Biology subjects

Zaman, M.

Publications and source records attributed to Zaman, M..

14 recordsLinked to original sources

bioRxiv2025

Drug Repurposing Screen Identifies an HRI Activating Compound that Promotes Adaptive Mitochondrial Remodeling in MFN2-deficient Cells

Pathogenic variants in the mitochondrial outer membrane GTPase MFN2 cause the peripheral neuropathy Charcot-Marie-Tooth Type 2A (CMT2A). These mutations disrupt MFN2-dependent regulation of diverse aspects of mitochondrial biology including organelle morphology, motility, mitochondrial-endoplasmic reticulum (ER) contacts (MERCs), and respiratory chain activity. However, no therapies currently exist to mitigate the mitochondrial dysfunction linked to genetic deficiencies in MFN2. Herein, we performed a drug repurposing screen to identify compounds that selectively activate the integrated stress response (ISR) - the predominant stress-responsive signaling pathway responsible for regulating mitochondrial morphology and function. This screen identified the compounds parogrelil and MBX-2982 as potent and selective activators of the ISR through the OMA1-DELE1-HRI signaling axis. We show that treatment with these compounds promotes adaptive, ISR-dependent remodeling of mitochondrial morphology and protects mitochondria against genetic and chemical insults. Moreover, we show that pharmacologic ISR activation afforded by parogrelil restores mitochondrial tubular morphology, promotes mitochondrial motility, rescues MERCs, and enhances mitochondrial respiration in MFN2-deficient cells. These results demonstrate the potential for pharmacologic HRI activation as a viable strategy to mitigate mitochondrial dysfunction in CMT2A and other pathologies associated with MFN2 deficiency.

cell biology↗

bioRxiv2025

Midkine Attenuates Aβ Fibril Assembly and Amyloid Plaque Formation

Proteomic profiling of Alzheimers disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with A{beta} since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates A{beta} assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both A{beta}40 and A{beta}42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdk gene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and detergent-insoluble proteome in these mouse models indicates significant accumulation of A{beta} and A{beta}-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimers disease.

biochemistry↗

bioRxiv2025

Drug repurposing reveals Posaconazole as a CYP11A1 inhibitor enhancing anti-tumour immunity

Steroid hormones regulate cell physiology and immune function, with dysregulated steroidogenesis promoting cancer progression by supporting tumour growth and suppressing anti-tumour immunity. Targeting CYP11A1, the first and rate-limiting enzyme in steroid biosynthesis, has shown promise in cancer therapy, but safe and effective inhibitors remain an unmet need. Undertaking in silico structure-based drug repurposing approach, we found Posaconazole as an inhibitor of CYP11A1. The docking pose analysis showed that Posaconazole can form multiple hydrogen bonds and hydrophobic interactions with the key residues at the binding site and the cofactor, stabilising the protein-ligand complex. We validated its inhibition efficiency in cell-based assays. In a mouse model of lung metastasis, we demonstrated that Posaconazole restricts metastatic cancer growth by stimulating anti-tumour immunity. These findings highlight Posaconazoles potential as a research tool to study steroidogenesis and as a candidate for further preclinical and clinical evaluation in pathological conditions associated with local steroid production, such as steroidogenic tumours.

immunology↗

bioRxiv2024

Human-mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome

Murine models of Alzheimers disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome (n > 10,000 for both) across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata, and prioritized novel components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Determining the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including A{beta}-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identify potential new targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.

biochemistry↗

bioRxiv2024

Pharmacologic Activation of Integrated Stress Response Kinases Inhibits Pathologic Mitochondrial Fragmentation

Excessive mitochondrial fragmentation is associated with the pathologic mitochondrial dysfunction implicated in the pathogenesis of etiologically-diverse diseases, including many neurodegenerative disorders. The integrated stress response (ISR) - comprising the four eIF2 kinases PERK, GCN2, PKR, and HRI - is a prominent stress-responsive signaling pathway that regulates mitochondrial morphology and function in response to diverse types of pathologic insult. This suggests that pharmacologic activation of the ISR represents a potential strategy to mitigate pathologic mitochondrial fragmentation associated with human disease. Here, we show that pharmacologic activation of the ISR kinases HRI or GCN2 promotes adaptive mitochondrial elongation and prevents mitochondrial fragmentation induced by the calcium ionophore ionomycin. Further, we show that pharmacologic activation of the ISR reduces mitochondrial fragmentation and restores basal mitochondrial morphology in patient fibroblasts expressing the pathogenic D414V variant of the pro-fusion mitochondrial GTPase MFN2 associated with neurological dysfunctions including ataxia, optic atrophy, and sensorineural hearing loss. These results identify pharmacologic activation of ISR kinases as a potential strategy to prevent pathologic mitochondrial fragmentation induced by disease-relevant chemical and genetic insults, further motivating the pursuit of highly selective ISR kinase-activating compounds as a therapeutic strategy to mitigate mitochondrial dysfunction implicated in diverse human diseases.

cell biology↗

bioRxiv2023

Wearable Disposable Electrotherapy

We design and validate a novel electrotherapy platform without electronic components, using printed abundant, environmentally benign materials. Whereas existing electrotherapy devices use an independent power source and electronics to generate and control stimulation currents, our design eliminates the need for these components. Device production relies only on scalable additive manufacturing and common materials, minimizing cost and environmental impact. The disposable single-use platform (as discreet as adhesive bandages) is activated simply by placement on the body. A prescribed electrotherapy discharge is regulated by a flexible 3D electrochemical architecture tailored to each application by a novel operational theory. The single-dose usability of this platform is a categorical shift from existing approaches with durable equipment that require programming and assembly to disposable electrodes for each use. Our Wearable Disposable Electrotherapy technology can be distributed like pharmacotherapy, with indications spanning neuromodulation of brain disorders, wound healing, transcutaneous drug delivery, bioelectronic medicine, and aesthetics.

bioengineering↗

bioRxiv2023

Collection of Non Timber Forest Products (NTFPs) and their contribution to sustainable rural livelihoods in selected areas around Ayubia National Park, Pakistan

This study shows the Collection of Non Timber Forest Products (NTFPs) and their contribution to sustainable rural livelihoods in selected areas around Ayubia National Park, Pakistan. Forests are an important component for daily life of rural residents living near forested areas. A protected area is a geographically designated area for the purpose of biological conservation. Ayubia National Park (ANP) is a protected area in KPK, Pakistan that was designated with the purpose of management and preservation of nature. Non Timber Forest Products (NTFPs) have been defined as "All biological materials, excluding timber, which are extracted from forests for human use". NTFPs play an important role in income generation for indigenous people. Malaach Village, Pasala Village and Khanuspur Town present around ANP were selected study areas. Purposive sampling was used for selection of study areas. Quantitative research was done. Field visits were done for Questionnaire survey. 50 questionnaires were filled from each selected village/town and results were analysed using SPSS. Cross tabulation was done and Chi Square test was applied. It was found that Wild Vegetables, Wild Fruits, Medicinal Plants and Mushrooms are collected from forests in and around ANP by indigenous people. Chi square results showed significant relationship between gender and collection of NTFPs. Poverty is found to be the main reason for collecting NTFPs. Contribution of NTFPs to annual income of people is mostly less than 20% but this contribution is also 21%-40% and even 41%-60% for few people. ANP should be managed properly to inhibit the collection of NTFPs within the park. Indigenous people should cooperate in sustainable collection and use of NTFPs. The role of NTFPs to livelihoods in and around ANP are clearly understood by study and will be useful in the awareness and implementation of the conservation practices in the Ayubia National Park.

ecology↗

bioRxiv2023

BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair

HighlightsO_LIGap suppression requires BRCA2 C-terminal RAD51 binding in mouse and human cells C_LIO_LIBrca2 heterozygosity in mice results in fork protection and gap suppression defects C_LIO_LIGap suppression mitigates sensitivity to hmdU, but only when HDR is unperturbed C_LIO_LIHDR deficiency is the primary driver of chemotherapeutic sensitivity C_LI eTOC blurbLim et al. report that gap suppression as well as fork protection require BRCA2 stabilization of RAD51 filaments in human and mouse cells but have minimal impact on genome integrity, oncogenesis, and drug resistance. BRCA2 suppression of PRIMPOL-mediated replication gaps confers resistance to the nucleotide hmdU, incorporation of which leads to cytotoxic abasic sites.This effect is diminished when HDR is abrogated. SummaryTumor suppressor BRCA2 functions in homology-directed repair (HDR), protection of stalled replication forks, and suppression of replicative gaps. The relative contributions of these pathways to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for both fork protection and gap suppression, but not HDR. Loss of fork protection and gap suppression do not compromise genome instability or shorten tumor latency in mice or cause replication stress in human mammary cells. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection and gap suppression defects are also observed in Brca2 heterozygous mouse cells, likely due to reduced RAD51 stabilization at stalled forks and gaps. Gaps arise from PRIMPOL activity, which is associated with sensitivity to 5-hydroxymethyl-2-deoxyuridine due to the formation of abasic sites by SMUG1 glycosylase and is exacerbated by poly(ADP-ribose) polymerase inhibition. However, HDR deficiency ultimately modulates sensitivity to chemotherapeutics, including PARP inhibitors.

molecular biology↗

bioRxiv2022

Multiscale Modeling of MT1-MMP-Mediated Cell Migration: Destabilization of Cell-Matrix Adhesion

One of several ways MT1-MMP promotes cell migration is by modifying cell adhesion properties. MT1-MMP directly processes cell adhesion properties by shedding cell transmembrane receptors that attach cells to the extracellular matrix (ECM). The shedding leads to the destabilization and disassembly of firm cell-matrix adhesion that holds cells in their stationary position, prompting cells to migrate. In this paper, we present a multiscale mathematical model of single cell migration driven by MT1-MMP destabilization of cell-matrix adhesion. The dynamics of MT1-MMP are modeled using a system of differential equations that are integrated with the Cellular Potts Model (CPM) for a combined modeling at the intracellular and cellular scale, respectively. The CPM is extended to include a local feedback mechanism from MT1-MMP on the membrane that enhances cell membrane fluctuations, resulting in actively migrating cells. The results of computational simulation show that MT1-MMP is capable of destabilizing strong cell-matrix adhesion and stimulating cell migration, and at the same time, also producing cell polarization and motile cell morphology.

biophysics↗

bioRxiv2022

The Ketogenic Diet Metabolite β-Hydroxybutyrate Promotes Mitochondrial Elongation via Deacetylation and Improves Autism-like Behavior in Zebrafish

The ketogenic diet (KD) is clinically beneficial and has therapeutic potential across a growing list of neurological disorders, including autism spectrum disorder (ASD). However, the underlying mechanisms mediating the benefits of the KD, which can also have undesirable side effects, remain undefined. To this end, improvements in mitochondrial morphology and function correlate with improved ASD behaviours in response to the KD, though how the KD influences mitochondrial morphology, and whether this is sufficient to improve behaviour remains unknown. Here, we investigate how beta-hydroxybutyrate (BHB), a key metabolite produced by the KD regulates mitochondrial morphology in HeLa cells, and whether this pathway could be exploited to alter phenotypes in a zebrafish model of ASD. We found that {beta}-oxidation of BHB promotes mitochondrial elongation in HeLa cells by increasing NAD+ levels, which in turn activates SIRT deacetylases that act on key regulators of both mitochondrial fusion and fission. Our data suggest that increasing NAD+ levels with its precursor, nicotinamide mononucleotide (NMN), is sufficient to promote mitochondrial hyperfusion. Finally, both BHB and NMN impact neurodevelopment in the shank3b+/- zebrafish model of ASD. Together, our findings elucidate a mechanism by which the ketogenic diet promotes mitochondrial elongation. Moreover, manipulation of this pathway may provide a novel avenue for the treatment of neurological disorders such as ASD that also may obviate potential complications of the KD in clinical practice.

molecular biology↗

bioRxiv2022

Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments

Cell stiffness and T-box transcription factor 3 (TBX3) expression have been identified as biomarkers of melanoma metastasis in 2D environments. This study aimed to determine how mechanical and biochemical properties of melanoma cells change during cluster formation in 3D environments. Vertical growth phase (VGP) and metastatic (MET) melanoma cells were embedded in 3D collagen matrices of 2 and 4 mg/ml collagen concentrations, representing low and high matrix stiffness. Mitochondrial fluctuation, intracellular stiffness, and TBX3 expression were quantified before and during cluster formation. In isolated cells, mitochondrial fluctuation decreased and intracellular stiffness increased with increase in disease stage from VGP to MET and increased matrix stiffness. TBX3 was highly expressed in soft matrices but diminished in stiff matrices for VGP and MET cells. Cluster formation of VGP cells was excessive in soft matrices but limited in stiff matrices, whereas for MET cells it was limited in soft and stiff matrices. In soft matrices, VGP cells did not change the intracellular properties, whereas MET cells exhibited increased mitochondrial fluctuation and decreased TBX3 expression. In stiff matrices, mitochondrial fluctuation and TBX3 expression increased in VGP and MET, and intracellular stiffness increased in VGP but decreased in MET cells. The findings suggest that soft extracellular environments are more favourable for tumour growth, and high TBX3 levels mediate collective cell migration and tumour growth in the earlier VGP disease stage but play a lesser role in the later metastatic stage of melanoma. Symbols O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/495509v4_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1444cf4org.highwire.dtl.DTLVardef@118427eorg.highwire.dtl.DTLVardef@1b56a0aorg.highwire.dtl.DTLVardef@144d41f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

Heparin promotes fibrillation of most phenol soluble modulin peptides from S. aureus: a possible strengthening of the bacterial biofilm

Phenol soluble modulins (PSMs) are virulence peptides secreted by different Staphylococcus aureus strains. In addition, PSMs are able to form amyloid fibrils which may strengthen the biofilm matrix. The highly sulfated glycosaminoglycan heparin promotes S.aureus infection but the basis for this is unclear. We hypothesized that heparin promotes PSM fibrillation and in this way aids bacterial colonization. Here we address this hypothesis using a combination of different biophysical techniques along with peptide microarrays. We find that heparin accelerates fibrillation of all -PSMs (except PSM2) and {delta}-toxin, but inhibits {beta}-PSMs fibrillation by blocking nucleation. Given that S. aureus secretes higher levels of -PSMs than {beta}-PSMs peptidess, heparin is likely to overall promote fibrillation. Heparin binding is driven by multiple positively charged lysine residues in -PSMs and {delta}-toxins, whose removal strongly reduces affinity. Binding of heparin does not alter the final fibril conformation. Rather, heparin provides a scaffold to catalyze or inhibit fibrillation. Our findings suggest that heparin may strengthen bacterial biofilm through increased PSM fibrillation. O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/434294v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@99c3bdorg.highwire.dtl.DTLVardef@101d9b6org.highwire.dtl.DTLVardef@7c4058org.highwire.dtl.DTLVardef@1647eca_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome

Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay and seizures. To date, clinical features have been described for eleven patients with (likely) pathogenic SETD1B sequence variants. We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Interestingly, males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. Finally, despite the possibility of non-redundant contributions of SETD1B and its paralogue SETD1A to epigenetic control, the clinical phenotypes of the related disorders share many similarities, indicating that elucidating shared and divergent downstream targets of both genes will help to understand the mechanism leading to the neurobehavioral phenotypes. Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.

genetics↗

bioRxiv2020

Cross-talk between individual phenol soluble modulins in S. aureus biofilm formation

The infective ability of the opportunistic pathogen Staphylococcus aureus is associated with biofilm mediated resistance to host immune response and even disinfectants and indeed S. aureus is recognized as the most frequent cause of biofilm associated infections. Phenol-soluble modulin (PSM) peptides serve various roles in pathogenicity while also comprising the structural scaffold of S. aureus biofilms through self-assembly into functional amyloids, but the role of the individual PSMs during biofilm formation remains poorly understood and the molecular pathways of PSM self-assembly have proved challenging to identify. Here, we show a high degree of cooperation between individual PSMs during the formation of functional amyloids in biofilm formation. The fast aggregating PSM3 initiates the aggregation by forming unstable aggregates capable of seeding the formation of aggregates by other PSM peptides into the formation of stable amyloid structures. Using chemical kinetics along with spectroscopic techniques we dissect the molecular mechanism of aggregation of the individual peptides to show that PSM1, PSM3 and PSM{beta}1 display secondary nucleation whereas {beta}PSM2 aggregates through primary nucleation and elongation. Our findings suggest that the various PSMs have evolved to ensure fast and efficient biofilm formation through cooperation between individual peptides.

biophysics↗