Biology subjects

Mirza, R.

Publications and source records attributed to Mirza, R..

3 recordsLinked to original sources

bioRxiv2025

Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing

Background and objectivesVisible-light optical coherence tomography (vis-OCT) has enabled the visualization of retinal structures and functions beyond the capabilities of conventional OCTs. However, to reconstruct high-quality images, vis-OCT requires special post-processing, including balanced detection. An open-source, standardized vis-OCT data processing software is essential for clinical applications and translation of vis-OCT. MethodsWe developed Vis-OCT Explorer, an open-source, modular Python-based software for processing vis-OCT images. In addition to the standard spectral-domain OCT processing pipeline - including k-space resampling, dispersion compensation, and fast Fourier transformation - Vis-OCT Explorer offers unique dual-spectrometer balanced detection, short-time-Fourier transformation (STFT) based dispersion compensation coefficient optimization, and GPU-accelerated processing. We evaluated the reconstruction performance by quantifying a quality index extracted from individual B-scan images. We also assessed the repeatability of retinal thickness measurements by five operators on images acquired from different testing sites using the intraclass correlation coefficient (ICC) analysis. ResultsBalanced detection and STFT-based dispersion compensation significantly increased the quality index of reconstructed B-scan images. ICC values of the retinal nerve fiber layer (RNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness measurements from four testing sites exceeded 0.8 in 87.5% of the macular-centered images. The ICC of RNFL thickness measurements on all optic nerve head-centered images is above 0.8, showing strong repeatability across users. ConclusionsVis-OCT Explorer provides high-quality image processing and enables highly repeatable measurements on vis-OCT human retinal images. It facilitates future multicenter clinical tests to validate vis-OCTs clinical efficacy.

bioengineering↗

bioRxiv2023

NEK1-Mediated Phosphorylation of YAP1 is key to Prostate Cancer Progression

Understanding how Androgen-dependent PCa cells progress to independence and modify accordingly their transcriptional repertoire is the key to preventing mCRPC progression. We recently identified a novel axis of the Hippo pathway characterized by the sequential kinase cascade induced by androgen deprivation: AR->TLK1B>NEK1>pYAP1-Y407 leading to CRPC adaptation. Phosphorylation of YAP-Y407 increases upon ADT or induction of DNA damage, correlated with the known increase in NEK1 expression/activity, and this is suppressed in the Y407F mutant. Dominant expression of YAP1-Y407F in Hek293 cells reprograms the YAP1-mediated transcriptome to reduced TEAD- and P73-regulated gene expression and mediates sensitivity to MMC. NEK1 haploinsufficient TRAMP mice display reduced YAP1 expression and if castrated fail to progress to overt prostate carcinomas, even while displaying reduced E-CAD expression in hyperplastic ductules. YAP1 overexpression, but not the Y407F mutant, transforms LNCaP cells to androgen independent growth and a mesenchymal morphology. Immunohistochemical examination of Prostate Cancer biopsies revealed that pYAP1-Y407 nuclear signal is low in samples of low-grade cancer but elevated in high GS specimens. We also found that J54, pharmacological inhibitor of the TLK1>NEK1>YAP1 nexus, leading to degradation of YAP1 can suppress the transcriptional reprogramming of LNCaP cells to Androgen-Independent growth and EMT progression even when YAP1-WT is overexpressed.

cancer biology↗

bioRxiv2019

Lipin-1 contributes to IL-4 mediated macrophage polarization

Macrophage responses contribute to a diverse array of pathologies ranging from infectious disease to sterile inflammation. Polarization of macrophages determines their cellular function within biological processes. Lipin-1 is a phosphatidic acid phosphatase in which its enzymatic activity contributes to macrophage pro-inflammatory responses. Lipin-1 also possesses transcriptional co-regulator activity and whether this activity is required for macrophage polarization is unknown. Using mice that lack only lipin-1 enzymatic activity or both enzymatic and transcriptional coregulator activities from myeloid cells, we investigated the contribution of lipin-1 transcriptional co-regulator function towards macrophage wound healing polarization. Macrophages lacking both lipin-1 activities did elicit IL-4 mediated gene expression to levels seen in either wild-type or lipin-1 enzymatically deficient macrophages. Furthermore, we provide evidence that the lack of myeloid-associated lipin-1 transcriptional co-regulator activity leads to impaired full thickness excisional wound healing. Our study demonstrates that lipin-1 transcriptional co-regulatory activity contributes to macrophage polarization and the macrophage contribution to wound healing in vivo.

immunology↗