Biology subjects

Tatu, U.

Publications and source records attributed to Tatu, U..

8 recordsLinked to original sources

bioRxiv2025

Identification of Novel Open Reading Frames on the Rabies Virus Antigenome Strand and Assessing Their Expression

Rabies disease can be caused by several lyssaviruses, which are a group of bullet-shaped, enveloped viruses with single-stranded, negative-sense RNA as their genome. Lyssaviruses are known to produce a full complement of genomic RNA (cRNA or antigenome) during their lifecycle. The rabies virus (RABV) is the prototype of the genus and has a genome of 12 kilobases. The RABV genome is known to encode five proteins from the genomic strand. In this study, we examined the coding potential of RABV and identified 17 novel ORFs (nORFs): one on the genomic strand and sixteen on the antigenomic strand. Synteny analysis revealed that several of these nORFs were conserved across the RABV clades. Additionally, five of the nORFs possessed Kozak sequences, and trRosetta predicted well-folded three-dimensional domains in these nORFs. Using LC-MS data of rabies-infected canine brain samples, we identified high-confidence peptides corresponding to the two nORF-coded proteins, nORF9 and nORF12. Furthermore, the structural and sequence similarity analyses indicated that these domains share homology with proteins involved in signalling and transcription.

microbiology↗

bioRxiv2025

Proteomic Profiling of Rabid Canine Brain Samples Reveals Dysregulation of Immune Signalling and Neuronal Pathways

Rabies is one of the most feared diseases and has been known to humans for approximately 4,000 years. It is caused by several lyssaviruses and leads to an encephalitis, which is 100% fatal after symptom onset. The most common cause of rabies is the rabies virus (RABV), which leads to around 59,000 human deaths globally every year. The infection leads to drastic changes in host behaviour, but the underlying mechanistic details remain unclear. Although interactions between the viral glycoprotein and host nicotinic acetylcholine receptors have been proposed as drivers of rabies-associated neurological dysfunction, clinical proteomic studies in naturally infected canines have been partially explored. In this study, we conducted a global proteomics analysis of RABV-infected and non-infected canine brain samples in India to unravel the changes in protein expression. Using liquid chromatography combined with mass spectrometry, we identified various host proteins and pathways dysregulated in the infected state. Approximately 700 proteins exhibited differential expression, with around 250 proteins involved in various pathways being significantly upregulated and approximately 500 proteins being significantly downregulated in the infected condition. Network clustering of the dysregulated proteins revealed functional modules, including clathrin-mediated endocytosis, actin cytoskeletal regulation, and the TCA cycle, indicating widespread alterations in cellular trafficking, energy metabolism, and structural integrity. Complementary pathway enrichment through PANTHER identified processes linked to axon guidance, integrin signalling, chemokine and cytokine-mediated inflammation, and cytoskeletal regulation, underscoring the profound impact of rabies virus infection on neuronal connectivity and host immune responses.

microbiology↗

bioRxiv2025

Stromal LOX/FAK/beta catenin pathway locks mammary fibroblasts into a tumor-promoting myCAF state

BackgroundCancer-associated fibroblasts (CAFs) sustain tumor progression, yet the soluble cues that maintain their myofibroblast (myCAF) state are poorly defined. Transforming growth factor beta (TGF-{beta}) is a canonical CAF activator. This study aims to identify TGF-{beta}-induced secreted mediators that reinforce the myCAF phenotype in breast cancer and map the downstream signaling cascade. Methods and ResultsSecretome profiling of primary patient-derived myCAFs and human mammary fibroblasts (HMF3s) engineered to over-express TGF-{beta}1 revealed 20 extracellular-matrix remodelers shared exclusively by both activated states; lysyl oxidase (LOX) was the top-ranked hit. LOX knockdown abrogated TGF-{beta}-driven -smooth-muscle actin (-SMA) induction, collagen-gel contraction and migration in HMF3s, and reduced constitutive -SMA and {beta}-catenin in myCAFs. Mechanistically, TGF-{beta} upregulated LOX, which activated focal-adhesion kinase (FAK), leading to p38 MAPK- and Akt-mediated Ser9 phosphorylation (inactivation) of GSK3{beta} and consequent {beta}-catenin stabilization. In HCC1806-luciferase orthotopic xenografts, CAFs accelerated tumor growth, whereas LOX-deficient CAFs lost this pro-tumoral effect. ConclusionLOX is a pivotal autocrine effector of TGF-{beta} that locks breast CAFs into a pro-tumoral myCAF state through a LOX/FAK/GSK3{beta}/{beta}-catenin axis. Targeting stromal LOX may disrupt CAF activation and curb breast cancer progression.

cancer biology↗

bioRxiv2024

Genomic analyses of recently emerging clades of mpox virus reveal gene deletion and single nucleotide polymorphisms that correlate with altered virulence and transmission

Mpox virus (MPXV) has consistently caused human infections since the first reported case in 1970, with the initial outbreaks primarily attributed to sporadic zoonotic transmissions. In recent years, an increase in human-to-human transmission has been observed, particularly during the 2022 outbreak caused by Clade IIb, which was declared a public health emergency by WHO. In 2024, the emergence of Clade Ib from Africa raised global concern once again. While several studies have provided valuable insights into the differences among MPXV clades, research on Clade Ib remains limited. In this study, we have conducted a comprehensive comparative genome sequence analysis and identified unique features across MPXV clade sequences. We report a [~]1141 bp long novel deletion resulting in loss of the complement control protein (CCP) in Clade Ib sequences, a deletion earlier exclusively reported in Clade II sequences. Additionally, B22R, a crucial host receptor-binding protein involved in viral entry and known for its high immunogenicity, shows clade-specific amino acid changes across three MPXV clades. Moreover, multiple extragenic mutations were identified in the 5 UTR of several genes, which may impact gene transcription. Other frequently mutated proteins are linked to immune evasion, translation, and viral entry and exit. The above results and APOBEC signatures associated with sustained human-to-human transmission highlight the viruss potential for rapid adaptation, underscoring the need for vigilance against reverse zoonosis and the risk of spillover to new hosts.

microbiology↗

bioRxiv2024

Odoribacter splanchnicus mitigates Salmonella-induced gut inflammation and its associated pathogenesis via its secreted bacteriocin

Foodborne pathogens pose a major global health hazard, worsened by drug-resistant strains. Therefore, designing novel therapeutic strategies is crucial. Here, we identified the protective role of gut-commensal Odoribacter splanchnicus (OS) against Salmonella in mice by promoting colonization resistance, preserving gut barrier integrity, and preventing acute inflammation and biofilm formation. In vitro, both OS and their culture supernatant inhibited Salmonella biofilm formation, intracellular proliferation in human intestinal cells, and virulence gene expression. Further, our results depicted that OSs protective role acts over a broad spectrum as it confers protection against Gram-positive, Listeria monocytogenes and Gram-negative, Salmonella Typhimurium. Notably, OS conferred protection even when administered post-infection in mice, highlighting its therapeutic potential. Using several biochemical and proteomics approaches, we characterized key OS-secreted molecules that limit intracellular Salmonella and Listeria replication in human intestinal epithelial cells by regulating key virulence effectors and flagella. Collectively, our study establishes OS as the broad-spectrum protective agent against Salmonella and Listeria infections, with promising therapeutic potential. Author SummaryFoodborne pathogens such as Salmonella and Listeria continue to threaten global health, especially with the rise of antibiotic resistance. In this study, we identify the gut commensal bacterium Odoribacter splanchnicus (OS) as a potent protectant against these pathogens. Using a mouse model, we show that OS enhances colonization resistance, maintains gut barrier integrity, and prevents both inflammation and biofilm formation during infection. Remarkably, OS also limits pathogen proliferation and virulence gene expression in human intestinal cells. These protective effects are mediated by both live OS and its secreted molecules within culture supernatant. Importantly, OS administration post-infection also conferred protection, indicating strong therapeutic potential. Biochemical and proteomic analyses revealed OS-secreted factors that suppress key virulence and motility pathways in pathogens. Our findings establish Odoribacter splanchnicus as a promising broad-spectrum biotherapeutic agent against major foodborne infections. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/609322v4_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@7ea42corg.highwire.dtl.DTLVardef@4c8074org.highwire.dtl.DTLVardef@855350org.highwire.dtl.DTLVardef@120decc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Identification of clade-specific single nucleotide polymorphisms for improved Rabies virus surveillance in Canis familiaris host

BackgroundRabies is an ancient disease that remains endemic in many countries. It causes many human deaths annually, predominantly in resource-poor countries. Over evolutionary timelines, several rabies virus (RABV) genotypes have stabilised, forming distinct clades. Extensive studies have been conducted on the origin, occurrence and spread of RABV clades. Single nucleotide polymorphisms (SNPs) distribution across the RABV genome and its clades remains largely unknown, highlighting the need for comprehensive whole-genome analyses. MethodsWe accessed whole genome sequences for RABV from public databases and identified SNPs across the whole genome sequences. Then, we annotated these SNPs using an R script, and these SNPs were categorised into different categories; universal, clade-specific, and clade-defining, based on the frequency of occurrence. ResultsIn this study, we present the SNPs occurring in the RABV based on whole genome sequences belonging to 8 clades isolated from 7 different host species likely to harbour dog-related rabies. We classified mutations into several classes based on their location within the genome and assessed the effect of SNP mutations on the viral glycoprotein. ConclusionsThe clade-defining mutations have implications for targeted surveillance and classification of clades. Additionally, we investigated the effects of these mutations on the Glycoprotein of the virus. Our findings contribute to expanding knowledge about RABV clade diversity and evolution, which has significant implications for effectively tracking and combatting RABV transmission.

microbiology↗

bioRxiv2023

Methods and techniques enabling multi-kilobase long-range genomic rewrite/replace editing

CRISPR enabled cell and gene therapies have the potential to revolutionize the field of genetic medicine. However, the vast majority of rare diseases remain untreatable due to the limitations of current tools and techniques. To date, most corrective therapeutic approaches have been restricted to mutation-by-mutation approaches, where either HDR, or newer techniques such as base or prime editing, rewrite small regions of DNA at a time ([~]1-100 bp). While these approaches are powerful, short editing windows (relative to the size of human genes) are financially and/or technically incompatible with most rare-disease mutation profiles. Here, we demonstrate for the first time that CRISPR/Cas9 can be used to "rewrite" 7kb+ sections of the human genome simultaneously via a selection-free process we have named "long-range rewriting". Long-range rewriting approaches are compatible with multiple nucleases, cell types and genomic loci, and can be used with both double-strand break (DSB) and non-DSB based approaches.

genetics↗

bioRxiv2021

Fibrinogen and Complement Factor H are promising CSF protein biomarker(s) for Parkinson's disease with cognitive impairment- A Proteomics and ELISA based study

Cognitive impairment is a debilitating non-motor symptom of Parkinsons disease (PD). The diagnosis of PD with cognitive impairment (PDCI) is essentially through clinical and neuropsychological examinations. There is an emerging need to identify biomarker(s) to foresee cognitive decline in PD patients, at an early stage. We performed label-free unbiased nontargeted proteomics (Q-TOF LC/MS-MS) in CSF of non-neurological control (NNC); PDCI; PD and normal pressure hydrocephalus (NPH), followed by targeted ELISA for validation. The diagnosis was confirmed by neuropsychological and MRI assessments prior to CSF collection. Of the 282 proteins identified by mass spectrometry, 42 were differentially altered in PD, PDCI and NPH. Further, 28 proteins were altered in PDCI and 25 in NPH. An interesting overlap of certain proteins was noted both in PDCI and NPH. Five significantly upregulated proteins in PDCI were fibrinogen, gelsolin, complement factor-H, apolipoprotein A-IV and apolipoprotein A-I. Whereas carnosine dipeptidase 1, carboxypeptidase E, dickkpof 3 and secretogranin 3 precursor proteins were down-regulated. NPH also had few uniquely altered proteins viz. insulin-like growth factor-binding protein, ceruloplasmin, -1 antitrypsin, VGF nerve growth factor, neural cell adhesion molecule L1 like protein. Interestingly, the ELISA-derived protein concentrations correlated well with the neuropsychological scores of certain cognitive domains. Executive function was affected both in PDCI and NPH. In PD, Wisconsin card sorting test (WCST) percentile correlated positively with ApoA-IV and negatively with the ratio of ApoAI: ApoA-IV. Thus assessment of a battery of proteins like fibrinogen--chain, CFAH and ApoAI: ApoA-IV ratio alongside neuropsychological could be reliable biomarkers to distinguish PDCI and NPH.

neuroscience↗