Biology subjects

Shaham, S.

Publications and source records attributed to Shaham, S..

At least 19 recordsLinked to original sources

bioRxiv2026

C. elegans E3 ubiquitin ligase EBAX-1 promotes non-apoptotic linker cell-type death through target-directed miRNA degradation

Programmed cell death is essential for animal development and homeostasis, and its disruption accompanies many human disorders. Linker cell-type death (LCD) is a morphologically conserved non-apoptotic developmental cell death program with features resembling polyglutamine-dependent neurodegeneration. In C. elegans, LCD execution is mediated by ubiquitin proteasome system (UPS) components, but their proteolytic targets are unknown. Here we demonstrate that EBAX-1/ZSWIM8, a conserved E3 ligase, promotes C. elegans LCD by target directed miRNA degradation (TDMD). We show that EBAX-1 acts cell-autonomously as part of the UPS and requires its Cullin-2 binding motif to promote LCD. Loss of mir-35 family miRNAs, argonautes, or miRNA biogenesis factors, restores LCD to ebax-1 mutants. Furthermore, expression of viln-1/villin mRNA, a predicted mir-35 target, is upregulated in dying cells and is required for LCD. Together, our studies suggest that TDMD mediated by EBAX-1 is important for the fidelity of non-apoptotic developmental cell death.

developmental biology↗

bioRxiv2025

Non-apoptotic death of the C. elegans linker cell is primed by MYRF-1 activation of pqn-41/polyQ

Linker cell-type death (LCD) is a morphologically conserved non-apoptotic cell-death process with features resembling polyglutamine-dependent neurodegeneration. In C. elegans development, LCD eliminates the male-specific linker cell following its long-range migration. Using single-cell mRNA sequencing of migrating and dying linker cells, we identify myrf-1, encoding a membrane-bound transcription factor implicated in human developmental disorders, as a key LCD regulator. MYRF-1 translocates to the linker cell nucleus during early migration and, surprisingly, its auxin-inducible degradation then, but not later, blocks LCD. MYRF-1 directly binds known LCD genes, including pqn-41, encoding an aggregation-prone polyglutamine protein. Deleting a bona fide MYRF-1-binding site within pqn-41 promotes linker cell survival. Our findings reveal that linker cell death is primed well before cell demise takes place, temporally uncoupling death commitment and execution.

cell biology↗

bioRxiv2025

C. elegans astrocytes mature in two phases from lineally distinct progenitors through CEH-43/DLX-mediated convergent transcription

Mammalian radial glia can remodel to become astrocytes, which acquire common transcriptional states despite spatially and lineally distinct origins. To uncover molecular programs driving convergent radial-glia-to-astrocyte transformation, we investigated development of C. elegans CEPsh astrocytes, which also arise from distinct progenitors without cell division. Using lineage-restricted single-cell RNA sequencing, we delineate a two-phase program for CEPsh astrocyte formation. Transcriptionally disparate nascent CEPsh glia rapidly acquire a common radial-glia-like state, facilitating nerve ring (brain) assembly. Subsequently, convergent CEPsh glia upregulate astrocyte-specific gene expression. Both phases require the distal-less transcription factor CEH-43, expressed in CEPsh glia and their progenitors. CEH-43 binds conserved astrocyte-expressed genes, cell-autonomously activating both early and late CEPsh glia-specific gene expression. CEH-43 misexpression is sufficient to induce CEPsh astrocyte reporter expression. We demonstrate that CEH-43 homologs, DLX1/2, are expressed in mouse astrocytes, and comparative transcriptomics reveal additional parallels. Our findings provide a molecular foundation for understanding cell-division-independent radial-glia-to-astrocyte transformation.

neuroscience↗

bioRxiv2025

CED-3 caspase promotes dismantling but not onset of non-apoptotic linker cell death in C. elegans

Nuclear degradation accompanies cell death. To study this process, we followed nuclear dismantling of the C. elegans linker cell, which undergoes non-apoptotic morphologically-conserved cell death characterized by nuclear envelope crenellations and cell splitting. We show that although linker cell death is cell autonomous, nucleus elimination follows engulfment and is blocked in rab-35 and arf-6 phagosome maturation mutants. Surprisingly, although linker cell death is independent of the apoptotic caspase CED-3, CED-3 is partially required within the linker cell, and upstream of RAB-35 and ARF-6, for cell splitting, engulfment, and nucleus elimination. In parallel studies, we found that the kinase inhibitor staurosporine causes mouse embryonic fibroblasts to undergo caspase-independent non-apoptotic death accompanied by nuclear crenellations and, paradoxically, by Caspase-3/7 activation. Our findings suggest mechanistic similarities between staurosporine-induced and linker cell death, revealing that, in some contexts, caspases do not initiate cell death but instead promote subcellular tasks required for cell clearance.

cell biology↗

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↗

bioRxiv2024

Astrocyte-derived extracellular matrix proteins regulate synapse remodeling in stress-induced depression

Major depressive disorder (MDD) is a common mood condition affecting multiple brain regions and cell types. Changes in astrocyte function contribute to depressive-like behaviors. However, while neuronal mechanisms driving MDD have been studied in some detail, molecular mechanisms by which astrocytes promote depression have not been extensively explored. To uncover astrocyte contributions to MDD, we subjected male mice to chronic social defeat stress precipitated by encounters with a dominant male. Animals exposed to this treatment exhibit symptoms indicative of MDD, including reduced social interactions, anxiety, despair, and anhedonia. We then measured astrocyte translating mRNA expression changes in mice that underwent chronic social defeat and control animals using ribosome affinity purification. Bioinformatic analyses reveal significant alterations in the prefrontal cortex (PFC), consistent with previous studies implicating this brain region in MDD. Expression of genes encoding extracellular matrix (ECM) proteins, cell-cell interaction proteins, and proteins controlling glutamatergic synaptic function are significantly altered. These changes correlate with perturbation of glutamatergic transmission, measured by electrophysiology, and increased synaptic cleft size. Among ECM genes, increased expression of mRNA encoding the synaptic remodeling protein secreted protein acidic and rich in cysteine (Sparc) correlates the most with the depressive phenotype. Furthermore, presence of SPARC and other ECM proteins in synaptosomes is also increased and overexpressing Sparc in PFC partially alleviates stress symptoms. Our results raise the possibility that increased expression of Sparc may be a natural protective mechanism against stress-induced synaptic dysfunction in depression.

neuroscience↗

bioRxiv2024

C. elegans LET-381/FoxF and DMD-4/DMRT control development of the mesodermal HMC endothelial cell

Endothelial cells form the inner layer of blood vessels and play key roles in circulatory system development and function. A variety of endothelial cell types have been described through gene expression and transcriptome studies; nonetheless, the transcriptional programs that specify endothelial cell fate and maintenance are not well understood. To uncover such regulatory programs, we studied the C. elegans Head Mesodermal Cell (HMC), a non-contractile mesodermal cell bearing molecular and functional similarities to vertebrate endothelial cells. Here, we demonstrate that a Forkhead transcription factor, LET-381/FoxF, is required for HMC fate specification and maintenance of HMC gene expression. DMD-4, a Dmrt transcription factor, acts downstream of and in conjunction with LET-381 to mediate HMC fate specification and gene expression maintenance. DMD-4, independently of LET-381, also represses the expression of genes associated with a different, non-HMC, mesodermal fate. Our studies uncover essential roles for FoxF transcriptional regulators in endothelial cell development, and suggest that the identity of FoxF co-functioning target transcription factors promotes specific non-contractile mesodermal fates.

developmental 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↗

bioRxiv2023

Glia detect and mount a protective response to loss of dendrite substructure integrity in C. elegans

Neurons have elaborate structures that determine their connectivity and functions. Changes in neuronal structure accompany learning and memory formation and are hallmarks of neurological disease. Here we show that glia monitor dendrite structure and respond to dendrite perturbation. In C. elegans mutants with defective sensory-organ dendrite cilia, adjacent glia accumulate extracellular matrix-laden vesicles, secrete excess matrix around cilia, alter gene expression, and change their secreted protein repertoire. Inducible cilia disruption reveals that this response is acute. DGS-1, a 7-transmembrane domain neuronal protein, and FIG-1, a multifunctional thrombospondin-domain glial protein, are required for glial detection of cilia integrity, and exhibit mutually-dependent localization to and around cilia, respectively. While inhibiting glial secretion disrupts dendritic cilia properties, hyperactivating the glial response protects against dendrite damage. Our studies uncover a homeostatic protective dendrite-glia interaction and suggest that similar signaling occurs at other sensory structures and at synapses, which resemble sensory organs in architecture and molecules.

neuroscience↗

bioRxiv2023

LET-381/FoxF and UNC-30/Pitx2 control the development of C. elegans mesodermal glia that regulate motor behavior.

While most CNS glia arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which ensheath the brain neuropil and separate it from the circulatory-system cavity. Transcriptome analysis suggests GLR glia merge astrocytic and endothelial characteristics relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naive cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and induces salt hypersensitivity, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neurons, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.

neuroscience↗

bioRxiv2023

Nucleus-Independent Transgenerational Small RNA Inheritance in C. elegans

Studies using C. elegans nematodes demonstrated that, against the dogma, animals can transmit epigenetic information transgenerationally. While it is now clear that in these worms ancestral RNA interference (RNAi) responses continue to regulate gene expression for many generations, it is still debated whether the primary agent that perpetuates heritable silencing is RNA or chromatin, and whether the information is communicated to the next generation inside or outside of the nucleus. Here we take advantage of the tractability of gene-specific double stranded RNA-induced heritable silencing to answer these questions. We demonstrate that RNAi can be inherited independently of any changes to the chromatin or any other nuclear factors via mothers that are genetically engineered to transmit only their ooplasm but not the oocytes nuclei to the next generation. Nucleus-independent RNA inheritance depends on ZNFX-1, an RNA-binding germ granule resident protein. We find that upon manipulation of normal germ granules functions (in pptr-1 mutants) nucleus-independent RNA inheritance becomes stronger, and can occur even in znfx-1 mutants. Utilizing RNA sequencing, chimeric worms, and sequence polymorphism between different C. elegans isolates, we identify endogenous small RNAs which, similarly to exogenous siRNAs, are inherited in a nucleus-independent manner. From an historical perspective, nucleus-independent inheritance of small RNAs might be regarded as partial vindication of discredited cytoplasmic inheritance theories from the 19th century, such as Darwins "pangenesis" theory.

genetics↗

bioRxiv2022

A developmental pathway for epithelial-to-motoneuron transformation in C. elegans

Motoneurons and motoneuron-like pancreatic beta cells arise from radial glia and ductal cells, both tube-lining progenitors that share molecular regulators. To uncover programs underlying motoneuron formation, we studied a similar, cell-division-independent transformation of the C. elegans tube-lining Y cell into the PDA motoneuron. We find that lin-12/Notch acts through ngn-1/Ngn and its regulator hlh-16/Olig to control transformation timing. lin-12 loss blocks transformation, while lin-12(gf) promotes precocious PDA formation. Early basal expression of both ngn-1/Ngn and hlh-16/Olig depends on sem-4/Sall and egl-5/Hox. Later, coincident with Y-cell morphological changes, ngn-1/Ngn expression is upregulated in a sem-4/Sall and egl-5/Hox-dependent but hlh-16/Olig-independent manner. Subsequently, Y-cell retrograde extension forms an anchored process priming PDA axon extension. Extension requires ngn-1-dependent expression of the cytoskeleton organizers UNC-119, UNC-44/ANK, and UNC-33/CRMP, which also, unexpectedly, activate PDA terminal-gene expression. Our findings reveal key cell-division-independent regulatory events leading to motoneuron generation, suggesting a conserved pathway for epithelial-to-motoneuron/motoneuron-like differentiation.

neuroscience↗

bioRxiv2021

Nuclear hormone receptors promote gut and glia detoxifying enzyme induction and protect C. elegans from the mold P. brevicompactum

Animals encounter microorganisms in their habitats, adapting physiology and behavior accordingly. The nematode Caenorhabditis elegans is found in microbe-rich environments; however, its responses to fungi are not extensively studied. Here we describe interactions of C. elegans and Penicillium brevicompactum, an ecologically-relevant mold. Transcriptome studies reveal that co-culture upregulates stress-response genes, including xenobiotic metabolizing enzymes (XMEs), in C. elegans intestine and AMsh glial cells. The nuclear hormone receptors (NHR) NHR-45 and NHR-156 are key induction regulators, and mutants that cannot induce XMEs in the intestine when exposed to P. brevicompactum experience mitochondrial stress and exhibit developmental defects. Different C. elegans wild isolates harbor sequence polymorphisms in nhr-156, resulting in phenotypic diversity in AMsh glia responses to microbe exposure. We propose that P. brevicompactum mitochondria-targeting mycotoxins are deactivated by intestinal detoxification, allowing tolerance to moldy environments. Our studies support the idea that C. elegans NHR gene expansion/diversification underlies adaptation to microbial environments.

cell biology↗

bioRxiv2020

Heritable Sexual Attraction under Parental Control

It is unknown whether transient transgenerational epigenetic responses to environmental challenges affect the process of evolution, which typically unfolds over many generations. Here we show that in C. elegans, inherited small RNAs shape the hard-wired genome and control genetic variation by regulating the decision of whether to self-fertilize or outcross. We found that under stressful temperatures younger hermaphrodites secrete a male-attracting pheromone. Attractiveness transmits transgenerationally to unstressed progeny via heritable small RNAs and the Argonaute Heritable-RNAi-Deficient-1. We identified an endogenous small interfering RNA pathway, enriched in endo-siRNAs which target sperm genes, that transgenerationally regulates sexual attraction, male prevalence, and outcrossing rates. Multigenerational mating competitions and mathematical simulations revealed that over generations, animals that inherit attractiveness mate more, and their alleles spread in the population. We propose that sperm serves as a "stress sensor" which, via small RNA inheritance, can promote outcrossing in challenging environments, when increasing genetic variation is advantageous.

molecular biology↗

bioRxiv2020

Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior

Glia in the central nervous system engulf neuron fragments during synapse remodeling and recycling of photoreceptor outer-segments. Whether glia passively clear shed neuronal debris, or actively remove neuron fragments is unknown. How pruning of single-neuron endings impacts animal behavior is also unclear. Here we report that adult C. elegans AMsh glia engulf sensory endings of the AFD thermosensory neuron. Engulfment is regulated by temperature, AFDs sensory input, and tracks AFD activity. Phosphatidylserine (PS) flippase TAT-1/ATP8A, functions with glial PS-receptor PSR-1/PSR and PAT-2/-integrin to initiate engulfment. Glial CED-10/Rac1 GTPase, acting through a conserved GEF complex, executes phagocytosis using the actin-remodeler WSP-1/nWASp and the membrane-sealing factor EFF-1 fusogen. CED-10 levels determine engulfment rates, and engulfment-defective mutants exhibit altered AFD-ending shape and thermosensory behavior. Our findings reveal a molecular pathway underpinning glia-dependent phagocytosis in a peripheral sense-organ, and demonstrate that glia actively engulf neuron-fragments, with profound consequences on neuron shape and animal behavior.

neuroscience↗

bioRxiv2020

C. elegans REMO-1, a glial GPCR, regulates stress-induced nervous system remodeling and behavior

Animal nervous systems remodel following stress. Although global stress-dependent changes are well documented, contributions of individual neuron remodeling events to animal behavior modification are challenging to study. In response to environmental insults, C. elegans become stress-resistant dauers. Dauer entry induces amphid sensory-organ remodeling, in which bilateral AMsh glial cells expand and fuse, allowing embedded AWC chemosensory neurons to extend sensory receptive endings. We show that amphid remodeling accelerates dauer exit upon exposure to favorable conditions, and identify a G protein-coupled receptor, REMO-1, driving AMsh glia fusion, AWC neuron remodeling, and dauer exit. REMO-1 is expressed in and localizes to AMsh glia tips, is dispensable for other remodeling events, and promotes stress-induced expression of the remodeling receptor tyrosine kinase VER-1. Our results demonstrate how single-neuron structural changes affect animal behavior, identify key glial roles in stress-induced nervous system shape changes, and demonstrate that remodeling primes animals to respond to favorable conditions.

neuroscience↗

bioRxiv2019

Lineage-specific control of convergent cell identity by a Forkhead repressor

During convergent differentiation, multiple developmental lineages produce a highly similar or identical cell type. However, few molecular players that drive convergent differentiation are known. Here, we show that the C. elegans Forkhead transcription factor UNC-130 is required in only one of three convergent lineages that produce the same glial cell type. UNC-130 acts transiently as a repressor in progenitors and newly-born terminal cells to allow the proper specification of cells related by lineage rather than by cell type or function. Specification defects correlate with UNC-130:DNA binding, and UNC-130 can be functionally replaced by its human homolog, the neural crest lineage determinant FoxD3. We propose that, in contrast to terminal selectors that activate cell-type specific transcriptional programs in terminally differentiating cells, UNC-130 acts early and specifically in one convergent lineage to produce a cell type that also arises from molecularly distinct progenitors in other lineages.

developmental biology↗

bioRxiv2018

Glutamate spillover in C. elegans triggers repetitive behavior through presynaptic activation of MGL-2/mGluR5

Glutamate is a major excitatory neurotransmitter, and impaired glutamate clearance following synaptic release promotes spillover, inducing extra-synaptic signaling. The effects of glutamate spillover on animal behavior and its neural correlates are poorly understood. We developed a glutamate spillover model in Caenorhabditis elegans by inactivating the conserved glial glutamate transporter GLT-1. GLT-1 loss drives aberrant repetitive locomotory reversal behavior through uncontrolled oscillatory release of glutamate onto AVA, a major interneuron governing reversals. Repetitive glutamate release and reversal behavior require the glutamate receptor MGL-2/mGluR5, expressed in RIM and other interneurons presynaptic to AVA. mgl-2 loss blocks oscillations and repetitive behavior; while RIM activation is sufficient to induce repetitive reversals in glt-1 mutants. Repetitive AVA firing and reversals require EGL-30/Gq, an mGluR5 effector. Our studies reveal that cyclic autocrine presynaptic activation drives repetitive reversals following glutamate spillover. That mammalian GLT1 and mGluR5 are implicated in pathological motor repetition suggests a common mechanism controlling repetitive behaviors.

neuroscience↗