Biology subjects

Islam, F.

Publications and source records attributed to Islam, F..

11 recordsLinked to original sources

bioRxiv2026

Genotype-Dependent Dysregulation of the MDM2-p53 Axis and Breast Cancer Susceptibility in Bangladeshi Women: A Cas-Control Study

BackgroundThe MDM2-p53 signaling pathway plays a central role in tumor suppression, and genetic variants that disrupt this pathway may influence breast cancer (BC) susceptibility. However, data from South Asian populations, particularly Bangladesh, remain limited. MethodsA case-control study was conducted in Bangladeshi women, including BC patients and healthy controls (HCs). Genotyping of MDM2 polymorphisms was performed using PCR-based methods. Circulating MDM2 and p53 protein levels were measured using enzyme-linked immunosorbent assays (ELISA). Associations between genotype, protein levels, BC status, and clinicopathological features were evaluated using appropriate statistical models. ResultsA strong and genotype-specific association was observed for MDM2 rs2279744. Women carrying the heterozygous TG genotype had a markedly increased risk of BC across additive, dominant, and over-dominant models, whereas the GG genotype showed a protective effect under the recessive model. In contrast, rs937282 did not show a significant association with BC risk. Circulating MDM2 levels were significantly elevated in patients compared with controls and varied by rs2279744 genotype, while circulating p53 levels showed an opposite trend. A strong inverse correlation was observed between serum MDM2 and p53 levels, supporting dysregulation of the MDM2-p53 feedback loop. Elevated MDM2 levels were also noted in HER2-positive and triple-positive BC subtypes. ConclusionTogether, these findings indicate that the MDM2 rs2279744 polymorphism contributes to BC susceptibility in a genotype-specific manner, likely through disruption of the MDM2-p53 regulatory balance. However, the absence of functional validation limits direct causal inference.

cancer biology↗

bioRxiv2026

Structure-Activity Mapping of Intraperitoneal mRNA-LNPs: Decoupling Tumor and Liver Biodistribution in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) remains difficult to treat with nucleic acid therapeutics because efficient intratumoral delivery is limited and off-target liver accumulation is common. Here, we developed a structure-activity map for intraperitoneally administered mRNA lipid nanoparticles (mRNA-LNPs) to identify formulation features that improve delivery to pancreatic tumors while reducing liver expression. A full-factorial library of 48 mRNA-LNP formulations was generated by varying ionizable lipid, sterol, phospholipid, and PEG-lipid components. Formulations were characterized for size, polydispersity, zeta potential, and encapsulation, then evaluated in an orthotopic KPC8060 pancreatic tumor model after intraperitoneal administration of firefly luciferase mRNA-loaded LNPs. Biodistribution was assessed by Rhodamine B fluorescence and functional delivery by luciferase expression 12 h after dosing. Lipid composition strongly influenced both physicochemical properties and in vivo performance. G0-C14-based formulations produced the smallest and most homogeneous particles, whereas FTT5-containing formulations were generally larger. Across the 48-formulation library, mRNA expression and nanoparticle biodistribution varied significantly among tumor, pancreas, liver, and spleen. Statistical, decision-tree, and predictive modeling analyses identified composition rules associated with organ-selective delivery. High tumor expression was associated primarily with G0-C14 combined with DSPC and {beta}-sitosterol, whereas liver expression was favored by C12-200 or DLin-MC3-DMA with DOPE and DSPE-PEG. Notably, a G0-C14/DSPC/DSPE-PEG formulation emerged as a lead candidate, producing a greater than 6-fold increase in tumor luciferase signal relative to the library median while reducing liver exposure by approximately 60%. Histopathology showed no treatment-related liver or lung toxicity. These findings define actionable formulation rules for tuning intraperitoneal mRNA-LNP delivery in PDAC and support further development of tumor-selective mRNA therapeutics for pancreatic cancer.

bioengineering↗

bioRxiv2025

Host microRNA Target Prediction in SARS-CoV-2 and Hepatitis E Virus Genomes: Insights from RNAhybrid Analysis

MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression that can influence viral replication and pathogenesis by binding to viral RNA genomes. This study uses RNAhybrid to predict binding sites of three abundant human miRNAs--hsa-miR-155-5p, hsa-miR-21-5p, and hsa-let-7a-5p--within the genomes of SARS-CoV-2 (Bangladesh isolate OM967280.1) and Hepatitis E Virus genotype 1 (NC_001434.1). Our results show stable hybridization events with minimum free energy (mfe) values ranging from -23.8 to -28.1 kcal/mol, indicating strong potential interactions. These findings suggest that host miRNAs may modulate viral RNA stability or translation, impacting viral pathogenesis. Further experimental validation is necessary to confirm these regulatory relationships and explore their therapeutic potential.

bioinformatics↗

bioRxiv2025

Contrasting roles for IKK regulated inflammatory signalling pathways for development and maintenance of type 1 and adaptive γδ T cells

The inhibitor of kappa B kinase complex (IKK) is a critical regulator of cell death and inflammatory signaling in multiple cell types. Phosphorylation of I{kappa}B proteins by IKK results in their degradation and consequent activation of NF-{kappa}B transcription factors. RIPK1, a critical cell death regulator, is also a direct target of IKK kinase activity, thereby repressing its cell death activity. In {beta} T cells, the RIPK1 kinase activity of IKK is critical for normal thymic development while mature {beta} T cells require IKK for both activation of NF-{kappa}B dependent survival programmes, and repression of RIPK1. {gamma}{delta} T cells play a unique and versatile role in host immunity with specific effector functions that enables them to act as early responders in immune defence. The role of IKK regulated pathways in their development and survival is not known. Here, we use mouse genetics to dissect the function of IKK and downstream pathways in the normal homeostasis of {gamma}{delta} T cells. We find that IKK expression is critical to establish a replete {gamma}{delta} T cell compartment, but that requires vary between different subsets. Type 1 {gamma}{delta} T cells require IKK dependent NF-{kappa}B activation for their generation, while IKK is redundant for development of adaptive {gamma}{delta} T cells. Instead, IKK dependent NF-{kappa}B activation is required for their longterm survival. We also find evidence that IKK repression of RIPK1 is required for survival of peripheral but not thymic {gamma}{delta} T cells. Ablation of CASPASE8 did not rescue {gamma}{delta} T cells in the absence of IKK but rather revealed a potent sensitivity of all {gamma}{delta} subsets to necroptosis, that was rescued by kinase dead RIPK1. Overall, we reveal critical requirements for IKK regulated inflammatory pathways by {gamma}{delta} T cells that contrast with those of {beta} T cells, and between different subsets, highlighting the complexity of the regulation of these pathways in the adaptive immune system.

immunology↗

bioRxiv2025

Evidence for a RIPK1-independent survival mechanism for CASPASE-8 in αβ T cells

CASPASE8 promotes both cell death and survival by acting as a trigger of apoptosis but also a repressor of necroptosis. In T cells, CASPASE8 is required for FAS induced apoptosis, but protects activated T cells from necroptosis. The broader role and mechanisms of CASPASE8 in the wider T cell compartment is less certain. Here, we analysed mice in which Casp8 was conditionally deleted in the lymphoid compartment by huCD2iCre. In the thymus, we found evidence of a modest impairment of early thymic progenitors and a striking absence of NKT cell development. Amongst mature peripheral T cells, there was a substantial and specific reduction in the CD8 T cell compartment, that included naive, central memory and virtual memory subsets. While life spans and turnover of CD8 T cells appeared largely normal, we did identify an acute requirement for continued CASPASE8 expression for survival of a fraction of CD8 T cells, since induced Casp8 deletion by tamoxifen induced CD8CreERT resulted in an acute loss of CD8 T cells. CASPASE8 deficient T cells were resistant to FAS or TNF induced cell death in vitro. Generating Casp8 deficient mice that express a kinase dead RIPK1 confirmed that necroptosis contributed to death of thymic progenitors and some peripheral CD8 T cell subsets in the absence of CASPASE8. However, kinase dead RIPK1 failed to restore NKT cell development and only partially rescued CD8 VM T cells, while analysing mixed bone marrow chimeras suggested that CASPASE8 deficient CD4 and CD8 T cells were less competitively fit than WT T cells, even in the absence of RIPK1 kinase activity. These latter observations suggest the existence of a novel mechanism by which CASPASE8 promotes T cell survival that is independent of its established role in repressing necroptosis.

immunology↗

bioRxiv2023

Reprogramming megakaryocytes to engineer platelets as delivery vehicles

Platelets are anucleate cells naturally filled with secretory granules that store large amounts of protein to be released in response to certain physiological conditions. Cell engineering can endow platelets with the ability to deliver non-native proteins by modifying them as they develop during the cell fate process. This study presents a strategy to efficiently generate mouse platelets from pluripotent stem cells and demonstrates their potential as bioengineered protein delivery platforms. By modifying megakaryocytes, the progenitor cells of platelets, we successfully engineered platelets capable of packaging and delivering non-native proteins. These engineered platelets can offer flexible delivery platforms to release non-native proteins in a controlled manner upon activation when packaged into -granules or deliver active enzymes to genetically alter recipient cells. Our findings highlight platelets as a promising tool for protein delivery in cell therapy applications.

synthetic biology↗

bioRxiv2023

Unveiling the Holliday junction conformational dynamics upon binding with architectural proteins IHF

Integration host factor (IHF) of E. coli is a nucleoid-associated protein with diverse roles in DNA packaging, viral DNA integration, and recombination. IHF binds to duplex DNA containing a 13 bp consensus sequence with nanomolar affinity and induces a significant bend of approximately 160{degrees} upon binding. While the Wild type IHF (WtIHF) is involved in DNA bending, thereby facilitating the integration of foreign DNA into the host genome, its engineered version, Single chain IHF (ScIHF) was designed for specific genetic engineering and biotechnological applications. We investigated interaction of the two IHF variants with Holliday junctions (HJ), crucial intermediates in DNA repair and homologous recombination. Our finding demonstrate that both variant of IHF binds to HJs with high affinity in presence of the consensus sequence, indicating a structure-based recognition mechanism. HJs are dynamic structures that can adopt open or stacked conformation. The open conformation facilitates processes like branch migration and strand exchange. Through quantitative binding studies using microscale thermophoresis, we determined the binding of IHF to four-way DNA junctions that harboured two specific binding sequences H & H1. Circular dichroism (CD) experiments revealed the proteins impact on the junction conformation. This was further confirmed by Single molecule Forster resonance energy transfer (smFRET) technique that was used to examine the binding of IHF to the junction and its effect on the dynamicity of junction conformation. We also probed the population distribution of junction conformations. Interestingly, our results revealed that binding of both WtIHF & ScIHF shifts the population towards the open conformation of the junction and stabilised it in that conformation. In summary, our findings demonstrate that IHF binds HJs with a strong affinity and has a stabilizing effect on maintaining the junctions open conformation.

biophysics↗

bioRxiv2022

Evolutionary analysis of Quinone Reductases 1 and 2 suggest that NQO2 evolved to function as a pseudoenzyme

Quinone reductases 1 and 2 (NQO1 and NQO2) are paralogous FAD-linked enzymes found in all amniotes. NQO1 and NQO2 have similar structures and can both catalyze reduction of quinones and other electrophiles. The two enzymes differ in their cosubstrate specificity, with NQO1 using cellular redox couples NAD(H) and NADP(H), while NQO2 is almost completely inactive with these cosubstrates, and instead uses dihydronicotinamide riboside (NRH) and small synthetic cosubstrates such as N-benzyl-dihydronicotinamide (BNAH). We used ancestral sequence reconstruction to investigate the catalytic properties of a predicted common ancestor and 2 additional ancestors from each of the evolutionary pathways to extant NQO1 and NQO2. In all cases, the small nicotinamide cosubstrates NRH and BNAH were good cosubstrates for the common ancestor and the enzymes along the NQO1 and NQO2 lineages. In the case of NADH, however, extant NQO1 evolved to a catalytic efficiency 100x higher than the common ancestor, while NQO2 has evolved to a catalytic efficiency 1000x lower than the common ancestor. In addition, 13 chimeric enzymes were created to investigate the molecular basis of cosubstrate specificity, which was further elaborated by site-directed mutagenesis of the ancestral NQO2. Overall, the results suggest a selective pressure for evolution of NQO1 towards greater efficiency with NADH, and for NQO2 towards extremely low efficiency with NADH. These divergent trajectories have implications for the cellular functions of both enzymes, but particularly for NQO2 whose cellular functions are only beginning to be uncovered.

biochemistry↗

bioRxiv2021

Probing the molecular mechanism of action of Deinococcus radiodurans RecD2 at single-molecule resolution

Helicases are ATP-driven molecular machines that directionally remodel nucleic acid polymers in all three domains of life. Helicases are responsible for resolving double-stranded DNA (dsDNA) into separate single-strands and this activity is essential for DNA replication, nucleotide excision repair, and homologous recombination. RecD2 from Deinococcus radiodurans (DrRecD2) has important contributions towards the organisms unusually high tolerance to gamma radiation and hydrogen peroxide. Although previous X-ray Crystallography studies have revealed the structural characteristics of the protein, the direct experimental evidence regarding the dynamics of the DNA unwinding process by DrRecD2 in the context of other accessory proteins is yet to be found. In this study, we have probed the exact binding event and processivity of DrRecD2 at single-molecule resolution using Protein-induced fluorescence enhancement (smPIFE) and Forster resonance energy transfer (smFRET). We have found that the protein prefers to bind at the 5 terminal end of the single-stranded DNA (ssDNA) by Drift and has helicase activity even in absence of ATP. However, a faster and iterative mode of DNA unwinding was evident in presence of ATP. The rate of translocation of the protein was found to be slower on dsDNA compared to ssDNA. We also showed that DrRecD2 is recruited at the binding site by the single-strand binding protein (SSB) and during the unwinding, it can displace RecA from ssDNA.

biophysics↗

bioRxiv2020

BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response

Effective vaccine against SARS-CoV-2 is the utmost importance in the current world. More than 1 million deaths are accounted for relevant pandemic disease COVID-19. Recent data showed that D614G genotype of the virus is highly infectious and responsible for almost all infection for 2nd wave. Despite of multiple vaccine development initiatives, there are currently no report that has addressed this critical variant D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine considering the D614G variant and characterization of the vaccine in preclinical trial. The surface plasmon resonance (SPR) data with spike protein as probe and competitive neutralization with RBD and S2 domain revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, immunization protected mice lungs from pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+ cells with a Th1 bias. The IgG2a to IgG1 and (IgG2a+IgG2b) to (IgG1+IgG3) ratios were found 1{+/-}0.2 and 1.24{+/-}0.1, respectively. These values are comparatively higher than relevant values for other published SARS-CoV-2 vaccine in development,1, 2 and suggesting higher viral clearance capacity for our vaccine. The data suggested great promise for immediate translation of the technology to the clinic.

immunology↗

bioRxiv2019

Suppression of GABAergic transmission in the spinal dorsal horn induces pain-related behavior in a chicken model of spina bifida

Spina bifida aperta (SBA), one of the most common congenital malformations, causes various neurological disorders. Pain is a common complaint of patients with SBA. However, little is known about the neuropathology of SBA-related pain. Because loss of {gamma}-aminobutyric acid (GABA)ergic neurons in the spinal cord dorsal horn is associated with pain, we hypothesized the existence of cross-talk between SBA-related pain and alterations in GABAergic transmission in the spinal cord. Therefore, we investigated the kinetics of GABAergic transmission in the spinal cord dorsal horn in a chicken model of SBA. Neonatal chicks with SBA exhibited various pain-like behaviors, such as an increased number of vocalizations with elevated intensity (loudness) and frequency (pitch), reduced mobility, difficulty with locomotion, and escape reactions. Furthermore, the chicks with SBA did not respond to standard toe-pinching, indicating disruption of the spinal cord sensorimotor networks. These behavioral observations were concomitant with loss of GABAergic transmission in the spinal cord dorsal horn. We also found apoptosis of GABAergic neurons in the superficial dorsal horn in the early neonatal period, although cellular abnormalization and propagation of neurodegenerative signals were evident at middle to advanced gestational stages. In conclusion, ablation of GABAergic neurons induced alterations in spinal cord neuronal networks, providing novel insights into the pathophysiology of SBA-related pain-like complications.

neuroscience↗