Biology subjects

Srivastava, S.

Publications and source records attributed to Srivastava, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

PERK arm of UPR selectively regulates ferroptosis in colon cancer cells by modulating the expression of SLC7A11 (System Xc-)

Ferroptosis, a genetically and biochemically distinct form of programmed cell death, is characterised by an iron-dependent accumulation of lipid peroxides. Therapy-resistant tumor cells display vulnerability toward ferroptosis. Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) play a critical role in cancer cells to become therapy resistant. Tweaking the balance of UPR to make cancer cells susceptible to ferroptotic cell death could be an attractive therapeutic strategy. To decipher the emerging contribution of ER-stress in the ferroptotic process, we observe that ferroptosis inducer RSL3 promotes UPR (PERK, ATF6, and IRE1), along with overexpression of cystine-glutamate transporter SLC7A11 (System Xc-). Exploring the role of a particular UPR arm in modulating SLC7A11 expression and subsequent ferroptosis, we notice that PERK is selectively critical in inducing ferroptosis in colorectal carcinoma. PERK inhibition reduces ATF4 expression and recruitment to the promoter of SLC7A11 and results in its downregulation. Loss of PERK function not only primes cancer cells for increased lipid peroxidation but also limits in vivo colorectal tumor growth, demonstrating active signs of ferroptotic cell death in situ. Further, by performing TCGA data mining and using colorectal cancer patient samples, we demonstrate that the expression of PERK and SLC7A11 is positively correlated. Overall, our experimental data indicate that PERK is a negative regulator of ferroptosis and loss of PERK function sensitizes colorectal cancer cells to ferroptosis. Therefore, small molecule PERK inhibitors hold huge promise as novel therapeutics and their potential can be harnessed against the apoptosis-resistant condition.

cancer biology↗

bioRxiv2023

Wat1/mLst8, a TOR complex protein regulates mitochondrial integrity and calcium ion homeostasis in fission yeast S. pombe

The mTOR complexes play a fundamental role in mitochondrial biogenesis and cellular homeostasis. Wat1, an ortholog of mammalian Lst8 is an important component of TOR complex and is essential for the regulation of downstream signaling. Earlier we reported the role of Wat1 in oxidative stress response. Here, we show that the inactivation of wat1 leads to respiratory defects and mitochondrial depolarization leading to decrease in ATP production. The confocal and electron microscopy in wat1{Delta} cells revealed the fragmented mitochondrial morphology implying its role in mitochondrial fission. Furthermore, we also showed its role in autophagy and the maintenance of calcium ion homeostasis. Additionally, tor2-287 mutant cells also exhibit defects in mitochondrial integrity indicating the TORC1-dependent involvement of Wat1 in the maintenance of mitochondrial homeostasis. The interaction studies of Wat1 and Tor2 with Por1 and Mmm1 proteins revealed a cross-talk between mitochondria and endoplasmic reticulum through the Mitochondria-associated membranes (MAM) and endoplasmic reticulum-mitochondria encounter structure (ERMES) complex, involving TORC1. Taken together, this study demonstrates involvement of Wat1/mLst8 in harmonizing various mitochondrial functions, redox status, and Ca2+ homeostasis.

cell biology↗

bioRxiv2023

Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients

Respiratory infections disrupt the microbiota in the upper respiratory tract (URT), putting patients at a risk for subsequent infections. During the pandemic, cases of COVID-19 were aggravated by secondary infections because of impaired immunity and medical interventions, which was clearly evident in the second wave of COVID-19 in India. The potential dangers and clinical difficulties of bacterial and fungal secondary infections in COVID-19 patients necessitate microbial exploration of the URT. In this regard, mass spectrometry (MS)-based proteome data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. The MS datasets were searched against a comprehensive protein sequence database of common URT pathogens using multiple search platforms (MaxQuant, MSFragger, and Search GUI/PeptideShaker). The detected microbial peptides were verified using PepQuery, which analyses peptide-spectrum pairs to give statistical output for determining confident microbial peptides. Finally, a protein sequence database was generated using the list of verified microbial peptides for identification and quantitation of microbial peptides and proteins, respectively. The taxonomic analysis of the detected peptides revealed several opportunistic pathogens like Streptococcus pneumoniae, Rhizopus microsporus, Clavispora lusitaniae, and Syncephalastrum racemosum among others. Using parallel reaction monitoring (PRM), we validated a few identified microbial peptides in clinical samples. The analysis also revealed proteins belonging to species like Pseudomonas fluorescens, Enterobacter, and Clostridium to be up-regulated in severe COVID-19 samples. Thus, MS can serve as a powerful tool for untargeted detection of a wide range of microorganisms. Metaproteomic analysis in COVID-19 patients for early identification and characterisation of co-infecting microorganisms can significantly impact the diagnosis and treatment of patients.

microbiology↗

bioRxiv2022

AP2XII-2 coordinates transcriptional repression for Toxoplasma gondii sexual commitment

Toxoplasma gondii is a widespread protozoan parasite that has significant impact on human and veterinary health. The parasite undergoes a complex life cycle involving multiple hosts and developmental stages. How Toxoplasma transitions between life cycle stages is poorly understood, yet central to controlling transmission. Of particular neglect are the factors that contribute to its sexual development, which takes place exclusively in feline intestines. While epigenetic repressors have been shown to play an important role in silencing spurious gene expression of sexually committed parasites, the specific factors that recruit this generalized machinery to the appropriate genes remains largely unexplored. Here, we establish that a member of the AP2 transcription factor family, AP2XII-2, is targeted to genomic loci associated with sexually committed parasites along with the epigenetic regulators of transcriptional silencing, HDAC3 and MORC. Despite widespread association with gene promoters, AP2XII-2 is required for silencing of relatively few genes. Using CUT&Tag methodology, we identify two major genes associated with sexual development downstream of AP2XII-2 control, AP2X-10 and the amino acid hydroxylase AAH1. Our findings show that AP2XII-2 is a key contributor to the gene regulatory pathways modulating Toxoplasma sexual development. IMPORTANCEToxoplasma gondii is a parasite that undergoes its sexual stage exclusively in feline intestines, making cats a major source of transmission. A better understanding of the proteins controlling the parasites life cycle stage transitions is needed for the development of new therapies aimed to treat toxoplasmosis and transmission of the infection. Genes that regulate the sexual stages need to be turned on and off at the appropriate times, activities that are mediated by specific transcription factors that recruit general machinery to silence or activate gene expression. In this study, we identify a transcription factor called AP2XII-2 as being important for repression of a subset of sexual stage genes, including a sexual stage-specific AP2 factor (AP2X-10) and a protein (AAH1) required to construct the infectious oocysts expelled by infected cats.

microbiology↗

bioRxiv2022

, a prion-form of Cut4/ Apc1, enforces non-Mendelian inheritance of heterochromatin silencing defect in Fission Yeast

Prions represent epigenetic regulator proteins that can self-propagate their structure and confer their misfolded structure and function on normally folded proteins. Like the mammalian prion PrPSc, prions also occur in fungi. While a few prions, like Swi1, affect gene expression, none are shown to affect heterochromatin structure and function. In fission yeast and metazoans, histone methyltransferase Clr4/Suv39 causes H3-Lys9 methylation, which is bound by the chromodomain protein Swi6/HP1 to assemble heterochromatin. Earlier, we showed that sng2-1 mutation in the Cut4 subunit of Anaphase Promoting Complex abrogates heterochromatin structure due to defective binding and recruitment of Swi6. Here, we demonstrate that the Cut4p forms a non-canonical prion form, designated as [SNG2], which abrogates heterochromatin silencing. [SNG2] exhibits various prion-like properties, e.g., non-Mendelian inheritance, requirement of Hsp proteins for its propagation, de novo generation upon cut4 overexpression, reversible curing by guanidine, cytoplasmic inheritance and formation of infectious protein aggregates, which are converted into monomers upon overexpression of hsp genes. Interestingly, [SNG2] prion imparts an enhanced tolerance to stress conditions, supporting its role in promoting cell survival under environmental stress during evolution.

genetics↗

bioRxiv2022

Novel Multi-Epitope Vaccine candidate derived from critically important proteins of Monkeypox isolates

BackgroundOn May 7, 2022, a case of monkeypox virus (MPXV) has been reported to the WHO. It causes a viral zoonotic disease with characteristics comparable to that of smallpox cases. Monkeypox could be a serious health concern as it is already spreading to multiple countries worldwide. To prevent the monkeypox infection and for its early detection, a potential vaccine and diagnostic candidate is urgently required. MethodIn present study we have used different in silico methods to screen the entire genome with its approximately 191 genes for potential epitopes present in proliferation and virulent proteins of monkeypox virus. All protein sequences were retrieved from different genomic and proteome databases listed in Uniprot or NCBI. ResultsIn the present study we have screened potential epitopes from 11 different proteins of Monkeypox. All the included protein play an important role in pathogenesis and/or proliferation of Monkeypox virus. We have identified in total 984 CTL and 168 HTL epitopes with highest score in our epitope screening. The reported epitopes could be potential candidates for the design of an early detection diagnostic kit specific for the monkeypox virus. Out of these target peptides we have included a total of 39 CTL epitopes and 39 HTL epitopes in design of multi-epitope vaccine candidates. These shortlisted epitopes are highly conserved amongst different strains and origin of monkeypox viruses. The population coverage by joint administration of CTL and HTL MEVs is predicted to be high with the epitopes showing potential to bind upto 24 different CTL and HTL HLA allele molecules. The epitopes used in MEVs are examined to be highly immunogenic, non allergic but antigenic, and non toxic. All the CTL and HTL MEVs designed utilizing the epitopes have physiochemical properties favor its over expression in human cells. The optimized cDNA constructs of CTL and HTL MEVs also favor over expression of MEVs in human cells. Overall, the MEV construct proposed by us are fissile for expression in the lab and for further in vivo studies. ConclusionControl and fight against emerging diseases such as MPXV requires pathogen diagnostic and novel vaccine approaches. We screened for several epitopes and designed a MEV providing a potential solution for both purposes. Our method allows rapid screening and provides a rational strategy for the development of vaccine candidate effective in fighting MPXV and other unexpected upcoming diseases.

immunology↗

bioRxiv2022

Novel 'GaEl antigenic patches' identified by 'reverse epitomics' approach to design multi-patch vaccines against NIPAH infection, a silent threat to global human health

BackgroundNipah virus (NiV) is a zoonotic virus that causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. Several NiV outbreaks have been reported since 1999 with nearly annual occurrences in Bangladesh. The outbreaks had high mortality rates ranging from 40 to 90%. No specific vaccine has yet been reported against NiV. MethodologyRecently, several vaccine candidates and different designs of vaccines composed of epitopes against NiV were proposed. Most of the vaccines target single protein or protein complex subunits of the pathogen. The Multi-epitope vaccines proposed also cover a largely limited number of epitopes and hence their efficiency is still pending. To address the urgent need for a specific and effective vaccine against NiV infection in the present study, we have utilized the Reverse Epitomics approach ("overlapping-epitope-clusters-to-patches" method) to identify antigenic patches (Ag-Patches) and utilize them as immunogenic composition for Multi-Patch vaccine (MPV) design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and interaction with Toll-like receptor 3 ectodomain. ResultsIn total 30 CTL (Cytotoxic T lymphocyte) and 27 HTL (Helper T lymphocytes) antigenic patches were identified from the entire NiV proteome based on the clusters of overlapping epitopes. These identified Ag-Patches cover a total of discreet 362 CTL and 414 HTL epitopes from entire proteome of NiV. The antigenic patches were utilized as immunogenic composition for the design of two CTL and two HTL multi-patch vaccines. The 57 antigenic patches utilized here cover 776 overlapping epitopes targeting 52 different HLA class I and II alleles providing a global ethnically distributed human population coverage of 99.71%. Such large number of epitope coverage resulting in large human population coverage cannot be reached with single protein/subunit or multi-epitope based vaccines. The reported antigenic patches also provide potential immunogenic composition for early detection diagnostic kits for NiV infection. Further, all the MPVs & Toll-Like Receptor ectodomain complexes show stable nature of molecular interaction with numerous hydrogen bonds, salt bridges and non-bounded contacts formation and acceptable root mean square deviation and fluctuation. The cDNA analysis show a favorable large scale expression of the MPV constructs in human cell line. ConclusionBy utilizing the novel Reverse epitomics approach highly immunogenic novel GaEl antigenic patches (GaEl Ag-Patches) a synonym term for antigenic patches, were identified and utilized as immunogenic composition to design four MPVs against NiV. We conclude that the novel Multi-Patch Vaccines is a potential candidate to combat NiV, with greater effectiveness, high specificity and large human population coverage worldwide.

immunology↗

bioRxiv2022

Asparagine starvation suppresses histone demethylation through iron depletion

Nutrient availability can impact epigenome to modify gene expression and dictate cell fate decision (Etchegaray and Mostoslavsky, 2016; Kinnaird et al., 2016). -ketoglutarate is an indispensable substrate for the Jumonji family of histone demethylases (JHDMs) mediating most of the cellular demethylation reactions on histone subunits (Schvartzman et al., 2018). Since -ketoglutarate is an intermediate of the tricarboxylic acid (TCA) cycle and a product of transamination, its intracellular levels are regulated by the metabolism of several amino acids (Baksh et al., 2020; Carey et al., 2015; Raffel et al., 2017; Vardhana et al., 2019). Here we show that asparagine starvation suppresses global histone demethylation. This process is neither due to the change of expression of histone modifying enzymes, nor due to the change of intracellular level of -ketoglutarate. Rather, asparagine starvation reduces intracellular pool of labile iron (Fe2+), which is a key cofactor for the JHDMs to function. Mechanistically, asparagine starvation post-transcriptionally suppresses the expression of iron responsive element binding protein 2 (IREB2), an iron sensing protein, which then reduces the mRNA expression of the transferrin receptor (TFRC), a major carrier for iron uptake (Hentze et al., 2010). Furthermore, iron supplementation to the culture medium restores histone demethylation and alters global gene expression to accelerate cell death under conditions of asparagine starvation. Collectively, our results uncover that suppression of iron-dependent histone demethylation is part of the cellular adaptive response to asparagine starvation.

cell biology↗

bioRxiv2022

Targeting Epsins by nanotherapy regulates lipid metabolism and promotes 1 ABCG1-mediated cholesterol efflux to fortify atheroma regression

BACKGROUNDExcess cholesterol accumulation in lesional macrophages elicits complex responses in atherosclerosis. Epsins, a family of endocytic adaptors, fuel the progression of atherosclerosis; however, the underlying mechanism and therapeutic potential of targeting Epsins remains unknown. In this study, we determined the role of Epsins in macrophage-mediated metabolic regulation. We then developed an innovative method to therapeutically-target macrophage Epsins with specially-designed S2P-conjugated lipid nanoparticles (NPs), which encapsulate small interfering RNAs to suppress Epsins. METHODSWe used single cell RNA sequencing (scRNA-seq) with our newly developed algorithm MEBOCOST to study cell-cell communications mediated by metabolites from sender cells and sensor proteins on receiver cells. Biomedical, cellular and molecular approaches were utilized to investigate the role of macrophage Epsins in regulating lipid metabolism and transport. We performed this study using myeloid-specific Epsin double knockout (LysM-DKO) mice and mice with a genetic reduction of ABCG1 (LysM-DKO-ABCG1fl/+). The NPs targeting lesional macrophages were developed to encapsulate interfering RNAs to treat atherosclerosis. RESULTSWe revealed that Epsins regulate lipid metabolism and transport in atherosclerotic macrophages. Inhibiting Epsins by nanotherapy halts inflammation and accelerates atheroma resolution. Harnessing lesional macrophage-specific NP delivery of Epsin siRNAs, we showed that silencing of macrophage Epsins markedly diminished atherosclerotic plaque size and promoted plaque regression. Mechanistically, we demonstrated that Epsins bound to CD36 to facilitate lipid uptake by enhancing CD36 endocytosis and recycling. Conversely, Epsins promoted ABCG1 degradation via lysosomes and hampered ABCG1-mediated cholesterol efflux and reverse cholesterol transport. In a LysM-DKO-ABCG1fl/+ mouse model, enhanced cholesterol efflux and reverse transport due to Epsin deficiency was suppressed by the reduction of ABCG1. CONCLUSIONSOur findings suggest that targeting Epsins in lesional macrophages may offer therapeutic benefits for advanced atherosclerosis by reducing CD36-mediated lipid uptake and increasing ABCG1-mediated cholesterol efflux. Novelty and SignificanceO_ST_ABSWHAT IS KNOWN?C_ST_ABSO_LIEpsin endocytic adaptor proteins are upregulated in human and mouse atherosclerotic lesions C_LIO_LILesional macrophages internalize lipids primarily through scavenger receptor-mediated endocytosis such as CD36 and SR-A C_LIO_LIMacrophage-mediated cholesterol efflux and reverse cholesterol transport is crucial to atheroma resolution C_LI WHAT NEW INFORMATION DOES THIS ARTICLE CONTRIBUTE?O_LIScRNA-seq combined with the newly-developed algorithm MEBOCOST reveals that Epsins are involved in macrophage-mediated lipid metabolic regulation C_LIO_LIMacrophage epsins promote lipid uptake by targeting CD36 endocytosis and membrane recycling via the Epsin ENTH domain C_LIO_LIEpsins bind ubiquitinated ABCG1--resulting in the endocytosis and lysosomal degradation of this cholesterol transporter, which reduces cholesterol efflux. C_LIO_LIMacrophage-specific, nanoparticle-mediated RNAi delivery exhibits a therapeutic benefit for the treatment of atherosclerosis C_LIO_LIAtherosclerotic plaque regression using this nanoparticle delivery platform represents a clinically-relevant approach for the treatment of advance atherosclerosis C_LI BRIEF SUMMARYDespite the development of new cholesterol-lowering therapies, including the recently approved PCSK9 small interfering RNA (siRNA) antagonists, patients still face a tremendous risk of developing major acute cardiovascular events resulting from chronic inflammation in the plaque. We employed a novel nanomedicine platform containing a stabilin-2 targeting peptide (S2P) to deliver Epsin-specific siRNAs to lesional macrophages. We discovered that inhibition of these adaptor proteins in lesional macrophages significantly diminished plaque size and necrotic core area, increased fibrous cap thickness, and promoted plaque regression.

cell biology↗

bioRxiv2022

Pink1-mediated mitophagy in the endothelium releases proteins encoded by mitochondrial DNA and activates neutrophil responses

Given their ancient evolutionary origins, eukaryotic mitochondria possess multiple vestiges of their prokaryotic ancestors. One such factor is the N-terminal formylation of proteins encoded by mitochondrial DNA. N-formylated proteins are also released by bacteria and trigger activation of immune cells such as neutrophils. Growing evidence indicate that circulating levels of mitochondrial formyl proteins are elevated in the serum of patients with excessive inflammatory responses and trigger neutrophil activation like their bacterial counterparts. However, the cellular source of these proteins, and the mechanism by which they are released into the circulation is not known. In this study, we have identified vascular endothelial cells as a source of mitophagy induced release of formyl proteins in response to inflammatory mediators in vitro. Mechanistically, endothelial mitophagy required activation of the Pink1 pathway. Using liposomal delivery of sgRNA targeting Pink1 in mice expressing endothelial-specific Cas9, we developed a mouse model in which Pink1 is specifically depleted in the endothelium. Deletion of endothelial Pink1 was remarkably protective in endotoxin-induced lung inflammation, resulting in reduced neutrophil infiltration and significantly reduced death in mice. We thus propose that endothelial cells upregulate pro-inflammatory mitophagy in response to inflammation, leading to release of mitochondrial formyl peptides and detrimental neutrophil recruitment into the lung.

cell biology↗

bioRxiv2022

Collective invasion of the basement membrane in breast cancer driven by forces from cell volume expansion and local contractility

Breast cancer becomes invasive when carcinoma cells collectively invade through the basement membrane (BM), a nanoporous layer of matrix that physically separates the primary tumor from the stroma, in a first step towards metastasis. Single cells can invade through nanoporous three-dimensional (3D) matrices via protease-mediated degradation or, when the matrix exhibits sufficient mechanical plasticity, force-mediated widening of pores. However, how cells invade collectively through physiological BM layers in cancer remains unclear. Here, we developed a 3D in vitro model of collective invasion of the BM during breast cancer. We show that cells utilize both proteases and forces to breach the BM. Forces are generated from a combination of global cell volume expansion that stretch the BM with local contractile forces that act in the plane of the BM to breach it, allowing invasion. These results uncover a mechanism by which cells collectively interact to overcome a critical barrier to metastasis.

cancer biology↗

bioRxiv2022

Structural bases for blockade and activation of BK channels by Ba2+ ions

Ba2+ increases open probability and blocks the permeation pathway of BK channels. Here we discuss Cryo-EM structures of BK channels with Ba2+. They reveal that Ba2+ occupies site S3 in the selectivity filter, leading to blockade. Ba2+ are also detected at all high affinity Ca2+ binding sites of the gating ring. However, the architectures of this region in these structures represent intermediate transitions between the extreme close and open configurations.

biophysics↗

bioRxiv2022

Adgrg6/Gpr126 is required for myocardial Notch activity and N-cadherin localization to attain trabecular identity

How adhesion G protein-coupled receptors (aGPCRs) control development remains unclear. The aGPCR Adgrg6/Gpr126 has been associated with heart trabeculation. Defects in this process cause cardiomyopathies and embryonic lethality. Yet, how cardiomyocytes attain trabecular identity is poorly understood. Here, we show that Gpr126 regulates Notch activity and N-cadherin localization that are necessary for attaining trabecular identity in zebrafish. Maternal zygotic gpr126stl47 early truncation mutants exhibit hypotrabeculation whereby N-cadherin distributes randomly at apical/basal membranes of compact layer cardiomyocytes. In contrast, gpr126st49 mutants expressing a N-terminal fragment lacking the GPS motif (NTF{Delta}GPS) exhibit a multilayered ventricular wall consisting of polarized cardiomyocytes with normal N-cadherin expression and increased Notch signaling. Notably, endocardially expressed C-terminal fragment (CTF) reinstates trabeculation in gpr126st49 mutants. Collectively, our data indicate domain-specific roles of Gpr126 during trabeculation whereby the NTF maintains cell-cell adhesion and is required for compact wall integrity, while the CTF is essential to provide trabecular identity

developmental biology↗

bioRxiv2022

A critical role for touch neurons in a skin-brain pathway for stress resilience

Social touch can act as a stress buffer, reducing behavioral and physiological responses to stressful scenarios. However, skin-brain touch pathways that promote stress resilience remain unknown. Here, we show that mice with an early life genetic ablation of Mrgprb4-lineage touch neurons display stress vulnerability behaviors in adulthood. Chemogenetic activation of these touch neurons reduced corticosterone levels under mild acute stress conditions. In addition, whole-brain c-Fos activity mapping while chemogenetically turning on these neurons uncovered differential neural activity patterns in brain areas relevant to somatosensation, reward, and affect. To gain mechanistic insight into this skin-brain touch pathway for stress susceptibility, we used multi-circuit neurophysiological recordings across seven brain regions at baseline and after stress in mice that had Mrgprb4-lineage touch neurons ablated in early life. Interestingly, the Mrgprb4-lineage neuron-ablated mice have alterations in local field potential phase directionality and power in the theta frequencies in mesolimbic reward regions, which may underlie our observed stress susceptibility phenotype. Together, these studies revealed that sensory neurons in the skin engage networks across the brain to promote stress resilience.

neuroscience↗

bioRxiv2022

Cell-to-cell variability of dynamic CXCL12-CXCR4 signaling and morphological processes in chemotaxis

Chemotaxis drives critical processes in cancer metastasis. While commonly studied at the population scale, metastasis arises from small numbers of cells that successfully disseminate, underscoring the need to analyze chemotaxis at single-cell resolution. Here we focus on chemotaxis driven by the CXCL12-CXCR4 pathway, a signaling network that promotes metastasis in more than 20 different human cancers. CXCL12-CXCR4 activates ERK and Akt, kinases known to promote chemotaxis, but how cells couple signaling to chemotaxis remain poorly defined. To address this challenge, we implemented single-cell analysis of MDA-MB-231 breast cancer cells migrating in a chemotaxis device towards chemokine CXCL12. We integrated live, single-cell imaging with advanced computational analysis methods to discover processes defining subsets of cells that move efficiently toward a CXCL12 gradient. We identified dynamic oscillations in ERK and Akt signaling and associated morphological transitions as key determinants of successful chemotaxis. Cells with effective chemotaxis toward CXCL12 exhibit faster and more persistent movement than non-migrating cells, but both cell populations show similar random motion. Migrating cells exhibit higher amplitude fluctuations in ERK and Akt signaling and greater frequencies of generating lateral cell membrane protrusions. Interestingly, computational analysis reveals less correlated network coupling of signaling and morphological changes in migrating cells. These data reveal processing events that enable cells to convert a signaling input to chemotaxis and highlight how cells in a uniform environment produce heterogeneous responses.

cancer biology↗

bioRxiv2022

MHC-II molecules present RhoC-derived peptides on the surface of tumour cells

RhoC is an important regulator of metastasis and tumour progression across various tumour models. Since RhoC has been found to have no major contribution towards normal embryogenic development, it has emerged as a suitable therapeutic target for effective cancer treatment. Recent evidence has shown that Rho-based peptide vaccines have favourable outcomes in prostate cancer patients, by bringing about activation of CD4+ T-cells. Antigen presentation on the surface of cells is brought about by the MHC-I/MHC-II complex. This work provides conclusive evidence to show that the seemingly cytosolic protein, RhoC, is in fact, present on the surface of tumour cells. This report goes on to prove that the presentation of RhoC peptides is brought about in association with MHC-II, becoming the first piece of scientific evidence to report this phenomenon.

cancer biology↗

bioRxiv2022

Novel tuberculosis combination regimens of two and three-months therapy duration

The tuberculosis treatment duration is 4-6 months, but can be 18-20 months with multidrug resistance. Ultrashort regimens that cure regardless of resistance status ["pan-tuberculosis regimens"] would be a major step towards global tuberculosis control. Starting with seven drugs [bedaquiline, delamanid, pretomanid, OPC-167832, sutezolid, moxifloxacin, and pyrazinamide] in clinical testing, we calculated that there were thousands of possible novel combinations to evaluate. We used mathematical and pharmacokinetics/pharmacodynamic-based hollow fiber modeling to reduce this complexity to nine combinations, which we tested. Each regimens fast and slow growth bacteria kill-slope trajectories and times-to-extinction were estimated and translated to minimum required therapy duration in patients. Sputum microbial kill trajectories of two combination regimens that have undergone clinical testing were correctly predicted by this approach. Four pan-tuberculosis regimens were predicted to achieve relapse-free cure after 2-3 months therapy in patients. The kill-slopes were used to design expedited clinical trials that minimize patients risks.

pharmacology and toxicology↗

bioRxiv2021

Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita

Aeromonas hydrophila (Ah) is an opportunistic Gram-negative bacterium and a serious global pathogen causing Motile Aeromonas Septicaemia (MAS) in fish and many other vertebrates. The pathogenesis of aeromonas septicaemia is complex and involves multiple perturbed pathways. Molecular analysis of host tissues could be a powerful approach to identify mechanistic and diagnostic immune signatures of disease. We performed a deep proteomic analysis of Labeo rohita liver tissue to examine changes in the host proteome during Ah infection. A total of 2525 proteins were identified of which 158 were found differentially expressed during Ah infection. Functional analysis of significant proteins identified the dysregulation of several metabolic enzymes, antioxidative proteins, cytoskeletal proteins and immune related proteins. Proteomic analysis revealed the alterations in the cellular defence mechanisms including phagolysosomal killing and apoptosis during Ah infection. Our systemic approach revealed the protein dynamics in the host cells to explore the putative biological processes underlying the metabolic reprogramming of the host cells during Ah infection. Our findings paved the way for future research into the role of Toll-like receptors (Tlr3), C-type lectins (Clec4e) and metabolic enzymes in Ah pathogenesis leading towards host directed immunotherapies to tackle the Ah infection in fish. IMPORTANCEBacterial disease is one of the most serious problems in aquaculture industry. Aeromonas hydrophila (Ah), a Gram-negative bacterium causes motile aeromonas septicaemia (MAS) in fish. Small molecules that target the metabolism of the host have recently emerged as potential treatment possibilities in infectious diseases. However, the ability to develop new therapies is hampered due to lack of knowledge about pathogenesis mechanisms and host-pathogen interactions. Molecular level analysis of host tissues could be helpful in finding mechanistic immunological markers of diseases. We examined alterations in the host proteome during Ah infection in Labeo rohita liver tissue to find cellular proteins and processes affected by Ah infection. Our systemic approach revealed protein dynamics underlying the host cells metabolic reprogramming during Ah infection. Our work is an important step towards leveraging host metabolism in targeting the disease by providing a bigger picture on proteome pathology correlation during Ah infection.

systems biology↗