Biology subjects

Patel, S.

Publications and source records attributed to Patel, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

Aptamers are single-stranded oligonucleotides that bind molecular targets with high affinity and specificity. However, their discovery remains time-consuming, expensive, and susceptible to experimental biases. Here we present AptaBLE, a deep learning framework for predicting aptamer-protein binding. Additionally, we demonstrate two de novo generation methods that produce novel aptamers with desired specificity profiles and Kds as low as 31 nM to-date. AptaBLE represents a significant advance towards therapeutic and diagnostic aptamer development.

bioinformatics↗

bioRxiv2025

Intestinal Stem and Progenitor Cells Exhibit Distinct Adaptive Responses to Inflammatory Stress in IBD

BackgroundIntestinal epithelial stem cells (SCs) and their transit-amplifying (TA) progeny are critical for mucosal repair and regeneration. However, their behaviour under chronic inflammatory conditions, such as those observed in Inflammatory Bowel Disease (IBD), remains incompletely understood. MethodsWe investigated the impact of chronic inflammation on intestinal stem/progenitor cells by integrating bulk RNA sequencing from the largest IBD biopsy cohort to date with single-cell transcriptomic analysis and experimental assays using patient-derived intestinal organoids. ResultsActive inflammation was associated with a reduction in canonical LGR5 intestinal stem cells and a concurrent expansion of OLFM4 populations, consistent with an inflammation-induced epithelial repair program. Notably, SC/TA cells from both inflamed and non-inflamed IBD tissues exhibited persistent transcriptional changes that were distinct from those in healthy controls. Single-cell analysis identified transcriptionally heterogeneous SC/TA subpopulations, including a previously uncharacterized inflammation-associated cluster enriched in immune signalling pathways. Pseudotime trajectory analysis demonstrated a shift in differentiation toward deep crypt secretory (Paneth-like) cell lineages under inflammatory conditions. ConclusionsChronic intestinal inflammation reshapes the epithelial stem and progenitor cell compartment, promoting altered differentiation and the emergence of immune-responsive epithelial states. These findings highlight the plasticity of the human intestinal epithelium in IBD and point to new avenues for therapeutic strategies aimed at maintaining epithelial integrity during chronic inflammation.

molecular biology↗

bioRxiv2025

ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed loss of ATRX protein in 14% of soft tissue leiomyosarcoma (STLMS, n =127), 53% of uterine leiomyosarcoma (ULMS, n = 95), 37% of undifferentiated pleomorphic sarcoma (UPS, n = 82), and 8% of dedifferentiated liposarcoma (DDLPS, n = 84). ATRX loss was associated with significantly worse outcomes in ULMS, UPS, and DDLPS. ATRX knockout in sarcoma cells increased proliferation in cooperation with TP53 deletion. ATRX knockout led to chromatin de-repression and enrichment of PRDM4 and NFIX transcription factor (TF) motifs. PRDM4 and NFIX knockdown in ATRX-mutant sarcoma lines resulted in reduced proliferation and invasion suggesting epistatic relationship. Consistent with the known functional relationship between PRMD4 and YAP1, we observed that ATRX/TP53 KO cells were more sensitive to the TEAD inhibitor VT103 compared to TP53 KO and ATRX WT controls. Overall, our results identify ATRX loss as a prognostic factor of worse outcomes, implicate the ATRX-PRDM4-YAP1 axis as a novel underlying mechanism, and suggest use of TEAD inhibition as a potential therapeutic strategy for ATRX-deficient sarcomas. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/689992v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@a759ecorg.highwire.dtl.DTLVardef@100c580org.highwire.dtl.DTLVardef@1a675c9org.highwire.dtl.DTLVardef@17f1f91_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy

Revealing how individual axons create a brain-wide connectome would be indispensable for understanding brain function and behavior, yet remains technically challenging. We introduce MAPL3, an end-to-end pipeline that integrates self-supervised learning with an innovative deep architecture to capture local and global brain-wide axonal projections. MAPL3 enables subject- and population-level quantitative laminar analysis, generalizes across experiments, and outperforms state-of-the-art methods. We showcase its ability to map the circuitry of the orbitofrontal cortex from single axons to whole-brain projectome.

neuroscience↗

bioRxiv2025

Co-Hyperpolarized Dehydroascorbate and Pyruvate MRI Predicts Radiation Response in Glioblastoma Models

PurposeEarly noninvasive assessments of treatment response are desperately needed to improve outcomes in glioblastoma (GBM). Molecular imaging techniques that measure glycolytic metabolism are being increasingly studied, but limitations such as variable substrate delivery present significant barriers to clinical interpretation. To develop more robust translational imaging biomarkers, we propose utilizing the interrogation of oxidative stress, a critical component of tumor metabolism for which no method of clinical measurement currently exists. This study investigates the simultaneous measure of oxidative stress and glycolytic flux using co-hyperpolarized [1-13C] dehydroascorbate and [1-13C] pyruvate (HP DHA/PA) as a predictor of treatment response in GBM. Experimental DesignTo establish a model that exhibits known metabolic responses to oxidative stress, we characterize radiation induced metabolic reprogramming in four human GBM lines (U87, U251, A172, T98) in vitro. We extend this in vivo and establish radiosensitive and radioresistant orthotopic xenograft models to investigate HP DHA/PA magnetic resonance imaging as a predictor of treatment response. ResultsIn vitro analyses revealed that radiation upregulates the pentose phosphate pathway and response is augmented by glutathione depletion. In vivo metabolomic profiling identified preferential nucleotide metabolism pathways in each tumor type. HP DHA/PA imaging revealed that DHA perfusion was not impacted by blood-brain-barrier integrity and detected reductions in DHA-to-vitamin C and pyruvate-to-lactate conversion in treatment-sensitive tumors, reflecting diminished reductive capacity following radiation. ConclusionsThese findings demonstrate successful prediction of radiosensitivity in GBM utilizing measurement of oxidative stress and establish HP DHA/PA imaging as an innovative method to address existing clinical limitations in treatment response assessment.

cancer biology↗

bioRxiv2025

Beyond retinotopy: exploiting native visual representations in cortical neuroprostheses for vision loss remediation

Cortical prosthetic systems offer a promising path to restoring vision in blindness by stimulating neurons in the visual cortex to evoke visual percepts. To effectively encode visual information, however, it is essential to target neurons based on their functional encoding properties. Current stimulation protocols focus on retinotopic information, ignoring other key encoding properties, and therefore fail to reproduce complex visual percepts. We demonstrate that incorporating orientation selectivity alongside retinotopy to guide stimulation dramatically improves fidelity of the evoked activity to the underlying neural code. We propose a Bottlenecked Rotation-Equivariant CNN (BRCNN) and demonstrate that neural responses can be predicted to a large degree using only retinotopy and orientation preference. Using this model, we design a retinotopy-and-orientation aware stimulation protocol and validate it in a state-of-the-art large-scale optogenetic stimulation simulation framework of primary visual cortex. Our protocol elicits neural activity patterns exhibiting substantially higher correlation with natural vision responses compared to retinotopic-only approaches.

neuroscience↗

bioRxiv2025

Microbial-inspired antidotes to repurpose toxic compounds as antibiotics

Antibiotic-resistant (AMR) bacterial infections are a major global health threat. Despite the critical need for new antimicrobials, progress is constrained by protracted development timelines, as well as the requirement for chemical novelty to avoid cross-resistance. Although advances in high-throughput screening, genome mining, and machine learning have greatly accelerated antimicrobial discovery, insufficient separation between antibacterial efficacy and host toxicity remains a bottleneck, precluding the clinical development of many promising compounds. Here, we establish a generalizable, two-component strategy to engineer antimicrobial safety and mobilize otherwise inaccessible chemical space for antimicrobial therapy, using calicheamicin, a potent cytotoxin with unacceptable host toxicity, as a proof of concept. In the first arm, we engineer a conditionally-active drug conjugate that limits calicheamicin activity to infected tissue, thereby reducing systemic toxicity. In the second arm, we co-administer a re-engineered self-resistance enzyme from Micromonospora echinospora, the natural producer of calicheamicin, as an "antidote" to neutralize calicheamicin present outside of infected tissue, further mitigating off-target toxicity. The conditionally-active conjugate exhibits activity against Gram-negative and Gram-positive pathogens in response to a protease present within the infected microenvironment. When delivered in combination with the antidote, antibacterial efficacy is maintained while off-target toxicity is reduced in mouse models of Gram positive and negative bacterial pneumonia. We anticipate that our dual strategy, which engineers, rather than selects for enhanced drug safety, by combining conditional drug activity with antidote-driven neutralization of off-target effects, provides a generalizable framework for mobilizing other promising but toxic compounds as antimicrobials.

bioengineering↗

bioRxiv2025

Development of a Time-based Drug Screening Platform for Improved Clinical Translation

In 2022, the average cost for a single drugs development increased by 15%, reaching $2.3 billion. In drug development, oncology has the highest attrition rate with 95% of new drugs failing Phase 2 clinical trials alone. Consequently, innovative approaches are needed to assess clinical utility prior to proceeding with human trials. Current drug development follows the theory that "Best Potency = Best Drug" which is a concentration-centric paradigm focused on optimizing drug-target interaction (Kd) to improve the concentration of drug necessary to elicit its therapeutic effect (IC50). However, both drug concentration and exposure time contribute to clinical efficacy, yet most laboratory studies focus on IC50 alone. This manuscript characterizes drug potency and kinetics of ten oncology drugs in three different cancer cell lines and integrates in vivo pharmacokinetic-pharmacodynamic models to identify how these parameters relate to real-world clinical outcomes. Our analyses revealed that Cmax normalization is necessary for concentration response data as IC50 alone does not account for drugs that are studied at sub-therapeutic concentrations. Additionally, the temporal effect of drug efficacy varies between cell lines and dose, where some drugs are unable to overcome the proliferation rate of the cells to induce a decrease in disease progression. This work aims to enhance the design and implementation of drug regimens by understanding the time-dependence of clinical efficacy and cytotoxicity.

pharmacology and toxicology↗

bioRxiv2025

LIS1 is critical for axon integrity in adult mice

Mutations in human LIS1 cause lissencephaly, a severe developmental brain malformation. Although most studies focus on development, LIS1 is also expressed in adult mouse tissues. We previously induced LIS1 knockout (iKO) in adult mice using a Cre-Lox approach with an actin promoter driving CreERT2 expression. This proved to be rapidly lethal, with evidence pointing toward nervous system dysfunction. CreERT2 activity was observed in astrocytes, brainstem and spinal motor neurons, and axons and Schwann cells in the sciatic and phrenic nerves, suggesting dysfunctional cardiorespiratory and motor circuits. However, it is unclear how LIS1 knockout in these different cell types contributes to the lethal phenotype. We now report that LIS1 depletion from astrocytes is not lethal to mice (male or female), although glial fibrillary protein (GFAP) expression is increased in all LIS1-depleted astrocytes. In contrast, LIS1 depletion from projection neurons causes motor deficits and rapid lethality in both males and females. This is accompanied by progressive, widespread axonal degeneration along the entire length of both motor and sensory axons. Interestingly, sensory neurons harvested from iKO mice initially extend axons in culture but soon develop axonal swellings and fragmentation, indicating axonal degeneration. LIS1 is a prominent regulator of cytoplasmic dynein 1 (dynein, hereafter), a microtubule motor whose disruption can cause both cortical malformations and later-onset neurodegenerative diseases, such as Charcot-Marie-Tooth disease. Our results raise the possibility that LIS1 depletion, through disruption of dynein function in mature axons, may lead to Wallerian-like axon degeneration without traumatic nerve injury. Significance StatementA healthy nervous system requires that proper brain wiring is maintained throughout the life of the animal. Connectivity often involves the long axons of projection neurons. Some axons drive cognition, others contribute to sensory and motor systems, while still others subserve vitally important cardiorespiratory processes. We show that LIS1, a protein linked to congenital brain abnormalities, also plays a crucial role in fully developed projection neurons in the adult mouse. LIS1 depletion from these cells causes severe axonal degeneration resembling the Wallerian degeneration that occurs in response to nerve injury. Because LIS1 regulates dynein, and because defective dynein can cause neurodegenerative disorders in humans, our study suggests that drugs targeting Wallerian degeneration may have therapeutic potential for dynein-related diseases.

neuroscience↗

bioRxiv2025

Single-cell spatial mapping reveals dynamic bone marrow microarchitectural alterations and enhances clinical diagnostics in MDS

Myelodysplastic neoplasms (MDS) disrupt bone marrow hematopoiesis, yet clinical assessment relies largely on blast enumeration and qualitative morphology, which incompletely capture marrow architecture and disease state. We applied whole-slide multiplex immunofluorescence imaging with single-cell phenotyping to map bone marrow microarchitecture in MDS. Diagnostic biopsies (n=36), longitudinal treatment samples (n=29), precursor states (n=13), and normal controls (n=21) were analyzed, comprising >5 million spatially resolved cells. MDS marrow exhibited coordinated, genotype-imprinted architectural remodeling, including altered progenitor composition and spatial patterning, disrupted erythroid island organization, and displacement of hematopoietic stem and progenitor cells from perivascular niches. Interrogation of 82 cellular and spatial features yielded a composite Microarchitectural Perturbation Score (MDS-MAPS), derived from diagnostic samples and fixed prior to longitudinal analyses. In leave-one-patient-out cross-validation, MDS-MAPS discriminated remission from active disease more accurately than blast percentage (AUC 0.883 vs 0.660) and distinguished low-blast MDS from clonal cytopenia of undetermined significance (CCUS) (AUC 0.815). Mixed-effects modeling showed MAPS decreased in remission statistically independent of blast burden, with architectural normalization during remission and re-emergence at relapse. These findings define quantitative bone marrow architecture as a dynamic tissue-state biomarker that complements molecular and blast-based assessment in MDS.

pathology↗

bioRxiv2025

Alternate Splicing Directs PMCA2 to Lysosomes and is Linked to Neurodegeneration

Plasma membrane calcium ATPases (PMCAs) are believed to function exclusively at the plasma membrane where they expel calcium from the cytosol. We have unexpectedly identified a splice variant-dependent localisation of the PMCA isoform PMCA2 to the lysosome, where it forms an evolutionarily conserved complex with NPC1, the lysosomal membrane protein defective in the rare lysosomal storage disease Niemann-Pick disease type C (NPC). This interaction is required for lysosomal Ca2+ homeostasis and implicates PMCA2 as a mediator of Ca2+ uptake into lysosomes. Disruption of the NPC1-PMCA2 complex contributes to the pathophysiology of both Niemann-Pick disease type C and Parkinsons disease, revealing an unrecognised intracellular function for PMCA2 and a shared mechanism linking lysosomal Ca2+ and lipid regulation in neurodegeneration.

cell biology↗

bioRxiv2025

Persistence and near persistence via trait evolution: pathways to coexistence

Modern coexistence theory relies on the invasion criterion: each species must be able to increase when rare in a resident community at ecological equilibrium. However, when considering trait evolution, for example of competing species, this concept must be refined to account for evolution potentially feeding back on population dynamics. We analyze a model of two competing species whose quantitative traits evolve under stabilizing selection, assuming fixed but potentially unequal intraspecific trait variances. Using persistence theory, we derive conditions under which both species persist for all initial trait values, and we introduce the concept of near persistence, in which coexistence holds for a specific, biologically relevant, subset of initial trait configurations. Our analysis reveals that equal trait variances between species, which is commonly assumed in previous work, yield highly specific outcomes and obscure a broader set of coexistence scenarios that emerge under asymmetric trait variation. We identify fifteen distinct qualitative dynamical regimes as a function of initial conditions and trait variances. Moreover, we show that invasion analysis must often be performed at multiple eco-evolutionary equilibria, as invader dynamics may converge to different trait values depending on the ecological and evolutionary context. We discuss the biological implications of these results and perspectives for future work.

ecology↗

bioRxiv2025

Lower Airway Dysbiosis in NTM+ Bronchiectasis is Associated with NET-Predominant Severe Phenotypes

RationaleThe discoveries of neutrophilic inflammation and Pseudomonas-dominant pulmonary dysbiosis have helped pave the way for host-directed therapy in bronchiectasis. Substantial knowledge gaps remain about the interplay between neutrophilic signatures and microbes in non-tuberculous mycobacterial lung disease (NTM-LD), a phenotypically diverse lung infection that is increasingly prevalent in the United States and other parts of the world. ObjectivesEvaluate the lower airway microbiota and neutrophilic traits in NTM- and NTM+ bronchiectasis. Methods16S rRNA gene sequencing, cell counts and neutrophil extracellular trap (NET) immunoassays were performed on bronchoscopic lower airway samples in 200 bronchiectasis subjects (108 NTM-, 92 NTM+). A preclinical model of oral commensal micro-aspiration and NTM infection was used to profile the murine lower airways with flow cytometry and a NET assay. Measurements and Main ResultsLower airways of NTM+ bronchiectasis patients were enriched with Mycobacterium and oral commensals (e.g., Veillonella, Prevotella). NET levels were higher in NTM+ BAL. Mycobacterium and oral commensals co-occurred with NET and neutrophils in network studies. Distinct oral commensal taxa associated with severe disease phenotypes such as cavitary disease and exacerbators. In a murine micro-aspiration model, the combination of oral commensals and Mycobacterium led to a sustained pro-inflammatory immune response marked by an increase in Th17, {gamma}8T cells, PD-1+ T lymphocytes as well as higher NET levels. ConclusionsOur analyses showed that distinct microbiome features beyond the primary pathogen can contribute to neutrophilic inflammation and severe disease phenotypes in bronchiectasis/ NTM-LD.

immunology↗

bioRxiv2025

Chaperone AIP Couples mTORC1 Activation and Catabolic Metabolism During Neonatal Development

To grow and divide cells must tightly coordinate anabolic programs with the availability of nutrients and growth factors. This balance is especially critical during postnatal development, when biosynthetic and energetic demands are high, and nutrient supply and neonates have to adapt to periods of fasting. These conditions place acute stress on the proteostasis network, making autophagy essential for nutrient recycling. We found that the chaperone aryl hydrocarbon receptor-interacting protein (AIP) supports both arms of this metabolic balance: promoting anabolic PI3K-AKT signaling for mTORC1 activation and enabling catabolic processes such as proteasomal degradation and autophagy. Loss of AIP causes a severe neonatal metabolic disorder, where affected infants fail to thrive postnatally. Our findings establish AIP as a central regulator of neonatal metabolic adaptation and cellular homeostasis. One Sentence SummaryAIP integrates nutrient sensing and protein recycling to sustain neonatal survival.

developmental biology↗

bioRxiv2025

How the Drosophila Cryptochrome C-terminus mediates magnetosensitivity

The Earths magnetic field plays an important role in the seasonal migrations of many species of animals. A Cryptochrome (CRY)-based radical pair mechanism (RPM) has been suggested to underlie the mechanistic basis of animal magnetosensitivity and navigation. The quantum spin state of a radical pair involving flavin adenine dinucleotide (FAD) bound to CRY in the canonical pocket is sensitive to external magnetic fields that can alter the signalling concentration of activated CRY1-5. However, several experimental observations challenge this model including the finding that the C-terminal fragment of Drosophila CRY (DmCRY), which lacks any canonical FAD binding pocket, and human CRY2, which lacks affinity for FAD, are sufficient to support magnetosensitivity6-9. Here, we use all-atom molecular dynamic (MD) simulations, alongside in vitro and in vivo analyses to reveal that the C-terminus of Drosophila CRY (DmCRY-CT) binds FAD. FAD binding is required for transduction of a magnetic signal within cells, and, in vitro, initiates formation of high molecular weight DmCRY-CT oligomers, including large insoluble aggregates reminiscent of CRY photobodies observed in plants10-14. These results provide a plausible mechanistic basis for several experimental observations that have reported non-canonical magnetosensitivity in animals.

biochemistry↗

bioRxiv2025

Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4⁺ T Cells

In vivo genetic engineering of T cells could overcome the logistical, biological, and safety challenges of ex vivo modification, but effective and safe delivery systems remain limited by a lack of cellular specificity. Here, we developed aptamer-functionalized lipid nanoparticles (LNPs) for targeted mRNA delivery to CD4+ T cells, employing both a validated CD4-binding aptamer (Apt62) and novel aptamers generated using our proprietary transformer-based AI language model, AptaBLE. LNPs formulated with ionizable lipid SM102 or MC3 and conjugated with aptamers at controlled densities were physiochemically characterized and assessed for binding, in vitro transfection, in vivo biodistribution, and safety evaluation. Aptamer-functionalized LNPs demonstrated selective nanomolar binding to recombinant CD4, achieved enhanced transfection of CD4+ versus CD4- T cells in vitro, and significantly enriched mRNA delivery to immune-rich tissues in vivo, achieving up to 70-fold spleen signal enhancement with SM102 formulations compared to non-targeted controls, while maintaining suitable safety profiles. Overall, these findings demonstrate aptamer-functionalized LNPs, augmented by AI-guided aptamer design, as a tunable, non-immunogenic platform for in vivo T cell engineering. HighlightsO_LIAptamer-functionalized LNPs enable selective mRNA delivery to CD4+ immune cells rich organs. C_LIO_LIAptamer-functionalized LNPs maintain a favorable systemic safety profile in vivo. C_LIO_LIAI-guided AptaBLE platform generated functional aptamers validated in nanoparticle delivery. C_LI

molecular biology↗

bioRxiv2025

Structural basis for the function of long noncoding RNA Pnky in neural stem cells

LncRNA Pnky is a trans-acting regulator of neural stem cell (NSC) differentiation, but the molecular mechanisms by which Pnky regulates neurogenesis is unknown. A fundamental step towards mechanistic understanding is to determine whether a lncRNA has folded structure that underlies biological function. Using chemical probing and high-throughput analysis, we determined the secondary structure of Pnky folded in vitro and in cellulo. Pnky adopts a compact structure in vitro with distinct modules and evidence of tertiary interactions. In cellulo, Pnky structure is remarkably similar to the in vitro conformation. We used locked nucleic acid oligonucleotides to interrogate the entire Pnky transcript for function in NSCs and identified regions that when targeted increased neurogenesis - phenocopying Pnky knockdown - without decreasing transcript abundance. Our findings provide a structural basis for the role of Pnky in neurogenesis and, more broadly, illustrate how structural maps combined with phenotypic data can advance fundamental understanding of lncRNA mechanism. HIGHLIGHTSPnky folds into highly structured conformation in vitro with distinct modules. Pnky is a compact lncRNA with evidence of tertiary interactions. Pnky structure in neural stem cells is similar to its in vitro conformation. LNA ASO perturbations identify structured regions of Pnky involved in neuronal differentiation.

molecular biology↗

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes (ACTG) program. Originating from a clone of Auburn Universitys historic "Toomers Oak," this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

genomics↗