Biology subjects

Elkhalil, A.

Publications and source records attributed to Elkhalil, A..

3 recordsLinked to original sources

bioRxiv2025

Mitochondria transported by Kinesin 3 prevent localized calcium spiking to inhibit caspase-dependent specialized cell death

Polarized cells (such as neurons), defined by distinct compartments are, like many cell types, subject to developmental elimination, as in neurite pruning. The molecular mechanism behind specialized elimination remains a largely open question. We previously introduced the "tri-partite" embryonic cell death program Compartmentalized Cell Elimination (CCE) in the scaffolding tail-spike epithelial cell and sex-specific CEM neurons of C. elegans. CCE is stereotyped and ordered, with three distinct programs eliminating three cell compartments, and bearing morphological hallmarks reminiscent of neurite pruning. Here we report first, that, prior to CCE onset, mitochondria undergo UNC-116/Kinesin 1-dependent irreversible retrograde transport; and second, that the caspase protease CED-3 promotes the completion of the proximal nicking event of CCE by helping inhibit the kinesin 3 homolog UNC-104. While known canonically to carry only synaptic vesicles, UNC-104/Kinesin 3, in the CCE context, and in the absence of CED-3/Caspase, can transport mitochondria anterogradely to the severing site. We observe both caspase activity and Ca2+ spiking at this site prior to nicking. Mitochondria appear to protect against nicking in the absence of CED-3 via their MCU-1 uniporter-dependent Ca2+ uptake capacity. Our study sheds light on the molecular machinery of specialized cell elimination and pruning, highlighting involvement of region-specific Ca2+ signaling, an anti-death function of mitochondria via local Ca2+ uptake, mitochondrial transport as a regulatory strategy, with UNC-116/kinesin 1-mediated retrograde transport important for cell elimination priming and UNC-104/kinesin 3 in a previously undescribed role as a non-canonical anterograde mitochondrial motor.

cell biology↗

bioRxiv2025

SQST-1/p62-regulated SKN-1/Nrf mediates a phagocytic stress response via transcriptional activation of lyst-1/LYST

Cells may be intrinsically fated to die to sculpt tissues during development or to maintain homeostasis. Cells can also die in response to various stressors, injury or pathological conditions. Additionally, cells of the metazoan body are often highly specialized with distinct domains that differ both structurally and with respect to their neighbors. Specialized cells can also die, as in normal brain development or pathological states and their different regions may be eliminated via different programs. Clearance of different types of cell debris must be performed quickly and efficiently to prevent autoimmunity and secondary necrosis of neighboring cells. All cells, including those programmed to die, may be subject to various stressors. Some largely unexplored questions include whether predestined cell elimination during development could be altered by stress, if adaptive stress responses exist and if polarized cells may need compartment-specific stress-adaptive programs. We leveraged Compartmentalized Cell Elimination (CCE) in the nematode C. elegans to explore these questions. CCE is a developmental cell death program whereby three segments of two embryonic polarized cell types are eliminated differently. We have previously employed this in vivo genetic system to uncover a cell compartment-specific, cell non-autonomous clearance function of the fusogen EFF-1 in phagosome closure during corpse internalization. Here, we introduce an adaptive response that serves to aid developmental phagocytosis as a part of CCE during stress. We employ a combination of forward and reverse genetics, CRISPR/Cas9 gene editing, stress response assays and advanced fluorescence microscopy. Specifically, we report that, under heat stress, the selective autophagy receptor SQST-1/p62 promotes the nuclear translocation of the oxidative stress-related transcription factor SKN-1/Nrf. This in turn allows SKN-1/Nrf to transcribe the lysosomal trafficking associated gene lyst-1/LYST which subsequently promotes the phagocytic resolution of the developmentally-killed internalized cell even under stress conditions. Author SummaryDuring development, cells can have many fates, one of which is to deliberately die. If a cells inherent ability to die is lost, unwanted cells remain, which can lead to pathologies such as abnormal brain development or cancer. Dead cell remains must also be fully and efficiently cleared away by being ingested and digested by other cells, to avoid autoimmunity. Cells that are destined to die, like any cell, can be subject to stress, which can change cell behavior. Moreover, cells fated to die often have highly intricate shapes, such as nerve cells in the brain, and their removal may entail different strategies for different regions of the cell. In this study, we have used the pre-destined "3-in-1" death of a structurally-complex cell in the roundworm C. elegans as a platform to describe the genetics behind how one cell bolsters its inherent ability to consume an area of another dying cell by mounting a response to environmental stress. Specifically, we report, to our knowledge for the first time, that a well-known stress-protective protein helps turns on a gene that helps ensure that ingested parts of dead cells are fully digested and removed.

cell biology↗

bioRxiv2024

EOR-1/PLZF-regulated WAH-1/AIF sequentially promotes early and late stages of non-apoptotic corpse removal

AbstractProgrammed cell death (PCD) is a crucial, genetically-encoded, and evolutionarily-conserved process required for development and homeostasis. We previously identified a genetically non-apoptotic, highly ordered, and stereotyped killing program called Compartmentalized Cell Elimination (CCE) in the C. elegans tail-spike epithelial cell (TSC). Here we identify the transcription factor EOR-1/PLZF as an important coordinator of CCE. Loss of EOR-1 results in a large, persisting, un-engulfed soma with enlarged nuclei. We find that EOR-1 and its partners positively regulate the transcription of the Apoptosis Inducing Factor AIF homolog, WAH-1/AIF. We report stereotyped and sequential spatiotemporal dynamics of WAH-1/AIF1 during phagocytosis, with defined roles acting early and late, within the dying cells. Mitochondria to plasma membrane translocation within the TSC soma is required its internalization by its phagocyte, and plasma membrane to nuclear translocation is required for DNA degradation and ultimately, corpse resolution. Our study suggests that EOR-1 serves as a master regulator for the transcriptional control of DNA degradation is essential for changes in nuclear morphology required for cellular dismantling and infers that tight spatiotemporal regulation of WAH-1/AIF is required for this function. Summary StatementThis work describes the genetic control and cellular dynamics of a factor linked to cancer, metabolic and degenerative disease acting in developmentally dying cells to instruct their own removal.

cell biology↗