Biology subjects

Wang, J. T.

Publications and source records attributed to Wang, J. T..

12 recordsLinked to original sources

bioRxiv2025

Loss of Sarm1 Mitigates Axonal and Neuronal Degeneration and Promotes Neuronal Repair After Ischemic Stroke

Axonal degeneration is a core feature of ischemic brain injury that limits functional recovery. The pro-degenerative molecule Sarm1 is required for Wallerian axon degeneration after traumatic and chemotoxic nerve injuries, however it is unclear if a similar mechanism mediates axonal degradation after ischemic injury. Here we show that loss of Sarm1 results in profound attenuation of axonal degeneration after focal ischemia to the subcortical white matter as well as to the cortex. Moreover, absence of Sarm1 significantly promotes the survival of neurons remote from but connected to the infarct after ischemic injuries to the subcortical white matter as well as to the cortex. Notably, loss of Sarm1 also significantly ameliorates early and late motor as well as cognitive deficits following white matter stroke. To further understand the mechanism of Sarm1-/- mediated neuronal protection, we performed differential gene expression analyses of wildtype and Sarm1-/- stroke-injured neurons and found that the loss of Sarm1 activates a pro-growth molecular program that promotes gene expression programs involved in axonogenesis and synaptogenesis after white matter ischemia. Using a functional genomics approach to recapitulate such a molecular program in Sarm1-/- neurons, we identify molecular compounds sufficient to enhance cortical neurite outgrowth in vitro, and all of which elicit a conserved epigenetic signature promoting axonogenesis. These results indicate that Sarm1 promotes axonal degeneration and concurrently inhibits an axonal reparative program encoded at the level of the epigenome that can be modulated pharmacologically. Our findings thus reveal a novel role for Sarm1 as a crucial regulator of both axonal degeneration and axonal repair after ischemic stroke.

neuroscience↗

bioRxiv2024

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

Multiple Myeloma (MM) remains incurable despite advances in treatment options. Although tumor subtypes and specific DNA abnormalities are linked to worse prognosis, the impact of immune dysfunction on disease emergence and/or treatment sensitivity remains unclear. We established a harmonized consortium to generate an Immune Atlas of MM aimed at informing disease etiology, risk stratification, and potential therapeutic strategies. We generated a transcriptome profile of 1,149,344 single cells from the bone marrow of 263 newly diagnosed patients enrolled in the CoMMpass study and characterized immune and hematopoietic cell populations. Associating cell abundances and gene expression with disease progression revealed the presence of a proinflammatory immune senescence-associated secretory phenotype in rapidly progressing patients. Furthermore, signaling analyses suggested active intercellular communication involving APRIL-BCMA, potentially promoting tumor growth and survival. Finally, we demonstrate that integrating immune cell levels with genetic information can significantly improve patient stratification.

genomics↗

bioRxiv2024

A delta-tubulin/epsilon-tubulin/Ted protein complex is required for centriole architecture

Centrioles have a unique, conserved architecture formed by three linked "triplet" microtubules arranged in nine-fold symmetry. The mechanisms by which these triplet microtubules are formed are not understood and likely involve the noncanonical tubulins delta-tubulin and epsilon-tubulin. Previously, we found that human cells deficient in delta-tubulin or epsilon-tubulin form abnormal centrioles, characterized by an absence of triplet microtubules, lack of central core protein POC5, and a futile cycle of centriole formation and disintegration (Wang et al., 2017). Here, we show that human cells lacking either of the associated proteins TEDC1 and TEDC2 have these same phenotypes. Using ultrastructure expansion microscopy, we find that mutant centrioles elongate to the same length as control centrioles in G2-phase. These mutants fail to recruit inner scaffold proteins of the central core and have an expanded proximal region. During mitosis, the mutant centrioles elongate further before fragmenting and disintegrating. All four proteins physically interact and TEDC1 and TEDC2 are capable forming a subcomplex in the absence of the tubulins. These results support an AlphaFold Multimer model of the tetramer in which delta-tubulin and epsilon-tubulin are predicted to form a heterodimer. TEDC1 and TEDC2 localize to centrosomes and are mutually dependent on each other and on delta-tubulin and epsilon-tubulin for localization. Our results demonstrate that delta-tubulin, epsilon-tubulin, TEDC1, and TEDC2 function together to promote robust centriole architecture. This work also lays the groundwork for future molecular studies of this complex, providing a basis for determining the mechanisms that underlie the assembly and interplay between the triplet microtubules and inner centriole structure.

cell biology↗

bioRxiv2023

Integrated characterization of cell types, states and molecular programs in disseminated appendiceal neoplasms

Appendiceal neoplasms include a heterogeneous group of epithelial and non-epithelial tumors with varying malignant potential. Despite the rise in incidence of appendiceal neoplasms in recent years, limited progress has been made in the understanding, management and therapeutic treatment. To comprehensively characterize the cell types and molecular mechanisms driving cellular remodeling in epithelial appendiceal neoplasms, we performed an integrated scRNA-seq study. We analyzed 126,998 cells from 16 appendix samples (11 peritoneal metastases samples, 5 healthy controls) and identified 33 distinct cell types/cell states with seven being cancer-specific. Highlights of our study include the characterization of tumor cells across the histologic spectrum, the identification of a novel cancer-associated-fibroblast (CAF) subtypes (fiCAFs) and the identification of pathologic-specific cellular crosstalk between tumor cells and the tumor microenvironment (TME). Together, our study provides a high-resolution insight into the complexity and heterogeneity of epithelial appendiceal neoplasms and a valuable resource for therapeutic strategies.

genomics↗

bioRxiv2023

MAP9/MAPH-9 supports axonemal microtubule doublets and modulates motor movement

Microtubule doublets (MTDs) are a well conserved compound microtubule structure found primarily in cilia. However, the mechanisms by which MTDs form and are maintained in vivo remain poorly understood. Here, we characterize microtubule-associated protein 9 (MAP9) as a novel MTD-associated protein. We demonstrate that C. elegans MAPH-9, a MAP9 homolog, is present during MTD assembly and localizes exclusively to MTDs, a preference that is in part mediated by tubulin polyglutamylation. Loss of MAPH-9 caused ultrastructural MTD defects, dysregulated axonemal motor velocity, and perturbed cilia function. As we found that the mammalian ortholog MAP9 localized to axonemes in cultured mammalian cells and mouse tissues, we propose that MAP9/MAPH-9 plays a conserved role in supporting the structure of axonemal MTDs and regulating ciliary motors.

cell biology↗

bioRxiv2022

Spindle assembly checkpoint-dependent mitotic delay is required for cell division in absence of centrosomes

The spindle assembly checkpoint (SAC) temporally regulates mitosis by preventing progression from metaphase to anaphase until all chromosomes are correctly attached to the mitotic spindle. Centrosomes refine the spatial organization of the mitotic spindle at the spindle poles. However, centrosome loss leads to elongated mitosis, suggesting that centrosomes also inform the temporal organization of mitosis in mammalian cells. Here we find that the mitotic delay in acentrosomal cells is enforced by the SAC in a MPS1-dependent manner, and that a SAC-dependent mitotic delay is required for bipolar cell division to occur in acentrosomal cells. Although acentrosomal cells become polyploid, polyploidy is not sufficient to cause dependency on a SAC-mediated delay to complete cell division. Rather, the division failure in absence of MPS1 activity results from mitotic exit occurring before acentrosomal spindles can become bipolar. Furthermore, prevention of centrosome separation suffices to make cell division reliant on a SAC-dependent mitotic delay. Thus, centrosomes and their definition of two spindle poles early in mitosis provide a "timely two-ness" that allows cell division to occur in absence of a SAC-dependent mitotic delay.

cell biology↗

bioRxiv2022

Calcineurin associates with centrosomes and regulates cilia length maintenance

Calcineurin, or PP2B, the Ca2+ and calmodulin-activated phosphatase and target of immunosuppressants, has many substrates and functions that remain undiscovered. By combining rapid proximity-dependent labeling with cell cycle synchronization, we mapped calcineurins spatial distribution in different cell cycle stages. While calcineurin-proximal proteins did not vary significantly between interphase and mitosis, calcineurin consistently associated with multiple centrosomal/ciliary proteins. These include POC5, which binds centrin in a Ca2+-dependent manner and is a component of the luminal scaffold that stabilizes centrioles. We show that POC5 contains a calcineurin substrate motif (PxIxIT-type) that mediates calcineurin binding in vivo and in vitro. Using indirect immunofluorescence and expansion microscopy, we demonstrate that calcineurin co-localizes with POC5 at the centrosome, and further show that calcineurin inhibitors alter POC5 distribution within the centriole lumen. Our discovery that calcineurin directly associates with centrosomal proteins highlights a role for Ca2+ and calcineurin signaling at these organelles. Calcineurin inhibition promotes primary cilia elongation without affecting ciliogenesis. Thus, Ca2+ signaling within cilia includes previously unknown functions for calcineurin in cilia length maintenance, a process frequently disrupted in ciliopathies. Summary statementCalcineurin phosphatase participates in centrosome and cilia regulation. Calcineurin localizes to centrosomes, where it interacts with partner POC5, and its inhibition promotes cilia elongation.

cell biology↗

bioRxiv2021

Long-range migration of centrioles to the apical surface of the olfactory epithelium

Olfactory sensory neurons (OSNs) in vertebrates detect odorants using multiple cilia, which protrude from the end of the dendrite and require centrioles for their formation. In mouse olfactory epithelium, the centrioles originate in progenitor cells near the basal lamina, often 50 to 100 m from the apical surface. It is unknown how centrioles traverse this distance or mature to form cilia. Using high-resolution expansion microscopy, we found that centrioles migrate together, with multiple centrioles per group and multiple groups per OSN, during dendrite outgrowth. Centrioles were found by live imaging to migrate slowly, with a maximum rate of 0.18 m/min. Centrioles in migrating groups were associated with microtubule nucleation factors, but acquired rootletin and appendages only in mature OSNs. The parental centriole had preexisting appendages, formed a single cilium prior to other centrioles, and retained its unique appendage configuration in the mature OSN. We developed an air-liquid interface explant culture system for OSNs and used it to show that centriole migration can be perturbed ex vivo by stabilizing microtubules. We consider these results in the context of a comprehensive model for centriole formation, migration, and maturation in this important sensory cell type.

cell biology↗

bioRxiv2019

Systematic discovery of Short Linear Motifs decodes calcineurin phosphatase signaling

Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches for SLiM discovery to elucidate the regulatory network of calcineurin (CN)/PP2B, the Ca2+-activated phosphatase that recognizes LxVP and PxIxIT motifs. In vitro proteome-wide detection of CN-binding peptides, in vivo SLiM-dependent proximity labeling, and in silico modeling of motif determinants uncovered unanticipated CN interactors, including NOTCH1, which we establish as a CN substrate. Unexpectedly, CN shows SLiM-dependent proximity to centrosomal and nuclear pore complex (NPC) proteins - structures where Ca2+ signaling is largely uncharacterized. CN dephosphorylates human and yeast NPC proteins and promotes accumulation of a nuclear transport reporter, suggesting conserved NPC regulation by CN. The CN network assembled here provides a resource to investigate Ca2+ and CN signaling and demonstrates synergy between experimental and computational methods, establishing a blueprint for examining SLiM-based networks.

cell biology↗

bioRxiv2018

Assembly of functionally antagonistic visual circuits for controlling pupil dynamics

HighlightsO_LITbx20 plays a role in the development of non-image-forming pathways.\nC_LIO_LILoss of Tbx20-expressing RGCs alters specific aspects of the pupil reflex arc.\nC_LIO_LIPreviously unknown role for a specific subset of Tbx20-expressing RGCs in modulating pupil size.\nC_LI\n\neTOCDhande et al. identify a novel genetic program that marks and is required for the development of non-image-forming parallel visual pathways. Moreover, chemogenetic activation of a specific retina-to-OPN pathway reveals a novel circuit element controlling pupil size. These findings provide new insight into the mechanisms that establish defining features of functionally specialized sensory pathways.\n\nSummaryThe functional attributes of parallel sensory circuits are determined by the properties of the individual cell types that comprise them, and their connectivity. The mechanisms controlling the specification and establishment of parallel sensory pathways remain unclear. Here we report the non-uniform distribution of retinal ganglion cells (RGCs) expressing the transcription factor Tbx20 in mice. Owing to their layout within the retina, Tbx20-RGCs are positioned to preferentially encode light information from dorsal visual space. We discovered that Tbx20 expression is mostly restricted to three RGC-types: M1 intrinsically photosensitive RGCs (ipRGCs), M2 ipRGCs and diving RGCs. The axonal projections of Tbx20-RGCs innervate non-image-forming brain centers including the suprachiasmatic nucleus, the medial division of the posterior pretectal nucleus, and the olivary pretectal nucleus (OPN), a principal station in the neural pathway for generating the pupillary light reflex (PLR). Conditional deletion of Tbx20 resulted in reduced Tbx20-RGC axonal innervation of these targets and revealed a key role of these neurons in driving specific phases of the PLR. Furthermore, chemogenetic activation uncovered a novel role for a specific subset of Tbx20-RGCs in controlling pupil dilation. These data offer a new understanding of the genetic and molecular mechanisms that establish specific, behaviorally-relevant visual circuits.

neuroscience↗

bioRxiv2018

Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include architectural proteins--such as CTCF, RAD21 and SMC3--that are involved in tethering chromatin loops and marking domain boundaries. The 3D organization of the mammalian genome is intimately linked to its function and is remarkably conserved. However, the mechanisms by which these structural intricacies emerge and evolve have not been thoroughly probed. Here we show that TEs contribute extensively to both the formation of species-specific loops in humans and mice via deposition of novel anchoring motifs, as well as to the maintenance of conserved loops across both species via CTCF binding site turnover. The latter function demonstrates the ability of TEs to contribute to genome plasticity and reinforce conserved genome architecture as redundant loop anchors. Deleting such candidate TEs in human cells leads to a collapse of such conserved loop and domain structures. These TEs are also marked by reduced DNA methylation and bear mutational signatures of hypomethylation through evolutionary time. TEs have long been considered a source of genetic innovation; by examining their contribution to genome topology, we show that TEs can contribute to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture globally, revealing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation.\n\nOne-sentence summaryCo-option of transposable elements maintains conserved 3D genome structures via CTCF binding site turnover in human and mouse.

genomics↗

bioRxiv2017

Centriole triplet microtubules are required for stable centriole formation and inheritance in human cells

Centrioles are composed of long-lived microtubules arranged in nine triplets. In unicellular eukaryotes, loss of the noncanonical tubulins, delta-tubulin and epsilon tubulin, result in loss of the triplet microtubule structure. However, the contribution of triplet microtubules to mammalian centriole formation and stability is unknown. Here, we report the first characterization of delta-tubulin and epsilon-tubulin null human cells. Centrioles in cells lacking either delta-tubulin or epsilon-tubulin lack triplet microtubules and fail to undergo centriole maturation. These aberrant centrioles are formed de novo each cell cycle, but are unstable and do not persist to the next cell cycle, leading to a futile cycle of centriole formation and disintegration. Disintegration can be suppressed by paclitaxel treatment. Delta-tubulin and epsilon-tubulin physically interact, indicating that these tubulins act together to maintain triplet microtubules and that these are necessary for inheritance of centrioles from one cell cycle to the next.

cell biology↗