Biology subjects

Akhtar, A.

Publications and source records attributed to Akhtar, A..

13 recordsLinked to original sources

bioRxiv2026

Temozolomide-associated inflammatory-repair remodeling in recurrent glioblastoma exposes a ROCK-linked therapeutic vulnerability

Background: Glioblastoma (GBM) adapts to therapy through coordinated malignant-cell and microenvironmental responses, but the mechanisms linking treatment-associated inflammation to tumor-cell phenotypic plasticity remain poorly defined. Here, we investigated whether preoperative temozolomide exposure is associated with inflammatory-repair remodeling and a ROCK-linked therapeutic vulnerability in recurrent GBM using a window-of-opportunity clinical trial cohort. Methods: We integrated patient-resolved single-cell transcriptomics, spatial RNA profiling and multiplex protein imaging with experimental perturbations and orthotopic glioblastoma models. In the presurgical window-of-opportunity subgroup of NCT05236036, four patients with recurrent glioblastoma received additional preoperative temozolomide (TMZ; 150 mg/m2/day for 5 days) before resection and were compared with three recurrent comparators who did not receive additional preoperative TMZ. Results: Across seven tumors, malignant-cell inflammatory activity covaried with integrin-binding and wound-healing programs (median partial {rho} = 0.45 and 0.42, respectively). Tumors exposed to preoperative TMZ showed enrichment of inflammatory, chemokine, adhesion and wound-healing programs (GSEA q < 0.05), with the direction of enrichment preserved in all leave-one-patient-out analyses. In two tumors exposed to preoperative TMZ, CXCL12 localized to vascular territories, whereas chemokine and wound-repair programs increased near injury-reference regions. Across seven specimens analyzed by multiplex protein imaging, MYL9 abundance correlated with local CXCL12 ({rho} = 0.61), phosphorylated MYPT1 ({rho} = 0.48) and nuclear phosphorylated STAT3 ({rho} = 0.45), with positive associations in every specimen. Experimentally, TMZ increased CXCL8 and reactive-state markers and enhanced subsequent scratch closure, while CXCL8 and CXCL12 increased MLC2 phosphorylation. Fasudil attenuated TNF-NF-{kappa}B, inflammatory-response and IFN-{gamma}-response programs in TMZ-treated cells and reduced scratch closure and p-MLC2 in complementary assays. Across three orthotopic models, fasudil plus TMZ prolonged survival versus TMZ alone (model-stratified HR, 0.21; 95% CI, 0.07-0.61; P = 0.001). Conclusions: These findings link treatment-associated inflammatory-repair programs with cytoskeletal remodeling and support further translational evaluation of fasudil plus TMZ in glioblastoma.

cancer biology↗

bioRxiv2026

Preclinical evaluation of Brincidofovir in glioblastoma demonstrates improved long term-survival and cytomegalovirus-dependent and independent effects

Cytomegalovirus (CMV) has been implicated in glioblastoma (GBM) progression. Ongoing clinical trials are assessing therapeutic approaches targeting CMV in GBM but to date no new therapy has been approved outside the standard of care. Previous preclinical studies have highlighted the potential of the antiviral drug Cidofovir (CDV) in GBM; however, its clinical use is limited by dose-dependent nephrotoxicity and poor cellular uptake, necessitating high intravenous doses to achieve therapeutic activity. Brincidofovir (BCV), a lipid conjugate of CDV has been developed, which does not induce nephrotoxicity and has significantly greater cellular bioavailability. Here we examined the effects of BCV in a newly established CMV-driven GBM model (SB28) and in patient-derived tumor neurospheres. We show that BCV prolongs survival in vivo and exerts both CMV-dependent and independent antitumor effects. Mechanistically, BCV induces DNA damage and cell cycle dysregulation in GBM cells and inhibits proliferation of patient-derived neurospheres in a dose-dependent manner. These data identify BCV as a dual-action therapeutic that suppresses viral oncomodulation while directly targeting tumor cell viability.

cancer biology↗

bioRxiv2026

Dynamin 2–dependent endocytosis differentially regulates ligand and receptor contributions to Notch signaling during neural precursor cell fate determination

A critical event in the development of the highly structured cerebral cortex is the appropriate generation of differentiated daughter cell populations from asymmetric precursor cell divisions. Internalization of extracellular receptors and ligands in the process of endocytosis is key to the establishment of asymmetry. However, the detailed mechanisms mediating this exchange are incompletely understood. The dynamin family of membrane remodeling GTPases is considered critical for many forms of clathrin-mediated endocytosis (CME) but its role in brain development is unexplored. Here we found that dynamin 2 (Dnm2), a protein involved in CME through vesicle release from the plasma membrane, is essential for the maintenance of neural stem cells. Conditional deletion of Dnm2 leads to early exhaustion of neural precursor cells and premature neurogenesis, resulting in gross structural abnormalities, periventricular hemorrhaging and increased perinatal mortality. Notably, Notch ligands accumulate at the cell surface and cleaved NICD is reduced in neural stem cells, consistent with impaired ligand-mediated activation. In contrast, inhibition of CME in receptor-expressing cells increases cell autonomous Notch signaling, likely by promoting receptor accumulation at the plasma membrane. Further, dynamin 1, 2, and 3 can rescue loss of Dnm2 to different extents. Taken together, these findings reveal that Dnm2 is the essential isoform for physiological non-cell autonomous Notch-mediated neural stem cell maintenance, and that CME exerts fundamentally distinct roles in Notch signaling, promoting ligand activity while restricting receptor signaling through control of surface receptor abundance.

Developmental Biology↗

bioRxiv2026

Simultaneous TCR and IL-2 agonism selectively enhances epitope-specific CD8 T cell responses during chronic viral infection

Interleukin-2 (IL-2) remains an attractive cytokine for enhancing antigen-specific CD8 T cell responses in cancer immunotherapy, but systemic toxicity hinders its broad clinical application. To address this, various IL-2-based therapeutics have been engineered with altered IL-2 receptor bias or targeted delivery to tumors, the tumor microenvironment, or immune cell populations. Ideally, IL-2 signals should be selectively delivered to antigen-specific CD8 T cells, boosting their responses and promoting effector differentiation while sparing non-targeted populations. Immuno-STATTM (Selective Targeting and Alteration of T cells) is a fusion protein platform comprising a bivalent peptide-MHC class I complex and an affinity-attenuated IL-2 mutein that co-stimulates TCR and IL-2 signaling in epitope-specific CD8 T cells. Here, we investigated whether a DbGP33-41-targeted Immuno-STAT enhances DbGP33-specific CD8 T cell responses in a mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection. Immuno-STAT treatment selectively expanded DbGP33-specific CD8 T cells with an effector-like phenotype. Non-targeted DbGP276-specific CD8 T cells showed little to no expansion in response to DbGP33-41-targeted Immuno-STAT therapy, underscoring the selectivity of this approach. However, minor changes in phenotypic markers, including increased expression of CD25 and CX3CR1, were observed in non-targeted CD8 T cells, likely reflecting bystander IL-2 signaling. Combining Immuno-STAT with PD-1 blockade augmented DbGP33-specific CD8 T cell responses more effectively than PD-1 blockade alone, with minor effects on the non-targeted DbGP276-specific population. These findings inform the clinical development of Immuno-STAT and other IL-2 therapeutics and highlight the value of coordinated TCR and IL-2 stimulation during chronic antigen exposure, alone or in combination with PD-1 blockade. IMPORTANCEInterleukin-2 (IL-2) is a key cytokine for promoting effector differentiation of antigen-specific CD8 T cells and remains an attractive agent in cancer immunotherapy, but systemic toxicity limits its clinical use. This study addresses a central challenge in IL-2-based immunotherapy: delivering IL-2 to cognate antigen-specific CD8 T cells while minimizing activation of non-targeted populations. Using a mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection, we show that the Immuno-STAT (Selective Targeting and Alteration of T cells) platform selectively expands targeted virus-specific CD8 T cells and enhances their function while limiting effects on non-targeted populations. We also show that combining Immuno-STAT with PD-1 blockade further enhances targeted virus-specific CD8 T cell responses during chronic LCMV infection. These findings provide mechanistic and preclinical support for integrating T cell receptor (TCR) specificity with IL-2 signaling to advance cancer immunotherapy and guide next-generation IL-2 therapeutics for cancer and chronic infection.

immunology↗

bioRxiv2025

Acetylation-dependent clustering of BRD2 instructs transcription dynamics

BET protein inhibitors represent one of the most prominent classes of epigenetic drugs. However, the specific contributions of individual BET family members to transcription regulation remain largely unknown. Here, by acutely co-depleting BET proteins, we uncover an essential role of BRD2 in maintaining RNA Polymerase II recruitment at promoters, which becomes especially critical in the absence of BRD4 or when pause release is inhibited. Combining rapid protein degradation, chemogenomics, and super-resolution microscopy, we show that H4 acetylation, particularly H4K16ac, serves as a template for BRD2 function, driving sub-diffraction BRD2 cluster formation at chromatin. Accordingly, depletion of BRD2 or the writer of H4K16ac, MOF decreases sub-diffraction RNA Polymerase II clusters, which are associated with transcription initiation. Thus, this study highlights the importance of acetylated chromatin in transcriptional coactivator organization and the distinct role of BRD2 in transcription initiation dynamics.

genomics↗

bioRxiv2025

AI-Guided Design and AKT3 Degradation Synergize to Enhance Bispecific and Trispecific CAR-T Cell Persistence and Overcome Antigen Escape

The structural design of chimeric antigen receptors (CARs) is critical for achieving robust and durable anti-tumor responses, particularly when targeting multiple antigens to prevent tumor antigen escape. However, increasing CAR complexity can introduce structural vulnerabilities, leading to antigen-independent T cell activation, activation-induced cell death, and reduced CAR-T cell persistence. To overcome these challenges, we designed 10,824 CAR molecules across diverse formats and screened 1,452 constructs in-vitro to develop an artificial intelligence model, termed CAR-Mediated Self-Destruction (CARMSeD), which predicts CAR designs susceptible to self-activation and dysfunction. Guided by CARMSeD and structural CAR-CAR interaction modeling, we identified optimized CAR architectures incorporating ICOS and 4-1BB co-stimulatory domains. Humanized bispecific CARs targeting CD20/CD19 and CD22/CD19 demonstrated superior anti-tumor efficacy and persistence both in-vitro and in various xenograft mice models. To further extend CAR-T cell persistence, we engineered bispecific CARs integrated with an AKT3-targeted PROTAC strategy. Targeted degradation of AKT3 enhanced anti-tumor potency, promoted memory T cell formation, and enabled sustained responses even under tumor rechallenge and CD19 antigen-loss conditions. Mechanistically, these effects were mediated by metabolic reprogramming involving FOXO4; notably, FOXO4-deficient CAR-T cells exhibited impaired long-term persistence. Leveraging these mechanistic insights, we developed a trispecific CAR-T cell platform incorporating a bispecific T cell engager (BiTE) targeting CD22/CD3, combined with AKT3 PROTACs. These trispecific CAR-T cells achieved potent tumor eradication, even against malignancies lacking both CD19 and CD20 expression. Collectively, this study presents a comprehensive strategy combining structure-based design, AI-guided screening, and targeted protein degradation to engineer next-generation bi and trispecific CAR-T cells with enhanced persistence, broad antigen coverage, and superior therapeutic durability.

cancer biology↗

bioRxiv2024

Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome

CD8 T cell exhaustion impedes immune responses to cancer and chronic infections, and a biochemical understanding of exhaustion is essential to improving immunotherapy. Here, we present the first longitudinal protein abundance and phosphoproteomic analysis of antigen-specific CD8 T cells undergoing differentiation in vivo during acute (LCMV-Armstrong) and chronic (LCMV-Clone 13) infection. Comparing protein abundance across the two infection conditions identified over 180 known and novel exhaustion-associated proteins, including proteins missed by transcriptional analyses. Phosphoproteomic analysis identified >900 differentially regulated phosphosites on >400 proteins, including known inhibitory phosphosites on PD1, PAG1, SHP-1/PTPN6, SLAMF1/CD150. We also calculated phosphosite conservation across mammals, to direct follow-up studies towards sites with likely essential function. Lastly, our analysis uncovers exhaustion-associated kinases with clinical-stage inhibitors, underscoring the translational utility of our dataset to guide immunotherapy development. Together, our datasets define a biochemical atlas of T cell exhaustion in vivo, shedding light on the molecular mechanisms of T cell dysfunction.

immunology↗

bioRxiv2022

Characterization of Plasmodium falciparum RAP domain proteins-RAP291 and RAP070, and their association with ribosomal RNAs

Plasmodium genomes encode multiple RAP (RNA-binding domain abundant in Apicomplexan) domain proteins that contain a conserved module of 56 to 73 amino acids. Here, we characterized two of the P. falciparum RAP domain proteins; PfRAP291 & PfRAP070, for their expression and role at asexual blood stages. RNA binding assays and high-throughput CLIP-seq analysis showed that these proteins mainly bind ribosome associated RNAs. Blue-native PAGE and protein-protein interaction studies suggested association of these proteins with MSP-1 complex. Anti-PfRAP291 and anti-PfRAP070 antibodies showed moderate inhibitions in in-vitro merozoite invasion assays. Together, these results suggest multiple roles of these proteins; PfRAP291 and PfRAP070, in merozoite invasion and in ribosome regulation during asexual stages of the parasite.

microbiology↗

bioRxiv2019

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs) and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.

genomics↗

bioRxiv2018

Optimisation and validation of hydrogel-based brain tissue clearing shows uniform expansion across anatomical regions and spatial scales

Imaging of fixed tissue is routine in experimental neuroscience, but is limited by the depth of tissue that can be imaged using conventional methods. Optical clearing of brain tissue using hydrogel-based methods (e.g. CLARITY) allows imaging of large volumes of tissue and is rapidly becoming commonplace in the field. However, these methods suffer from a lack of standardised protocols and validation of the effect they have upon tissue morphology. We present a simple and reliable protocol for tissue clearing along with a quantitative assessment of the effect of tissue clearing upon morphology. Tissue clearing caused tissue swelling (compared to conventional methods), but this swelling was shown to be similar across spatial scales and the variation was within limits acceptable to the field. The results of many studies rely upon an assumption of uniformity in tissue swelling, and by demonstrating this quantitatively, research using these methods can be interpreted more reliably.

neuroscience↗

bioRxiv2018

The NSL complex mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise

Nucleosomal organization at gene promoters is critical for transcription, with a nucleosome-depleted region (NDR) at transcription start sites (TSSs) being required for transcription initiation. How NDR and the precise positioning of the +1 nucleosome is maintained on active genes remains unclear. Here, we report that the Drosophila Non-Specific Lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner. The NSL complex interacts with the NURF chromatin remodeling complex and is necessary and sufficient to recruit NURF to target promoters. The NSL complex is not only essential for transcription but is required for accurate TSS selection for genes with multiple TSSs. Further, loss of NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity.

genomics↗

bioRxiv2017

uvCLAP: a fast, non-radioactive method to identify in vivo targets of RNA-binding proteins

RNA-binding proteins (RBPs) play important and essential roles in eukaryotic gene expression regulating splicing, localization, translation and stability of mRNAs. Understanding the exact contribution of RBPs to gene regulation is crucial as many RBPs are frequently mis-regulated in several neurological diseases and certain cancers. While recently developed techniques provide binding sites of RBPs, they are labor-intensive and generally rely on radioactive labeling of RNA. With more than 1,000 RBPs in a human cell, it is imperative to develop easy, robust, reproducible and high-throughput methods to determine in vivo targets of RBPs. To address these issues we developed uvCLAP (UV crosslinking and affinity purification) as a robust, reproducible method to measure RNA-protein interactions in vivo. To test its performance and applicability we investigated binding of 15 RBPs from fly, mouse and human cells. We show that uvCLAP generates reliable and comparable data to other methods. Unexpectedly, our results show that despite their different subcellular localizations, STAR proteins (KHDRBS1-3, QKI) bind to a similar RNA motif in vivo. Consistently a point mutation (KHDRBS1Y440F) or a natural splice isoform (QKI-6) that changes the respective RBP subcellular localization, dramatically alters target selection without changing the targeted RNA motif. Combined with the knowledge that RBPs can compete and cooperate for binding sites, our data shows that compartmentalization of RBPs can be used as an elegant means to generate RNA target specificity.

molecular biology↗

bioRxiv2017

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Eukaryotic chromatin is partitioned into domains called TADs that are broadly conserved between species and virtually identical among cell types within the same species. Previous studies in mammals have shown that the DNA binding protein CTCF and cohesin contribute to a fraction of TAD boundaries. Apart from this, the molecular mechanisms governing this partitioning remain poorly understood. Using our new software, HiCExplorer, we annotated high-resolution (570 bp) TAD boundaries in flies and identified eight DNA motifs enriched at boundaries. Known insulator proteins bind five of these motifs while the remaining three motifs are novel. We find that boundaries are either at core promoters of active genes or at non-promoter regions of inactive chromatin and that these two groups are characterized by different sets of DNA motifs. Most boundaries are present at divergent promoters of constitutively expressed genes and the gene expression tends to be coordinated within TADs. In contrast to mammals, the CTCF motif is only present on 2% of boundaries in flies. We demonstrate that boundaries can be accurately predicted using only the motif sequences, along with open chromatin, suggesting that DNA sequence encodes the 3D genome architecture in flies. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogeome.ie-freiburg.mpg.de.

genomics↗