Biology subjects

Chawla, A.

Publications and source records attributed to Chawla, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Biomechanical effects of load-carrying in adolescent idiopathic scoliosis: a subject-specific musculoskeletal modelling study

Load carrying is a common activity during adolescence, yet its biomechanical consequences for the structurally asymmetric spine in adolescent idiopathic scoliosis (AIS) remain poorly understood. This study investigated how load magnitude, carrying height, and side of application influence spinal loading and paraspinal muscle forces in AIS. A subject-specific musculoskeletal model of a 16-year-old female with a 59{degrees} right-convex thoracic curve was used to simulate bilateral and unilateral load carrying at the hand, chest, and above-shoulder levels, with loads corresponding to 5%, 10%, and 15% of body weight. Intervertebral compressive and lateral forces and erector spinae (ES) and multifidus (MF) muscle forces were evaluated. Spinal loading increased progressively with load magnitude and carrying height. At 15% body weight, compressive forces at the curve apex increased from 511-566 N at hand level to 721-831 N above the shoulder. Unilateral carrying produced distinct side-dependent responses: convex-side carrying generated greater compressive forces, whereas concave-side carrying generated greater lateral forces, which were concentrated around the curve apex. Paraspinal muscles also exhibited muscle-specific responses. ES forces primarily reflected the imposed external asymmetry, with unilateral carrying eliciting predominantly contralateral recruitment, whereas MF maintained a characteristic convex-side dominance concentrated around the curve apex. These findings demonstrate that load carrying in AIS produces a coupled biomechanical response governed by both the external loading configuration and the pre-existing structural asymmetry of the spine, highlighting the importance of considering loading direction and muscular adaptation alongside load magnitude when evaluating everyday carrying activities in AIS.

bioengineering↗

bioRxiv2026

Influence of trunk posture on spinal loading and paraspinal muscle forces in adolescent idiopathic scoliosis: a subject-specific musculoskeletal modelling study

Adolescent idiopathic scoliosis (AIS) alters spinal geometry and may influence the biomechanical response of the spine during functional postures. However, posture-dependent changes in spinal loading and paraspinal muscle forces in AIS remain poorly understood. This study investigated the effects of trunk posture on intervertebral loading and paraspinal muscle forces using a subject-specific musculoskeletal model of an adolescent with AIS. The spinal deformity was reconstructed from biplanar radiographs and incorporated into a full-body musculoskeletal model. Flexion, extension, lateral bending, and axial rotation were simulated at three incremental magnitudes, with motion distributed across the thoracolumbar spine. Intervertebral compressive and lateral forces around the curve apex and forces in the erector spinae (ES) and multifidus (MF) muscles were evaluated. Trunk flexion produced the greatest compressive loading, reaching 337 N at the curve apex and 372 N two levels below the apex at 30{degrees} flexion. Lateral bending produced pronounced direction-dependent loading: concave-side bending increased lateral forces, whereas convex-side bending increased compressive forces. Axial rotation produced similar but smaller direction-dependent changes. Paraspinal muscle forces were consistently asymmetric, with concave-side dominance of the ES and convex-side dominance of the MF. Flexion and convex-sided movements generally produced greater muscle imbalance, while increasing posture magnitude amplified spinal loading and muscle forces. These findings demonstrate that trunk posture, movement direction, and magnitude substantially influence the biomechanical environment of the scoliotic spine and should be considered when evaluating spinal mechanics in AIS.

bioengineering↗

bioRxiv2026

Multi-omics characterization of astrocyte subtypes reveals spatially coordinated astrocyte downregulation in depression

Major depressive disorder (MDD) is a complex psychiatric disorder affecting millions of individuals worldwide. Astrocytes, which have been implicated in MDD by several studies, are the most abundant non-neuronal cells in the brain and play critical roles in synaptic regulation, blood-brain barrier maintenance, and immune modulation. While astrocytic molecular and morphological abnormalities are well-established features of MDD, these alterations have not been resolved within their spatial context. Here, we combine spatial transcriptomics with matched snRNA-seq and snATAC-seq datasets to spatially map molecularly distinct astrocyte subtypes and define their regional contributions to MDD pathology. This spatial context further enables the characterization of astrocyte interactions with neighboring cell populations, providing a more holistic assessment of how dysfunctional astrocytes influence local brain microenvironments and circuit function in MDD. We identified spatially localized astrocytic dysfunction in deep cortical layers of the MDD dlPFC, converging across transcriptomic, chromatin, and spatial modalities and centering on the PSAP-GPR37L1 signaling axis. Together, these findings identify astrocyte dysfunction as a key feature of MDD and demonstrate the value of spatially resolved molecular profiling for uncovering how altered astrocyte-neuron communication within deep cortical layers may contribute to disease pathology.

neuroscience↗

bioRxiv2026

Sex-specific hormone-sensitive regulatory architecture in adolescence as a scaffold for depression vulnerability

Adolescence is a critical developmental period during which sex differences in depression risk emerge, yet the underlying molecular mechanisms remain unclear. Here, we integrated longitudinal transcriptomic, epigenomic, and gene regulatory network analyses to characterize sex-specific regulatory dynamics of the brain across adolescence under normative conditions and elucidate how baseline molecular differences may shape later vulnerability. We observed that immediate early genes exhibited the strongest sex-biased signals, with males and females showing opposing developmental trajectories, suggesting a role in sex-specific stress-responsive programs. Across analyses, a consistent pattern emerged: males showed stronger activity-dependent neuronal signatures, whereas females showed stronger stress- and immune-related signatures. Extending these findings to a disease context using single-nucleus chromatin accessibility data, we identified hormone-responsive regulatory elements enriched in depression-associated regions, with sex- and cell type-specific links to genetic risk. Grounded in established models of sex-specific stress responses, these findings offer a developmental regulatory framework for understanding the differential presentation of, and vulnerability to, depression.

genomics↗

bioRxiv2026

A multimodal characterization of the human uncinate fasciculus

The uncinate fasciculus (UF) is a hook-shaped long-range association white matter tract that serves to bidirectionally transmit information between the anterior temporal lobe and the orbitofrontal cortex. Neuroimaging studies have suggested that changes in UF microstructure are involved in the neurobiological sequalae of childhood abuse (CA). Given that the UF is not present in rodents, it is vastly understudied with no cellular and molecular information available. To this end, we aimed to perform a multimodal characterization of the UF between individuals diagnosed with depression who died by suicide with (DS-CA) and without a history of severe CA (DS) and psychiatrically healthy individuals (CTRL). Fresh frozen UF tissue was obtained from the Douglas Bell-Canada Brain Bank, with phenotypic information collected via psychological autopsy. Immunohistochemistry with PDGFR and NogoA was used to label oligodendrocyte precursor cell (OPC) and oligodendrocyte (OL), respectively, and stereology was performed to ascertain cell density and soma volume. Single nucleus RNA sequencing (snRNAseq) was used to generate a transcriptomic survey of the cell types found in the UF. Finally, spectral focusing Coherent Anti-Stokes Raman Scattering (sf-CARS) microscopy was employed in tandem with a custom AxonDeepSeg segmentation model to measure axon diameter, myelin thickness, and g-ratio. No group differences were observed in histology or ultrastructure metrics, but nearly 50 differentially expressed genes (DEG) were identified between groups. Interestingly NECTIN3, the top DEG downregulated in OL1 and OL3 of DS-CA, is a computationally predicted target of the microRNA MIR646, the host gene of which was significantly downregulated in multiple cell types in DS-CA. Age-associated changes were pronounced and observed in all modalities, including an age-related increase in OL density, extensive changes in glial gene expression, as well as decreases in axon diameter and g-ratio. This study serves as a foundational resource on the molecular and cellular properties of the human UF. Our results suggest that observable myelin-related traces of depression or CA are limited in the UF and highlights the need for future research on the cellular and molecular properties of white matter tracts during aging.

neuroscience↗

bioRxiv2025

Enrichment of a CD4-CD8- NK-like cytotoxic Vδ1/3 T cell subset in tuberculosis disease

Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a leading cause of global morbidity and mortality. Although gamma-delta ({gamma}{delta}) T cells have increasingly been suggested to contribute to the TB immune response, quantitative and qualitative differences in this immune cell compartment between healthy and TB diseased individuals are not well-characterized. In this study, we used single-cell RNA sequencing to provide a high-resolution characterization of CD4-CD8- {gamma}{delta} T cells in peripheral blood across healthy Mtb-non-sensitized, healthy Mtb-sensitized, and TB disease pre-/post-treatment cohorts. We found upregulation of an activated and cytotoxic gene signature in {gamma}{delta} T cells of TB disease compared to both healthy cohorts. Strikingly, these differences persisted through one year following diagnosis of TB disease (corresponding to six months after completion of anti-TB therapy). We found that these transcriptomic differences were largely mediated by an NK-like cytotoxic V{delta}1 and V{delta}3 subset that was enriched in TB disease, with a unique V{delta}3 TCR gene usage. Our findings suggest long-lasting changes in the CD4-CD8- {gamma}{delta} T cell compartment and highlight V{delta}3 cells, a previously underappreciated {gamma}{delta} T cell subset, as potentially important in TB.

immunology↗

bioRxiv2025

Bmal1 expression is minimal or absent in human and mouse cerebral microglia

Microglia orchestrate immunological responses in the brain and play an important role in maintaining homeostatic brain functions. Several studies have reported clock gene expression in microglia and the circadian rhythm they drive has been linked to the modulation of immune responses and neuronal functions. In the current study, complementary approaches, including immunofluorescence, multiplexed fluorescence in situ hybridization, and liquid chromatography-mass spectrometry proteomics of isolated CD11b+ microglia, were combined with publicly available transcriptomic and epigenomic datasets to investigate the expression of the core clock gene BMAL1 in human post-mortem cortical and limbic areas as well as mouse brain. The majority of BMAL1-expressing cells were found to be neurons, with microglia representing a negligeable proportion. We also identified significantly lower chromatin accessibility or "openness" for BMAL1 gene regulatory regions (such as promoters and enhancers) in microglia compared to neurons. These regulatory regions in microglia were enriched for ETS domain transcription factor (TF) binding sites. Together, this suggests a strong role of chromatin remodeling factors in suppressing BMAL1 gene expression in microglia. Finally, while we observed a very low expression, BMAL1 TF motifs were accessible in open chromatin landscape of microglia, which may lead to downstream gene-regulatory effects upon binding, even if BMAL1 expression is constitutively low. Overall, our results reveal low or absent expression of BMAL1 in microglia and point towards potential epigenetic mechanisms regulating its expression in these cells.

neuroscience↗

bioRxiv2025

Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis

Assigning antigen specificity to T cell receptor (TCR) sequences is challenging due to the TCR repertoires diversity and the complexity of TCR:antigen recognition. We developed the Peptide-Driven Identification of TCRs (PDI-TCR) assay that combines in vitro expansion of cells with peptide pools, bulk TCR sequencing, and statistical analysis to identify antigen-specific TCRs from human blood. A key feature of PDI-TCR is the ability to distinguish true antigen-specific TCR clonotypes from TCRs associated with unspecific bystander activation by comparing responses to non-overlapping peptide pools. We applied PDI-TCR to Tuberculosis (TB) patients, sampling blood at diagnosis and throughout treatment, and Mycobacterium tuberculosis (Mtb)-sensitized healthy individuals (IGRA+). We identified hundreds of Mtb-specific TCRs, as well as unspecific TCRs, and characterized their phenotype in each cohort by single-cell RNA sequencing ex vivo. Mtb-specific T cells were highly diverse, with short-lived effector phenotypes only present in TB at diagnosis, while memory phenotypes were maintained through treatment. In contrast, unspecific expanded T cells were more clonally restricted, had a cytotoxic phenotype, and were maintained throughout treatment. This showcases PDI-TCR as a powerful tool for identifying antigen-specific TCRs, which enables direct ex vivo identification and monitoring of antigen-specific T cells.

immunology↗

bioRxiv2025

Influence of simplifications on FE modelling of mandible and TMJ implants

End-stage temporomandibular joint (TMJ) disorders often necessitate joint replacement to restore bilateral mastication. Patient-specific TMJ implants typically rely on detailed in silico modelling derived from subject-specific computed tomography (CT) scans of the mandible. However, generating highly detailed finite element (FE) models is computationally expensive. Although structural simplifications of the mandible are known to influence mechanical behaviour, their quantitative impact on TMJ implant evaluation has not been systematically investigated. This study examines the influence of three modelling simplifications on stress-strain predictions in intact and implanted mandibles: (i) a detailed segmented mandible with tissue-specific material properties (Model 1), (ii) a simplified mandible comprising cortical bone only (Model 2), and (iii) a further simplified mandible excluding dental crowns (Model 3). Both narrow and standard TMJ implants were analysed under osseointegrated and non-osseointegrated conditions, resulting in fifteen FE models. Physiological clenching activities were simulated. Compared with the detailed model, simplified models showed reductions of up to 50% in maximum principal strain in bone and up to 44% in von Mises stress in TMJ implants, while preserving spatial stress-strain trends. These findings indicate that simplified models may be suitable for preliminary implant design, whereas detailed FE modelling remains essential for final pre-clinical evaluation.

bioengineering↗

bioRxiv2024

Biomechanical Evaluation of Femoral Neck Fracture Fixation Based on Finite Element Analysis

Pauwels type III fracture, wherein the fracture plane makes an angle of 50{degrees}-70{degrees} with the transverse plane, is the most unstable femoral neck fracture. Although there are various types of internal fixation devices, including Cannulated cancellous screws (CCS), dynamic hip screw (DHS), dynamic hip screw along with anti-rotation screws (DHS+ARS), and a newly introduced femoral neck system (FNS), patients with Pauwels type III fracture often experience implant failure. There was no study investigating the performance of these internal fixators under physiological musculoskeletal loading. The objective of the present study was to compare the biomechanical performance of CCS, DHS, DHS+ARS and FNS under daily physiological activities like normal walking and stair climbing. The unstable Pauwels type III fracture was virtually induced in a composite femur bone model and was fixed with all four internal fixators. Second-order tetrahedral elements were used to develop the FE models. The stresses, strains, and deformations of intact and reconstructed femur and implant components were compared to understand the biomechanical efficacy. FNS showed the highest inferior axial displacement of the femoral head while DHS+ARS exhibited the least inferior axial displacement. Among the four fracture fixation systems, DHS+ARS offered the highest post-fixation stability in terms of fracture gap opening (normal walking: 0.82mm and stair climbing: 0.95mm) and contact sliding, while the performance of single hole locking plated FNS was the worst (normal walking: 2.65mm, stair climbing: 3.72mm). Based on this computational study, DHS+ARS seems to be a better performing system in Pauwels type III fracture fixation.

bioengineering↗

bioRxiv2024

A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique signatures in blood T cell-monocyte complexes during infection

Communication between immune cells through direct contact is a critical feature of immune responses. Here, we developed a novel high-throughput method to study the transcriptome and adaptive immune receptor repertoire of single cells forming complexes without needing bioinformatic deconvolution. We found that T cells and monocytes forming complexes in blood during active tuberculosis (TB) and dengue hold unique transcriptomic signatures indicative of TCR/MCH-II immune synapses. Additionally, T cells in complexes showed enrichment for effector phenotypes, imaging and transcriptomic features of active TCR signaling, and increased immune activity at diagnosis compared to after anti-TB therapy. We also found evidence for bidirectional RNA exchange between T cells and monocytes, since complexes were markedly enriched for "dual-expressing" cells (i.e., co-expressing T cell and monocyte genes). Thus, studying immune cell complexes at a single-cell resolution offers novel perspectives on immune synaptic interactions occurring in blood during infection. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=59 SRC="FIGDIR/small/612103v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@f90023org.highwire.dtl.DTLVardef@178007corg.highwire.dtl.DTLVardef@167e53corg.highwire.dtl.DTLVardef@1faff48_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Biomechanical Evaluation of Temporomandibular Joint Implants Under Complete Mastication Cycle

To ensure the long-term success of temporomandibular joint (TMJ) implants, it is imperative to understand their biomechanical performances. This study aims to compare the biomechanical performance of two stock implants (narrow and standard) under unilateral and bilateral clenching during both osseointegrated and non-osseointegrated conditions. Finite element models of a human mandible were developed from QCT data, with the left TMJ being replaced by the implants. Six clenching tasks were simulated to evaluate stress and strain distributions in the mandible and implants. Ipsilateral clenching produced higher mandibular strains, while contralateral clenching generated larger implant stresses. Furthermore, intercuspal biting was found to have produced the highest strain (1750-1880 {micro}{varepsilon}) and stress ([~]17 MPa) in the mandible. Osseointegration reduced stresses (up to 0.14 MPa) and strains (up to 30 {micro}{varepsilon}) in mandible as well as stresses in mandibular components (up to 48 MPa) and screws (up to 71 MPa). However, during non-osseointegrated conditions, stresses in cortical bone were higher for standard TMJ implant as compared to narrow implant. This suggests possible preference of narrow implant over standard ones.

bioengineering↗

bioRxiv2024

Pervasive neurovascular dysfunction in the ventromedial prefrontal cortex of female depressed suicides with a history of childhood abuse

Exposure to early life adversity (ELA) poses a significant global public health concern, with profound pathophysiological implications for affected individuals. Studies suggest that ELA contributes to endothelial dysfunction, bringing into question the functional integrity of the neurovascular unit in brain regions vulnerable to chronic stress. Despite the importance of the neurovasculature in maintaining normal brain physiology, human neurovascular cells remain poorly characterized, particularly with regard to their contributory role in ELA-associated pathophysiologies. In this study, we present the first comprehensive transcriptomic analysis of intact microvessels isolated from postmortem ventromedial prefrontal cortex samples from adult healthy controls (CTRL) and matched depressed suicides with histories of ELA. Our findings point to substantive differences between men and women, with the latter exhibiting widespread gene expression changes at the neurovascular unit, including the key vascular nodal regulators KLF2 and KLF4, alongside a broad downregulation of immune-related pathways. These results suggest that the neurovascular unit plays a larger role in the neurobiological consequences of ELA in human females.

neuroscience↗

bioRxiv2023

Differential Chromatin Architecture and Risk Variants in Deep Layer Excitatory Neurons and Grey Matter Microglia Contribute to Major Depressive Disorder

Major depressive disorder (MDD) associated genetic variants reside primarily in the non-coding, regulatory genome. Here we investigate genome-wide regulatory differences and putative gene-regulatory effects of disease risk-variants by examining chromatin accessibility combined with single-cell gene-expression profiles in over 200,000 cells from the dorsolateral prefrontal cortex (DLPFC) of 84 individuals with MDD and neurotypical controls. MDD-associated accessibility alterations were prominent in deep-layer excitatory neurons characterized by transcription factor (TF) motif accessibility and binding of nuclear receptor (NR)4A2, an activity-dependent TF responsive to pathological stress. The same neurons were significantly enriched for MDD-associated genetic variation disrupting cis-regulatory sites and TF binding associated with genes involved in synaptic communication. Furthermore, a grey matter microglial cluster exhibited differentially closed chromatin in MDD affecting binding sites bound by TFs known to regulate immune homeostasis. In summary, our study points to specific cell types and regulatory mechanisms whereby genetic variation may increase predisposition to MDD.

genomics↗

bioRxiv2023

Temporal dynamics and genomic programming of plasma cell fates

Affinity-matured plasma cells (PCs) of varying lifespans are generated through a germinal center (GC) response. The developmental dynamics and genomic programs of antigen-specific PC precursors remain to be elucidated. Using a model antigen, we demonstrate biphasic generation of PC precursors, with those generating long-lived bone marrow PCs preferentially produced in the late phase of GC response. Clonal tracing using scRNA-seq+BCR-seq in spleen and bone marrow compartments, coupled with adoptive transfer experiments, reveal a novel PC transition state that gives rise to functionally competent PC precursors. The latter undergo clonal expansion, dependent on inducible expression of TIGIT. We propose a model for the proliferation and programming of precursors of long-lived PCs, based on extended antigen encounters followed by reduced antigen availability.

immunology↗

bioRxiv2023

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation

Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~[1/3] of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.

molecular biology↗

bioRxiv2022

On an Analogy Between Ephaptic Coupling in Large Tracts and Cross-Modal Integration During Illusory Percept

In this paper, the authors report simulations analogous to cross-modal integration which can be modeled by thinking of large (in terms of numbers of axons) axon tracts with distinctly demarcated subsets of axons. In such a tract, when the demarcated regions are separately stimulated they fire in response to the stimulation. Due to extracellular current-based coupling, at a later time, unstimulated axons also begin to cross-talk. The simulation graphical result, though on a faster time scale, is analogous to the multi-channel MEG recordings of "AV-(A+V)" obtained by Shams et. al. When the coupling parameter is weakened, this cross-talk disappears. In Shams et. al., the appearance and disappearance of cross-talk are related to the perception of an illusory flash by the subject. Our extrapolated conclusion is that ephaptic coupling might be a part of the mechanism for cross-talk between brain regions mediating, say, audio and visual-processing. We also study noisy ephaptic coupling and additionally do a comparative study with the Kuramoto model, which yields insight into the exact and detailed mechanism of ephaptic synchronization.

neuroscience↗

bioRxiv2022

Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes

Major depressive disorder (MDD) is a common, heterogenous, and potentially serious psychiatric illness. Diverse brain cell types have been implicated in MDD etiology. Significant sexual differences exist in MDD clinical presentation and outcome, and recent evidence suggests different molecular bases for male and female MDD. We evaluated over 160,000 nuclei from 71 female and male donors, leveraging new and pre-existing single-nucleus RNA-sequencing data from the dorsolateral prefrontal cortex. Cell type specific transcriptome-wide threshold-free MDD-associated gene expression patterns were similar between the sexes, but significant differentially expressed genes (DEGs) diverged. Among 7 broad cell types and 41 clusters evaluated, microglia and parvalbumin interneurons contributed the most DEGs in females, while deep layer excitatory neurons, astrocytes, and oligodendrocyte precursors were the major contributors in males. Further, the Mic1 cluster with 38% of female DEGs and the ExN10_L46 cluster with 53% of male DEGs, stood out in the meta-analysis of both sexes.

neuroscience↗