Biology subjects

Amiri, S.

Publications and source records attributed to Amiri, S..

8 recordsLinked to original sources

bioRxiv2025

Multi-cohort, multi-sequence harmonisation for cerebrovascular brain age

IntroductionHigher brain-predicted age gaps (BAG), based on anatomical brain scans, have been associated with cognitive decline among elderly participants. Adding a cerebrovascular component, in the form of arterial spin labelling (ASL) perfusion MRI, can improve the BAG predictions and potentially increase sensitivity to cardiovascular health, a contributor to brain ageing and cognitive decline. ASL acquisition differences are likely to influence brain age estimations, and data harmonisation becomes indispensable for multi-cohort brain age studies including ASL. In this multi-cohort, multi-sequence study, we investigate harmonisation methods to improve the generalisability of cerebrovascular brain age. MethodsA multi-study dataset of 2608 participants was used, comprising structural T1-weighted (T1w), FLAIR, and ASL 3T MRI data. The single scanner training dataset consisted of 806 healthy participants, age 50{+/-}17, 18-95 years. The testing datasets comprised four cohorts (n=1802, age 67{+/-}8, 37-90 years). Image features included grey and white matter (GM/WM) volumes (T1w), WM hyperintensity volumes and counts (FLAIR), and ASL cerebral blood flow (CBF) and its spatial coefficient of variation (sCoV). Feature harmonisation was performed using NeuroComBat, CovBat, NeuroHarmonize, OPNested ComBat, AutoComBat, and RELIEF. ASL-only and T1w+FLAIR+ASL brain age models were trained using ExtraTrees. Model performance was assessed through the mean absolute error (MAE) and mean BAG. ResultsASL feature differences between cohorts decreased after harmonisation for all methods (p<0.05), mostly for RELIEF. Negative associations between age and GM CBF (b=-0.37, R2=0.13, unharmonised) increased after harmonisation for all methods (b<-0.42, R2>0.12) but weakened for RELIEF (b=-0.28, R2=0.14). In the ASL-only model, MAE improved for all harmonisation methods from 11.1{+/-}7.5 years to less than 8.8{+/-}6.2 years (p<0.001), while BAGs changed from 0.6{+/-}13.4 years to less than -1.03{+/-}7.92 years (p<0.001). For T1w+FLAIR+ASL, MAE (5.9{+/-}4.6 years, unharmonised) increased for all harmonisation methods non-significantly to above 6.0{+/-}4.9 years (p>0.42) and significantly for RELIEF (6.4{+/-}5.2 years, p=0.02), while BAGs non-significantly differed from -1.6{+/-}7.3 years to between -1.3{+/-}4.7 and -2.0{+/-}8.0 years (p>0.82). In general, the ASL-specific parameter harmonisation method AutoComBat performed nominally best. DiscussionHarmonisation of ASL features improves feature consistency between studies and also improves brain age estimations when only ASL features are used. ASL-specific parameter harmonisation methods perform nominally better than basic mean and scale adjustment or latent-factor approaches, suggesting that ASL acquisition parameters should be considered when harmonising ASL data. Although multi-modal brain age estimations were improved less by ASL-only harmonisation, possibly due to weaker associations between age and ASL features compared to T1w features feature importance, studies investigating pathological ASL-feature distributions might still benefit from harmonisation. These findings advocate for ASL-parameter specific harmonisation to explore associations between cardiovascular risk factors, brain ageing, and cognitive decline using multi-cohort ASL and cerebrovascular brain age studies.

neuroscience↗

bioRxiv2025

Antimuscarinic drugs exert β-arrestin-biased agonism at the muscarinic acetylcholine type 1 receptor

Previous studies indicate that both pirenzepine (PZ), a selective orthosteric muscarinic acetylcholine type 1 receptor (M1R) antagonist, and muscarinic toxin 7 (MT7), a negative M1R allosteric modulator (NAM), act via M1R to promote neuritogenesis in cultured adult rodent primary dorsal root ganglia (DRG) sensory neurons, in part, through {beta}-arrestin-dependent activation of extracellular signal-regulated protein kinase 1/2 (ERK1/2). Furthermore, these antagonists reverse nerve degeneration in a variety of rodent models of peripheral neuropathy through multiple complementary pathways. To understand the therapeutic effects and mechanism of M1R antagonist-induced ERK1/2 phosphorylation, we tested the hypothesis that PZ and MT7 possess {beta}-arrestin-biased agonism at M1R to drive activation of ERK and enhance neurite outgrowth. Treatment for up to 30 min with PZ and MT7 dose-dependently recruited {beta}-arrestin2 to M1R (analyzed using nano-BRET) and increased ERK phosphorylation in both HEK293 cells and DRG neurons. DRG neurons of different sub-types express M1R, and ERK activation by MT7 was only observed in M1R-positive neurons. These novel pharmacological effects occurred in the absence of activation of G protein signaling or receptor internalization. PZ phosphorylated M1R at six specific serine/threonine residues (T230, S251, T254, S321, T354, S356) of intracellular loop 3 (ICL3) and deletion mutation of these sites suppressed PZ and MT7 induction of {beta}-arrestin binding to M1R and inhibited ERK activation. With regard to PZ signaling, alanine substitution at S251 and T254 was sufficient to impede {beta}-arrestin binding and ERK activation. {beta}-arrestin-biased activity of PZ and MT7 involved the mobilization of casein kinase 2 (CK2) and this occurred in the absence of Gq or G protein receptor kinase (GRK) activity. Pharmacological or siRNA-based inhibition of CK2 blocked PZ-induction of {beta}-arrestin association, ERK activation and neurite outgrowth in DRG neurons. In conclusion, PZ/MT7 activated M1R toward the {beta}-arrestin signaling pathway in both HEK293 cells and DRG neurons to augment ERK activation and neurite outgrowth via engagement of CK2. One-sentence summaryAntimuscarinic drugs act as {beta}-arrestin-biased agonists via casein kinase 2 activation to promote ERK1/2 phosphorylation and neurite outgrowth O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/649213v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1bb8da7org.highwire.dtl.DTLVardef@510218org.highwire.dtl.DTLVardef@608d69org.highwire.dtl.DTLVardef@e40d9e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO Schematic presentation of the effect of muscarinic ligands at M1R associated signaling pathway. (A) Muscarine/carbachol acts as a balanced ligand by engaging both Gq and -arrestin signaling pathways and treatment with pirenzepine/MT7 blocks these effects. (B) Pirenzepine/MT7 acts as a -arrestin biased ligand by 1) phosphorylating of ICL3 region of M1R via CK2 (but not GRKs), 2) no activation of G protein signaling, 3) recruitment of -arrestin 2 and 4) ERK1/2 activation leading to neurite outgrowth in DRG sensory neurons. This figure was generated by BioRender under license number EK285MUOPQ. C_FIG

pharmacology and toxicology↗

bioRxiv2024

The nuclear lamin network passively responds to both active or passive cell movement through confinements

Physical models of cell motility rely mostly on cytoskeletal dynamical assembly. However, when cells move through the complex 3D environment of living tissues, they have to squeeze their nucleus that is stiffer than the rest of the cell. The lamin network, organised as a shell right underneath the nuclear membrane, contributes to the nuclear integrity and stiffness. Yet, its response during squeezed cell motility has never been fully characterised. As a result, up to now, the interpretations on the lamin response mechanism are mainly speculative. Here, we quantitatively map the lamin A/C distribution in both a microfluidic migration device and a microfluidic aspiration device. In the first case, the cell is actively involved in translocating the nucleus through the constriction, while in the second case, the cell behaves as a passive object that is pushed through the constriction by an external pressure. Using a quantitative description of the lamin shell response based on mass conservation arguments applied on the fluorescence signal of lamin, we show that in both cases of migration and aspiration, the response of the lamin network is passive. In this way, our results not only further elucidate the lamin response mechanism, but also allow to distinguish this passive deformation response from other active responses that may occur when the nucleus is squeezed through constrictions.

biophysics↗

bioRxiv2024

Ensemblex: an accuracy-weighted ensemble genetic demultiplexing framework for population-scale scRNAseq sample pooling

Multiplexing samples from distinct individuals prior to sequencing is a promising step toward achieving population-scale single-cell RNA sequencing by reducing the restrictive costs of the technology. Individual genetic demultiplexing tools resolve the donor-of-origin identity of pooled cells using natural genetic variation but present diminished accuracy on highly multiplexed experiments, impeding the analytic potential of the dataset. In response, we introduce Ensemblex: an accuracy-weighted, ensemble genetic demultiplexing framework that integrates four distinct algorithms to identify the most probable subject labels. Using computationally and experimentally pooled samples, we demonstrate Ensemblexs superior accuracy and illustrate the implications of robust demultiplexing on biological analyses.

genomics↗

bioRxiv2024

T2R14 mediated antimicrobial responses through interactions with CFTR

Bitter taste receptors (T2Rs), are a subset of G protein-coupled receptors (GPCRs) that play a key role in responding to microbial presence at epithelial surfaces. In epithelia, the activities of ion channels and transporters, and of T2Rs, mutually affect each other. The normal function of one such anion channel, cystic fibrosis transmembrane conductance regulator (CFTR), is essential for the maintenance of healthy epithelia, not just in the respiratory but in the digestive and reproductive system as well. Based on evidence that T2R14 activity is affected upon mutations in CFTR, we explored the possibility that T2R14 and CFTR directly interact in cell membranes. The biophysical interaction between these proteins was mapped to specific regions of the CFTR, and was dependent on agonist stimulation of T2R14. Further, T2R14 was found to couple to Gq, in addition to the canonical Gi, in response to bacterial and fungal quorum sensing molecules. Whether the interaction with CFTR affects T2R14 driven responses to microbial signals is under investigation.

biochemistry↗

bioRxiv2023

ScRNAbox: Empowering Single-Cell RNA Sequencing on High Performance Computing Systems

MotivationSingle-cell RNA sequencing (scRNAseq) offers powerful insights, but the surge in sample sizes demands more computational power than local workstations can provide. Consequently, high-performance computing (HPC) systems have become imperative. Existing web apps designed to analyze scRNAseq data lack scalability and integration capabilities, while analysis packages demand coding expertise, hindering accessibility. ResultsIn response, we introduce scRNAbox, an innovative scRNAseq analysis pipeline meticulously crafted for HPC systems. This end-to-end solution, executed via the SLURM workload manager, efficiently processes raw data from standard and Hashtag samples. It incorporates quality control filtering, sample integration, clustering, cluster annotation tools, and facilitates cell type-specific differential gene expression analysis between two groups. ImplementationOpen-source code and comprehensive usage instructions with examples are available at https://neurobioinfo.github.io/scrnabox/site/. Supplementary InformationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures

SummaryMitochondrial dysfunction is implicated in a wide array of human diseases ranging from neurodegenerative disorders to cardiovascular defects. The coordinated localization and import of proteins into mitochondria are essential processes that ensure mitochondrial homeostasis and consequently cell survival. The localization and import of most mitochondrial proteins are driven by N-terminal mitochondrial targeting sequences (MTSs), which interact with import machinery and are removed by the mitochondrial processing peptidase (MPP). The recent discovery of internal MTSs - those which are distributed throughout a protein and act as import regulators or secondary MPP cleavage sites - has expanded the role of both MTSs and MPP beyond conventional N-terminal regulatory pathways. Still, the global mutational landscape of MTSs remains poorly characterized, both from genetic and structural perspectives. To this end, we have integrated a variety of tools into one harmonized R/Shiny database called MTSviewer (https://neurobioinfo.github.io/MTSvieweR/) which combines MTS predictions, cleavage sites, genetic variants, pathogenicity predictions, and N-terminomics data with structural visualization using AlphaFold models of human and yeast mitochondrial proteomes. Availability and ImplementationMTSviewer is freely available on the web at https://neurobioinfo.github.io/MTSvieweR/. Source code is available at https://github.com/neurobioinfo/MTSvieweR. Contacteanfrancois.trempe@mcgill.ca; sali.farhan@mcgill.ca

bioinformatics↗

bioRxiv2020

Tissue pressure and cell traction compensate to drive robust aggregate spreading

In liquid droplets, the balance of interfacial energies and substrate elasticity determines the shape of the droplet and the dynamics of wetting. In living cells, interfacial energies are not constant, but adapt to the mechanics of their environment. As a result, the forces driving the dynamics of wetting for cells and tissues are unclear and may be context specific. In this work, using a combination of experimental measurements and modeling, we show the surface tension of cell aggregates, as models of active liquid droplets, depends upon the size of the aggregate and the magnitude of applied load, which alters the wetting dynamics. Upon wetting rigid substrates, traction stresses are elevated at the boundary, and tension drives forward motion. By contrast, upon wetting compliant substrates, traction forces are attenuated, yet wetting occurs at a comparable rate. In this case, capillary forces at the contact line are elevated and aggregate surface tension contributes to strong outward, pressure-driven cellular flows. Thus, cell aggregates adapt to the mechanics of their environments, using pressure and traction as compensatory mechanisms to drive robust wetting.

biophysics↗