Biology subjects

Alkuraya, F. S.

Publications and source records attributed to Alkuraya, F. S..

6 recordsLinked to original sources

bioRxiv2026

Quantitative 3D cytoarchitecture of human brain organoids using light-sheet microscopy

Human brain organoids are valuable models for studying human brain development and disorders. Although organoids enable multi-omics analyses, understanding developmental mechanisms requires precise three-dimensional mapping of cell types and their dynamics within their cytoarchitecture. Traditional thin-section immunohistochemistry and imaging provide insights but disrupt spatial information. Light-sheet microscopy allows volumetric imaging of intact organoids, but methods and analytical algorithms remain technically challenging. Here, we introduce LUCID-org, an optimized and reproducible technique for Light-sheet imaging of Unsectioned, Cleared, Immunolabeled, and Depth-resolved human brain organoids. Coupled with machine-learning-based quantitative analysis, LUCID-org enables unbiased 3D characterization of cell-type composition and cytoarchitecture. We validated this approach using brain organoids derived from a patient with CENPJ-mutated microcephaly, revealing quantifiable defects in the ventricular zone (VZ), progenitor density, dynamics, cell-type variability, VZ lumen volume, and neuronal distribution compared with healthy controls. The LUCID-org pipeline is straightforward, taking approximately one week, significantly cheaper, non-toxic, and compatible with standard light-sheet microscopes. Therefore, the LUCID-org method could serve as a benchmark for comprehensive 3D analysis of human brain organoids.

developmental biology↗

bioRxiv2025

tRNA thiolation defects disrupt cellular proteostasis and tissue homeostasis in mammals

Sulfur modification of tRNA wobble uridines is an evolutionarily conserved mechanism that ensures efficient protein synthesis. In humans, loss of this anticodon modification due to mutations in CTU2 (cytosolic thiouridylase 2) causes DREAM-PL syndrome, a severe congenital disorder often leading to early postnatal death. However, the mechanisms by which loss of tRNA thiolation drives pathology remain unclear. Here, we show that loss of CTU2 triggers significant cellular proteostasis defects in patient cells and model cell lines. Structural and biochemical analyses reveal that the pathogenic CTU2L63P mutation destabilizes the CTU1/CTU2 complex and abolishes tRNA binding and thiolation. Acute loss of CTU2 caused codon-specific ribosome pausing at A-ending codons decoded by thiolated tRNAs, and decreased ribosome occupancy of A-rich transcripts in a dosage-dependent manner. Codon-biased mRNAs transcribed from genes critical for ciliogenesis are predicted to be most affected, linking their reduced translation to DREAM-PL etiology in humans. Surprisingly, Ctu2L63P mice display severe thiolation defects, but develop normally, are viable and fertile. Our findings highlight the importance of functional tRNA thiolation for organismal health in humans and identify species-specific vulnerabilities during embryonic development in mammals.

cell biology↗

bioRxiv2023

Bi-allelic variants in WDR47 lead to neuronal loss causing a rare neurodevelopmental syndrome with corpus callosum dysgenesis in humans.

The corpus callosum (CC) is the largest interhemispheric connection that is largely formed by the axons of layer 2/3 callosal projection neurons (CPNs) through a series of tightly regulated cellular events, including neuronal specification, migration, axon extension and branching. Defects in any of those steps may prevent the proper development of the corpus callosum resulting in a spectrum of disorders collectively referred to as corpus callosum dysgenesis (CCD). Here, we report four unrelated families carrying bi-allelic variants in WDR47 presenting with CCD together with other neuroanatomical phenotypes such as microcephaly, cerebellar abnormalities and hydrocephalus. Using a combination of in vitro and in vivo mouse models and complementation assays, we show that independently from its previously identified functions in neuronal migration and axonal extension, WDR47 is required for survival of callosal neurons by contributing to the maintenance of mitochondrial and microtubule homeostasis. We further provide evidence that severity of the CCD phenotype is determined by the degree of the loss of function caused by the human variants. Taken together, we identify WDR47 as a causative gene of a new neurodevelopmental syndrome characterized by corpus callosum abnormalities and other neuroanatomical malformations.

neuroscience↗

bioRxiv2021

WDR31 is a novel ciliopathy protein displaying functional redundancy with GTPase-activating proteins ELMOD and RP2 in recruiting BBSome to cilium

The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caenorhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into cilia and exit from cilia are impacted. Furthermore, anterograde IFT in the middle segment travel at increased speed in wdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into cilia of wdr-31;rpi-2;elmd-1 possible due to IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.

genetics↗

bioRxiv2018

EROS is required for phagocyte NADPH oxidase function in humans and its deficiency causes Chronic Granulomatous Disease.

The phagocyte respiratory burst is mediated by the phagocyte NADPH oxidase, a multi-protein subunit complex that facilitates production of reactive oxygen species and which is essential for host defence. Monogenic deficiency of individual subunits leads to chronic granulomatous disease (CGD), which is characterized by an inability to make reactive oxygen species, leading to severe opportunistic infections and auto-inflammation. However, not all cases of CGD are due to mutations in previously identified subunits. We recently showed that Eros, a novel and highly conserved ER-resident transmembrane protein, is essential for the phagocyte respiratory burst in mice because it is required for expression of gp91phox-p22phox heterodimer, which are the membrane bound components of the phagocyte NADPH oxidase. We now show that the function of EROS is conserved in human cells and describe a case of CGD secondary to a homozygous EROS mutation that abolishes EROS protein expression. This work demonstrates the fundamental importance of EROS in human immunity and describes a novel cause of CGD.\n\nClinical ImplicationsChronic granulomatous disease is caused by an inability to make reactive oxygen species via the phagocyte NADPH oxidase. Mutations in C17ORF62/EROS, which controls gp91phox- p22phox abundance, are a novel cause of chronic granulomatous disease.\n\nKey MessagesO_LIThe murine gene, Eros, is known to regulate abundance of gp91phox-p22phox heterodimer and Eros deficient mice are susceptible to infection\nC_LIO_LIWe show that the function of EROS is conserved in human cells and that a homozygous mutation in EROS causes chronic granulomatous disease\nC_LI

immunology↗

bioRxiv2018

Formation of tRNA wobble inosine in humans is perturbed by a millennia-old mutation linked to intellectual disability

The formation of inosine at the wobble position of eukaryotic tRNAs is an essential modification catalyzed by the ADAT2/ADAT3 complex. In humans, a valine to methionine mutation (V144M) in ADAT3 that originated [~]1,600 years ago is the most common cause of autosomal-recessive intellectual disability (ID) in Arabia. Here, we show that ADAT3-V144M exhibits perturbations in subcellular localization and has increased propensity to form aggregates associated with cytoplasmic chaperonins. While ADAT2 co-expression can suppress the aggregation of ADAT3-V144M, the ADAT2/3 complexes assembled with ADAT3-V144M exhibit defects in adenosine deaminase activity. Moreover, extracts from cell lines derived from ID-affected individuals expressing only ADAT3-V144M display a reduction in tRNA deaminase activity. Notably, we find that the same cell lines from ID-affected individuals exhibit decreased wobble inosine in certain tRNAs. These results identify a role for ADAT2-dependent localization and folding of ADAT3 in wobble inosine modification that is crucial for the developing human brain.

molecular biology↗