Biology subjects

Zaki, H.

Publications and source records attributed to Zaki, H..

5 recordsLinked to original sources

bioRxiv2026

Inflammation is an essential trigger for POLE-driven ultramutated colorectal cancer

Pathogenic variants in the exonuclease (proofreading) domain of DNA polymerase {varepsilon} (POLE) are frequently detected in colorectal cancers (CRC) with high tumor mutational burden (TMB), yet their functional role in intestinal tumorigenesis remains unknown. Here, we investigated the impact of mutation in POLE on intestinal homeostasis using a conditional mouse model expressing the PoleP286R pathogenic driver in intestinal epithelial cells. PoleP286R mutant mice developed invasive adenocarcinomas in the small intestine with incomplete penetrance and extremely long latency but did not spontaneously develop colorectal tumors. However, induction of colitis with dextran sodium sulfate (DSS) resulted in a striking phenotypic shift to colorectal adenocarcinomas at high frequency. Molecular and histological analyses revealed hyperactivation of Wnt/{beta}-catenin, NF-{kappa}B, ERK and STAT3 pathways, accompanied by markedly higher proliferation of intestinal epithelial cells, in DSS-treated PoleP286R mutant mouse colons. Whole genome sequencing of the tumor demonstrated exceptionally high TMB (>100 mutations/megabase) and characteristic trinucleotide signatures, consistent with human POLE tumors. Recurrent mutations in Apc and Ctnnb1 underscored the central role of Wnt signaling in POLE-driven hypermutated CRC. In addition, intestinal organoids derived from PoleP286R mutant mice exhibited accelerated growth and increased expression of pro-proliferative genes. Together, these findings highlight POLE as a gatekeeper of intestinal genomic integrity and identify inflammation as the key driver that unleashes POLE-mutant CRC. Furthermore, this work establishes a mechanistically faithful preclinical platform for studying the molecular pathogenesis of CRC and advancing therapeutic drug discovery.

cancer biology↗

bioRxiv2024

Genetic removal of Nlrp3 protects against sporadic and R345W Efemp1-induced basal laminar deposit formation

Chronic, unresolved inflammation has long been speculated to serve as an initiating and propagating factor in numerous neurodegenerative diseases, including a leading cause of irreversible blindness in the elderly, age-related macular degeneration (AMD). Intracellular multiprotein complexes called inflammasomes in combination with activated caspases facilitate production of pro-inflammatory cytokines such as interleukin 1 beta. Specifically, the nucleotide-binding oligomerization (NOD)-like receptor protein 3 (NLRP3) has received heightened attention due to the wide range of stimuli to which it can respond and its potential involvement in AMD. In this study, we directly tested the role of Nlrp3 and its downstream effector, caspase 1 (Casp1) in mediating early AMD-like pathology (i.e., basal laminar deposits [BLamDs]) in wild-type (WT) mice and the Malattia Leventinese/Doyne honeycomb retinal dystrophy (ML/DHRD) mouse model (p.R345W mutation in Efemp1). Compared to aged-matched controls, R345W+/+ knockin mice demonstrated increased Muller cell gliosis, subretinal Iba-1+ microglial cells, higher Nlrp3 immunoreactivity in the retina, as well as significant transcriptional upregulation of complement component 3, Nlrp3, pro-Il1b, pro-caspase-1, and tissue inhibitor of matrix metalloproteinase 3 in the retinal pigmented epithelium (RPE)/choroid. These findings were accompanied by an age-related increase in BLamD formation in the R345W+/+ mice. Genetic elimination of either Nlrp3 or Casp1 significantly reduced both the size and coverage of BLamDs in the R345W+/+ background, highlighting an important and underappreciated pathway that could affect ML/DHRD onset and progression. Moreover, Nlrp3 knockout reduced spontaneous, idiopathic BLamDs in WT mice, suggesting translatability of our findings not only to rare inherited retinal dystrophies, but also potentially to AMD itself.

immunology↗

bioRxiv2022

Distinct mechanisms of germ cell factor regulation for an inductive germ cell fate

Specification of primordial germ cells (PGCs), the lineage which gives rise to eggs and sperm, is essential for sexually reproducing organisms. The mechanism by which animals specify their PGCs generally falls into two categories: inherited or inductive. The inductive mechanism, used by mammals, relies on cell signaling interactions to direct a subset of embryonic cells to a germ cell fate. Previous work suggested that sea star embryos, which develop in simple culture and are markedly transparent, also use inductive mechanisms to specify their germline. The germ cell factors Nanos and Vasa become restricted during early development into a localized region of cells within the posterior enterocoel (PE), the presumptive germline. Nodal signaling was observed to negatively regulate Vasa and Nanos mRNAs outside of the PE and restrict the germline to the PE. Here we employed single cell RNA sequencing to identify the transcriptional program of germ cells and their changes during development. We never see Nodal pathway members within Nanos/Vasa positive cells in the region known to give rise to the PE, and instead see members of the Wnt-signaling pathway and the FoxY family of transcription factors. We learned that Wnt and Delta/Notch signaling enhances expression of both Nanos and Vasa, whereas a test of cell interactions reveals that Nanos and Vasa are regulated distinctly. This work provides insights into the sequence of events that leads to PGC specification and enables deeper mechanistic studies in a tractable in vivo model. HighlightsO_LISingle-cell RNA-sequencing of sea star embryos demonstrates temporal differences in cell fate commitment among echinoderms. C_LIO_LISea urchin and sea star embryos appear to ascribe their germ line by two extreme different mechanisms but share similar pathways in regulation of the germline genes. C_LIO_LIExpression of the germline factors, Vasa and Nanos, is regulated by distinct mechanisms in the sea star. C_LIO_LIGermline induction in the sea star uses similar signaling mechanisms as mammals. C_LI

developmental biology↗

bioRxiv2021

Larval zebrafish exhibit collective motion behaviors in constrained spaces

Collective behavior may be elicited or can spontaneously emerge by a combination of interactions with the physical environment and conspecifics moving within that environment. To investigate the relative contributions of these factors in a small millimeter-scale swimming organism, we observed larval zebrafish, interacting at varying densities under circular confinement. Our aim was to understand the biological and physical mechanisms acting on these larvae as they swim together inside circular confinements. If left undisturbed, larval zebrafish swim intermittently in a burst and coast manner and are socially independent at this developmental stage, before shoaling behavioral onset. We report here our analysis of a new observation for this well-studied species: in circular confinement and at sufficiently high densities, the larvae collectively circle rapidly alongside the boundary. This is a new physical example of self-organization of mesoscale living active matter driven by boundaries and environment geometry. We believe this is a step forward toward using a prominent biological model system in a new interdisciplinary context to advance knowledge of the physics of social interactions.

animal behavior and cognition↗

bioRxiv2021

SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-κB pathway

Pathogenesis of COVID-19 is associated with a hyperinflammatory response; however, the precise mechanism of SARS-CoV-2-induced inflammation is poorly understood. Here we investigated direct inflammatory functions of major structural proteins of SARS-CoV-2. We observed that spike (S) protein potently induces inflammatory cytokines and chemokines including IL-6, IL-1{beta}, TNFa, CXCL1, CXCL2, and CCL2, but not IFNs in human and mouse macrophages. No such inflammatory response was observed in response to membrane (M), envelope (E), and neucleocapsid (N) proteins. When stimulated with extracellular S protein, human lung epithelial cells A549 also produce inflammatory cytokines and chemokines. Interestingly, epithelial cells expressing S protein intracellularly are non-inflammatory, but elicit an inflammatory response in macrophages when co-cultured. Biochemical studies revealed that S protein triggers inflammation via activation of the NF-{kappa}B pathway in a MyD88-dependent manner. Further, such an activation of the NF-{kappa}B pathway is abrogated in Tlr2-deficient macrophages. Consistently, administration of S protein induces IL-6, TNF-a, and IL-1 {beta} in wild-type, but not Tlr2-deficient mice. Together these data reveal a mechanism for the cytokine storm during SARS-CoV-2 infection and suggest that TLR2 could be a potential therapeutic target for COVID-19.

immunology↗