Biology subjects

Ali, M. M.

Publications and source records attributed to Ali, M. M..

7 recordsLinked to original sources

bioRxiv2026

BMP2 signaling cooperates with retinoic acid to activate a meiotic-entry transcriptional program in chicken primordial germ cells

The initiation of meiosis in germ cells is largely regulated by extrinsic cues from the gonadal environment, but the logic of these signals remains poorly understood in non-mammalian vertebrates. Retinoic acid has long been considered a principal meiosis-inducing signal, yet recent genetic and reconstitution studies indicate that retinoic acid alone is insufficient. In mice, bone morphogenetic protein 2 cooperates with retinoic acid to establish the oogenic program through the bone morphogenetic protein-responsive transcriptional regulator Zglp1, but whether this regulatory logic is conserved beyond mammals is unknown. Here, using cultured chicken (Gallus gallus) primordial germ cells, we show that bone morphogenetic protein 2 cooperates with retinoic acid to promote a meiotic-entry transcriptional program. Retinoic acid alone induced a limited retinoic acid-responsive state, whereas combined treatment reduced the primordial germ cell program and activated early meiotic genes. The resulting transcriptome matched the premeiotic-to-meiotic-entry transition of the embryonic ovary in a single-cell atlas of chicken germ cells. We also generated a genome-edited primordial germ cell line carrying an SYCP3 promoter-green fluorescent protein reporter as a platform for dissecting meiotic-entry signals in culture. Comparative genomic analysis revealed Gallus-specific pseudogenization of ZGLP1, which is intact in closely related galliform species. Retinoic acid and bone morphogenetic protein may therefore act through a different downstream regulator in chicken. Article summaryEggs and sperm are produced by meiosis, a specialized cell division that starts during embryonic development. Retinoic acid, a signal derived from vitamin A, was long thought to be enough to start meiosis, but on its own it is not. In mice, a second signal, bone morphogenetic protein 2 (BMP2), works alongside retinoic acid to push germ cells toward the egg-producing program. We asked whether birds use the same combination. Giving both signals to chicken primordial germ cells in culture switched on genes for egg development and for the first steps of meiosis; retinoic acid alone did not. Birds and mammals last shared an ancestor more than 300 million years ago, so the pairing of these two signals appears to be an old feature of vertebrate germ cells. The cells stopped short of completing meiosis, which means other signals are still missing. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/740788v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@10b8b22org.highwire.dtl.DTLVardef@db9a08org.highwire.dtl.DTLVardef@15d9726org.highwire.dtl.DTLVardef@16e4dd3_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Structure of ER chaperone complex GRP170-ATP-BiP suggests a new model for substrate engagement

Molecular chaperones are essential for maintaining protein homeostasis in all living cells1. In the endoplasmic reticulum (ER), BiP and GRP170 are the sole representatives of Hsp70 and Hsp110 family and are critical for ER function. GRP170 is a relatively large and unusual chaperone that possess both nucleotide exchange and chaperoning activity2. The molecular mechanism by which these chaperones collaborate to engage substrate protein and how GRP170 couples its dual functionalities are not currently known. Here, we report the 2.7 [A] cryo-electron microscopy structure of GRP170-ATP-BiP chaperone complex purified from HEK293 cells that reveals a C-terminal curved hook domain, suggesting a role in substrate engagement in coordination with BiP. Additionally, we uncover the structural basis for GRP170 pseudo-ATPase chaperone activity - making it, to our knowledge, the first chaperone with this type of regulation. Our ER chaperone complex structure, together with prior cellular data3, suggests a new paradigm for how GRP170-BiP chaperones collaborate in ER protein quality control, broadening our understanding of how BiP/Hsp70 chaperones engage with substrates.

biochemistry↗

bioRxiv2025

A microfluidic gradient and parallel-track system uncovers spatial control of endocytosis and adhesion formation in breast cancer cell migration

Cell migration through confined spaces is a critical step in cancer metastasis, yet the spatial regulation of endocytosis and adhesion dynamics during this process remains poorly understood. To address this, we developed a microfluidic platform that generates stable, spatially linear biochemical gradients across 5 m-tall migration channels while limiting confounding flow-induced shear stress (<0.05 dyn/cm2). COMSOL simulations and optical calibration using FITC-dextran confirmed that gradients form reliably within 5 minutes. The microdevice also supports long-term live imaging and is compatible with both spinning disk confocal and total internal reflection fluorescence structured illumination microscopy modalities, enabling high-resolution visualization of adhesion and endocytic structures. Localized application of the endocytic inhibitor Dyngo-4a to the front or rear of migrating cells revealed that front-targeted inhibition significantly increased the enrichment of paxillin and the clathrin adaptor AP-2 at the leading edge, whereas rear-targeted inhibition completely abolished their front-rear asymmetry. These changes were accompanied by enhanced migration speed and persistence, particularly under front-targeted inhibition. Together, these findings highlight the critical role of spatially coordinated endocytosis in sustaining polarized adhesion and persistent cell movement. Our platform offers a powerful tool for dissecting subcellular mechanisms of migration under confinement and provides a broadly applicable framework for probing spatially localized signaling in engineered microenvironments.

cell biology↗

bioRxiv2025

Mechanisms of mitochondrial reactive oxygen species action in bone mesenchymal cells

Mitochondrial reactive oxygen species (mtROS), insufficient NAD+, and cellular senescence all contribute to the decrease in bone formation with aging. ROS can cause senescence and decrease NAD+, but it remains unknown whether these mechanisms mediate the effects of ROS in vivo. Here, we generated mice with deletion of the mitochondrial antioxidant enzyme Sod2 in Osx1-Cre (Sp7-tTA, tetO-EGFP/cre) targeted cells designated Sod2{Delta}Osx1 mice. We showed that Sod2 deletion caused low bone mass. Osteoblastic cells from these mice had impaired mitochondrial respiration and attenuated NAD+ levels. Administration of an NAD+ precursor improved mitochondrial function in vitro but failed to rescue the low bone mass of Sod2{Delta}Osx1 mice. Single-cell RNA-sequencing of bone mesenchymal cells indicated that ROS had no significant effects on markers of senescence but disrupted parathyroid hormone signaling, iron metabolism, and proteostasis. Our data support the rationale that treatment combinations aimed at decreasing mtROS and senescent cells and increasing NAD+ should confer additive effects in delaying age-associated osteoporosis.

cell biology↗

bioRxiv2024

OST component RPN1 is a novel regulator of IRE1 RNase activity that interacts with multiple distinct IRE1 and PERK complexes

The unfolded protein response (UPR) is an essential cell signalling system that regulates ER protein homeostasis. IRE1 and PERK are receptor proteins that propagate the UPR signal from the ER to the cytosol. Both receptors are suggested to interact with various proteins from different biological pathways, although the scale and scope of such interactions are unclear. Previous reconstitution experiments have utilized purified isolated domains of IRE1 and PERK to understand mechanism. Here, we affinity purify full length IRE1 and PERK from mammalian cells and characterise the complexes they form by biochemical techniques and assess RNase function in vivo. We identify RPN1 as a novel interacting protein present in complexes with IRE1 and PERK. In the Drosophila eye, RNAi knockdown of RPN1 results in loss of IRE1 RNase activity. This work provides a basis for understanding of protein interaction networks for IRE1 and PERK and identifies OST subunit RPN1 as a novel regulator of IRE1 RNase activity.

biochemistry↗

bioRxiv2024

Imipridones inhibit tumor growth and improve survival in an orthotopic liver metastasis mouse model of human uveal melanoma

PurposeUveal melanoma (UM) is a highly aggressive disease with very few treatment options. We previously demonstrated that mUM is characterized by high oxidative phosphorylation (OXPHOS). Here we tested the anti-tumor, signaling and metabolic effects of imipridones, CLPP activators which reduce OXPHOS indirectly and have demonstrated safety in patients. Experimental DesignWe assessed CLPP expression in UM patient samples. We tested the effects of imipridones (ONC201, ONC212) on the growth, survival, signaling and metabolism of UM cell lines in vitro, and for therapeutic effects in vivo in UM liver metastasis models. ResultsCLPP expression was confirmed in primary and mUM patient samples. ONC201/212 treatment of UM cell lines in vitro decreased OXPHOS effectors, inhibited cell growth and migration, and induced apoptosis. ONC212 increased metabolic stress and apoptotic pathways, inhibited amino acid metabolism, and induced cell death-related lipids. ONC212 also decreased tumor burden and increased survival in vivo in two UM liver metastasis models. ConclusionImipridones are a promising strategy for further testing and development in mUM.

cancer biology↗

bioRxiv2018

Epitope - based peptide vaccine against Fructose-bisphosphate aldolase (FBA) of Madurella mycetomatis using immunoinformatics approaches

BackgroundMycetoma is a distinct flesh eating and destructive neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections (actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi (eumycetoma) such as Madurella mycetomatis. Until date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma.\n\nThe aim of this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches.\n\nMethods and MaterialsFructose-bisphosphate aldolase of Madurella mycetomatis Sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominees epitopes in Immune Epitope Database for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.\n\nResults and ConclusionsThe proposed and promising peptides KYLQ shows a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC1 alleles and FFKEHGVPL that show a very strong binding affinity to MHC11and MHC1 alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against Fructose-bisphosphate aldolase of Madurella mycetomatis. This study recommends an in-vivo assessment for the most promising peptides especially FFKEHGVPL.

bioinformatics↗