissue specific manner

Consumption of sugar-sweetened beverages (SSBs) have been linked to metabolic dysfunction, obesity, diabetes and enhanced risk of cardiovascular diseases across all age-groups globally. Decades of work that have provided insights into pathophysiological manifestations of sucrose overfeeding have employed paradigms that rarely mimic human consumption of SSBs. Thus, our understanding of multi-organ cross-talk and molecular and/or cellular mechanisms, which operate across scales and drive physiological derangement is still poor. By employing a paradigm of sucrose water feeding in mice that closely resembles chronic SSB consumption in humans (10% sucrose in water), we have unraveled hitherto unknown tissue-specific mechanistic underpinnings, which contribute towards perturbed physiology. Our findings illustrate that systemic impaired glucose homeostasis, mediated by hepatic gluconeogenesis and insulin resistance, does not involve altered gene expression programs in the liver. We have discovered the pivotal role of the small intestine, which in conjunction with liver and muscles, drives dyshomeostasis. Importantly, we have uncovered rewiring of molecular mechanisms in the proximal intestine that is either causal or consequential to systemic ill-effects of chronic sucrose water consumption including dysfunction of liver and muscle mitochondria. Tissue-specific molecular signatures, which we have unveiled, clearly indicate that inefficient utilization of glucose is exacerbated by enhanced uptake by the gut. Besides providing systems-wide mechanistic insights, we propose that consumption of SSBs causes intestinal molecular addiction for deregulated absorption of hexose-sugars, and drives diseases such as diabetes and obesity.

physiology↗

Mutant p53 Exploits Enhancers to Elevate Immunosuppressive Chemokine Expression and Impair Immune Checkpoint Inhibitors in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer without effective treatments. It is characterized by activating KRAS mutations and p53 alterations. However, how these mutations dysregulate cancer-cell-intrinsic gene programs to influence the immune landscape of the tumor microenvironment (TME) remains poorly understood. Here, we show that p53R172H establishes an immunosuppressive TME, diminishes the efficacy of immune checkpoint inhibitors (ICIs), and enhances tumor growth. Our findings reveal that the upregulation of the immunosuppressive chemokine Cxcl1 mediates these pro-tumorigenic functions of p53R172H. Mechanistically, we show that p53R172H associates with the distal enhancers of the Cxcl1 gene, increasing enhancer activity and Cxcl1 expression. p53R172H occupies these enhancers in an NF-{kappa}B-pathway-dependent manner, suggesting NF-{kappa}Bs role in recruiting p53R172H to the Cxcl1 enhancers. Our work uncovers how a common mutation in a tumor-suppressor transcription factor appropriates enhancers, stimulating chemokine expression and establishing an immunosuppressive TME that diminishes ICI efficacy in PDAC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/609802v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@b2354dorg.highwire.dtl.DTLVardef@1c96300org.highwire.dtl.DTLVardef@829f26org.highwire.dtl.DTLVardef@19e7d2e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Characterizing the role of exosomal miRNAs in metastasis

BackgroundExosomal microRNAs (exomiRs), transported via exosomes, play a pivotal role in intercellular communication. In cancer, exomiRs influence tumor progression by regulating key cellular processes such as proliferation, angiogenesis, and metastasis. Their role in mediating communication between cancer cells and the tumor microenvironment highlights their significance as potential diagnostic and therapeutic targets. MethodologyIn this study, we aimed to characterize the role of exomiRs in influencing the pre-metastatic niche (PMN). Across 7 tumor types, including 4 cell lines and three tumors, we extracted high confidence exomiRs (Log FC >= 2 in exosomes relative to control) and their targets (experimentally identified and targeted by at least 2 exomiRs). Subsequently, we identified enriched pathways and selected the top 100 high-confidence exomiR targets based on the frequency of their appearance in the enriched pathways. These top 100 targets were consistently used throughout the analysis. ResultsCancer cell line and tumor derived ExomiRs have significantly higher GC content relative to genomic background. Pathway enriched among the top exomiR targets included general cancer-associated processes such as "wound healing" and "regulation of epithelial cell proliferation", as well as cancer-specific processes, such as "regulation of angiogenesis in kidney" (KIRC), "ossification" in lung (LUAD), and "positive regulation of cytokine production" in pancreatic cancer (PAAD). Similarly, Pathways in cancer and MicroRNAs in cancer ranked among the top 10 enriched KEGG pathways in all cancer types. ExomiR targets were not only enriched for cancer-specific tumor suppressor genes (TSG) but are also downregulated in pre-metastatic niche formed in lungs compared to normal lung. Motif analysis shows high similarity among motifs identified from exomiRs across cancer types. Our analysis recapitulates exomiRs associated with M2 macrophage differentiation and chemoresistance such as miR-21 and miR-222-3p, regulating signaling pathways such as PTEN/PI3/Akt, NF-{kappa}B, etc. Cox regression indicated that exomiR targets are significantly associated with overall survival of patients in TCGA. Lastly, a Support Vector Machine (SVM) model using exomiR target gene expression classified responders and non-responders to neoadjuvant chemotherapy with an AUROC of 0.96 (in LUAD), higher than other previously reported gene signatures. ConclusionOur study characterizes the pivotal role of exomiRs in shaping the PMN in diverse cancers, underscoring their diagnostic and therapeutic potential.

bioinformatics↗

Enhanced Piezoelectric Performance of PVDF-TrFE Nanofibers through Annealing for Tissue Engineering Applications

This study investigates bioelectric stimulations role in tissue regeneration by enhancing the piezoelectric properties of tissue-engineered grafts using annealed poly(vinylidene fluoride-trifluoroethylene) (PVDF-TrFE) scaffolds. Annealing at temperatures of 80{degrees}C, 100{degrees}C, 120{degrees}C, and 140{degrees}C was assessed for its impact on material properties and physiological utility. Analytical techniques such as Differential Scanning Calorimetry (DSC), Fourier-Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) revealed increased crystallinity with higher annealing temperatures, peaking in {beta}-phase content and crystallinity at 140{degrees}C. Scanning Electron Microscopy (SEM) showed that 140{degrees}C annealed scaffolds had enhanced lamellar structures, increased porosity, and maximum piezoelectric response. Mechanical tests indicated that 140{degrees}C annealing improved elastic modulus, tensile strength, and substrate stiffness, aligning these properties with physiological soft tissues. In vitro assessments in Schwann cells demonstrated favorable responses, with increased cell proliferation, contraction, and extracellular matrix attachment. Additionally, genes linked to extracellular matrix production, vascularization, and calcium signaling were upregulated. The foreign body response in C57BL/6 mice, evaluated through Hematoxylin and Eosin (H&E) and Picrosirius Red staining, showed no differences between scaffold groups, supporting the potential for future functional evaluation of the annealed group in tissue repair.

bioengineering↗

AVJ16 inhibits the RNA binding protein IGF2BP1 in lung adenocarcinomas and prevents tumor growth in mice

IGF2BP1 is an oncofoetal RNA binding protein that is expressed in many tumors. We have recently described a small molecule inhibitor of IGF2BP1, termed AVJ16, that prevents binding of the protein to its RNA targets by directly associating with the protein. Here, using a multi-omics approach, we have analyzed the effects of this inhibition on RNA binding, RNA expression, and protein expression. AVJ16 treatment downregulates RNAs encoding members of several pro-oncogenic signaling pathways, including Hedgehog, Wnt, and PI3K-Akt, and there is a strong correlation between IGF2BP1 RNA binding, RNA expression, and protein expression. AVJ16 treatment of lung adenocarcinoma (LUAD) cells in culture causes a strong reduction in proliferation, colony formation, invasion, and spheroid growth while enhancing apoptosis and cell death. All of these effects are limited to cells expressing IGF2BP1. LUAD cells treated with AVJ16 show a pronounced reduction in vital dye efflux, often correlated with enhanced chemosensitivity. In syngeneic LUAD xenografts in mice, IP injection of AVJ16 prevents tumor growth, and incubation with AVJ16 induces cell death in human organoids derived from IGF2BP1-expressing LUADs but not from healthy lung tissue. These results suggest that AVJ16 is a promising candidate for mono- and/or adjuvant therapy directed against tumors expressing IGF2BP1.

cancer biology↗

A multi-model approach defines function altering MECP2 missense variants identified in individuals with autism spectrum disorder

Pathogenic variants in MECP2 commonly lead to Rett syndrome, where MECP2s function as a DNA cytosine methylation reader is believed critical. MECP2 variants are also catalogued in individuals with autism spectrum disorder (ASD), including nine missense variants which had no known clinical significance at the start of this study. To assess these nine variants as risk alleles for ASD, we developed MECP2 variant functional assays using budding yeast and Drosophila. We calibrated these assays with known pathogenic and benign variants. Our data predict that four ASD variants are loss of function and five are functional. Protein destabilization offers insight into the altered function of some of these variants. Notably, yeast and Drosophila lack DNA methylation, yet all Rett pathogenic and ASD variants located in the methyl DNA binding domain that we analyzed proved to be loss of function, suggesting a clinically-relevant role for non-methyl DNA-binding by MECP2.

neuroscience↗

Caught in the act of triplication: TNF superfamily

In humans, the signaling mechanisms of the 19 paralogs of the tumor necrosis factor superfamily (TNFSF) and the 29 receptor paralogs of the tumor necrosis factor receptor superfamily (TNFRSF) are extensively characterized because of their therapeutic relevance. The functional expansion of TNFSF in vertebrates from a single ancestral gene through successive duplication events is also well established. However, apart from the first identification of a TNFSF homolog, Eiger (dmEiger), in Drosophila melanogaster in 2002, together with its receptor homologs Wengen (dmWgn) and Grindelwald (dmGrnd), this signaling system has remained largely unexplored in invertebrates. More recently, the implication of an Eiger homolog in Plasmodium resistance in malaria vectors has further highlighted the need for a systematic investigation of this pathway in lower invertebrates. Structural comparison of the dmEiger-dmGrnd complex with the canonical 3:3 ligand-receptor configuration observed in human TNFSF-TNFRSF signaling suggests either conservation of this signaling modality since before the bilaterian split or convergent evolution of a similar architecture in both branches. The recent explosion in high-quality proteomes spanning diverse phyla, together with advances in protein-complex prediction using AlphaFold-multimer, now enables large-scale exploration of ligand-receptor evolution across invertebrates. Here, we analyzed 148 near-complete proteomes spanning major invertebrate phyla and identified 290 TNFSF, 336 wengen (wgn), and 115 grindelwald (grnd) homologs, including homologs from lower invertebrates. Structural characterization of 140 selected complexes using AlphaFold and AlphaFold-multimer revealed several key findings: (i) TNFSF and TNFRSF homologs are present in majority of the phyla under invertebrates (ii) the canonical 3:3 ligand-receptor signaling configuration is conserved across invertebrates; (iii) orthologs of 25 out of the 26 genes implicated in TNF signaling pathways are present in lower invertebrates; and (iv) signaling through grnd-like receptors containing a single cysteine-rich domain with CXXCXXXC signature is the predominant signaling mode in invertebrates and becomes highly prevalent in Arthropoda. We also elaborate a hypothesize on the evolutionary trajectories toward a genetically parsimonious signaling by this complex system before functional expansion in vertebrates and species diversification in Arthropoda.

bioinformatics↗

Hysteresis and noise floor in gene expression optimised for persistence against lethal events

Bacterial cell persistence, crucial for survival under adverse conditions like antibiotic exposure, is intrinsically linked to stochastic fluctuations in gene expression. Certain genes, while inhibiting growth under normal circumstances, confer tolerance to antibiotics at elevated expression levels. The occurrence of antibiotic events lead to instantaneous cellular responses with varied survival probabilities correlated with gene expression levels. Notably, cells with lower protein concentrations face higher mortality rates. This study aims to elucidate an optimal strategy for protein expression conducive to cellular survival. Through comprehensive mathematical analysis, we determine the optimal burst size and frequency that maximise cell proliferation. Furthermore, we explore how the optimal expression distribution changes as the cost of protein expression to growth escalates. Our model reveals a hysteresis phenomenon, characterised by discontinuous transitions between deterministic and stochastic optima. Intriguingly, stochastic optima possess a noise floor, representing the minimal level of fluctuations essential for optimal cellular resilience.

systems biology↗

Consequences of decoy site repair and feedback regulation on neurotransmission dynamics

Neurons form the fundamental unit of the central nervous system with the human brain containing close to 100 billion neurons. We present a systems-level model of a chemical synapse by which signals from a presynaptic neuron are transmitted to a postsynaptic neuron. In this model, neurotransmitter-filled synaptic vesicles (SVs) dock with a given rate at a fixed number of docking sites in the axon terminal of the presynaptic neuron. Upon the arrival of an action potential (AP), each docked SV has a certain probability to fuse with the presynaptic membrane and release neurotransmitters into the synaptic cleft. After the SV fusion event, the corresponding docking site undergoes repair before becoming available to be reoccupied by an SV. We develop a stochastic model of these coupled processes and derive exact analytical results quantifying the mean and the degree of random fluctuations (i.e., noise) in the levels of docked SVs and released neurotransmitters in response to a train of APs. Our results show that the repair of docking sites exacerbates synaptic depression, i.e., reduces the ability of the chemical synapse to release neurotransmitters in response to an AP. Moreover, repair amplifies statistical fluctuations in neurotransmission for fixed mean neurotransmitter levels. We next consider feedback regulation where the released neurotransmitters affect the rate of SV docking. Counterintuitively, our analysis reveals that for certain physiological parameter spaces, positive feedback loops can reduce noise levels in both the number of docked SVs and neurotransmitters in the cleft.

neuroscience↗

Intestinal serotonergic vagal signaling as a mediator of microbiota-induced hypertension

Hypertension is a pervasive global health challenge, impacting over a billion individuals worldwide. Despite strides in therapeutic strategies, a significant proportion of patients remain resistant to the currently available therapies. While conventional treatments predominantly focus on cardiac, renal, and cerebral targets, emerging research underscores the pivotal role of the gut and its microbiota. Yet, the precise mechanisms governing interactions between the gut microbiota and the host blood pressure remain unclear. Here we describe a neural host-microbiota interaction that is mediated by the intestinal serotonin (5-HT) signaling via vagal 5HT3a receptors and which is crucial for maintenance of blood pressure homeostasis. Notably, a marked decrease in both intestinal 5-HT and vagal 5HT3aR signaling is observed in hypertensive rats, and in rats subjected to fecal microbiota transplantation from hypertensive rats. Leveraging an intersectional genetic strategy in a Cre rat line, we demonstrate that intestinal 5HT3aR vagal signaling is a crucial link between the gut microbiota and blood pressure homeostasis and that recovery of 5-HT signaling in colon innervating vagal neurons can alleviate hypertension. This paradigm-shifting finding enhances our comprehension of hypertensive pathophysiology and unveils a promising new therapeutic target for combating resistant hypertension associated with gut dysbiosis.

physiology↗

Controlled and orthogonal partitioning of large particles into biomolecular condensates

Biomolecular condensates arising from liquid-liquid phase separation contribute to diverse cellular processes, such as gene expression. Partitioning of client molecules into condensates is critical to regulating the composition and function of condensates. Previous studies suggest that client size limits partitioning, with dextrans >5 nm excluded from condensates. Here, we asked whether larger particles, such as macromolecular complexes, can partition into condensates based on particle-condensate interactions. We sought to discover the biophysical principles that govern particle inclusion in or exclusion from condensates using polymer nanoparticles with tailored surface chemistries as models of macromolecular complexes. Particles coated with polyethylene glycol (PEG) did not partition into condensates. We next leveraged the PEGylated particles as an inert platform to which we conjugated specific adhesive moieties. Particles functionalized with biotin partitioned into condensates containing streptavidin, driven by high-affinity biotin-streptavidin binding. Oligonucleotide-decorated particles exhibited varying degrees of partitioning into condensates, depending on condensate composition. Partitioning of oligonucleotide-coated particles was tuned by altering salt concentration, oligonucleotide length, and oligonucleotide surface density. Remarkably, beads with distinct surface chemistries partitioned orthogonally into immiscible condensates. Based on our experiments, we conclude that arbitrarily large particles can controllably partition into biomolecular condensates given sufficiently strong condensate-particle interactions, a conclusion also supported by our coarse-grained molecular dynamics simulations and theory. These findings may provide insights into how various cellular processes are achieved based on partitioning of large clients into biomolecular condensates, as well as offer design principles for the development of drug delivery systems that selectively target disease-related biomolecular condensates. Significance StatementBiomolecular condensates are subcellular compartments that selectively recruit or exclude client molecules, even though condensates lack an enclosing membrane. Many biochemical reconstitution experiments have investigated mechanisms by which membraneless organelles control partitioning, modeling how cells spatiotemporally recruit components into condensates to regulate cellular functions. One outstanding question is whether partitioning is strictly limited by client size. In this work, we engineered nanoparticles with various sizes and surface functionalities and measured how these variables determine partitioning. We observed controlled and orthogonal partitioning of large particles into several condensate types, driven by strong particle-condensate interactions. Molecular simulations recapitulated key results. Our work advances understanding of how condensate composition is regulated, and our nanoparticle toolbox may also inspire a platform for drug delivery.

biophysics↗

Glioma-associated tertiary lymphoid structures are sites of lymphocyte clonal expansion and plasma cell formation

Adult-type diffuse gliomas, the most common primary brain tumors, pose significant clinical challenges due to limited treatment options, restricted anti-tumor immune response and dismal patient prognosis. In this study, we elucidate the immunological function and clinical relevance of intra-tumoral tertiary lymphoid structures (TLS) in adaptive anti-glioma immunity. We conducted a comprehensive, unbiased analysis of lymphoid aggregation in 642 gliomas using a multi-modal approach that combines RNA sequencing with spatial transcriptome and proteome profiling. Our findings reveal that TLS are present in 15% of tumors and correlate with improved overall survival. Gliomas with TLS exhibit a remodeled perivascular space, marked by transcriptional upregulation and spatial redistribution of collagens associated with barrier functions. Furthermore, we demonstrate that TLS maturation into sites of dynamic adaptive immune responses, characterized by clonal T and B cell expansion and IgA+ and IgG+ plasma-cell formation, is driven by efficient early T cell recruitment to the perivascular space.

immunology↗

DNA walk of specific fused oncogenes exhibit distinct fractal geometric characteristics in nucleotide patterns

Background/ObjectivesThe complex system of cancer has led to an emphasis on understanding the more general causal relationship within the disease. In this context, concepts of symmetry and symmetry-breaking in distinct biological cell features or components have been examined as an approach to cancer investigation. However, there can be possible limitations in directly interpreting the symmetry-based approach from a physical viewpoint due to the lack of understanding of physical laws governing symmetry in complex systems like cancer. MethodsFractal geometry and DNA walk representation were employed to investigate the geometric features i.e., self-similarity and heterogeneity in DNA nucleotide coding sequences of wild-type and mutated oncogenes, tumour-suppressor, and other unclassified genes. The mutation-facilitated self-similar and heterogenous features were quantified by the fractal dimension and lacunarity coefficient measures, respectively. Additionally, the geometrical orderedness and disorderedness in the analyzed sequences were interpreted from the combination of the fractal measures. ResultsThe findings showed distinct fractal geometric features in the case of fusion mutations. It also highlights the possible interpretation of the observed fractal features as geometric analogues concerning explicit observations corresponding to specific cancer types. In addition, the two-dimensional multi-fractal analysis highlighted the presence of a single exponent in the scaling of mutation-mediated gene sequence self-similarity/complexity and heterogeneity. ConclusionsThe approach identified mutation-induced geometric features in gene sequences, demonstrating the potential of DNA walks and fractal analysis in translational research regarding cancer. The findings suggest that investigating fractal parameters can capture unique geometric features in nucleotide sequences, contributing to the understanding of cancers molecular complexity.

bioinformatics↗

Stochastic Gene Expression in Proliferating Cells: Differing Noise Intensity in Single-Cell and Population Perspectives

Random fluctuations (noise) in gene expression can be studied from two complementary perspectives: following expression in a single cell over time or comparing expression between cells in a proliferating population at a given time. Here, we systematically investigated scenarios where both perspectives lead to different levels of noise in a given gene product. We first consider a stable protein, whose concentration is diluted by cellular growth, and the protein inhibits growth at high concentrations, establishing a positive feedback loop. For a stochastic model with molecular bursting of gene products, we analytically predict and contrast the steady-state distributions of protein concentration in both frameworks. Although positive feedback amplifies the noise in expression, this amplification is much higher in the population framework compared to following a single cell over time. We also study other processes that lead to different noise levels even in the absence of such dilution-based feedback. When considering randomness in the partitioning of molecules between daughters during mitosis, we find that in the single-cell perspective, the noise in protein concentration is independent of noise in the cell cycle duration. In contrast, partitioning noise is amplified in the population perspective by increasing randomness in cell-cycle time. Overall, our results show that the commonly used single-cell framework that does not account for proliferating cells can, in some cases, underestimate the noise in gene product levels. These results have important implications for studying the inter-cellular variation of different stress-related expression programs across cell types that are known to inhibit cellular growth.

systems biology↗

Evolution of iGluR ligand specificity, polyamine regulation, and ion selectivity inferred from a placozoan Epsilon receptor

Epsilon ionotropic glutamate receptors (iGluRs) belong to a recently described sub-family of metazoan receptors that is distinct from the AMPA, Kainate, Delta, and Phi (i.e., AKDF) sub-family, the NMDA sub-family, and the Lambda subfamily. Here, we sought to better understand the evolutionary and functional properties of Epsilon receptors by focusing on homologues from the basal invertebrate Trichoplax adhaerens (phylum Placozoa). We provide an updated species-guided phylogeny of eukaryotic iGluRs, and a comprehensive phylogeny of placozoan receptors uncovering marked diversification of Epsilon receptors within three conserved subclades, and four invariable subclades of AKDF receptors. Detailed functional characterization of the T. adhaerens Epsilon receptor GluE1A revealed robust activation by glycine, alanine, serine, and valine, but not glutamate. Through combined of structural modeling and mutation experiments, we used GluE1A to test the hypothesis that only a small set of amino acids in the ligand binding domain determine ligand selectivity. Mutation of just three amino acids converted GluE1A selectivity to glutamate, resulted in nascent sensitivity to AMPA, and increased sensitivity to the AMPA/Kainate receptor blocker CNQX. Lastly, combined modeling and mutation experiments revealed that an atypical serine residue in the pore NQR site of GluE1A, along with an aspartate four amino acids downstream, confers sensitivity to voltage-dependent polyamine block, while the serine alone diminishes both polyamine block and Ca2+ permeation compared to asparagine and glutamine residues of AMPA and Kainate receptors. Altogether, we demonstrate conserved molecular determinants for polyamine regulation between Epsilon and AKDF receptors, and evidence that natural variations in NQR residues have important implications for ion permeation and regulation by polyamines.

neuroscience↗

Insights into the metabolic consequences of type 2 diabetes

Circulating metabolite levels have been associated with type 2 diabetes (T2D), but the extent to which these are affected by T2D and the involvement of genetics in mediating these relationships remain to be elucidated. In this study, we investigate the interplay between genetics, metabolomics and T2D risk in the UK Biobank dataset. We find 79 metabolites with a causal association to T2D, mostly spanning lipid-related classes, while twice as many metabolites are causally affected by T2D liability, including branched-chain amino acids. Secondly, using an interaction quantitative trait locus (QTL) analysis, we describe four metabolites, consistently replicated in an independent dataset from the Estonian Biobank, for which genetic loci in two different genomic regions show attenuated regulation in T2D cases compared to controls. The significant variants from the interaction QTL analysis are significant QTLs for the corresponding metabolites in the general population, but are not associated with T2D risk, pointing towards consequences of T2D on the genetic regulation of metabolite levels. Finally, we find 165 metabolites associated with microvascular, macrovascular, or both types of T2D complications, with only a few discriminating between complication classes. Of the 165 metabolites, 40 are not causally linked to T2D in either direction, suggesting biological mechanisms specific to the occurrence of complications. Overall, this work provides a map of the metabolic consequences of T2D and of the genetic regulation of metabolite levels and enable to better understand the trajectory of T2D leading to complications.

genomics↗

Flagellar Motility is Mutagenic

Flagella are highly complex rotary molecular machines that enable bacteria to not only migrate to optimal environments but to also promote range expansion, competitiveness, virulence, and antibiotic survival. Flagellar motility is an energy-demanding process, where the sum of its production (biosynthesis) and operation (rotation) costs has been estimated to total [~]10% of the entire energy budget of an E. coli cell. The acquisition of such a costly adaptation process is expected to secure short-term benefits by increasing competitiveness and survival, as well as long-term evolutionary fitness gains. While the role of flagellar motility in bacterial survival has been widely reported, its direct influence on the rate of evolution remains unclear. We show here that both production and operation costs contribute to elevated mutation frequencies. Our findings suggest that flagellar movement may be an important player in tuning the rate of bacterial evolution.

microbiology↗