Biology subjects

Sinha, I.

Publications and source records attributed to Sinha, I..

14 recordsLinked to original sources

bioRxiv2026

Restoring multiple TDP-43 cryptic targets, but not solely Unc13a, rescues motor neuron disease

Dysfunction of TAR DNA-binding protein 43kDa (TDP-43) underlies amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder with limited therapeutic options. While current therapeutic approaches are designed to individually target unique cryptic exons of TDP-43 such as UNC13A, the sufficiency of such a strategy to mitigate motor neuron disease remains unclear. Using a mouse model lacking TDP-43 in spinal motor neurons which mimics early stages of ALS, we show that the exclusion of Unc13a cryptic exon fails to mitigate motor neuron disease. In contrast, the restoration of multiple TDP-43 cryptic targets, including Unc13a, attenuated motor neuron loss, and rescued motor neuron disease. Additionally, compared to brain neurons, spinal motor neurons accumulate markedly lower amounts of Unc13a cryptic exons in mice and humans, suggesting that the contribution of this TDP-43 cryptic target to spinal motor neuron loss may be limited. Together, these results strongly support ALS therapeutic strategies designed to simultaneously restore multiple TDP-43 cryptic targets to attenuate spinal motor neuron loss.

neuroscience↗

bioRxiv2026

HALPred-B: Host-Aware Linear B-Cell Epitope Prediction: Challenges, Limitations, and Variability Across Species

Predicting linear B-cell epitopes is a basic immunoinformatics task that has a direct impact on vaccine design and antibody engineering. Recent advances in machine learning have improved predictive performance, but most existing approaches are trained on aggregated datasets and assume that antigenic patterns are conserved across host organisms. This assumption ignores the immunological variability depending on the host and prevents generalizing the model across species. This is the first systematic host-wise evaluation where we present a systematic machine learning-based analysis of host-aware linear B-cell epitope prediction using curated datasets from the Immune Epitope Database (IEDB). We build separate datasets for human, mouse, and non-human primate hosts and assess several classification models, including Random Forest, Support Vector Machine (SVM), Gradient Boosting, XGBoost, and K-Nearest Neighbors (KNN). The models exploit feature representations derived from sequences, such as AAIndex descriptors, biochemical properties from ExPASy, and dipeptide composition. Our results show that predictive performance differs substantially across hosts. Models achieve up to 86.07% accuracy and 0.93 ROC-AUC on human datasets but lower performance on mouse and non-human primate datasets. This gap underlies dataset bias and sequence distribution differences, as well as the inability of existing features to capture host-specific immunological context. These results indicate that the prediction of linear B-cell epitopes is intrinsically host-specific, and a single global model does not generalize well across species. We propose to incorporate host-aware modeling strategies and organism-specific features for enhanced predictive reliability and biological relevance.

bioinformatics↗

bioRxiv2026

RNA degradation by DIS3 is a necessary step in the resolution of backtracked transcription complexes

The RNA exosome is known to participate in transcription, but the contribution of its ribonuclease activities to this process remains unclear. Here we investigated the role of DIS3, one of the exosome ribonucleases, in transcription by RNA polymerase II (RNAPII). Rapid depletion of DIS3 reduced RNA synthesis and induced RNAPII elongation defects that were exacerbated by UV irradiation, a treatment that generates transcription-blocking DNA lesions and promotes RNAPII backtracking. Notably, DIS3 itself was redistributed following UV irradiation in a manner that closely paralleled RNAPII dynamics, which suggested that DIS3 acts in concert with the transcription machinery. We also investigated whether RNA degradation by DIS3 was required for transcription elongation and found that the 3-5 exoribonucleolytic activity of DIS3, but not its endonucleolytic activity, is essential for efficient transcription elongation. More specifically, DIS3 degrades the 3 ends of backtracked RNA, as shown by sequencing of RNA fragments released by TFIIS-induced transcript cleavage in vitro. This DIS3-dependent degradation of backtracked RNA is critical for resolving stalled RNAPII complexes and enabling productive transcription elongation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/703186v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@c080dorg.highwire.dtl.DTLVardef@1e4b375org.highwire.dtl.DTLVardef@1c1f575org.highwire.dtl.DTLVardef@d9d640_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDIS3 depletion leads to severely reduced rates of RNA synthesis in human cells. C_LIO_LITranscription-blocking lesions reveal a critical role for DIS3 in RNA polymerase II elongation. C_LIO_LIThe 3 to 5 exoribonuclease activity of DIS3 is necessary for transcription elongation. C_LIO_LIDIS3-mediated degradation of backtracked RNA is required for the resolution of stalled transcription complexes. C_LI

molecular biology↗

bioRxiv2025

CDR Conformation Aware Antibody Sequence Design with ConformAb

Antibody lead optimization methods seek to enhance a lead candidates therapeutic properties through targeted sequence mutation. However, the mutations introduced during this process can inadvertently induce structural changes that disrupt binding, particularly by altering CDR loop conformations which destabilize CDR-target binding interactions. To address this, we present ConformAb, a guided discrete diffusion model for designing antibody sequences that explicitly conform to the CDR canonical conformation of the lead. With seed sequences as the starting point, we show that our method is capable of generating 3- 5x better binders that conform to the same CDR backbone structure in a one-shot design setup, and in some cases, binders with better affinity than seed repertoire picks without any target-specific data included in training. Across the targets tested, ConformAb demonstrated binding rates ranging from 15 -60% in wet lab experiments, a result obtained using fewer than 100 designs for each target. ConformAb offers a unique one-shot approach for antibody lead optimization in data-scarce scenarios where experimental/repertoire data cannot be leveraged for model training.

biophysics↗

bioRxiv2025

METTL13 Promotes Pre-Leukemic Transformation and the Development of Pediatric Leukemia

Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A) methylation and adenosine to inosine (A-to-I) editing, are critical regulators of hematopoietic stem cell (HSC) self-renewal and differentiation, yet their precise contributions to malignant transformation are not fully elucidated. In this study, we uncovered the epitranscriptomic landscape caused by knockdown of genes from the methyltransferase (METTL)-family in hematopoietic stem and progenitor cells (HSPCs). We identified both converging and distinct roles of METTL3 and METTL14, known members of the m6A writer complex, as well as orphan gene METTL13. Notably, METTL13 was uniquely upregulated by adenosine deaminase acting on RNA 1 (ADAR1) overexpression, while other METTL genes were downregulated. Knockdown of METTL13 altered the expression of multiple genes involved in oncogenic development in HSPCs. Furthermore, METTL13 was associated with a high-risk profile in pediatric T-cell acute lymphoblastic leukemia (T-ALL), and functional studies confirmed that METTL13 is required for T-ALL cell proliferation and survival both in vitro and in vivo. Collectively, our results indicate a previously unrecognized, oncogenic role for METTL13 in pre-leukemic transformation and T-ALL pathogenesis. SignificanceIn this study we uncovered a novel regulatory link between ADAR1 and the METTL-family of RNA methyltransferases in hematopoietic stem cells. Overexpression of ADAR1 uniquely upregulated METTL13 while suppressing other METTL genes. Loss of orphan gene METTL13 affected proliferation, apoptosis and p53 signaling in hematopoietic stem cells. Furthermore, loss of METTL13 suppressed cell proliferation and survival in pediatric T-cell acute lymphoblastic leukemia. Our findings suggest a potential role for METTL13 in pre-leukemia transformation and oncogenic development.

cancer biology↗

bioRxiv2024

A Distinct Alternative mRNA Splicing Profile Identifies the Oncogenic CD44 Transcript Variant 3 in KMT2A-Rearranged Pediatric T-cell Acute Lymphoblastic Leukemia Cells

T-cell acute lymphoblastic leukemia (T-ALL), which constitutes of 10-15% of all pediatric ALL cases, is known for its complex pathology due to pervasive genetic and chromosomal abnormalities. Although most children are successfully cured, chromosomal rearrangements involving the KMT2A (KMT2A) gene is considered a poor prognostic factor. In a cohort of 171 pediatric T-ALL samples we have studied differences in gene and splice variant patterns in KMT2A rearranged (KMT2A-r) T-ALL compared to KMT2A negative (KMT2A-wt) T-ALL samples. Our results have identified a distinct gene expression and splice variant expression pattern in pediatric KMT2A-r patient samples including significant expression of splicing regulatory markers ESRP1 and MBNL3. Additionally, the pro-survival long transcript variant of BCL2 were upregulated in KMT2A-r compared to KMT2A-wt T-ALL samples. Lastly, increased levels of activating methylation in the promoter region of CD44 were identified followed by an upregulation of the oncogenic transcript variant CD44v3 in KMT2A-r T-ALL. Together this suggests that CD44v3 could play a potential role as gene expression-based risk stratification of KMT2A-r rearranged T-ALL and could possibly serve as a therapeutic target using splicing modulators.

cancer biology↗

bioRxiv2023

Serial dilution shapes genetic variation and defines conservation units in Asian elephants

Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analysed 34 whole genomes (between 11X - 32X) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern) India, Central India and three in Southern India. Our genetic data reveal signatures of serial colonisation, and a dilution of genetic diversity from north to south of India. The Northern populations diverged from other populations more than 70,000 years ago, have higher genetic diversity, and low inbreeding/high effective size (Pi = 0.0016{+/-}0.0001; FROH> 1MB= 0.09{+/-}0.03). Two of three populations in Southern India (South of Palghat Gap: SPG, and South of Shencottah Gap:SSG) have low diversity and are inbred, with very low effective population sizes compared to current census sizes (Pi = 0.0014{+/-}0.00009 and 0.0015{+/-}0.0001; FROH> 1MB= 0.25{+/-}0.09 and 0.17{+/-}0.02). Analyses of genetic load reveals purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the Southern populations and potential dilution of all deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity make these populations (SPG and SSG) high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to geographic signatures of serial founding events, even in large, highly mobile, endangered mammals.

evolutionary biology↗

bioRxiv2023

The CNS Microenvironment Promotes Leukemia Cell Survival by Disrupting Tumor Suppression and Cell Cycle Regulation in Pediatric T-cell Acute Lymphoblastic Leukemia

A major obstacle in improving survival in pediatric T-cell acute lymphoblastic leukemia is understanding how to predict and treat leukemia relapse in the CNS. Leukemia cells are capable of infiltrating and residing within the CNS, where they interact with the microenvironment and remain sheltered from systemic treatment. These cells can survive in the CNS niche, by hijacking the microenvironment and disrupting normal functions, thus promoting malignant transformation. While the protective effects of the bone marrow niche have been widely studied, the mechanisms behind leukemia infiltration into the CNS and the role of the CNS niche in leukemia cell survival remain unknown. We have identified a dysregulated gene expression profile in CNS infiltrated T-ALL and CNS relapse, promoting cell survival, chemoresistance and disease progression. Furthermore, we discovered that interactions between leukemia cells and CNS microenvironment induce epigenetic alterations, such as changes in gene regulation and histone modifications, including H3K36me3 levels. These findings can be utilized to predict CNS infiltration and CNS relapse, therefore avoiding overtreatment and adverse effects caused by CNS directed therapy. Additionally, the identified genetic drivers of disease progression can serve as a first step towards identifying therapeutic targets, to sensitize the CNS niche to current therapeutic strategies.

cancer biology↗

bioRxiv2023

Expanding the Evo-Devo Toolkit: Generation of 3D mammary tissue from diverse mammals

The divergent events during mammary gland development between species and across evolution are not well studied mainly due to the lack of tractable model systems. In theory, advancements in the field of organoid technology now make it possible to study developmental processes adapted throughout species evolutions to accommodate advantageous phenotypes. However, its application to the mammary gland remains limited to rodents and humans. In the current study, we successfully created next-generation 3D mammary gland organoids from eight eutherian mammals and the first 3D organoid of a marsupial mammary gland (the gray short-tailed opossum), representing a more ancient version of the mammary gland. Using mammary organoids, we identified a role for ROCK protein in regulating branching morphogenesis, a role that manifests differently in human and opossum mammary organoids. This finding demonstrates the utility of 3D organoid model for understanding the evolution and adaptations of signaling pathways. Overall, the establishment of mammary organoids as animal model surrogates is a significant advancement in the field of mammary gland biology and evolution and paves the way for future studies utilizing this model. This achievement highlights the potential of organoid models to expand our understanding of mammary gland biology and evolution and their utility in studying milk production and breast cancer research.

developmental biology↗

bioRxiv2023

A fluid biomarker reveals loss of TDP-43 splicing repression in pre-symptomatic ALS

Loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well-documented in postmortem tissues of amyotrophic lateral sclerosis (ALS), yet whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects functional loss of TDP-43, and thus detection of cryptic exon-encoded peptides in cerebrospinal fluid (CSF) could reveal the earliest stages of TDP-43 dysregulation in patients. Here, we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found in HDGFL2) to show that loss of TDP-43 splicing repression occurs in C9ORF72-associated ALS, including pre-symptomatic mutation carriers. In contrast to neurofilament light and heavy chain proteins, cryptic HDGFL2 accumulates in CSF at higher levels during early stages of disease. Our findings indicate that loss of TDP-43 splicing repression occurs early in disease progression, even pre-symptomatically, and that detection of HDGFL2s cryptic neoepitope may serve as a prognostic test for ALS which should facilitate patient recruitment and measurement of target engagement in clinical trials.

molecular biology↗

bioRxiv2021

Epigenetic clock and methylation studies in gray short-tailed opossums

The opossum (Monodelphis domestica), with its sequenced genome, ease of laboratory care and experimental manipulation, and unique biology, is the most used laboratory marsupial. Using the mammalian methylation array, we generated DNA methylation data from n=100 opossum tissues including blood, liver, and tail. We contrast age-related changes in the opossum methylome to those of C57BL/6J mice. We present several epigenetic clocks for opossums that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (opossum and human). Two dual-species human-opossum pan-tissue clocks accurately measure chronological age and relative age, respectively. These human-opossum epigenetic clocks are expected to provide a significant boost to the attractiveness of opossum as a biological model.

evolutionary biology↗

bioRxiv2020

The RNA binding protein hnRNP-U is required for physiological hypertrophy of skeletal muscle

Skeletal muscle has the remarkable ability to modulate its mass in response to physiological changes associated with nutritional input, functional utilization, systemic disease, and age. A decreased responsiveness to anabolic stimuli is thought to contribute significantly to the loss of skeletal muscle mass and strength associated with sarcopenia, however the molecular mechanisms precipitating this are unclear. The signal transduction pathways that control the relative balance between anabolic and catabolic processes are tightly regulated at the transcriptional and post-transcriptional levels. Alternative splicing produces multiple protein isoforms from a single gene in a cell-type-specific manner and in response to environmental cues. We show that sustained activation of Akt1 in Hnrnpu deficient mice leads to premature muscle wasting, in part, through impaired autophagy while providing mechanistic insights into the development of anabolic resistance.

cell biology↗

bioRxiv2019

Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures

An understanding of the factors affecting the diet composition of critically endangered Gyps vultures in the Indian subcontinent has important applications to the design of effective conservation strategies. After suffering a massive decline (~99%) in numbers caused by veterinary use of the nephrotoxic drug diclofenac, vultures now persist in very low numbers, mostly concentrated within or near National Parks. This spatial association might be attributed to the availability of wild ungulate carcasses free from toxic veterinary drugs. Hence, quantification of vulture diets and the factors affecting them is critical to test this hypothesis. Here, we describe and validate a robust \"field-to-benchtop-to-desktop\" metabarcoding workflow for assessing the species- and sex-specific diet of these obligate scavengers from non-invasively collected faecal samples. Seven metabarcodes targeting mitochondrial and nuclear genes were used to simultaneously determine the vulture species identity, sex and species consumed. The amplicons were sequenced using an Illumina Miseq platform. We included controls and three replicates per sample to establish a series of non-arbitrary thresholds to filter the sequence data and eliminate cross-contamination, PCR/sequencing errors and false positives. Using this strategy enabled identification of species and sex for all samples. Diet species-specific sequences could be identified with high taxonomic resolution for 93% of samples. Out of the seven metabarcodes, just four were sufficient to meet the objectives. From this preliminary analysis, domestic livestock seem to be the most frequently consumed diet item across samples from inside and outside protected habitats. Our method provides a rapid and reliable tool for describing large-scale variation in consumption of domestic versus wild species in the diet of these species, paving the way for a better understanding of the role protected areas play in persistence and recovery of the remaining Gyps vulture populations in the wild.

genetics↗

bioRxiv2018

The geography of malaria elimination in Bangladesh: combining data layers to estimate the spatial spread of parasites

Malaria control programs face difficult resource allocation decisions. Of particular concern for countries aiming for malaria elimination, the regular movement of individuals to and from endemic areas undermines local interventions by reintroducing infections and sustaining local transmission. Quantifying this movement of malaria parasites around a country has become a priority for national control programs, but remains methodologically challenging, particularly in areas with highly mobile populations. Here, we combined multiple data sources to measure the geographical spread of malaria parasites, including epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data. We collected parasite genetic barcodes and travel surveys from 2,090 patients residing in 176 unions in southeast Bangladesh. We developed a genetic mixing index to quantify the likelihood of samples being local or imported. We then inferred the direction and intensity of parasite flow between locations using an epidemiological model, and estimated the proportion of imported cases assuming mobility patterns parameterized using the travel survey and mobile phone calling data. Our results show that each data source provided related but different information about the patterns of geographic spread of parasites. We identify a consistent north/south separation of the Chittagong Hill Tracts region in Bangladesh, and found that in addition to imported infections from forested regions, frequent mixing also occurs in low transmission but highly populated areas in the southwest. Thus, unlike risk maps generated from incidence alone, our maps provide evidence that elimination programs must address ongoing movement of parasites around the lower transmission areas in the southwest.

epidemiology↗