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Singh, S.

Publications and source records attributed to Singh, S..

At least 235 records · Page 13Linked to original sources

KAT5 Acetylates Human Chromatin Protein PC4 to promote DNA Repair

Human positive coactivator 4 (PC4), is a highly abundant non-histone chromatin protein involved in diverse cellular processes, including transcription regulation, genome organization, DNA repair, etc. The majority of PC4 exists in a phosphorylated state in cells, which impinges its acetylation by p300 and thereby inhibits its double-stranded DNA binding ability and transcriptional co-activator function. Recently, we have shown that PC4 interacts with linker histone H1 in its phosphorylated state, and this interaction is important for PC4- mediated chromatin compaction. PC4 was also found to be an activator of non-homologous end joining and DSB repair activity. Knockdown of PC4 causes drastic decompaction and enhanced autophagy in the cells. Mechanistically, in the absence of PC4, the genome becomes highly vulnerable to DNA damage with an altered epigenetic landscape. Here, we report that other than p300, PC4 also gets acetylated by DNA repair facilitating lysine acetyltransferase KAT5 (Tip60), at K80 residue when the cells are subjected to DNA damage. The vulnerability of DNA in PC4 devoid cells could be substantially reduced by reintroducing wild-type PC4 to the cells but not the mutant PC4 (K80R PC4), defective in KAT5-mediated acetylation. Presumably, KAT5-mediated acetylation of PC4 at K80 residue facilitates the DNA repair machinery at the damage site and thus contributes to DNA damage repair, a process that could be of high significance both in cancer and in aging.

molecular biology↗

CREB activation drives acinar to ductal reprogramming and promote pancreatic cancer progression in animal models of alcoholic chronic pancreatitis

BACKGROUND & AIMSChronic alcoholism often leads to pancreatitis, which exacerbates pancreatic damage through acinar cell injury, fibrotic inflammation and activates AKT/mTOR/cyclic adenosine monophosphate response element binding protein 1 (CREB) signaling axis. However, the molecular interplay between oncogenic KrasG12D/+(Kras*) and CREB in promoting pancreatic cancer progression under chronic inflammation remains poorly understood. METHODSExperimental alcoholic chronic pancreatitis (ACP) induction was established in multiple mouse models, with euthanasia during the recovery stage to evaluate tumor latency. CREB was selectively deleted (Crebfl/fl) in Ptf1aCreERTM/+;LSL-KrasG12D/+(KC) genetic mouse models (KCC-/-). Pancreata from Ptf1aCreERTM/+, KC, and KCC-/- mice were analyzed using histological profiling, western blotting, phosphokinase array, and quantitative PCR. Single-cell RNA sequencing was performed in ACP-induced KC mice. Lineage tracing analysis in YFP reporter mice and acinar cell explant cultures analysis were also conducted. RESULTSACP induction in KC mice significantly impaired pancreas repair mechanism. Acinar cell-derived ductal lesions demonstrated sustained CREB hyperactivation in acinar-to-ductal metaplasia (ADM)/pancreatic intraepithelial neoplasia (PanIN) lesions associated with pancreatitis and pancreatic cancer. Persistent CREB activity reprogrammed acinar cells, and increased profibrotic inflammation. Notably, acinar specific Creb deletion in ACP induced models suppressed high grade PanIN development, restrained tumor progression, and improved acinar cell function. CONCLUSIONSOur findings demonstrate that CREB and Kras* promote irreversible ADM, accelerating pancreatic cancer progression with ACP. Targeting CREB may present a promising strategy to mitigate inflammation-driven pancreatic tumorigenesis.

cancer biology↗

Unveiling the Immune Dynamics of Neisseria Persistent Oral Colonization: A Roadmap for Innovative Vaccine Strategies

Commensal bacteria are crucial in maintaining host physiological homeostasis, immune system development, and protection against pathogens. Despite their significance, the factors influencing persistent bacterial colonization and their impact on the host still need to be fully understood. Animal models have served as valuable tools to investigate these interactions, but most have limitations. The bacterial genus Neisseria, which includes both commensal and pathogenic species, has been studied from a pathogenicity to humans perspective, but lacks models that study immune responses in the context of long-term persistence. Neisseria musculi, a recently described natural commensal of mice, offers a unique opportunity to study long-term host-commensal interactions. In this study, for the first time we have used this model to study the transcriptional, phenotypic, and functional dynamics of immune cell signatures in the mucosal and systemic tissue of mice in response to Neisseria musculi colonization. We found key genes and pathways vital for immune homeostasis in palate tissue, validated by flow cytometry of immune cells from lung, blood and spleen. This study offers a novel avenue for advancing our understanding of host-bacteria dynamics and may provide a platform for developing efficacious interventions against mucosal persistence by pathogenic Neisseria. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/572139v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1728fdaorg.highwire.dtl.DTLVardef@426a5forg.highwire.dtl.DTLVardef@55a90forg.highwire.dtl.DTLVardef@1ce3ff6_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Boosting bactericidal immunity of a recombinant Mycobacterium smegmatis strain via zinc-dependent ribosomal proteins

Tuberculosis (TB) continues to be a major global health burden and kills over a million people annually. New immunization strategies are required for the development of an efficacious TB vaccine that can potentially induce sterilizing immunity. In this study, we first confirmed that various strains of the IKEPLUS vaccine confer a higher survival benefit than BCG in a murine model of intravenous Mycobacterium tuberculosis (Mtb) infection. We have shown that there was a significant increase in the expression of the Rv0282 when IKEPLUS was grown in low zinc and iron containing Sauton medium. We confirmed on biofilm assays that zinc plays a vital role in the growth and formation of Mycobacterium smegmatis (M. smegmatis) biofilms. IKEPLUS grown in low zinc media led to better protection of mice after intravenous challenge with very high dosage of Mtb. We also showed that various variants of IKEPLUS induced apoptotic cell-death of infected macrophages at a higher rate than wild type M. smegmatis. We next attempted to determine if zinc containing ribosomal proteins such as rpmb2 could contribute to protective efficacy against Mtb infection. Since BCG has an established role in anti-mycobacterial efficacy, we boosted BCG vaccinated mice with rmpb2 but this did not lead to an increment in the protection mediated by BCG.

microbiology↗

G6PD deficiency mediated impairment of iNOS and lysosomal acidification affecting phagocytotic clearance in microglia in response to SARS-CoV-2

The glucose-6-phosphate dehydrogenase (G6PD) deficiency is X-linked and is the most common enzymatic deficiency disorder globally. It is a crucial enzyme for the pentose phosphate pathway and produces NADPH, which plays a vital role in the regulation of oxidative stress of many cell types. The deficiency of G6PD causes hemolytic anemia, diabetes, cardiovascular and neurological disorders. Notably, the patient with G6PD deficiency was severely affected by SARS-CoV-2 and showed prolonged COVID-19 symptoms, neurological impacts, and high mortality. However, the mechanism of COVID-19 severity in G6PD deficient patients is still ambiguous. Here, using a CRISPR-edited G6PD deficient human microglia cell culture model, we observed a significant reduction in NADPH and an increase in basal reactive oxygen species (ROS) in microglia. Interestingly, the deficiency of the G6PD-NAPDH axis impairs induced nitric oxide synthase (iNOS) mediated nitric oxide (NO) production which plays a fundamental role in inhibiting viral replication. Surprisingly, we also observed that the deficiency of the G6PD-NADPH axis reduced lysosomal acidification, which further abrogates the lysosomal clearance of viral particles. Thus, impairment of NO production and lysosomal acidification as well as redox dysregulation in G6PD deficient microglia altered innate immune response, promoting the severity of SARS-CoV-2 pathogenesis.

cell biology↗

Development and clinical validation of molecular subgrouping in medulloblastoma by targeted methylation sequencing

BackgroundThe WHO classification of CNS tumors confers promising prognostic value to the molecular classification of medulloblastoma (MB). Next-generation sequencing (NGS) has been the primary method employed for molecular classification through transcriptomic, genomic, or methylation profiling. However, due to cost and infrastructural needs, particularly in developing countries, we propose a relatively simple, rapid, and economical Sanger sequencing-based targeted methylation sequencing method for MB classification and prognostication. MethodsEleven epigenetic targets were amplified using optimized primers and bisulfite-converted DNA for Sanger sequencing. Chromas software was used for low-quality data trimming and NCBIs Needleman Wunsch alignment tool was used for sequence alignment to reference. The developed method was applied to tissues from twelve cases of medulloblastoma. ResultsSuccessful interpretation of methylation status in ten out of eleven targets was achieved which was sufficient for classification according to the latest WHO classification of Medulloblastoma tumors. Twelve medulloblastoma cases were classified into WNT (n=2), Group 3 (n=5), and Group 4 (n=5). ConclusionThe developed Sanger sequencing method is a cost-effective, in-house solution that can be used for molecular subgrouping of medulloblastoma. It offers an alternative to NGS, can be done on a case-to-case basis, and does not require high-end infrastructure, sample pooling, or extensive bioinformatics knowledge. Impact statementMolecular classification is imperative for determining the prognosis of medulloblastoma and is recommended by WHO. However, NGS proves to be an expensive option in developing countries. This study has come up with an affordable targeted methylation Sanger sequencing method requiring minimal bioinformatic skills, by utilizing epigenetic targets, for prognostication and risk stratification in medulloblastoma patients. The molecular subgroups of all recruited cases were successfully determined according to WHO classification which is crucial information that, when combined with clinical findings, will enable the clinicians to determine effective treatment strategies.

cancer biology↗

Androgen deprivation triggers a cytokine signaling switch to induce immune suppression and prostate cancer recurrence

Androgen deprivation therapy (ADT) is an effective but not curative treatment for advanced and recurrent prostate cancer (PC). We investigated the mechanisms controlling the response to androgen-deprivation by surgical castration in genetically-engineered mouse models (GEMMs) of PC, using high frequency ultrasound imaging to rigorously measure tumor volume. Castration initially causes almost all tumors to shrink in volume, but many tumors subsequently recur within 5-10 weeks. Blockade of tumor necrosis factor (TNF) signaling a few days in advance of castration surgery, using a TNFR2 ligand trap, prevents regression in a PTEN-deficient GEMM. Following tumor regression, a stem cell-like population within the tumor increases along with TNF protein levels. Tumor cell lines in culture recapitulate these in vivo observations, suggesting the possibility that stem cells are the source of TNF. When TNF signaling blockade is administered immediately prior to castration, tumors regress but recurrence is prevented. This implies that a late wave of TNF secretion within the tumor - which coincides with the expression of NF{kappa}B regulated genes - drives recurrence. The inhibition of signaling downstream of an NF{kappa}B-regulated protein - chemokine C-C motif ligand 2 (CCL2) - prevents post-castration tumor recurrence, phenocopying post-castration (late) TNF signaling blockade. CCL2 was originally identified as a macrophage chemoattractant and indeed at late times after castration gene sets related to chemotaxis and migration are up-regulated. Importantly, enhanced CCL2 signaling during the tumor recurrence phase coincides with an increase in pro-tumorigenic macrophages and a decrease in CD8 T cells, suggesting that recurrence is driven at least in part by tumor immunosuppression. In summary, we demonstrate that a therapy-induced switch in TNF signaling induces an immunosuppressive tumor microenvironment and concomitant tumor recurrence.

cancer biology↗

gQuant: A Robust and Generalizable Algorithm for Identifying Normalizer Genes in qRT-PCR Data: A Case Study on Urinary Exosomal miRNAs

The emergent role of nucleic acid-based biomarkers, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs), is becoming increasingly prominent in the realms of disease diagnostics and risk assessment. Quantitative reverse transcription PCR (qRT-PCR) is the primary analytical method for quantitative measurement of biomarkers. Yet, the relative infancy of non-coding RNAs (ncRNAs) recognition as biomarkers poses a challenge due to the absence of a consensus on a universally accepted normalizer gene, which is pivotal for accurate quantification. Current tools for selecting normalizer genes in qRT-PCR are fraught with limitations, including inadequate handling of null values, reliance on elementary statistical tools, use of a biased integrated approach, outlier sensitivity, and suboptimal graphical user interface for data visualization. These deficiencies underscore the necessity for a more nuanced and algorithmically balanced tool tailored to handle qRT-PCR datasets and facilitate the discernment of the most appropriate normalizer gene for specific datasets. Addressing the identified challenges, we have developed gQuant, a tool crafted to address the limitations present in existing methods. In gQuant we employed voting classifiers as an ensemble technique that combines predictions from multiple statistical methods to make more accurate rankings than any individual statistical measures. The tools efficacy was substantiated through rigorous validation against datasets from the Gene Expression Omnibus (GEO) database and corroborated with experimental data derived from urinary exosomal miRNAs. Comparative analysis with existing tools revealed that their integrated methodologies could skew the ranking of normalizer genes, whereas gQuant consistently yielded rankings characterized by lower standard deviation, reduced covariance, and enhanced kernel density estimation (KDE) values. Given gQuants promising performance, normalizer gene identification will be greatly improved, improving the precision of gene expression quantification in a variety of research scenarios.

molecular biology↗

Predicting Cortical Bone Resorption in Disuse Condition Caused by Transient Muscle Paralysis

Load removal from the load-bearing bone, such as in the case of extended space travel and prolonged bed rest, harms bone health and leads to severe bone loss. However, the constitutive idea relating the quantity of bone loss to the absence of physiological loading is poorly understood. This work attempts to develop a mathematical model that predicts cortical bone loss at three sections: distal, mid-section, and proximal along the length of a mouse tibia. Load-induced interstitial fluid flow-based dissipation energy density has been adopted as a stimulus to trigger mechanotransduction. The developed model takes the loss of stimulus due to the disuse of bone as an input and predicts the quantity of bone loss with spatial accuracy. We hypothesized that the bone loss site would be the site of maximum stimulus loss due to disuse. To test the hypothesis, we calculated stimulus loss, i.e., loss of dissipation energy density due to bone disuse, based on the poroelastic analysis of the bone using a finite element method. A novel mathematical model has been then developed that successfully relates this loss of stimulus to the in-vivo bone loss data in the literature. According to the developed model, the site-specific mineral rate is found to be proportional to the square root of the loss of dissipation energy density. To the authors best knowledge, this model is the first of its kind to compute site-specific bone loss. The developed model can be extended to predict bone loss due to other disuse conditions such as long space travel, prolonged bed rest, etc.

bioengineering↗

The Impact of Electrophysiological Diversity on Pattern Completion in Lithium Nonresponsive Bipolar Disorder: A Computational Modelling Approach

Patients with bipolar disorder (BD) demonstrate episodic memory deficits, which may be hippocampal-dependent and may be attenuated in lithium responders. Induced pluripotent stem-cell derived CA3 pyramidal cell-like neurons show significant hyperexcitability in lithium responsive BD patients, while lithium nonresponders show marked variance in hyperexcitability. We hypothesize that this variable excitability will impair episodic memory recall, as assessed by cued retrieval (pattern completion) within a computational model of the hippocampal CA3. We simulated pattern completion tasks using a computational model of the CA3 with different degrees of pyramidal cell excitability variance. Since pyramidal cell excitability variance naturally leads to a mix of hyperexcitability and hypoexcitability, we also examined what fraction (hyper-vs. hypoexcitable) was predominantly responsible for pattern completion errors in our model. Pyramidal cell excitability variance impaired pattern completion (linear model {beta}=-1.94, SE=0.01, p<0.001). The effect was invariant to the number of patterns stored in the network, as well as general inhibitory tone and pyramidal cell sparsity in the network. Excitability variance, and more specifically hyperexcitability, increased the number of spuriously active neurons, increasing false alarm rates and producing pattern completion deficits. Excessive inhibition also induces pattern completion deficits by limiting the number of correctly active neurons during pattern retrieval. Excitability variance in CA3 pyramidal cell-like neurons observed in lithium nonresponders may predict pattern completion deficits in these patients. These cognitive deficits may not be fully corrected by medications that minimize excitability. Future studies should test our predictions by examining behavioural correlates of pattern completion in lithium responsive and nonresponsive BD patients. Author summaryPatients with bipolar disorder experience debilitating cognitive impairments whose mechanisms are unknown, and these deficits may be greater in patients who do not respond to the mood stabilizer lithium. Studies using induced pluripotent stem cell (iPSC) derived neurons have suggested that CA3 pyramidal cells in lithium nonresponders may have wide diversity of excitability. Our study examines how this diversity of neuronal excitability would impact the computation of pattern completion in the CA3. In a computational model of the CA3, we found that variance in pyramidal cell excitability reliably impaired pattern completion abilities. Furthermore, we found that both the hyperexcitable and hypoexcitable fractions of cells were each responsible for distinct pattern completion errors, depending on the overall level of network inhibition. These results suggest that lithium nonresponsive patients with bipolar disorder will have worse performance on behavioural tasks that are sensitive to pattern completion, potentially including cued recall paradigms. Our results also suggest that mood stabilizers that simply reduce cellular hyperexcitability may not be sufficient to correct micro-circuit level computations in lithium nonresponsive bipolar disorder. Rather, these patients may require development of mood stabilizers that normalize the distribution of neuronal hyperexcitability among CA3 pyramidal cells.

neuroscience↗

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning

Image-based cell profiling is a powerful tool that compares perturbed cell populations by measuring thousands of single-cell features and summarizing them into profiles. Typically a sample is represented by averaging across cells, but this fails to capture the heterogeneity within cell populations. We introduce CytoSummaryNet: a Deep Sets-based approach that improves mechanism of action prediction by 30-68% in mean average precision compared to average profiling on a public dataset. CytoSummaryNet uses self-supervised contrastive learning in a multiple-instance learning framework, providing an easier-to-apply method for aggregating single-cell feature data than previously published strategies. Interpretability analysis suggests that the model achieves this improvement by downweighting small mitotic cells or those with debris and prioritizing large uncrowded cells. The approach requires only perturbation labels for training, which are readily available in all cell profiling datasets. CytoSummaryNet offers a straightforward post-processing step for single-cell profiles that can significantly boost retrieval performance on image-based profiling datasets.

bioinformatics↗

The helminth TGF-beta mimic TGM4 is a modular ligand that binds CD44, CD49d and TGF-beta receptors to preferentially target myeloid cells

The murine helminth parasite Heligmosomoides polygyrus expresses a family of modular proteins which, replicating the functional activity of the immunomodulatory cytokine TGF-{beta}, have been named TGM (TGF-{beta} Mimic). Multiple domains bind to different receptors, including TGF-{beta} receptors T{beta}RI (ALK5) and T{beta}RII through domains 1-3, and prototypic family member TGM1 binds the cell surface co-receptor CD44 through domains 4-5. This allows TGM1 to induce T lymphocyte Foxp3 expression, characteristic of regulatory (Treg) cells, and to activate a range of TGF-{beta}-responsive cell types. In contrast, a related protein, TGM4, targets a much more restricted cell repertoire, primarily acting on myeloid cells, with less potent effects on T cells and lacking activity on other TGF-{beta}-responsive cell types. TGM4 binds avidly to myeloid cells by flow cytometry, and can outcompete TGM1 for cell binding. Analysis of receptor binding in comparison to TGM1 reveals a 10-fold higher affinity than TGM1 for TGF{beta}R-I (T{beta}RI), but a 100-fold lower affinity for T{beta}RII through Domain 3. Consequently, TGM4 is more dependent on co-receptor binding; in addition to CD44, TGM4 also engages CD49d (Itga4) through Domains 1-3, as well as CD206 and Neuropilin-1 through Domains 4 and 5. TGM4 was found to effectively modulate macrophage populations, inhibiting lipopolysaccharide-driven inflammatory cytokine production and boosting interleukin (IL)-4-stimulated responses such as Arginase-1 in vitro and in vivo. These results reveal that the modular nature of TGMs has allowed the fine tuning of the binding affinities of the T{beta}R- and co-receptor binding domains to establish cell specificity for TGF-{beta} signalling in a manner that cannot be attained by the mammalian cytokine.

immunology↗

A vasopressin circuit that modulates sex-specific social interest and anxiety-like behavior in mice

One of the largest sex differences in brain neurochemistry is the male-biased expression of the neuropeptide arginine vasopressin (AVP) within the vertebrate social brain. Despite the long-standing implication of AVP in social and anxiety-like behavior, the precise circuitry and anatomical substrate underlying its control are still poorly understood. By employing optogenetic manipulation of AVP cells within the bed nucleus of the stria terminalis (BNST), we have unveiled a central role for these cells in promoting social investigation, with a more pronounced role in males relative to females. These cells facilitate male social investigation and anxiety-like behavior through their projections to the lateral septum (LS), an area with the highest density of sexually-dimorphic AVP fibers. Blocking the vasopressin 1a receptor (V1aR) in the LS eliminated stimulation-mediated increases in these behaviors. Together, these findings establish a distinct BNST AVP [->] LS V1aR circuit that modulates sex-specific social interest and anxiety-like behavior. Significance StatementThe function of sex differences in the brain is poorly understood. Here we test the function of one of the most consistently found sex differences in vertebrate brains, the male-biased vasopressin projections from the bed nucleus of the stria terminalis. Using optogenetic techniques, we demonstrate that these cells and their projection to the lateral septum are much more important in driving male than female social investigation. These studies make a strong contribution to understanding how sexually dimorphic circuitry controls social behavior.

neuroscience↗

Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling

Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial in understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Although still rare, studies combining these three technologies would comprehensively capture the humoral immune response. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy donors and sequenced BCRs at bulk and single-cell level, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.

immunology↗

Adjusted vascular contractility relies on integrity of progranulin pathway: Insights into mitochondrial function

ObjectiveCardiovascular disease (CVD) is a global health crisis and a leading cause of mortality. The intricate interplay between vascular contractility and mitochondrial function is central to CVD pathogenesis. The progranulin gene (GRN) encodes glycoprotein progranulin (PGRN), a ubiquitous molecule with known anti-inflammatory property. However, the role of PGRN in CVD remains enigmatic. In this study, we sought to dissect the significance of PGRN in the regulation vascular contractility and investigate the interface between PGRN and mitochondrial quality. MethodOur investigation utilized aortae from male and female C57BL6/J wild-type (PGRN+/+) and B6(Cg)-Grntm1.1Aidi/J (PGRN-/-) mice, encompassing wire myograph assays to assess vascular contractility and primary aortic vascular smooth muscle cells (VSMCs) for mechanistic insights. ResultsOur results showed suppression of contractile activity in PGRN-/- VSMCs and aorta, followed by reduced -smooth muscle actin expression. Mechanistically, PGRN deficiency impaired mitochondrial oxygen consumption rate (OCR), complex I activity, mitochondrial turnover, and mitochondrial redox signaling, while restoration of PGRN levels in aortae from PGRN-/- mice via lentivirus delivery ameliorated contractility and boosted OCR. In addition, VSMC overexpressing PGRN displayed higher mitochondrial respiration and complex I activity accompanied by cellular hypercontractility. Furthermore, increased PGRN triggered lysosome biogenesis by regulating transcription factor EB and accelerated mitophagy flux in VSMC, while treatment with spermidine, an autophagy inducer, improved mitochondrial phenotype and enhanced vascular contractility. Finally, angiotensin II failed to induce vascular contractility in PGRN-/- suggesting a key role of PGRN to maintain the vascular tone. ConclusionOur findings suggest that PGRN preserves the vascular contractility via regulating mitophagy flux, mitochondrial complex I activity, and redox signaling. Therefore, loss of PGRN function appears as a pivotal risk factor in CVD development.

pharmacology and toxicology↗

Neutrophil-derived complement factor P induces cytotoxicity in basal-like cells via caspase 3/7 activation in pancreatic cancer

Due to profound heterogeneity within stromal immune tumor microenvironment (TME), pancreatic ductal adenocarcinoma (PDAC) remains a hard to treat disease, with the lowest 5-year survival below 10%. Large-scale transcriptomic analysis has revealed two main, clinically relevant PDAC signatures: therapy responsive Classical subtype with better prognosis, and poorly-differentiated Basal-like with poor prognosis. It has also become evident that the cellular and humoral components in the immune TME considerably influence the outcome of tumorigenesis. Complement system, a potent humoral innate immune mechanism, also forms a part of this immune TME. In addition to the regular production of various complement components in the liver, certain infiltrating immune cells such as macrophages, dendritic cells and neutrophils, can produce a few complement components locally at the site of infection and inflammation including TME, and modulate tumorigenic outcomes. Neutrophils are the most prevalent innate immune cells in the PDAC TME; however, its role has been attributed as either pro-tumorigenic or anti-tumorigenic. Neutrophils, when stimulated or under stress, are capable of releasing their secretory granules that also contain the only known up-regulator of the complement alternative pathway, Complement Factor P (CFP) or properdin. Properdin can not only facilitate alternative pathway activation by stabilising the C3 convertase, but also act as a pattern recognition receptor on its own and modify inflammatory response. Here, by combining multicenter transcriptome analysis of PDAC patient tumors, single-cell-RNA-seq analysis, preclinical mouse models and human PDAC specimens, we show that properdin expression and neutrophil surveillance are linked to better prognosis in PDAC patients. Furthermore, properdin expression is substantially higher in well-to-moderately differentiated Classical subtype compared to the highly aggressive basal-like PDAC tumours. Mechanistically, exogenous properdin binds to the cell membrane and activates caspase 3/7 to induce apoptosis in basal-like PDAC cells. Together, these findings suggest that the complement protein, properdin, could be a favorable prognostic factor and exhibit anti-tumorigenic functions in PDAC.

immunology↗

G protein activation occurs via a largely universal mechanism

Understanding how signaling proteins like G proteins are allosterically activated is a long-standing challenge with significant biological and medical implications. Because it is difficult to directly observe such dynamic processes, much of our understanding is based on inferences from a limited number of static snapshots of relevant protein structures, mutagenesis data, and patterns of sequence conservation. Here, we use computer simulations to directly interrogate allosteric coupling in six G protein -subunit isoforms covering all four G protein families. To analyze this data, we introduce automated methods for inferring allosteric networks from simulation data and assessing how allostery is conserved or diverged among related protein isoforms. We find that the allosteric networks in these six G protein -subunits are largely conserved and consist of two pathways, which we call pathway-I and pathway-II. This analysis predicts that pathway-I is generally dominant over the second pathway, which we experimentally confirmed by showing that mutations to pathway-I perturb nucleotide exchange more than mutations to pathway-II. In the future, insights into unique elements of each G protein family could inform the design of isoform-specific drugs. More broadly, our tools should also be useful for studying allostery in other proteins and assessing the extent to which this allostery is conserved in related proteins.

biophysics↗

Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank

Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of various chemical and biological data to predict cardiotoxicity, using the recently released Drug-Induced Cardiotoxicity Rank (DICTrank) dataset from the United States FDA. We analyzed a diverse set of data sources, including physicochemical properties, annotated mechanisms of action (MOA), Cell Painting, Gene Expression, and more, to identify indications of cardiotoxicity. We found that such data, including protein targets, especially those related to ion channels (such as hERG), physicochemical properties (such as electrotopological state) as well as peak concentration in plasma offer strong predictive ability as well as valuable insights into DICT. We also found compounds annotated with particular mechanisms of action, such as cyclooxygenase inhibition, could distinguish between most-concern and no-concern DICT compounds. Cell Painting features related to ER stress discern the most-concern cardiotoxic compounds from non-toxic compounds. While models based on physicochemical properties currently provide substantial predictive accuracy (AUCPR = 0.93), this study also underscores the potential benefits of incorporating more comprehensive biological data in future DICT predictive models. With the availability of - omics data in the future, using biological data promises enhanced predictability and delivers deeper mechanistic insights, paving the way for safer therapeutic drug development. All models and data used in this study are publicly released at https://broad.io/DICTrank_Predictor O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/562398v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@755906org.highwire.dtl.DTLVardef@27c43borg.highwire.dtl.DTLVardef@c430dborg.highwire.dtl.DTLVardef@63b2ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗