bioRxiv Science⌕ Search

Biology subjects

Singh, P.

Publications and source records attributed to Singh, P..

At least 73 records · Page 4Linked to original sources

An interpretable alphabet for local protein structure search based on amino acid neighborhoods

MotivationRecent advancements in protein structure prediction methods have vastly increased the size of databases of protein structures, necessitating fast methods for protein structure comparison. Search methods that find structurally similar proteins can be applied to find remote homologs, study the functional relationships among proteins, and aid in protein engineering tasks. The structure comparison method Foldseek represents each protein structure as a sequence of "3Di" characters and uses highly optimized sequence comparison software to search with this alphabet. An alternate alphabet encoding richer features has the potential to improve search accuracy while leaving the underlying search algorithm unchanged. ResultsWe design a "3Dn" structural alphabet that encodes the local neighborhoods around each amino acid in an interpretable way. In a search benchmark task, a combination of our alphabet and Foldseeks 3Di alphabet, outperforms each alphabet individually and ranks best among local search methods that do not require amino acid identity information. We provide software tools that enable the exploration of novel alphabets and combinations of alphabets for protein structure search. Availability and implementationThe code is freely available at https://github.com/spetti/structure_comparison.

bioinformatics↗

Integrative plasma lipidomics and proteomics profiling to decipher potential biomarkers of dilated cardiomyopathy

BackgroundDilated cardiomyopathy (DCM), primarily characterised by left ventricular dilatation and systolic dysfunction, is one of the leading causes of heart failure and requires a critical clinical investigative strategy. However, conventional imaging techniques such as echocardiography and MRI, along with some classical CVD markers (NTproBNP, cTnT), fall short in diagnosing DCM-specific phenotypes. Thus, the need for biochemical markers with enhanced accuracy to DCM is of enormous importance. Lipids and proteins play essential roles in maintaining myocardial function. The homeostatic disruption of such biomolecules might contribute to DCM pathogenesis, thus offering to serve as potential biomarkers for DCM. Moreover, the lack of global lipidomics studies and specific protein markers in DCM patients prompted us to explore the disease pathophysiology through an integrative omics-based analysis coupled with an ML-derived approach. ObjectiveTo identify accurate, precise and specific circulatory lipidomic and proteomic biomarkers of DCM using high-resolution mass spectrometry and machine learning (ML)-based approaches. MethodsHigh-resolution-mass-spectrometry-based lipidomics and proteomics were applied to identify lipid and protein biomarkers in a cohort (n=360) of healthy and DCM patients. Top protein classifiers were further evaluated using single-cell transcriptomics on publicly available datasets from DCM myocardium and validated using ELISA. A biomarker panel was built by the integration of lipidomics and validated proteomics data using machine-learning-based approaches. ResultsA total of 125 lipids and 10 proteins have been primarily discovered with significant alterations in DCM (0.8 [&ge;] FC [&ge;] 1.2; padj < 0.05). Using a Boruta-based ML approach, we identified 39 lipids and 10 proteins as primary discriminators between DCM and controls. ELISA validation confirmed the potential of B2M (6.85 {+/-} 2.86 g/ml vs. 4.26 {+/-} 1.25 g/ml; p < 0.0001) and Tetranectin (CLEC3B) (1.99 {+/-} 0.88 g/ml vs. 2.49 {+/-} 0.90 g/ml; p = 0.0006) to emerge as protein biomarkers of DCM. In line with that, the single-cell transcriptomic analysis showed a similar trend of alteration of tetranectin (CLEC3B) in cardiomyocytes and {beta}2microglobulin (B2M) in varied cell types of the myocardium. Further, Integrated ROC analysis combining the top 8 lipid discriminators with B2M and CLEC3B achieved an AUC of 0.995, demonstrating enhanced diagnostic precision compared to the classical CVD marker NTproBNP (0.965). ConclusionThis study offers a system-omics-based perspective on first-global lipidomic and proteomic changes associated with DCM pathophysiology, with a high potential for diagnostic application.

systems biology↗

A systems biology investigation to identify potential bi-omarkers in leprosy-affected host cells.

M. leprae adapts to the host cell environment and disrupts protein-protein interactions inside the host cell for its own survival and proliferation. This study is attempts to comprehend these host-pathogen interactions at the systems level. We utilised RNA-Seq data set of leprosy-resistant and leprosy-susceptible armadillos and investigated how five different human signaling pathways get hijacked by M. leprae. We also identified the corresponding human homolog proteins. By applying graph theory on these protein networks, we predicted 25 proteins which play important role in these pathways related to leprosy pathogenesis and/progression. The study is also supported by wet lab experiments identifying 69 proteins in armadillos upon leprosy progression after experimental infection which get differentially expressed. Our study found that 69.5% of these experimentally identified proteins are part of either M. leprae-affected signaling pathways or possibly contribute to leprosy pathogenesis based on their GO terms. This study identified three human proteins: LC3-II, PI3K and IDO1 which have been implicated in M. leprae pathogenesis in other studies also leprosy patients. Thus, upon further experimentally validation, such markers can be potentially useful to diagnose leprosy in patients at an early stage .

systems biology↗

Inducible estrogen receptor alpha in normal breast epithelial cells demonstrate estrogen receptor-dependent DNA damage

BackgroundSignaling by estrogen-receptor alpha (ER) plays a major role in breast cancer initiation Investigations of the mechanism of DNA damage mediated by ER signaling are carried out in breast cancer cell lines due to the lack of ER+ normal human breast epithelial cells lines (HBEC). Defining the mechanisms by which ER induces DNA damage and initiates tumorigenesis requires normal HBECs that express ER, demonstrate estrogenic responses, and are amenable to long term propagation in culture. MethodsWe utilized lentiviral expression of an inducible ER construct to generate four HBEC lines (HBEC-ESR1). We studied these cells for ER-dependent responses using a luciferase reporter, endogenous gene expression and proliferation assays. RNA-Seq was performed to characterize the ER-mediated transcriptomic patterns in the four HBEC lines. ER mediated DNA double strand breaks (DSBs) were analyzed using {gamma}H2AX immunofluorescence. ResultsExpression and functional activation of ER were observed in all HBEC-ESR1 lines, whereas proliferation in response to 17{beta}-estradiol (E2) was observed in 3 of the cell lines. Proliferative responses were due to intrinsic signaling within the HBECs as conditioned media from the cells failed to cause proliferation. A total of 682 genes were differentially expressed at 24h following treatment with 10nM E2 with 43% of these genes were also observed in ER+ breast cancer cell lines (MCF7 or T47D). Gene-set enrichment analysis identified differential expression of genes in ER signaling pathways and DNA repair pathways in E2-treated cells. E2-induced ER signaling also increased {gamma}H2AX foci in 3 of the 4 cell lines. Levels of DSBs were increased by inhibition of the non-homologous end-joining (NHEJ) and homologous recombination (HR) pathways. DSBs were also increased in MCF10A-ESR1 cells heterozygous for the BRCA1185delAG mutation causing a truncated protein. ConclusionsInducible expression of ER in immortalized HBECs recapitulate transcriptional, replicative and DNA damage responses. Increased DSBs in MCF10A-ESR1 cells with heterozygous mutation of BRCA1 indicate haploinsufficiency and the potential for increased genetic instability due to ER signaling.

cancer biology↗

Antibody-Free Immunopeptide Nano-Conjugates for Brain-Targeted Drug Delivery in Glioblastoma Multiforme

Glioblastoma Multiforme (GBM) represents a significant clinical challenge amongst central nervous system (CNS) tumors, with a dismal mean survival rate of less than 8 months, a statistic that has remained largely unchanged for decades (National Brain Society, 2022). The specialized intricate anatomical features of the brain, notably the blood-brain barrier (BBB), pose significant challenges to effective therapeutic interventions, limiting the potential reach of modern advancements in immunotherapy to impact these types of tumors. This study introduces an innovative, actively targeted immunotherapeutic nanoconjugate (P12/AP-2/NCs) designed to serve as an immunotherapeutic agent capable of traversing the BBB via LRP-1 receptor-mediated transcytosis. P12/AP-2/NCs exert its immune-modulating effects by inhibiting the PD-1/PD-L1 axis through a small-size PD-L1/ PD-L2 antagonist peptide Aurigene NP-12 (P12). P12/AP-2/NCs are synthesized from completely biodegradable, functionalized high molecular weight {beta}-poly(L-malic acid) (PMLA) polymer, conjugated with P12 and Angiopep-2 (AP2) to yield P12/AP-2/NCs. Evaluating nanoconjugates for BBB permeability and 3-D tumor model efficacy using an in vitro BBB-Transwell spheroid based model demonstrating successful crossing of the BBB and internalization in brain 3D tumor environments. In addition, the nanoconjugate mediated T cells cytotoxicity on 3D tumor region death in a U87 GBM 3-D spheroid model. AP2/P12/NCs is selectively inhibited in PD1/PDL1 interaction on T cells and tumor site, increasing inflammatory cytokine secretion and T cell proliferation. In an in-vivo murine brain environment, rhodamine fluorophore-labeled AP2/P12/NCs displayed significantly increased accumulation in the brain during 2-6 h time intervals post-injection with a prolonged bioavailability over unconjugated peptides. AP2/P12/NCs demonstrated a safety profile at both low and high doses based on major organ histopathology evaluations. Our findings introduce a novel, programmable nanoconjugate platform capable of penetrating the BBB for directed delivery of small peptides and significant immune environment modulation without utilizing antibodies, offering promise for treating challenging brain diseases like glioblastoma multiforme and beyond.

immunology↗

Small Molecule Modulators of TOX protein to Re-invigorate T cell Activity

The TOX protein (thymocyte selection-associated high mobility group box) is a critical transcription factor implicated in both T acute lymphoblastic leukemia (T-ALL) and CD8+ T cell exhaustion. Gene perturbation studies suggest that inhibiting TOX may have therapeutic implications for both leukemia and T cell exhaustion. However, due to its complex molecular mechanisms and intrinsically disordered structure, TOX has not been effectively targeted by small molecules to date. In this study, we used small molecule microarray (SMM) screening and biochemical assays to identify a series of TOX protein-protein interaction (PPI) inhibitors. We identified KI-TOX-A3 as a TOX protein binder and potent TOX PPI inhibitor. In T-ALL, KI-TOX-A3 revealed selective cytotoxicity and proteosome-dependent TOX degradation. In CD8+ T cells, KI-TOX-A3 potently reversed T cell exhaustion by decreasing surface inhibitory receptors, increasing expression of effector cytokines, and enhancing cancer cell killing activity. We also demonstrate the utility of KI-TOX-A3 to probe potential epigenetic regulatory mechanisms of TOX via KAT7 acetylation in T cells.

biochemistry↗

Predicting allergy and postpartum depression from incomplete compositional microbiome

Time series of compositional data are a common format for many high-throughput studies of biological molecules, e.g., analyzing the response to a treatment or with the aim of predicting an outcome. However, data from some time points may be missing, which reduces the size of the complete dataset. We propose a method for binary classification that includes imputation for missing values and logarithmic transformation of compositional data. Imputation approaches entail models that incorporate artificial data alongside true measurements, thereby supplementing the dataset. We consider two datasets from prospective analyses with as-sociated target labels, aiming to improve prediction accuracy. We predict infants food allergies from their gut microbiome with a balanced accuracy of 0.72. We forecast postpartum depression based on gut microbiome data collected during pregnancy, with a balanced accuracy of 0.62. Features extracted from the microbiome time series, specifically ratios of bacterial abundance, are statistically significant indicators of depression.

bioinformatics↗

Three species, three labs, three experiments: testing the reproducibility of ecological studies on insect behaviour in a multi-laboratory setting

The reproducibility of studies involving insect species is an underexplored area in the broader discussion about poor reproducibility in science. Our study addresses this gap by conducting a systematic multi-laboratory investigation into the reproducibility of ecological studies on insect behaviour. We implemented a 3x3 experimental design, incorporating three study sites, and three independent experiments on three insect species from different orders: the turnip sawfly (Athalia rosae, Hymenoptera), the meadow grasshopper (Pseudochorthippus parallelus, Orthoptera) and the red flour beetle (Tribolium castaneum, Coleoptera). Using random-effect meta-analysis, we compared the consistency and accuracy of treatment effects on insect behavioural traits across replicate experiments. We successfully reproduced the overall statistical treatment effect in 83% of the replicate experiments, but overall effect size replication was achieved in only 66% of the replicates. Thus, though demonstrating sufficient reproducibility in some measures, this study also provides first experimental evidence for cases of poor reproducibility in insect experiments. Our findings further show that reasons causing poor reproducibility established in rodent research also hold for other study organisms and research questions. We believe that a rethinking of current best practices is required to face reproducibility issues in insect studies, but also across disciplines. Specifically, we advocate for adopting open research practices and the implementation of methodological strategies that reduce bias and problems arising from over-standardization. With respect to the latter, the introduction of systematic variation through multi-laboratory or heterogenized designs may contribute to improved reproducibility in studies involving any living organisms.

animal behavior and cognition↗

Growth Hormone Excess Drives Liver Aging via increased Glycation stress

Growth hormone (GH) plays a crucial role in various physiological functions, with its secretion tightly regulated by complex endocrine mechanisms. Pathological conditions such as acromegaly or pituitary tumors result in elevated circulating GH levels, which have been implicated in a spectrum of metabolic disorders, potentially by regulating liver metabolism. In this study, we focused on the liver, a key organ in metabolic regulation and a primary target of GH, to investigate the impact of high circulating GH on liver metabolism. We used bovine GH overexpressing transgenic (bGH-Tg) mice to conduct a comprehensive transcriptomic analysis of hepatic tissues. The bGH-Tg mouse livers exhibit dysregulated fatty acid metabolism and heightened inflammatory responses. Notably, the transcriptomic profile of young bGH-Tg mouse livers resembled that of aged livers and displayed markers of increased cellular senescence. Furthermore, these mice exhibited a significant accumulation of advanced glycation end products (AGEs). Intervention with glycation-lowering compounds effectively reversed the insulin resistance and aberrant transcriptomic signatures in the liver that are associated with elevated GH levels. These findings underscore the potential therapeutic value of glycation-lowering agents in mitigating the deleterious effects of chronic GH overexpression. HighlightsO_LIOverexpression of bovine growth hormone impacts transcriptional changes in liver fat metabolism and inflammatory response in mice. C_LIO_LIHigh circulating growth hormone leads to transcriptional changes that suggest enhanced liver aging and induce cellular senescence. C_LIO_LIDetoxification pathways in bGH-Tg mice are inhibited, leading to the accumulation of Advanced Glycation End (AGE) products. C_LIO_LIGlycation-lowering compounds can mitigate pathologies associated with high GH levels. C_LI

physiology↗

Adipocyte Aldosterone in Obstructive Sleep Apnea

Aldosterone, a hormone synthesized by the adrenal glands, plays a pivotal role in regulating both blood pressure and electrolyte balance and may contribute to long term cardiovascular risk. Recent findings suggest that adipose tissue might serve as a source for aldosterone production and secretion. Patients suffering from obstructive sleep apnea (OSA) often exhibit elevated blood pressure levels and increased cardiovascular risk. Therefore, we sought to investigate whether increased aldosterone synthesis in fat tissue could contribute to the increase in hypertension and cardiovascular disease in OSA patients. To address this, we conducted a comparative analysis of adipocyte aldosterone level in OSA patients versus Age and BMI matched healthy individuals. Our data revealed no significant differences in aldosterone content between the two groups. Further examination involved measuring the expression of the key enzyme CYP11B2 responsible for aldosterone synthesis. We observed comparable expression levels of CYP11B2 in both the OSA and control groups. To corroborate these findings, we isolated stromal vascular fraction (SVF) from human fat tissues. The SVF cells were cultured in preadipocyte medium and subjected to normoxia and intermittent hypoxia (IH), mimicking OSA conditions as per established protocol. Subsequent analysis of aldosterone levels in cell lysates and conditioned medium revealed no significant differences. Similarly, in vitro examination of CYBP11B2 expression was not different in normoxic versus IH conditions. In conclusion, our study did not discern significant differences in adipocyte aldosterone production and secretion between patients with OSA and matched control subjects, nor in human preadipocytes under normoxic versus IH conditions.

molecular biology↗

Methylglyoxal-induced glycation stress promotes aortic stiffening: Putative mechanistic roles of oxidative stress and cellular senescence

BackgroundHere, we assessed the role of the advanced glycation end-product (AGE) precursor methylglyoxal (MGO) and its non-crosslinking AGE MGO-derived hydroimidazolone (MGH)-1 in aortic stiffening and explored the potential of a glycation stress-lowering compound (Gly-Low) to mitigate these effects. MethodsYoung (3-6 month) C57BL/6 mice were supplemented with MGO (in water) and Gly-Low (in chow). Aortic stiffness was assessed in vivo via pulse wave velocity (PWV) and ex vivo through elastic modulus. Putative mechanisms underlying MGO- and MGH-1-induced aortic stiffening were explored using complementary experimental approaches in aortic tissue and cultured human aortic endothelial cells (HAECs). Moreover, aortic stiffness was assessed in old (24 month) mice after consumption of Gly-Low-enriched chow. ResultsMGO-induced glycation stress increased PWV in young mice by 21% (P<0.05 vs. control), which was prevented with Gly-Low (P=0.93 vs. control). Ex vivo, MGO increased aortic elastic modulus 2-fold (P<0.05), superoxide production by [~]40% (P<0.05), and MGH-1 expression by 50% (P<0.05), which were all mitigated by Gly-Low. Chronic MGO exposure elevated biomarkers of cellular senescence in HAECs, comparable to a known senescence inducer Doxorubicin, an effect partially blocked by Gly-Low. Moreover, elevated aortic elastic modulus induced by Doxorubicin (P<0.05 vs. control) was prevented with Gly-Low (P=0.71 vs. control). Aortic RNA sequencing implicated preservation of endogenous cellular detoxification pathways with Gly-Low following exposure to MGH-1. Old mice supplemented with Gly-Low had lower PWV (P<0.05) relative to old control mice. ConclusionsMGO-induced glycation stress contributes to aortic stiffening and glycation stress lowering compounds hold promise for mitigating these effects. What Is New?This study provides the first comprehensive line of evidence that methylglyoxal (MGO)-induced glycation stress directly contributes to aortic stiffening and does so through mechanisms involving oxidative stress and cellular senescence. Using complementary in vivo, ex vivo, and in vitro experimental models, we establish that MGO-mediated glycation stress independently induces aortic stiffening. Furthermore, we demonstrate that the glycation-lowering compound, Gly-Low, mitigates MGO-induced aortic stiffening by mitigating excessive oxidative stress and cellular senescence, and can lower aortic stiffness in old mice. Mechanistically, activation of the detoxification enzyme, glyoxalase-1 (Glo-1), is a novel pathway by which Gly-Low mediates its therapeutic effects on aortic stiffening. Lastly, we show that Gly-Low holds promise for lowering aortic stiffness in old age. What Is Relevant?Aortic stiffening is a major risk factor for cardiovascular diseases (CVD) and a significant predictor of CV-related morbidity and mortality. Yet, the underlying mechanisms driving this process remain incompletely understood. This study identifies MGO-derived glycation stress as a critical and modifiable factor contributing to aortic stiffening through pathways involving excessive oxidative stress and cellular senescence. By establishing the efficacy of Gly-Low in mitigating these effects, our findings underscore the importance of targeting glycation stress in the context of aging, and likely in other settings of glycation stress, to improve arterial health and reduce CVD risk. Clinical/Pathophysiological ImplicationsThese findings have significant clinical implications, as they demonstrate that glycation stress is a viable and modifiable therapeutic target for the prevention and treatment of aortic stiffening. Gly-Low offers a promising therapeutic approach to ameliorate glycation stress- and age-related aortic stiffening, by directly targeting excess glycation stress, oxidative stress, and cellular senescence. Additionally, the involvement of the Glo-1 detoxification pathway suggests a specific molecular target for future interventions aimed at improving arterial health and mitigating the progression of CVD.

molecular biology↗

Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes

BackgroundSmall intestinal neuroendocrine tumours (SI-NETs) are the most common malignancy of the small intestine and around 50% of patients present in clinic with multifocal disease. Recent investigations into the genomic architecture of multifocal SI-NETs have found evidence that these synchronous primary tumours evolve independently of each other. They also have extremely low mutational burden and few known driver genes, suggesting that epigenetic dysregulation may be driving tumorigenesis. Very little is known about epigenetic gene regulation, metabolism and ageing in these tumours, and how these traits differ across multiple tumours within individual patients. MethodsIn this study, we performed the first investigation of genome-wide DNA methylation in multifocal SI-NETs, assessing multiple primary tumours within each patient (n=79 primary tumours from 14 patients) alongside matched metastatic tumours (n=12) and normal intestinal epithelial tissue (n=9). We assessed multifocal SI-NET differential methylation using a novel method, comparing primary tumours with matched normal epithelial tissue and an enterochromaffin-enriched cell line to enrich for tumour-specific effects. This method reduced the identification of false positive methylation differences driven by cell composition differences between tumour and normal epithelial tissue. We also assessed tumour ageing using epigenetic clocks and applied metabolic predictors in the dataset to assess methylation variation across key metabolic genes. ResultsWe have identified 12,392 tumour-specific differentially methylated positions (Bonferroni corrected p<0.05) which were enriched for neural pathways. The expression levels of the genes associated with top sites were also found to be significantly altered in SI-NETs. Age acceleration was observed across SI-NETs and a variability in epigenetic age of tumours within each patient, which we believe is reflecting the order in which tumours have developed. This is supported by the correlation of age acceleration with somatic mutational count in the tumours. We have identified SI-NET associated alterations to the methylation patterns in key metabolic genes compared to matched normal tissue, which is more pronounced in metastatic tumours and tumours harbouring chromosome 18 loss of heterozygosity, indicating metabolic differences in these tumour subtypes. ConclusionsWe have identified accelerated ageing and changes to regulation of metabolic genes, alongside an epigenetic signature of multifocal SI-NETs. These findings add to our understanding of multifocal SI-NET biology and their molecular differences which may be instrumental in the development of these elusive tumours.

cancer biology↗

Deciphering Memory Patterns in Eco-Epidemiological systems through the lens of BaFOMS: A Bayesian Fractional Order Model Selection Method

The evolution of eco-epidemiological systems is significantly influenced by the memory or previous history of the system. These non-Markovian dynamics are effectively modelled using fractional derivatives (FDs), incorporating memory kernels that reflect long-term or short-term memory characteristics in corresponding nonlinear fractional differential evolution equations. We introduce BaFOMS, a framework for identifying and selecting the optimal FD model for eco-epidemiological processes based on historical data. Specifically, we evaluate a class of fractional logistic growth models defined by their time correlation functions and determine the optimal model through Bayesian inference, selecting the one with the highest posterior probability. We also demonstrated BaFOMS efficiency in parameter estimation and forecasting, producing reliable results with quantified uncertainties. The method is shown to be robust across a range of eco-epidemiological datasets, offering computational efficiency and reliable inference about the evolution dynamics.

ecology↗

Parallel cases of ring speciation within a rapid adaptive radiation of cichlid fishes

Speciation often emerges from the complex interplay of geography, demography, ecology, and sexual selection, yet disentangling their relative contributions remains a challenge. In this study, we examine two species complexes of rock-dwelling Lake Victoria cichlids in the genera Pundamilia and Neochromis that are distributed along a continuous geographic gradient of rocky shores. Using morphometric analyses and male nuptial coloration data, we reveal clinal craniofacial divergence following an isolation by distance model of evolution, punctuated by strong local effects. While the Pundamilia cline exhibited modular shifts in craniofacial anatomy linked to diet-specific morphology, variation in the Neochromis cline was dominated by allometric constraints, suggesting different evolutionary processes at play. At the single site where the terminal populations of both clines co-occur, each pair of sister species showed pronounced divergence in morphology and male nuptial coloration, consistent with ecological and sexual character displacement facilitating co-existence. Our findings highlight that clinal morphological variation in parapatry and more abrupt shifts in sympatry interact to generate and maintain species. These rocky shore cichlids provide a rare opportunity to investigate the speciation continuum in one of the worlds youngest adaptive radiations.

evolutionary biology↗

Loss of KDM6A-mediated genomic instability and metabolic reprogramming differentially regulates responses to immune checkpoint therapy and chemotherapy in bladder cancer.

Mutations in genes encoding critical epigenetic regulators are frequently noted in bladder cancer, however, the impact of these mutations on therapeutic efficacy is unclear. One of the most common driver mutations in bladder cancer occurs in the KDM6A gene, which encodes a histone demethylase that promotes gene transcription. Retrospective analyses of patients with bladder cancer demonstrated that KDM6A mutations correlate with improved overall survival (OS) with immune checkpoint therapy (ICT), while they are associated with lower OS in patients undergoing cisplatin-based chemotherapy. Mechanistic studies utilizing CRISPR-Cas9 mediated deletion of Kdm6a showed reduced expression of DNA mismatch repair (MMR) and DNA double-stranded base repair (DSBR) genes in tumor cells with improved response to anti-PD-1 therapy and attenuated sensitivity to cisplatin-based chemotherapy in preclinical models of bladder cancer. Additionally, the loss of Kdm6a-mediated reduction in glycolysis and intratumoral lactate accumulation impaired histone 3 lysine 9 lactylation (H3K9la) and histone 3 lysine 18 lactylation (H3K18la) in Tregs with concurrent decrease in the expression of key genes including Foxp3, Tgfb and Pdcd1 and their immune-suppressive function. Further, reduced expansion of PD-1hi Tregs improved the ratio of cytotoxic T cells to Tregs and response to anti-PD-1 therapy in Kdm6a deficient tumor-bearing mice. Collectively, this study provided key insights into the role of KDM6A-mediated epigenetic regulation of DNA repair and metabolic reprogramming which potentially govern response to chemotherapy and ICT thus highlighting the utility of KDM6A mutation status for patient stratification and development of personalized treatment algorithms.

immunology↗

Diabetes-Tuberculosis Comorbidity Characterized by Reduced Type-II Interferon and Elevated Th17 Responses.

Understanding the perturbed lung immune cells distribution and its functionality in tuberculosis (TB) is well documented; however, limited reports have covered their disruption, if any, in diabetes-tuberculosis (DM-TB) comorbid conditions. Here, we employed single-cell RNA-seq to investigate the molecular mechanisms that govern the heterogeneity in host immune response in DM-TB comorbid conditions. Diabetes is associated with chronic hyperinflammation and reduced lung-infiltrating immune cells, which delays the immune response to Mycobacterial infection. scRNA-seq of lung CD3 and CD11c cells revealed compromised adaptive and innate immunity, with decreased Th1 and M1 macrophage populations in DM-TB mice. A dampened immune response, marked by increased IL-16 signaling and reduced TNF and IFN-II responses, was observed in DM-TB. This study highlights chronic inflammation, hyperglycemia, and dyslipidemia associated with diabetes impairing anti-TB immunity. Selective inhibition of aberrant IL-16 secretion and Th17 cell activation might provide strategies for better managing DM-TB comorbidity.

immunology↗

Exploring New Horizons:A Novel Cdk5 Inhibitor Restoring Cognitive Function and Alleviating Type 2 Diabetes.

Type 2 diabetes (T2D) is a metabolic disorder frequently associated with cognitive decline, making T2D patients susceptible to dementia. Often referred to as type 3 diabetes, Alzheimers disease (AD) shares a close association with hyperglycemia and insulin dysregulation. Despite this, anti-diabetic medications have proven beneficial in reducing cognitive impairment induced by T2D. Previous research, including our own, has highlighted the dysregulation of Cdk5 activity in both T2D and AD, with downstream consequences contributing to the progression of pathophysiological changes in both disorders. Therefore, targeting the kinase Cdk5 may offer a more effective approach to treating T2D and cognitive deterioration. In our study, we present evidence supporting Cdk5 as a significant mediator between T2D and cognitive decline. Through the screening of the KINACore library, we identified novel brain-penetrant Cdk5 inhibitors, BLINK11 and BLINK15. Our study further validated the efficacy of these inhibitors in a high-fat diet-induced T2D model, demonstrating their rescue effects on T2D pathogenesis, including blood glucose levels, obesity, and cognitive impairment as assessed through behavioral studies. Notably, BLINK11 emerges as a promising Cdk5 inhibitor for improving the T2D phenotype and addressing cognitive impairment in T2D conditions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/615976v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1f6267aorg.highwire.dtl.DTLVardef@1583c99org.highwire.dtl.DTLVardef@1f27603org.highwire.dtl.DTLVardef@121f02b_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

Identifying Agronomic, Nutrition and Leaf Vein Quantitative Trait Loci in the Orphan Crop Gynandropsis gynandra

A sustainable food supply is vital for addressing the challenges of a growing global population and climate change. Gynandropsis gynandra, a nutritious C4 orphan crop native to Africa and Asia, thrives in low-input agricultural systems, making it a valuable candidate for future food security. This crop also serves as a model for studying C4 photosynthesis. However, research on its genetic improvement is limited. In this study, two mapping populations from diverse parental lines were used to identify Quantitative Trait Loci (QTL) linked to agronomically relevant traits like plant height, leaf area, flowering time, nutritional content, and photosynthesis. Fifteen QTL were identified, with two affecting both leaf size and flowering time across populations, which can be applied for marker assisted selection for crop improvement. Additionally, QTL linked to C4 photosynthesis provide insights into the genetic mechanisms behind this pathway. Overall, this research enhances the potential of G. gynandra as a climate-resilient crop. One sentence summaryLeveraging natural variation in Gynandropsis gynandra to identify QTL associated with important traits.

plant biology↗