Biology subjects

Salehi, M.

Publications and source records attributed to Salehi, M..

6 recordsLinked to original sources

bioRxiv2026

Termination dynamics set RNAPII elongation rate and gate the response to CDK12 inactivation

The transcriptional fidelity of RNA polymerase II (RNAPII) is governed by a tight equilibrium between elongation and termination activities, a balance frequently disrupted in human diseases such as cancer. The transcriptional cyclin-dependent kinase 12 (CDK12) maintains RNAPII elongation rate and processivity throughout the gene body. Inactivation of CDK12 disrupts this homeostatic balance and causes elongation stress, slowing RNAPII and triggering premature termination at intronic polyadenylation sites (IPAs). Despite this, the precise executors of intronic premature termination under CDK12-inactivation-induced elongation stress remain poorly understood. Using genome-wide CRISPR screening combined with chemical-genetic approach, we identified a pro-termination mechanism at intronic checkpoints; upon CDK12 inactivation, SCAF4 recruits the cleavage and polyadenylation (CPA) complex through its catalytic endonuclease CPSF3 to execute premature cleavage at IPAs. Disruption of SCAF4-CPA axis prevents early termination, restores full length transcription and confers resistance to CDK12/cyclin K inhibition. Genetic loss of SCAF4 restores the RNAPII elongation rate under CDK12 inhibition, revealing that termination dynamics actively shape the rate of transcription. Supporting this model, we uncovered an anti-termination mechanism driven by KHDRBS1/SAM68, whose depletion promotes proximal termination and sensitises cells to CDK12 targeting. Our findings mechanistically couple elongation and termination activities at intronic checkpoints as joint contributors to both the processivity and elongation rate of RNAPII. This establishes termination dynamics as an active and tractable axis of the cellular response to elongation stress.

molecular biology↗

bioRxiv2025

A TAK1Cytokine Toxicity Checkpoint Controls Anti-Cancer Immunity

The success of cancer immunotherapies is currently limited to a subset of patients, which underscores the urgent need to identify the processes by which tumours evade immunity. Through screening a kinome-wide CRISPR/Cas9 sgRNA library we identified MAP3K7 (TAK1) as a suppressor of CD8+ T cell mediated killing. We demonstrate that TAK1 acts as a cancer-intrinsic checkpoint by integrating signals from T cell-secreted TNF and IFNy effector cytokines to elicit a cytoprotective response. This cytoprotective response profoundly limits the anti-cancer activity these key effector molecules and completely abrogates bystander killing by perforin deficient T cells. Inhibition of the TAK1 checkpoint effectively redirects the combined TNF/IFNy pathway activation to promote inflammatory cell death via RIPK1 and Caspase-8 and simultaneously amplifies the output of the IFNy pathway, thereby priming cells for cytokine-induced cell death. Mechanistically, TAK1 deficiency led to proteasomal degradation of cFLIP, enhancing the formation of Complex II and subversion of other cytoprotective responses. Targeting the TAK1 checkpoint led to profound attenuation of tumour growth in immune competent mice, with minimal impact in immune deficient counterparts. Adoptive cell therapy led to preferential elimination of TAK1 deficient clones. Collectively, our study uncovers a cancer-intrinsic checkpoint controlled by TAK1 activity that switches TNF and IFNy responses from cytoprotective to apoptosis. Cancer cells exploit this to limit cell death in the presence of the cytotoxic lymphoctye cytokines TNF and IFN{gamma} and therapeutic intervention can fully unleash the impact of these effector molecules both on the direct target and bystander cells. These findings highlight the clinical development of TAK1 biologics as a potential strategy to improve cancer immunotherapies through harnessing and enhancing the cytotoxic potential of CTL-derived cytokines. In BriefDjajawi et al. identify TAK1 as a cancer-intrinsic cytokine toxicity checkpoint that limits the efficacy of anti-cancer immune responses. Cancer cells exploit TAK1 activity to confers resistance to CD8+ T cell-derived TNF and IFN{gamma}-induced apoptosis, limiting both direct and bystander killing. Mechanistically, TAK1 loss acts through 1. cFLIP and RIPK1 to promote cell death, 2. The inactivation of pro-survival signals and 3. Via amplification of the IFNy response. Targeting of this TAK1 checkpoint enhanced anti-tumour immunity in vivo and improved adoptive cellular therapy. These findings identify a strategy employed by transformed cells to avoid destruction by inflammatory cytokines and provide new therapeutic vulnerabilities for enhancing immunotherapies. HighlightsO_LICRISPR screens identify TAK1 as a tumour-intrinsic survival checkpoint limiting destruction by CD8+ T cells. C_LIO_LITAK1 protects tumour cells from combined TNF and IFN{gamma}-induced apoptosis. C_LIO_LITAK1 loss destabilizes cFLIP, priming cells for STAT1 and RIPK1-dependent cell death. C_LIO_LITAK1 loss promotes tumour control in immune competent animals and enhances the efficacy of adoptive cell therapy. C_LI

cancer biology↗

bioRxiv2019

Electrospun cellulose acetate/gelatin nanofibrous wound dressing containing berberine for diabetic foot ulcer healing: in vitro and in vivo studies

Functional dressing with tailored physicochemical and biological properties is vital for diabetic foot ulcer (DFU) treatment. Our main objective in the current study was to fabricate Cellulose Acetate/Gelatin (CA/Gel) electrospun nanofibrous mat loaded with berberine (Beri) as the DFU dressing. The results demonstrated that the diameter of the nanofibers was around 502 nm, the tensile strength, contact angle, porosity, water vapor permeability, and water uptake ratio of CA/Gel nanofibers were around 2.83 MPa, 58.07, 78.17 %, 11.23 mg/cm2 hr, and 12.78 respectively, while these values for CA/Gel/Beri nanofibers were 2.69 {+/-} 0.05 MPa, 56.93 {+/-} 1, 76.17 {+/-} 0.76 %, 10.17 {+/-} 0.21 mg/cm2 hr, 14.37 {+/-} 0.42 respectively. The bacterial evaluations demonstrated that the dressings are an excellent barrier against bacterial penetration with potent antibacterial activity. The animal studies depicted that the collagen density and angiogenesis score in the CA/Gel/Beri treated group were 88.8{+/-}6.7 % and 19.8{+/-}3.8, respectively. These findings implied that the incorporation of berberine did not compromise the physical properties of dressing, while improving the biological activates. In conclusion, our findings implied that the prepared mat is a proper wound dressing for DFU management and treatment.

bioengineering↗

bioRxiv2018

There is no single functional atlas even for a single individual: Parcellation of the human brain is state dependent

The goal of human brain mapping has long been to delineate the functional subunits in the brain and elucidate the functional role of each of these brain regions. Recent work has focused on whole-brain parcellation of functional Magnetic Resonance Imaging (fMRI) data to identify these subunits and create a functional atlas. Functional connectivity approaches to understand the brain at the network level, require such an atlas to assess connections between nodes and extract network properties. While no single functional atlas has emerged as the dominant atlas to date, there remains an underlying assumption that such an atlas exists. Using fMRI data from a highly sampled subject as well as two independent replication data sets, we demonstrate that functional atlases reconfigure substantially and in a meaningful manner, according to brain state.

neuroscience↗

bioRxiv2018

Exploring the prediction of emotional valence and pharmacologic effect across fMRI studies of antidepressants.

BackgroundClinically approved antidepressants modulate the brains emotional valence circuits, suggesting that the response of these circuits could serve as a biomarker for screening candidate antidepressant drugs. However, it is necessary that these modulations can be reliably detected. Here, we apply a cross-validated predictive model to classify emotional valence and pharmacologic effect across eleven task-based fMRI datasets (n=306) exploring the effect of antidepressant administration on emotional face processing.\n\nMethodsWe created subject-level contrast of parameter estimates of the emotional faces task and used the Shen whole-brain parcellation scheme to define 268 subject-level features that trained a cross-validated gradient-boosting machine protocol to classify emotional valence (fearful vs happy face visual conditions) and pharmacologic effect (drug vs placebo administration) within and across studies.\n\nResultsWe found patterns of brain activity that classify emotional valence with a statistically significant level of accuracy (70% across-all-subjects; range from 50-87% across-study). Our classifier failed to consistently discriminate drug from placebo. Subject population (healthy or unhealthy), treatment group (drug or placebo), and drug administration protocol (dose and duration) affected this accuracy with similar populations better predicting one another.\n\nConclusionsWe found limited evidence that antidepressants modulated brain response in a consistent manner, however found a consistent signature for emotional valence. Variable functional patterns across studies suggest that predictive modeling can inform biomarker development in mental health and in pharmacotherapy development. Our results suggest that case-controlled designs and more standardized protocols are required for functional imaging to provide robust biomarkers for drug development.

neuroscience↗

bioRxiv2018

State-specific individualized functional networks form a predictive signature of brain state

There is extensive evidence that human brain functional organization is dynamic, varying within a subject as the brain switches between tasks demands. This functional organization also varies across subjects, even when they are all engaged in similar tasks. Currently, we lack a comprehensive model that unifies the two dimensions of variation (brain state and subject). Using fMRI data obtained across multiple task-evoked and rest conditions (which we operationally define as brain states) and across multiple subjects, we develop a state-and subject-specific functional network parcellation (the assignment of nodes to networks). Our parcellation approach provides a measure of how node-to-network assignment (NNA) changes across states and across subjects. We demonstrate that the brains functional networks are not spatially fixed, but reconfigure with brain state. This reconfiguration is robust and reliable to such an extent that it can be used to predict brain state with accuracies up to 97%.

neuroscience↗