Biology subjects

Eldeeb, M.

Publications and source records attributed to Eldeeb, M..

4 recordsLinked to original sources

bioRxiv2023

TOM20 Gates PINK1 Activity And Mediates Its Tethering Of The TOM And TIM23 Translocases Upon Mitochondrial Stress

Mutations in PTEN-induced putative kinase 1 (PINK1) cause autosomal recessive early onset Parkinson disease (PD). PINK1 is a Ser/Thr kinase that regulates mitochondrial quality control by triggering mitophagy mediated by the ubiquitin ligase Parkin. Upon mitochondrial damage, PINK1 accumulates on the outer mitochondrial membrane (OMM) forming a high molecular weight complex with the translocase of the outer membrane (TOM). PINK1 then phosphorylates ubiquitin, which enables recruitment and activation of Parkin followed by autophagic clearance of the damaged mitochondrion. Thus, Parkin-dependent mitophagy hinges on the stable accumulation of PINK1 on the TOM complex. Yet, the mechanism linking mitochondrial stressors to PINK1 accumulation and whether the translocases of the inner membrane (TIMs) are also involved, remain unclear. Herein, we demonstrate that mitochondrial stress induces the formation of a PINK1-TOM-TIM23 supercomplex in human cultured cell lines, dopamine neurons, and midbrain organoids. Moreover, we show that PINK1 is required to stably tether the TOM to TIM23 complexes in response to stress, such that the supercomplex fails to accumulate in cells lacking PINK1. This tethering is dependent on an interaction between the PINK1 NT-CTE module and the cytosolic domain of the Tom20 subunit of the TOM complex, the disruption of which, by either designer or PD-associated PINK1 mutations, inhibits downstream mitophagy. Together, the findings provide key insight into how PINK1 interfaces with the mitochondrial import machinery, with important implications for the mechanisms of mitochondrial quality control and PD pathogenesis.

biochemistry↗

bioRxiv2021

Structure of PINK1 reveals autophosphorylation dimer and provides insights into binding to the TOM complex

Mutations in PINK1 causes autosomal-recessive Parkinsons disease. Mitochondrial damage results in PINK1 import arrest on the Translocase of the Outer Mitochondrial Membrane (TOM) complex, resulting in the activation of its ubiquitin kinase activity by autophosphorylation and initiation of Parkin-dependent mitochondrial clearance. Herein we report crystal structures of the entire cytosolic domain of insect PINK1. Our structures reveal a dimeric autophosphorylation complex targeting phosphorylation at the invariant Ser205 (human Ser228). The dimer interface requires insert 2, which is unique to PINK1. The structures also reveal how an N-terminal helix binds to the C-terminal extension and provide insights into stabilization of PINK1 on the core TOM complex.

biochemistry↗

bioRxiv2020

Nabo - a framework to define leukemia-initiating cells and differentiation in single-cell RNA-sequencing data

Single-cell transcriptomics facilitates innovative approaches to define and identify cell types within tissues and cell populations. An emerging interest in the cancer field is to assess the heterogeneity of transformed cells, including the identification of tumor-initiating cells based on similarities to their normal counterparts. However, such cell mapping is often confounded by the large effects on total gene expression programs introduced by strong perturbations such as an oncogenic event. Here, we present Nabo, a novel computational method that allows mapping of cells from one population to the most similar cells in a reference population, independently of confounding changes to gene expression programs initiated by perturbation. We validated this method on multiple datasets from different sources and platforms and show that Nabo achieves higher rates of accuracy than conventional classification methods. Nabo is available as an integrated toolkit for preprocessing, cell mapping, differential gene expression identification, and visualization of single-cell RNA-Seq data. For exploratory studies, Nabo includes methods to help evaluate the reliability of cell mapping results. We applied Nabo on droplet-based single-cell RNA-Seq data of healthy and oncogene-induced (MLL-ENL) hematopoietic progenitor cells (GMLPs) differentiating in vitro. Despite a substantial cellular heterogeneity resulting from differentiation of GMLPs and the large transcriptional effects induced by the fusion oncogene, Nabo could pinpoint the specific cell stage where differentiation arrest occurs, which included an immunophenotypic definition of the tumor-initiating population. Thus, Nabo allows for relevant comparison between target and control cells, without being confounded by differences in population heterogeneity.

bioinformatics↗

bioRxiv2018

HSCs contribute actively to native multilineage hematopoiesis but with reduced differentiation capacity upon aging

A hallmark of adult hematopoiesis is the continuous replacement of blood cells with limited lifespans. It is well established that adult hematopoietic stem cells (HSCs) are active contributors to these processes after transplantation, yet their role in native hematopoiesis has recently been called into question. Here, we use inducible lineage tracing from genetically marked adult HSCs to explore their roles in the steady state. We show that adult HSCs contribute robustly to all lineages via intermediate progenitor cells, but with neglible production of hematopoietic cells with a known fetal origin. We further reveal that the timing for regeneration of distinct blood lineages varies substantially. Finally, HSC contribution to multilineage hematopoiesis in aged animals declines with increasing age. Therefore, while HSCs are active contributors to native adult hematopoiesis, it appears that the numerical increase of HSCs is a physiologically relevant compensatory mechanism to account for a reduced differentiation capacity with age.

developmental biology↗