Biology subjects

Haque, F.

Publications and source records attributed to Haque, F..

6 recordsLinked to original sources

bioRxiv2026

Exo-LAMP: A Rapid Extraction-Free Isothermal Assay for Exosomal mRNA Detection

Preeclampsia arises from early placental dysfunction that precedes clinical presentation, creating a need for molecular readouts that enable timely risk assessment. Placenta derived exosomes carry nucleic acid biomarkers with diagnostic potential, yet current analytical workflows rely on multistep isolation and extraction procedures that are slow and resource intensive. Here, we report Exo-LAMP, an extraction-free isothermal assay for detecting placental exosomal KISS1 mRNA, representing the first isothermal approach for exosomal mRNA detection. Placental alkaline phosphatase (PLAP) positive syncytiotrophoblast derived exosomes are selectively captured from biofluids using PLAP antibody conjugated magnetic beads within 20 minutes. Captured exosomes are treated with RNase inhibitor and lysed at 90C for 5 minutes, enabling direct RNA release while preserving transcript integrity and eliminating conventional extraction steps. The released RNA is analyzed in the same vessel by colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP), providing semi-quantitative readout within 25 to 30 minutes. The assay quantifies KISS1 mRNA across 103 to 108 exosomes per reaction, with an estimated limit of detection of about 2 exosomes and a limit of quantification of 103 exosomes. Stoichiometric analysis indicates approximately one KISS1 transcript per 27 exosomes, compared with one per 38 exosomes measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR). In both the exosome-depleted serum spike-in and the plasma spike-in samples containing mixed vesicle populations, the assay detects target derived transcripts at 1% abundance and retains measurable signal at the quantification limit in the presence of up to 108 non-target exosomes. These results establish Exo-LAMP as a rapid and simplified platform for exosomal mRNA analysis that integrates selective capture, lysis, and amplification in a single workflow completed in less than 1 hour. The method provides a general framework for semi-quantitative detection of exosomal transcripts and can be adapted to other coding and non-coding RNA targets for liquid biopsy applications.

bioengineering↗

bioRxiv2026

Pil-Chp orchestrates a multi-level regulatory system to control type IV pilus dynamics in Pseudomonas aeruginosa

The cyclical extension and retraction dynamics of type IV pili (T4P) mediate critical virulence traits in many bacterial species, yet how these dynamics are regulated remain poorly understood. Here, by analyzing individual pilus dynamics across mutants covering the entire T4P system of Pseudomonas aeruginosa, we identified active pili in several mutants previously classified as non-piliated. Correlating these dynamics with intracellular cAMP levels, transcriptional profiles, and T4P protein abundances reveals how the chemosensory Pil-Chp system controls T4P fiber length, count, extension rate, and polarity in surface-naive cells by modulating cAMP levels. Specifically, fiber length is tuned by modulating the effective association and dissociation rates of the extension ATPase PilB; fiber count is regulated by controlling machine abundance; and extension rate is limited by the abundance of the major pilin (PilA). Furthermore, we demonstrate that these regulatory mechanisms of T4P length and count differentially impact T4P-dependent functions: phage infection efficiency increases continuously with fiber count or length, whereas twitching motility exhibits step-like activation thresholding. This indicates that the functional output of T4P dynamics is strictly context dependent. Because the Pil-Chp system is conserved across diverse human and plant pathogens, this multi-level regulatory logic may represent a widespread mechanism controlling T4P-mediated virulence.

microbiology↗

bioRxiv2026

How the non-motile kinesin KIF7 adapts conserved kinesin principles for itsfunction in Hedgehog signaling

KIF7 is an atypical, non-motile kinesin that regulates Hedgehog signaling by concentrating GLI transcription factors at the cilium tip. How canonical kinesin principles for intracellular transport are repurposed to support KIF7s function as a signaling scaffold remains unclear. KIF7 exists in an autoinhibited state that is relieved by GLI binding, promoting microtubule association. We examined this regulatory mechanism by combining HDX-MS and AlphaFold modeling of a minimal KIF7 dimer, both alone and in complex with the GLI2 zinc-finger domain. Our HDX-MS data indicate that the highly negatively charged neck-coil dimerization domain of KIF7, which serves as the GLI2-binding site, is intramolecularly protected in the absence of GLI2. Consistent with this, AlphaFold models suggest that the motor domain folds back onto the neck-coil via KIF7s unusually long neck-linker, sterically occluding the microtubule-binding interface. This occurs through a mechanism conceptually analogous to, but structurally distinct from, autoinhibition in motile kinesins. GLI2 binding to the KIF7 neck-coil displaces the motor domain and induces allosteric changes that propagate to the microtubule-binding surface, thereby activating microtubule binding. ATP turnover further modulates KIF7s microtubule binding-unbinding equilibrium. Together, these findings reveal how a kinesin is adapted for a non-motile function as a scaffold in Hedgehog signaling.

biochemistry↗

bioRxiv2022

XLID Syndrome Gene Med12 Promotes Ig Isotype Switching through Chromatin Modification and Enhancer RNA regulation

The transcriptional co-activator Med12 regulates gene expression through the function of its kinase module and by interacting with the larger Mediator complex and associated RNA Polymerase II (RNAPII). Here, we show a kinase module-independent function of Med12 in antibody class switching recombination (CSR). Med12 is essential for IgH 3 regulatory region (3RR) or super-enhancer activation and functions with p300 and Jmjd6/Carm1 coactivator complexes. Med12 deficiency leads to a dramatic decrease in H3K27 acetylation and enhancer RNA (eRNA) transcription at 3RR, with concomitant impairment of AID-induced DNA double strand breaks, long-range S-S synapse formation, and 3RR-E interaction. CRISPR/dCas9-mediated enhancer activation re-establishes the epigenomic and transcriptional hallmarks of the 3RR super-enhancer, fully restoring Med12 depletion defects. Notably, we find that 3RR derived eRNAs are critical for promoting proper S region epigenetic regulation, S-S synapse formation and recruitment of Med12 and AID to the IgH locus. We find specific X-Linked intellectual disability syndrome associated Med12 mutations are defective in both 3RR eRNA transcription and CSR, suggesting B and neuronal cells may have cell-specific super-enhancer dysfunctions. We conclude Med12 is essential for IgH3RR activation and eRNA transcription and plays a central role in AID-induced antibody gene diversification and genomic instability in B cells.

immunology↗

bioRxiv2021

Cytoskeletal regulation of a transcription factor by DNA mimicry

A long-established strategy for transcription regulation is the tethering of transcription factors to cellular membranes. In contrast, the principal effectors of Hedgehog signaling, the Gli transcription factors, are regulated by microtubules in the primary cilium and the cytoplasm. How Gli is tethered to microtubules remains unclear. We uncover DNA mimicry by the ciliary kinesin Kif7 as a mechanism for the recruitment of Gli to microtubules, revealing a new mode of tethering a DNA-binding protein to the cytoskeleton. Gli increases the Kif7-microtubule affinity and consequently modulates the localization of both proteins to microtubules and the cilium tip. Thus, the kinesin-microtubule system is not a passive Gli tether but a regulatable platform tuned by the kinesin-transcription factor interaction. We re-tooled the unique DNA-mimicry-based Gli-Kif7 interaction for inhibiting the nuclear and cilium localization of Gli. This strategy can be potentially exploited for downregulating erroneously activated Gli in human cancers.

cell biology↗

bioRxiv2020

Gold-standard diagnostics are tarnished by lytic bacteriophage

BackgroundA fundamental clinical and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. MethodsCholera was chosen as a model disease to investigate this important question. Patients with diarrheal disease were enrolled at two remote hospitals in Bangladesh. Diagnostic performance was assessed as a function of lytic bacteriophage detection, as well as exposure to the first-line antibiotic azithromycin detected by mass spectrometry. ResultsAmong diarrheal samples positive by nanoliter quantitative PCR for Vibrio cholerae (n=78/849), the odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by 89% (OR 0.108; 95%CI 0.002-0.872) and 87% (OR 0.130; 95%CI 0.022-0.649) when lytic bacteriophage were detected, respectively. The odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by more than 99% (OR 0.00; 95% CI: 0.00-0.28) and 89% (OR 0.11; 95% CI: 0.03-0.44) when azithromycin was detected, respectively. ConclusionsEstimations of cholera burden may improve by accommodating for the negative effect of antimicrobial exposure on diagnostic positivity. Furthermore, the findings herein challenge our current approach to interpreting and developing bacterial diagnostics given variable rates of lytic bacteriophage and antibiotic exposure.

microbiology↗