Biology subjects

So, C.

Publications and source records attributed to So, C..

7 recordsLinked to original sources

bioRxiv2026

Single-Cell Profiling Reveals Developmental Trajectories and identifies SYK and TIM3 as Targets in some T Cell Lymphomas

T cell lymphomas (TCL) are a heterogeneous collection of malignancies whose origins and pathogenesis are poorly understood and for which few efficacious therapeutic options exist. Here, we conduct single-cell transcriptomic profiling spanning eight TCL entities and describe entity-associated programmes. We predict the cell of origin for these tumours through an integrative analysis of transcriptome and T cell receptor (TCR) maturation states. By identifying tumours with TCR states ranging from the pre-TCR through non-productive and productive TCR alpha and beta chain rearrangements we shed new light on their developmental origins. Furthermore, we apply our drug2cell computational drug target predictions with drug screens using patient-derived cell models, systematically benchmarking the performance of drug2cell and validating compounds and targets. This process identifies SYK inhibitors as a therapeutic opportunity and prioritises TIM3 for immunotherapy based on combined spatial transcriptomics analysis. Overall, our data provide a resource for diagnostics and therapies for tumours of critical unmet need.

cancer biology↗

bioRxiv2025

Separately prestored proteasome components to prevent polyspermy

To ensure genome stability across generations, an egg must be fertilized by only a single sperm. However, how sperm actively contribute to preventing polyspermy has remained unknown. Here, we demonstrate that testis-specific 20S proteasome core particles (CPs) are pre-stored within the sperm heads of both mice and humans. Upon fertilization, these testis-specific 20S CPs assemble with oocyte-derived 19S regulatory particles (RPs), forming chimeric proteasomes that efficiently degrade Fetuin B, which is ubiquitinated by the E3 ligase MARCH3. The clearance of Fetuin B triggers ZP2 cleavage and subsequent zona pellucida hardening, thereby blocking additional sperm entry. The newly assembled chimeric proteasome in the zygote represents a novel strategy to prevent polyspermy during fertilization in mammals.

developmental biology↗

bioRxiv2025

The Kelch 3 motif on gigaxonin mediates the interaction with NUDCD3 and regulates vimentin filament morphology

Gigaxonin is an intermediate filament (IF)-interacting partner belonging to the Kelch-like (KLHL) protein family. Gigaxonin is encoded by the KLHL16 gene, which is mutated in Giant Axonal Neuropathy (GAN). The lack of functional gigaxonin in GAN patient cells impairs IF proteostasis, leading to focal abnormal accumulations of IFs and compromised neuronal function. We hypothesized that gigaxonin forms molecular interactions via specific sequence motifs to regulate IF proteostasis. The goal of this study was to examine how distinct Kelch motifs on gigaxonin regulate IF protein degradation and filament morphology. We analyzed vimentin IFs in HEK293 cells overexpressing wild type (WT) gigaxonin, or gigaxonin lacking each of the six individual Kelch motifs: K1 (aa274-326), K2 (aa327-374), K3 (aa376-421), K4 (aa422-468), K5 (aa470-522), and K6 (aa528-574). All six gigaxonin deletion mutants ({Delta}K1-{Delta}K6) promoted the degradation of soluble vimentin. The {Delta}K3 gigaxonin mutant exhibited soluble vimentin degradation and promoted the bundling of vimentin IFs relative to WT gigaxonin. Using mass spectrometry proteomic analysis we found that, relative to WT gigaxonin, {Delta}K3 gigaxonin had increased associations with ubiquitination-associated and mitochondrial proteins and lost the association with the NudC domain-containing protein 3 (NUDCD3), a molecular chaperone enriched in the nervous system. Collectively, our cell biological data show the induction of an abnormal GAN-like IF phenotype in cells expressing {Delta}K3-gigaxonin, while our mass spectrometry profiling links the loss of gigaxonin-NUDCD3 interactions with defective IF proteostasis, revealing NUDCD3 as a potential new target in GAN.

cell biology↗

bioRxiv2024

A new metoposaurid (Temnospondyli) bonebed from the lower Popo Agie Formation (Carnian, Triassic) and an assessment of skeletal sorting in temnospondyls

Metoposaurid-dominated bonebeds are relatively commonplace in Upper Triassic continental deposits with at least ten monodominant, densely populated bonebeds globally. The biostratinomy of several classic localities in India, North America, and Poland have been explored in detail, however, variability in methods and resultant conclusions point to the need for a more nuanced approach to understanding both the taphonomic and the ecological origins of metoposaurid-dominated bonebeds. Here we present the first monodominant metoposaurid mass mortality assemblage from the Late Triassic Popo Agie Formation and the stratigraphically lowest known record of several fauna from the Popo Agie Fm including the first occurrence of the Buettnererpeton bakeri in Wyoming. We employ previously used binning methods based on perceived hydrodynamic equivalence ("Voorhies groups") to assess pre-burial skeletal sorting. We suggest a simple counting and normalization method that avoids the inherent bias introduced by the interpretation of hydrodynamic equivalence of skeletal elements in taxa that lack actualistic experimental data. In contrast to other North American metoposaurid bonebeds, the sedimentology and skeletal sorting analyses of the Nobby Knob quarry support an autochthonous origin of this assemblage in a fluvio-lacustrine system with relatively little pre-burial sorting. Despite differences in underlying assumptions regarding the dispersal potential of specific skeletal elements, binning methods tend to follow similar trends regardless of framework used to assess different assemblages.

paleontology↗

bioRxiv2024

Reconstitution of chromatin reorganization during mammalian oocyte development

SignificanceThe generation of developmentally competent eggs requires oocyte growth and maturation. When compared to meiotic maturation, relatively little is known about the key processes that happen in growing oocytes. Since the first visualization of oocyte chromatin under the electron microscope, we have known that growing oocytes undergo a fundamental transition from the non-surrounded nucleolus (NSN) to surrounded nucleolus (SN) chromatin configuration. NSN-to-SN transition is crucial for subsequent embryonic development after fertilization, but what drives NSN-to-SN transition during mammalian oocyte development is still unknown. Here we show that natural degradation of RNA polymerase II (RNAPII) by segregase and proteasome drives NSN-to-SN transition, challenging the conventional view that transcriptional silencing and NSN-to-SN transition are driven by independent epigenetic mechanisms in mammalian oocytes. The final step of oocyte growth, which reorganizes chromatin from the uncondensed, non-surrounded nucleolus (NSN) configuration to the condensed, surrounded nucleolus (SN) configuration, is essential for embryonic development after fertilization. However, the mechanism of NSN-to-SN transition remains unknown. Here, we identify RNA polymerase II (RNAPII) degradation as the key driver of this process. RNAPII inhibitors, but not nucleoside-based transcription inhibitors, swiftly induced RNAPII degradation and NSN-to-SN transition in oocytes. Strikingly, induced SN-like nuclei recapitulated epigenetic features, chromatin interactions and developmental potential in SN oocytes. Using segregase and proteasome inhibitors and the newly established scFv miniTrim-Away for nuclear proteins, we further demonstrate that RNAPII degradation is necessary and sufficient for NSN-to-SN transition in mouse and human. RNAPII degradation globally cleared RNAPII from transcriptionally active chromatin and increased chromatin dynamics, concomitantly leading to transcriptional silencing and chromatin rearrangement in oocytes. Our study elucidates the framework of chromatin reorganization in growing mammalian oocytes and provides an alternative source of fully grown oocyte nuclei, representing a milestone for the potential use of growing oocytes in reproductive medicine.

developmental biology↗

bioRxiv2022

Reduced oocyte quality and exacerbation of the maternal age effect are enduring consequences of low-level atrazine exposure in mouse

BACKGROUNDEgg development has unique features that render it vulnerable to environmental perturbation. The herbicide atrazine is an endocrine disruptor shown to have detrimental effects on reproduction across a number of vertebrate species. OBJECTIVESTo determine whether exposure to low levels of atrazine impairs meiosis in female mammals using a mouse model; in particular, whether and how the fidelity of oocyte chromosome segregation is affected, and whether the aging-related aneuploidy is exacerbated. METHODSFemale C57BL/6J mice were exposed to two levels of atrazine in drinking water, with the lower level corresponding to detected environmental contamination. To model exposure during development, atrazine was ingested by pregnant females at 0.5 days post coitum and continued until pups were weaned at 21 days post-partum. For adult exposure, 2-month-old females ingested atrazine for 3 months. For each exposure group, various indicators of oocyte quality were determined, including developmental capacity and chromosomal abnormalities during the two meiotic divisions. RESULTSDevelopmental exposure caused only minor effects on the fetal events of meiotic prophase-I and establishment of initial follicle pools. However, ovulation was enhanced while oocyte quality was significantly reduced. At the chromosome level, misalignment and numerical and structural abnormalities were increased at both meiotic divisions. Furthermore, fertilization efficiency was impaired in vitro, and apoptosis was elevated in blastocysts derived from the eggs of atrazine-exposed females. Similar levels of chromosomal defects were seen in oocytes following both developmental and adult exposure regimens suggesting that quiescent primordial follicles may be the consequential targets of atrazine. Importantly, defects were observed long after exposure was terminated. Moreover, dramatic increases in chromosomally abnormal oocytes were seen in older mice indicating that atrazine exposure during development exacerbates the effects of maternal aging on oocyte quality. Indeed, analogous to the effects of maternal age, atrazine exposure resulted in weakened cohesion between sister chromatids. CONCLUSIONLow-level atrazine exposure causes persistent changes to the female mammalian germline with potential consequences for reproductive lifespan and congenital disease.

pharmacology and toxicology↗

bioRxiv2020

Genetic and Genomic Resources to Study Natural Variation in Brassica rapa

ABSTRACTThe globally important crop Brassica rapa, a close relative of Arabidopsis, is an excellent system for modeling our current knowledge of plant growth on a morphologically diverse crop. The long history of B. rapa domestication across Asia and Europe provides a unique collection of locally adapted varieties that span large climatic regions with various abiotic and biotic stress tolerance traits. This diverse gene pool provides a rich source of targets with the potential for manipulation towards the enhancement of productivity of crops both within and outside the Brassicaceae. To expand the genetic resources available to study natural variation in B. rapa, we constructed an Advanced Intercross Recombinant Inbred (AI-RIL) population using B. rapa subsp. trilocularis (Yellow Sarson) R500 and the B. rapa subsp. parachinensis (Cai Xin) variety L58. Our current understanding of genomic structure variation across crops suggests that a single reference genome is insufficient for capturing the genetic diversity within a species. To complement this AI-RIL population and current and future B. rapa genomic resources, we generated a de novo genome assembly of the B. rapa subsp. trilocularis (Yellow Sarson) variety R500, the maternal parent of the AI-RIL population. The genetic map for the R500 x L58 population generated using this de novo genome was used to map QTL for seed coat color and revealed the improved mapping resolution afforded by this new assembly.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗