Biology subjects

Dutta, A.

Publications and source records attributed to Dutta, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Microrobot and Cellbot Locomotion in Confined Hydrogels and Cardiac Tissue Surfaces

Biohybrid cellbots and microrobots are a promising platform for targeted drug delivery, minimally invasive surgery, and tissue engineering. Here, we present a comparative analysis of the locomotion dynamics across synthetic substrates and ex vivo cardiac tissue to help bridge the gap presented by translating locomotion dynamics from idealized environments to biological interfaces. By subjecting the microrobots and cellbots to different substrates (specifically, cell culture dish, hydrogel, and ex vivo tissue) and applying rotating magnetic fields at varying frequencies, we characterized how surface boundary interactions and driving frequency dictate translation speed. We reveal that particles moving on tissue exhibit restricted movement based on trajectory and tissue fiber orientation. Finally, we discuss that while cellular integration introduces significant adhesive drag that reduces translation speeds, it simultaneously offers a unique clinical advantage. This study highlights the potential of balancing magnetic driving parameters against biological environments to optimize for various treatment timelines and efficiency across diverse biomedical applications.

bioengineering↗

bioRxiv2026

Evaluating Brain Flow Index from a temple-worn wearable against depth-resolved time-domain NIRS during head-down tilt and postural transitions in healthy young men

Significance: Wearable optical sensors could make continuous cerebral hemodynamic monitoring practical in daily life. Because any surface head sensor also samples extracerebral tissue, demonstrating cerebral relevance requires a reference that separates deep from superficial hemodynamics. Aim: We evaluated whether the Temple Brain Flow Index (Temple-BF), derived from a temple-worn photoplethysmographic wearable, covaried more strongly with the deeper (brain-assigned) than the superficial (scalp-assigned) hemodynamics recovered from time-domain near-infrared spectroscopy (TD-NIRS) during controlled postural challenges. Approach: Sixty sessions from 44 healthy young adult men were analyzed across three physiological challenges: 30{degrees} head-down tilt, stand-to-squat, and stand-to-supine transitions. Optical density and mean time of flight from a three-module TD-NIRS system were inverted with a Monte Carlo-derived two-layer model to obtain scalp- and brain-layer hemoglobin time series. Temple-BF was compared with these model-derived signals using lag-adjusted and zero-lag correlations, paired brain-versus-scalp comparisons, heart rate and short-separation-HbO adjusted partial correlations. Results: Median lag-adjusted correlations between Temple-BF and brain-layer {Delta}HbO traces were 0.912, 0.843, and 0.839 for head-down tilt, stand-to-squat, and stand-to-supine transitions, respectively; corresponding scalp-layer medians were 0.494, 0.700, and 0.767. Paired brain-minus-scalp differences were significant for head-down tilt (median 0.333, p < 0.001) and stand-to-squat (0.110, p < 0.001) but not for stand-to-supine (0.036, p = 0.082) transitions. Zero-lag brain-layer medians were 0.826, 0.701, and 0.796, and the association persisted after adjustment for heart rate (partial r = 0.832, 0.850, 0.654) and for short-separation superficial HbO (0.649, 0.570, 0.438). Transition-window correlations had medians of 0.878, 0.861, and 0.876, with directionally concordant transition responses in 59 of 60 sessions. Conclusions: Temple-BF tracked model-derived brain-layer TD-NIRS {Delta}HbO across all three postural challenges, with larger median correlations against the brain-layer than the scalp compartment in all three protocols, and transition responses in the same direction for almost all sessions. These results support Temple-BF as a relative marker of cerebral hemodynamic change during postural perturbations. Establishing cerebral specificity at the temple, and excluding residual systemic and superficial contributions, will require flow-sensitive references and fuller systemic monitoring.

neuroscience↗

bioRxiv2026

Temple PPG Morphology Demonstrates a Stronger Cardiovascular Age Signal Than Wrist Sites

The features of the PPG (photoplethysmography) morphology are known to reflect age-related cardiac and vascular changes. In most contemporary wearables, PPG signals are acquired from distal sites such as the wrist and finger. The superficial temporal artery (STA), accessible at the temple region, is reached via a shorter arterial path from the aortic root than the radial circulation, and may therefore carry hemodynamic and aging information with less distance-dependent attenuation. We hypothesized that the morphology of the PPG at temple region (STA) would show stronger and more numerous age correlates than the PPG at the wrist. To test this, we extracted a common set of 89 pulse-morphology features, spanning raw-waveform timing/amplitude/area measures, ratios among them, derivative-based ratios, and spectral harmonic-ratio features. We compared an in-house temple-worn device which has PPG as one of the sensors, with a publicly available Microsoft Aurora-BP wrist-worn PPG dataset, and tested each feature's association with age. We identified 14 robust age correlates at the temple region, compared to 3 at the wrist. The temple's correlates spanned multiple morphological categories and showed a larger age-association than at the wrist. These results support the hypothesis that the temple region may be a more robust PPG measurement site than the wrist to extract age-related cardiovascular information, which motivates further investigation of temple-based cardiovascular sensing.

physiology↗

bioRxiv2026

Metazoan Orc6 Proteins Evolved Alternative Mechanisms for Association with the ORC Complex: Insights from Drosophila Modeling

In eukaryotes, DNA replication requires the origin recognition complex (ORC), a six-subunit assembly that promotes replisome formation on chromosomal origins. Orc6 is the smallest and least evolutionarily conserved among all ORC subunits. In Drosophila, Orc6 binds tightly with the core ORC(1-5) and is required for DNA binding and replication initiation, whereas in Xenopus and human systems Orc6 loosely associates with the rest of the complex resulting in some differences for replication-associated activities. Despite these variations, Orc6 remains essential for viability in all species. In current study we analyzed specific residues within the C-terminal 11 helix that is critical for stable association of Orc6 with the ORC complex in Drosophila. Human Orc6 lacks these residues, however it possesses a strong nuclear localization signal (NLS) that is absent in Drosophilidae. We propose that this NLS drives human protein to the nucleus and compensates for weaker Orc6-ORC(1-5) interactions by increasing the nuclear concentration of Orc6 and shifting the equilibrium toward formation of the fully assembled ORC complex at the DNA.

molecular biology↗

bioRxiv2026

Colistin resistance-mediated lipopolysaccharide modification in Klebsiella pneumoniae modulates host inflammatory response

Resistance to the polymyxin antimicrobial colistin in Gram-negative bacteria is associated with a modification of the immunogenic lipid A moiety of the lipopolysaccharide (LPS). Chromosomal and plasmid-borne colistin resistance results in the addition of L-Ara4N and pEtN groups to lipopolysaccharide (LPS), respectively. Here, using THP-1 cells, we studied the impact of different LPS modifications of Klebsiella pneumoniae in stimulating host immune response. K. pneumoniae clinical isolates were screened for colistin resistance using broth microdilution (BMD) and the MALDIxin test. LPS was extracted from colistin-resistant isolates and used to stimulate differentiated THP-1 cells. Luminex cytokine assay measured the immune induction via a panel of proinflammatory cytokines. Out of a collection of 72 clinical K. pneumoniae, eight (11.1%) exhibited phenotypic colistin resistance with a minimum inhibitory concentration (MIC) of 8 to 64 mg/L. In total, five isolates possessed genes associated with polymyxin resistance; three isolates had a mutation in the pmrB gene, and two were mcr-8.1 positive. MALDIxin demonstrated that all eight phenotypic colistin-resistant isolates elaborated peaks at m/z 1,955 and m/z 2,193, indicating an L-Ara4N group of LPS modification. For two mcr-8.1 positive isolates, LPS had a pEtN group. The LPS modification positively correlated with colistin MIC (correlation coefficient, r= 0.6 and R2= 0.4). Compared to the native structure, LPS modification was associated with greater production of IL-1{beta}, IL-6, and CXCL-8 (p<0.001). The pEtN-conjugated LPS triggered a significantly greater production of TNF-, IL-6, and CXCL-8 compared to L-Ara4N (p<0.05). This study reveals that the colistin MIC value can significantly predict lipid A modification in clinical K. pneumoniae, and differences in resistance-mediated lipid A modification result in variation in the immunological response. This study highlights the potential of dynamic host-pathogen interaction in the context of colistin resistance.

microbiology↗

bioRxiv2026

Myeloid STING restrains cardiac remodeling by suppressing macrophage amyloid precursor protein

Mitochondrial DNA (mtDNA) released into the cytosol activates innate immune signaling and promotes inflammation, yet its role in macrophages following sterile tissue injury remains poorly understood. Here, we show that cardiac macrophages from both patients and mice with myocardial infarction (MI) exhibit increased mitochondrial biogenesis, mitochondrial content, membrane potential, and expression of mitochondrial nucleases that facilitate mtDNA release. Consistently, macrophage-specific silencing of genes regulating mitochondrial biogenesis or mtDNA processing attenuated adverse cardiac remodeling after MI. Unexpectedly, despite the role of mtDNA in activating the cGAS-STING pathway, myeloid deletion or macrophage-specific silencing of Sting or cGas exacerbated ventricular dilation, fibrosis, and contractile dysfunction following MI. Single-cell transcriptomic and cell communication analyses identified amyloid precursor protein (APP) as a key downstream effector of STING in cardiac macrophages. Macrophage-specific in vivo App silencing rescued the detrimental effects of myeloid Sting deficiency, establishing APP as a critical mediator of adverse remodeling. Mechanistically, STING interacted with the transcriptional repressor MZF1, promoted its nuclear localization, facilitated its binding to the App promoter, and suppressed App transcription to restrain adverse cardiac remodeling. Together, our findings uncover an unexpected cardioprotective function of myeloid STING and identify the STING-MZF1-APP axis as a previously unrecognized mechanism governing cardiac repair after myocardial infarction.

cell biology↗

bioRxiv2026

CaMKII Activation Enhances Antioxidant Defence and Mitochondrial Function in human articular chondrocytes

BackgroundThe articular cartilage has limited vascular supply and repair capacity, making it particularly susceptible to reactive oxygen species (ROS)-driven oxidative damage. Excess ROS contributes to extracellular matrix breakdown and is a major factor in osteoarthritis (OA) progression. We previously identified Calcium/Calmodulin-dependent protein kinase II (CaMKII) as a regulator of cartilage homeostasis, prompting us to investigate its role during oxidative stress. MethodsPrimary adult human articular chondrocytes were isolated from OA cartilage. CaMKII activity was modulated using adenoviral overexpression of a constitutively active form of the kinase or of Autocamtide-2-related inhibitory peptide, a CaMKII inhibitor. Redox status and mitochondrial function were assessed by molecular and metabolic assays. ResultsOxidative stress increased CaMKII phosphorylation. CaMKII inhibition elevated cellular and mitochondrial ROS, whereas CaMKII activation enhanced mitochondrial respiration capacity, improved mitochondrial morphology, and was associated to NRF2 nuclear translocation. ConclusionCaMKII supports redox homeostasis in chondrocytes and may represent a therapeutic strategy to preserve cartilage integrity and delay disease onset.

cell biology↗

bioRxiv2026

Wnt stimulation and inhibition in the development and phenotype of patient-derived gallbladder organoids

Gallbladder cancer (GBC) is a highly lethal malignancy with limited experimental models to study disease biology or evaluate therapeutic responses. Although canonical Wnt activation is commonly used for patient-derived organoid (PDO) development and expansion, gallbladder PDOs has also been generated under Wnt-inhibitory conditions. No comparative assessment has determined how Wnt pathway modulation influences gallbladder PDO development, phenotype or drug response. This study systematically compared the impact of canonical Wnt activation (WNTAct medium containing CHIR99021) versus inhibition (WNTInh medium containing DKK1) on the establishment, propagation, molecular features and therapeutic responses of PDOs generated from malignant or non-malignant gallbladder tissues derived from the same patient. Both media supported successful PDO generation with comparable efficiency, preserving biliary epithelial functions and marker expression. Transcriptomic profiling confirmed selective enrichment of canonical Wnt target genes in PDOs generated in WNTAct cultures. WNTAct conditions enabled markedly superior long-term propagation, whereas WNTInh cultures more consistently retained the dysplastic features in malignant samples. Gemcitabine response assays demonstrated significantly greater drug sensitivity in PDOs grown in WNTAct medium, a phenotype reversible upon media switching but requiring extended adaptation, indicating a dynamic and context-dependent influence of Wnt signaling on chemotherapeutic vulnerability. Collectively, the findings reveal a trade-off between long-term propagation and histological fidelity in gallbladder PDOs and show that Wnt signaling modulates gemcitabine sensitivity in a reversible manner. This comparative framework provides practical guidance for selecting culture conditions for gallbladder PDO based disease modelling and precision oncology applications.

cell biology↗

bioRxiv2026

tRF-3021a, a tRNA-Ala-TGC derived 3' fragment, promotes glioblastoma cell invasion, suppresses apoptosis, and is required for normal levels of protein synthesis

tRNA-derived fragments (tRFs) are a relatively recently discovered class of small RNAs implicated in gene-regulatory processes in diverse biological contexts but there have been very few reports of a clear phenotypic role of these small RNAs in cancer progression. To select tRFs that should receive priority for mechanistic experiments, we analyzed small RNA-seq data from The Cancer Genome Atlas (TCGA) and found that high expression of three 3' tRFs (tRF-3a), tRF-3009a, tRF-3021a or tRF-3030a, is significantly associated with poor overall survival in low-grade glioma (LGG). In glioblastoma cells, tRF-3009a, tRF-3021a and tRF-3030a enhance cell invasion and migration but tRF-3021a was uniquely required for cell proliferation and suppression of apoptosis. Interestingly, tRF-3021a knockdown decreases global protein synthesis prior to and independent of apoptosis in a number of cancer cell lines, both from and outside the glioblastoma lineage. RNA-seq reveals that the results cannot be explained by microRNA-like functions of tRF-3021a. These data indicate that tRF-3021a supports cancer cell survival and particularly protein synthesis while promoting cellular invasion and migration and suggests that strategies to downregulate this short RNA could be a potential therapeutic approach in cancers. ImplicationtRF-3021a promotes malignant cell phenotypes, sustains global protein synthesis and prevents spontaneous apoptosis, motivating efforts to evaluate it as a biomarker and therapeutic target.

cancer biology↗

bioRxiv2026

Actin-dependent mechanotransduction controls nucleocytoplasmic partitioning of DNMT3a through ERK1/2 signaling during cutaneous wound healing

Cutaneous wound healing is a multifaceted physiological process that requires a cell state transition from homeostasis to tissue repair. An important contributor to this reprogramming is the wound-induced mechanical cues that are perceived by epidermal keratinocytes. Previously we identified that the nuclear translocation of the de novo DNA methyltransferase 3A (DNMT3a) upon wounding as an important regulator of this cell-state transition. However, the molecular mechanisms linking mechanotransduction to epigenetic regulation remain incompletely understood. Here we show that under homeostasis, active ERK1/2 phosphorylates DNMT3a, intramolecularly masking its nuclear localization signal (NLS), resulting in its cytoplasmic sequestration. Upon wounding actin cytoskeleton remodeling leads to the downregulation of the Extracellular Signal-Related Kinase 1/2 (ERK 1/2) pathway. Wound-induced ERK1/2 inactivation unmasks the NLS, enabling DNMT3a nuclear translocation. Collectively, these findings define a mechanotransduction-driven signaling axis linking cytoskeletal dynamics to epigenetic regulation and confirms an active role for differentiated keratinocytes in initiating early wound repair programs.

cell biology↗

bioRxiv2025

Population-scale chemical response revealed by a barcoded yeast collection

Natural genetic variation shapes how microbial populations adapt to environmental and chemical challenges, but scalable approaches to map genotype-phenotype relationships across diverse genetic backgrounds remain limited. Here, we developed a systematically barcoded collection of 520 Saccharomyces cerevisiae natural isolates that captures the ecological, geographical and genetic diversity of the species. Using pooled barcode sequencing, we profiled fitness responses to over 600 bioactive and natural compounds, revealing broader and more polarized bioactivity than the standard yeast gene-deletion collection. Fitness-based clustering defined six major compound groups with reproducible, population-structured sensitivity patterns. Genome-wide association analysis identified significant genetic variants across 107 compounds, linking natural polymorphisms to chemical responses and involving genes in genome maintenance, ribosome biogenesis, vesicular trafficking and stress tolerance. Together, our barcoded natural population provides a scalable framework for chemical-genetic screening, enabling systematic dissection of how genetic diversity shapes microbial fitness and adaptation.

evolutionary biology↗

bioRxiv2025

Predicting Toxicity and Bioactivity of the Chemical Exposome: A Case Study for the Blood Exposome Database

Humans are exposed to thousands of chemicals throughout their life. Many of these chemicals are detected in blood and have been catalogued in the Blood Exposome Database. Comprehensive hazard assessment of a chemical requires time-consuming and costly lab experiments using animal or cell-lines, which cannot be easily scaled up to the chemical exposome, highlighting the urgent need for computational approaches that can prioritize chemicals based on toxicological information. In this study, we trained direct message passing neural networks (D-MPNN) models using the Chemprop framework chemical structure and bioactivity data from 9,458 compounds profiled in the U.S. EPAs Tox21 program across 148 quantitative high-throughput screening assays. Additionally, we trained a complementary model using chemical structures (n=264,601) labeled with known UN GHS classifications for acute oral toxicity. Both models demonstrated strong predictive performance, with average AUCs exceeding 0.80 for 47 Tox21 assays. We applied these 48 models to 58,673 chemicals from the Blood Exposome Database to predict bioactivity and the GHS hazard classification, enabling scalable in-silico prioritization of understudied chemical exposures for further toxicological investigations. Data and code are available at https://zenodo.org/records/17560382 and https://github.com/idslme/exposome-toxicity-prediction.

bioinformatics↗

bioRxiv2025

Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing

Medulloblastomas are commonly considered immunologically cold and refractory to immunotherapy. One contributing factor to their low immunogenicity is impaired antigen presentation, which allows tumor cells to escape from cytotoxic T cells. Here we use a syngeneic mouse model of medulloblastoma to study the role of CD8+ T cells in medulloblastoma growth. We demonstrate that despite low expression of MHC Class I on tumor cells, depletion of CD8+ T cells accelerates tumor growth, whereas adoptive transfer of tumor-reactive CD8+ T cells prolongs survival. These anti-tumor effects rely on T cells secreting interferon gamma (IFN{gamma}), which induces MHC class I on tumor cells and facilitates tumor cell killing by T cells. Notably, this response is essential for CD8+ T cell-mediated tumor attack, as blocking IFN{gamma} signaling in vivo abrogates MHC class I induction and eliminates the beneficial effect of T cells. Importantly, delivering IFN{gamma} directly into tumors via convection-enhanced delivery (CED) enhances CD8+ T cell-mediated killing of tumor cells and significantly prolongs survival in tumor-bearing mice. These studies highlight the importance of T cells in controlling brain tumor growth and the value of IFN{gamma} as an adjuvant for T cell-based immunotherapy.

cancer biology↗

bioRxiv2025

Gain-of-function mutant p53 regulates long-noncoding RNA LINC00643 to modulate HIF1α in glioblastoma

Gain-of-function mutations of p53 (GOF-MUT-p53) act as oncogenes by regulating gene transcription. We screened for the genome-wide transcriptional targets of GOF-MUT-p53 in glioblastoma (GBM) and found that a significant subset of them were long non-coding RNAs (lncRNA). Among these, LINC00643 was strongly repressed by GOF-MUT-p53 but not wild-type p53. LINC00643 was downregulated in GBM and low-grade glioma and correlated with patient survival. LINC00643 and its conserved third exon (Exon3) suppressed GBM cell proliferation, migration, invasion, stem cell self-renewal, and in vivo tumor growth Mechanistically, ChIRP-seq identified HIF1 as a key LINC00643 interactor. Under hypoxia, LINC00643 repressed HIF1 expression and its target genes by interacting with the HIF1 enhancer. Knockdown of GOF-MUT-p53 upregulated LINC00643 and reduces HIF1, revealing a regulatory axis. These findings show extensive regulation of lncRNAs by GOF-MUT-p53 and uncover a novel mechanism by which GOF-MUT-p53 drives GBM through repression of LINC00643 and dysregulation of the HIF1 pathway.

cancer biology↗

bioRxiv2025

PATTY corrects open chromatin bias for improved bulk and single-cell CUT&Tag profiling

Precise profiling of epigenomes is essential for better understanding chromatin biology and gene regulation. Cleavage Under Targets & Tagmentation (CUT&Tag) is an efficient epigenomic profiling technique that can be performed on a low number of cells and at the single-cell level. With its growing adoption, CUT&Tag datasets spanning diverse biological systems are rapidly accumulating in the field. CUT&Tag assays use the hyperactive transposase Tn5 for DNA tagmentation. Tn5s preference toward accessible chromatin alters CUT&Tag sequence read distributions in the genome and introduces open-chromatin bias that can confound downstream analysis, an issue more substantial in sparse single-cell data. We show that open-chromatin bias extensively exists in published CUT&Tag datasets, including those generated with recently optimized high-salt protocols. To address this challenge, we present PATTY (Propensity Analyzer for Tn5 Transposase Yielded bias), a comprehensive computational method that corrects open-chromatin bias in CUT&Tag data by leveraging accompanying ATAC-seq. By integrating transcriptomic and epigenomic data using machine learning and integrative modeling, we demonstrate that PATTY enables accurate and robust detection of occupancy sites for both active and repressive histone modifications, including H3K27ac, H3K27me3, and H3K9me3, with experimental validation. We further develop a single-cell CUT&Tag analysis framework built on PATTY and show improved cell clustering when using bias-corrected single-cell CUT&Tag data compared to using uncorrected data. Beyond CUT&Tag, PATTY sets a foundation for further development of bias correction methods for improving data analysis for all Tn5-based high-throughput assays.

bioinformatics↗

bioRxiv2025

Mindin-α-M-Integrin endocytosis activates STAT3 to maintain keratinocyte stemness

Signalling networks rely not only on specific protein interactions but also on the subcellular locales at which these occur. Such spatial control is fundamental to cellular behaviour in both physiological and pathological scenarios. In studying keratinocyte stemness, we previously identified a Mindin-M{beta}2 (CD11b/CD18) interaction that triggers STAT3 activation. Here, we delineate the mechanism underlying this response and show that the F-Spondin domain of Mindin constitutes the minimal integrin-binding module required to initiate downstream signalling. F-Spondin binding to the integrin at the plasma membrane does not elicit the full activation state of the integrin. Instead, it promotes Src-kinase dependent endocytosis of the integrin receptor to the early endosomes. Analysis of integrin conformational dynamics reveals that this compartmental shift is essential as the acidic environment of early endosomes drives the transition into a signalling-competent state. This mechanism extends to pathological contexts, as we demonstrate a requirement for endocytosis in activating STAT3 signalling and preserving stem-like properties in a cancer stem cell model. Together, these findings highlight a previously unrecognized layer of spatial control in integrin signalling, confirming endosomal trafficking as a critical determinant of stem cell behaviour and offering new conceptual and therapeutic opportunities across regenerative biology and cancer.

cell biology↗

bioRxiv2025

Insights into gallbladder cancer pathogenesis from a living organoid gallbladder cholangiocyte biorepository

Gallbladder cancer (GBC) while rare worldwide has a high prevalence in India. Pathogenesis is unclear and outcomes poor. Gallbladder cholangiocyte organoids (GCOs) or gallbladder carcinoma organoids (GBCOs) were developed and serially propagated from surgically resected gallbladder tissues with benign or malignant diseases, respectively. Patient derived organoids (PDOs) were derived from 15 normal; 58 inflamed; 12 xanthogranulomatous cholecystitis (XGC); 5 pre-invasive neoplasm and 13 invasive malignant gallbladder pathologies. Protocol optimisation achieved 58% (69/119) success in organoid generation and expansion. Organoids maintained tight junction integrity; P-gp pump and enzymatic activity; preserved tissue-specific gene and protein marker expression; histological features and genetic variations. Cryopreserved organoids from 62 patients with primary tissue and high-quality DNA, RNA and protein derivatives have been banked. In gene expression analyses of tissue, XGC samples clustered with malignant subtypes, separate from benign pathologies. Derived XGC organoids showed a similar clustering. Enriched hallmark pathways in XGC support neoplastic change through chronic inflammation. PDOs generated from different gallbladder pathologies are a promising model to investigate the pathogenesis of GBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/651639v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@465f3dorg.highwire.dtl.DTLVardef@16c5f0org.highwire.dtl.DTLVardef@11d4807org.highwire.dtl.DTLVardef@163d072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A comprehensive pipeline for genome annotation across species: a case study on Schmidtea mediterranea

Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such as Schmidtea mediterranea. To address these challenges, we developed a flexible and scalable genome annotation pipeline that integrates short-read (Illumina) and long-read (PacBio) sequencing technologies. The pipeline combines reference-based and de novo assembly methods, effectively handling genomic variability and alternative splicing events. To improve splice site detection accuracy, DeepSplice deep learning predictions are used. Functional annotation is conducted to filter out low-confidence transcripts and ensure biological relevance. Applying this pipeline to the asexual strain of S. mediterranea revealed thousands of previously undescribed putative genes and transcripts, and improved the existing gene models, highlighting its utility in annotating complex, underexplored genomes. The modularity and comprehensiveness of our pipeline ensure its adaptability for genome annotation across diverse species, making it a valuable tool for annotating genomes of non-model organisms and supporting broader genomic research. The source code and implementation details are available at https://github.com/Norreanea/SmedAnno.

bioinformatics↗