Biology subjects

Ahmadi, S.

Publications and source records attributed to Ahmadi, S..

11 recordsLinked to original sources

bioRxiv2026

Hyperexcitable but seizure-free: hippocampal network dysfunction in a Wolfram syndrome model

Wolfram syndrome (WS) is a rare, life-limiting progressive neurodegenerative disorder caused by pathogenic variants in the WFS1 gene. It is a prototype endoplasmic reticulum (ER) stress disorder, and the mechanisms underlying neurological phenotypes in WS remain incompletely understood. Although WFS1 protein is abundant in the hippocampus, the role of this region in WS remains relatively understudied. Here we characterize hippocampal function across scales in mice carrying a patient orthologous Wfs1 variant (p.W542*) on both alleles. Male mutants lose excitatory synapses, and dissociated hippocampal neurons are markedly hyperexcitable yet generate no increase in network bursting and no shift in network criticality, indicating that their additional firing is not recruited into coordinated population activity. This finding translates in vivo wherein intracranial electroencephalogram (EEG) recordings show no epileptiform activity or seizures in either sex, with no hippocampal astrogliosis, alongside a male-specific reduction in hippocampal low-gamma power. Additionally, EEG demonstrates a sex-specific disruption of sleep, which parallels a sex-divergent synaptic phenotype. Mutant male mice show impaired hippocampus-dependent fear memory and reduced voluntary motor activity. Taken together, we propose that cellular hyperexcitability in the WS hippocampus does not translate into increased network bursting, potentially due to disproportionate loss of excitatory synapses. This dissociation may provide a functional substrate for the neurological features of WS.

neuroscience↗

bioRxiv2026

Head-level lesion-symptom mapping of picture naming in vision-language models

Researchers in artificial intelligence increasingly intervene on language models to study how their functions are organized, silencing weights and attention components in ways reminiscent of the brain lesions long used to map language in post-stroke aphasia. Under this program of mechanistic interpretability, a common move is to ablate an attention head and read the resulting drop in a behavior as evidence that the head implements it. How much that move can establish about where a behavior is computed remains unclear, because a head whose removal disrupts a behavior is necessary for it but need not be the site where it is computed. We examined this question for the picture naming task, taking the loss of naming (anomia) that defines aphasia as the behavior of interest. Across six vision-language models, spanning three language backbones and a range of parameter scales, we ablated each attention head in turn during single-word picture naming and measured accuracy before and after. The degree of localization varied widely across models. In LLaVA-1.6-Vicuna-13B, a single early head (layer 0, head 20) was necessary: removing it alone reduced naming accuracy from 0.99 to 0.006. The same head was not sufficient, because retaining it while ablating the other 1{,}599 heads also produced 0\% accuracy. Two Mistral-backbone models (LLaVA-Mistral-7B and Idefics2-8B) had no critical head. An early-layer dependence was present in every model but varied in strength, whereas dependence on any single head ranged from dominant to absent. Within Qwen2.5-VL, a dominant head was present in the 7B model but not the 3B model, indicating that this concentration emerged with scale rather than being fixed across a model family, and it was not explained by attention type. These results show that ablating the head whose removal disrupts naming does not establish that the head computes the behavior, that the result generalizes across models, or that the behavior localizes to a head at all.

neuroscience↗

bioRxiv2024

An epilepsy-associated CILK1 variant compromises KATNIP regulation and impairs primary cilia and Hedgehog signaling

Mutations in human CILK1 (ciliogenesis associated kinase 1) are linked to ciliopathies and epilepsy. Homozygous point and nonsense mutations that extinguish kinase activity impair primary cilia function, whereas mutations outside the kinase domain are not well understood. Here, we produced a knock-in mouse equivalent of the human CILK1 A615T variant identified in juvenile myoclonic epilepsy (JME). This residue is in the C-terminal region of CILK1 separate from the kinase domain. Mouse embryo fibroblasts (MEF) with either heterozygous or homozygous A612T mutant alleles exhibited a higher ciliation rate, shorter individual cilia and up-regulation of ciliary Hedgehog signaling. Thus, a single A612T mutant allele was sufficient to impair primary cilia and ciliary signaling in MEFs. Gene expression profiles of wild type versus mutant MEFs revealed profound changes in cilia-related molecular functions and biological processes. CILK1 A615T mutant protein was not increased to the same level as the wild type protein when co-expressed with scaffold protein KATNIP (katanin-interacting protein). Our data show that KATNIP regulation of a JME-associated single residue variant of CILK1 is compromised and this impairs the maintenance of primary cilia and Hedgehog signaling.

cell biology↗

bioRxiv2023

Phage display assisted discovery of a pH-dependent anti-alpha-cobratoxin antibody from a natural variable domain library

Recycling antibodies can bind to their target antigen at neutral pH in the blood stream and release them upon endocytosis when pH levels drop, allowing the antibodies to be recycled into circulation via FcRn-mediated pathway, while the antigens undergo lysosomal degradation. This enables recycling antibodies to achieve the same therapeutic effect at lower doses than their non-recyclable counterparts. The development of such antibodies is typically achieved by histidine doping of the variable regions of specific antibodies or by performing in vitro antibody selection campaigns utilizing histidine doped libraries. While often successful, these strategies may introduce sequence liabilities, as they often involve mutations that may render the resultant antibodies to be non-natural. Here, we present a methodology that employs a naive antibody phage display library, consisting of natural variable domains, to discover antibodies that bind -cobratoxin from the venom of Naja kaouthia in a pH-dependent manner. Upon screening of the discovered antibodies with immunoassays and bio-layer interferometry, a pH-dependent antibody was discovered that exhibits an 8-fold higher dissociation rate at pH 5.5 than 7.4. Interestingly, the variable domains of the pH-dependent antibody were found to be entirely devoid of histidines, demonstrating that pH-dependency may not always be driven by this amino acid. Further, given the high diversity available in a naive antibody library, the methodology presented here can likely be applied to discover pH-dependent antibodies against different targets ab initio without the need of histidine doping. For broader audienceHere, we present the discovery of an -cobratoxin targeting pH-dependent antibody, with a variable region devoid of histidines, from a naive antibody library with natural variable domains. Our findings suggest that the commonly taken approach of histidine doping to find pH-dependent antibodies may not always be required, and thus offer an alternative strategy for the discovery of pH-dependent antibodies.

bioengineering↗

bioRxiv2023

Proteomic Investigation of Neural Stem Cell to Oligodendrocyte Precursor Cell Differentiation Reveals Phosphorylation-Dependent Dclk1 Processing

Oligodendrocytes are generated via a two-step mechanism from pluripotent neural stem cells (NSCs): after differentiation of NSCs to oligodendrocyte precursor/NG2 cells (OPCs), they further develop into mature oligodendrocytes. The first step of this differentiation process is only incompletely understood. In this study, we utilized the neurosphere assay to investigate NSC to OPC differentiation in a time course-dependent manner by mass spectrometry-based (phospho-) proteomics. We identify double cortin like kinase 1 (Dclk1) as one of the most prominently regulated proteins in both datasets, and show that it undergoes a gradual transition between its short/long isoform during NSC to OPC differentiation. This is regulated by phosphorylation of its SP-rich region, resulting in inhibition of proteolytic Dclk1 long cleavage, and therefore Dclk1 short generation. Through interactome analyses of different Dclk1 isoforms by proximity biotinylation, we characterize their individual putative interaction partners and substrates.

cell biology↗

bioRxiv2022

Distinct roles of dentate gyrus and medial entorhinal cortex inputs for phase precession and temporal correlations in hippocampal CA3 place cells

The hippocampal CA3 subregion is a densely connected recurrent circuit that supports memory consolidation and retrieval by generating and storing sequential neuronal activity patterns that reflect recent experience. While theta phase precession is thought to be critical for generating sequential activity during memory encoding, the circuit mechanisms that support this computation across hippocampal subregions are unknown. By analyzing CA3 network activity in the absence of each of its theta modulated excitatory inputs, we show necessary and unique contributions of the dentate gyrus (DG) and the medial entorhinal cortex (MEC) to phase precession. DG inputs are essential for generating the preferential spiking of CA3 cells during late theta phases and for organizing the temporal order of neuronal firing, while MEC inputs modulate the general precision of phase precession. A computational model that accounts for the empirical findings suggests that DG inputs affect the phase and MEC inputs affect the amplitude of inhibitory subnetworks. Our results thus identify a novel and unique functional role of the DG for the generation of sequence coding in the CA3 recurrent circuit.

neuroscience↗

bioRxiv2021

High-throughput functional analysis of CFTR and other apically localized channels in iPSC derived intestinal organoids

Induced Pluripotent Stem Cells (iPSCs) can be differentiated into epithelial organoids that recapitulate the relevant context for CFTR and enable testing of therapies targeting Cystic Fibrosis (CF)-causing mutant proteins. However, to date, CF-iPSC-derived organoids have only been used to study pharmacological modulation of mutant CFTR channel activity and not the activity of other disease relevant membrane protein constituents. In the current work, we describe a high-throughput, fluorescence-based assay of CFTR channel activity in iPSC-derived intestinal organoids and describe how this method can be adapted to study other apical membrane proteins. In these proof-of-concept studies, we show how this fluorescence-based assay of apical membrane potential can be employed to study CFTR and ENaC channels and an electrogenic acid transporter in the same iPSC-derived intestinal tissue. This multiparameter phenotypic platform promises to expand CF therapy discovery to include strategies to target multiple determinants of epithelial fluid transport.

molecular biology↗

bioRxiv2021

Optimal Reinforcement Learning with Asymmetric Updating in Volatile Environments: a Simulation Study

AO_SCPLOWBSTRACTC_SCPLOWThe ability to predict the future is essential for decision-making and interaction with the environment to avoid punishment and gain reward. Reinforcement learning algorithms provide a normative way for interactive learning, especially in volatile environments. The optimal strategy for the classic reinforcement learning model is to increase the learning rate as volatility increases. Inspired by optimistic bias in humans, an alternative reinforcement learning model has been developed by adding a punishment learning rate to the classic reinforcement learning model. In this study, we aim to 1) compare the performance of these two models in interaction with different environments, and 2) find optimal parameters for the models. Our simulations indicate that having two different learning rates for rewards and punishments increases performance in a volatile environment. Investigation of the optimal parameters shows that in almost all environments, having a higher reward learning rate compared to the punishment learning rate is beneficial for achieving higher performance which in this case is the accumulation of more rewards. Our results suggest that to achieve high performance, we need a shorter memory window for recent rewards and a longer memory window for punishments. This is consistent with optimistic bias in human behavior.

neuroscience↗

bioRxiv2020

Combination of arsenic trioxide epigallocatechin-3-gallate and Resveratrol synergistically suppresses the growth and invasion in Brain tumor cell lines

The glioblastoma multiform has some properties including rapid growth, invasion, treatment resistance, and recurrence. Therefore, new therapies need to be developed that can be approved for using in patients. The previous study showed Arsenic Trioxide inhibits aggressive behavior in glioblastoma cells. Also, (-)-epigallocatechin-3-gallate prevents cellular proliferation, and invasion in multiple glioma cells. Resveratrol decreases cellular proliferation, induces cell death, and impaired the invasiveness of glioma cells. Combination therapy to inhibit cancer cells may have important clinical implications. Therefore, to assess the combination therapy of 2M Arsenic trioxide, 100M EGCG, and 100M Resveratrol, we examined the metabolic activity, colony formation, media pH, cell proliferation, Caspase 3 activity, and gene expression analysis of BCL2, Caspase 3, MMP2, MMP9, CA9, u-PA, u-PAR, and Cathepsin B genes in apoptosis and invasion by both quantitative PCR experiments and Western blot assay. Systems biology tools also were used to obtain, the related network, involved pathways, and identifying the key genes in our selected criteria. The results of the study confirmed that the combined therapy prevents cell proliferation and induces of apoptosis in the Brain tumor cell lines including: U87-MG, A-172, and 1321N1. Furthermore, over-expression of caspase-3 and down-regulation of BCL-2, MMP-2, and MMP-9 confirmed that combination therapy leads to induces apoptosis and decreases invasion. Nevertheless, the lowering of pharmacological doses and improving therapeutic efficacy through combination therapy may provide advantages to treat resistance cancer cells with lower side effects. Finally, the results might suggest new modality for Glioblastoma treatment.

cancer biology↗

bioRxiv2020

Phosphosite T674A mutation in kinesin family member 3A fails to reproduce tissue and ciliary defects characteristic of CILK1 loss of function

Background Kinesin family member 3A (KIF3A) is a molecular motor protein in the heterotrimeric kinesin-2 complex that drives anterograde intraflagellar transport. This process plays a pivotal role in both biogenesis and maintenance of the primary cilium that supports tissue development. Ciliogenesis associated kinase 1 (CILK1) phosphorylates human KIF3A at Thr672. CILK1 loss of function causes ciliopathies that manifest profound and multiplex developmental defects, including polydactyly, shortened and hypoplastic bones and alveoli airspace deficiency, leading to perinatal lethality. Prior studies have raised the hypothesis that CILK1 phosphorylation of KIF3A is critical for its regulation of organ development.Results We produced a mouse model with phosphorylation site Thr674 in mouse Kif3a mutated to Ala. Kif3a T674A homozygotes are viable and exhibit no skeletal abnormalities, and only mildly reduced airspace in alveoli. Mouse embryonic fibroblasts carrying Kif3a T674A mutation show a normal rate of ciliation and a moderate increase in cilia length.Conclusion These results indicate that eliminating Kif3a Thr674 phosphorylation by CILK1 is insufficient to reproduce the severe developmental defects in ciliopathies caused by Cilk1 loss of function. This suggests KIF3A phosphorylation by CILK1 is not essential for tissue development and other substrates are involved in Cilk1 ciliopathies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2020

The Landscape of Precision Cancer Combination Therapy: A Single-Cell Perspective

The availability of single-cell transcriptomics data opens new opportunities for rational design of combination cancer treatments. Mining such data, we employed combinatorial optimization techniques to explore the landscape of optimal combination therapies in solid tumors including brain, head and neck, melanoma, lung, breast and colon cancers. We assume that each individual therapy can target any one of 1269 genes encoding cell surface receptors, which may be targets of CAR-T, conjugated antibodies or coated nanoparticle therapies. As a baseline case, we studied the killing of at least 80% of the tumor cells while sparing more than 90% of the non-tumor cells in each patient, as a putative regimen. We find that in most cancer types, personalized combinations composed of at most four targets are then sufficient. However, the number of distinct targets that one would need to assemble to treat all patients in a cohort accordingly would be around 10 in most cases. Further requiring that the target genes be also lowly expressed in healthy tissues uncovers qualitatively similar trends. However, as one asks for more stringent and selective killing beyond the baseline regimen we focused on, we find that the number of targets needed rises rapidly. Emerging individual promising receptor targets include PTPRZ1, which is frequently found in the optimal combinations for brain and head and neck cancers, and EGFR, a recurring target in multiple tumor types. In sum, this systematic single-cell based characterization of the landscape of combinatorial receptor-mediated cancer treatments establishes first of their kind estimates on the number of targets needed, identifying promising ones for future development.

bioinformatics↗