Biology subjects

Wiley, D.

Publications and source records attributed to Wiley, D..

5 recordsLinked to original sources

bioRxiv2024

RNA methylation controls stress granule formation and function during erythropoiesis

Stress granules (SGs) are crucial in RNA regulation, affecting cell fate and function. SGs contain RNAs, some of which can be methylated. We studied m6A RNA modifications during the human CD34+ HSPCs (hCD34+) differentiating into erythroid cells and found that mRNAs encoding many erythroid-specific proteins had decreased methylation during differentiation. Increased levels ALKBH5 demethylase during erythropoiesis controls the levels of the 3UTR methylation of these mRNAs. hCD34+ carrying ALKBH5 mutations demonstrated a block in erythropoiesis, and mass-spectrometry studies of the mutant cells showed decreased levels of SG proteins, including the core granule protein ATXN2. ALKBH5 directly regulates the methylation of the mRNA of ATXN2. ATXN2 overexpression accelerated the erythroid differentiation of HSPCs and rescued the erythroid differentiation of ALKBH5 mutant cells. Very few SGs are found in normal human erythroid progenitors. SGs accumulated substantially in ALKBH5 mutant cells, and surprisingly overexpression of ATNX2 reduced SG numbers to normal. Polysome analysis demonstrated m6A-modified RNAs to be enriched in the pre-polysome fractions that were less translated. This work establishes a mechanism by which during stress, ATXN2 facilitates the release of SG-stored m6A-modified RNAs including erythroid-specific and SG-enriched RNAs that are loaded onto functional ribosomes, allowing better translation and accelerated erythroid differentiation during stress.

cell biology↗

bioRxiv2024

Reduction of Neuroinflammation and Seizures in a Mouse Model of CLN1 Batten Disease using the Small Molecule Enzyme Mimetic, N-Tert-Butyl Hydroxylamine.

Infantile neuronal ceroid lipofuscinosis (CLN1 Batten Disease) is a devastating pediatric lysosomal storage disease caused by pathogenic variants in the CLN1 gene, which encodes the depalmitoylation enzyme, palmitoyl-protein thioesterase 1 (PPT1). CLN1 patients present with visual deterioration, psychomotor dysfunction, and recurrent seizures until neurodegeneration results in death, typically before fifteen years of age. Histopathological features of CLN1 include aggregation of lysosomal autofluorescent storage material (AFSM), as well as profound gliosis. The current management of CLN1 is relegated to palliative care. Here, we examine the therapeutic potential of a small molecule PPT1 mimetic, N-tert-butyl hydroxylamine (NtBuHA), in a Cln1-/- mouse model. Treatment with NtBuHA reduced AFSM accumulation both in vitro and in vivo. Importantly, NtBuHA treatment in Cln1-/- mice reduced neuroinflammation, mitigated epileptic episodes, and normalized motor function. Live cell imaging of Cln1-/- primary cortical neurons treated with NtBuHA partially rescued aberrant synaptic calcium dynamics, suggesting a potential mechanism contributing to the therapeutic effects of NtBuHA in vivo. Taken together, our findings provide supporting evidence for NtBuHA as a potential treatment for CLN1 Batten Disease.

neuroscience↗

bioRxiv2024

CDKN1B (p27kip1) enhances drug tolerant persister CTCs by restricting polyploidy following mitotic inhibitors.

The mitotic inhibitor docetaxel (DTX) is often used to treat endocrine-refractory metastatic breast cancer, but initial responses are mitigated as patients eventually have disease progression. Using a cohort of ex vivo cultures of circulating tumor cells (CTCs) from patients with heavily pretreated breast cancer (n=18), we find two distinct patterns of DTX susceptibility, independent of clinical treatment history. In CTCs cultured from some patients, treatment with a single dose of DTX results in complete cell killing, associated with accumulation of non-viable polyploid ([≥]8N) cells arising from endomitosis. In others, a transient viable drug-tolerant persister (DTP) population emerges, ultimately enabling renewed proliferation of CTCs with preserved parental cell ploidy and DTX sensitivity. In these CTC cultures, efficient cell cycle exit generates a [≤]4N drug-tolerant state dependent on CDKN1B (p27Kip1). Exposure to DTX triggers stabilization of CDKN1B through AKT-mediated phosphorylation at serine 10. Suppression of CDKN1B reduces the number of persister CTCs, increases [≥]8N mitotic cells and abrogates regrowth after DTX exposure. Thus, CDKN1B-mediated suppression of endomitosis contributes to a reversible persister state following mitotic inhibitors in patient-derived treatment refractory breast cancer cells. Summary in bulletsO_LITransient DTX tolerant persister cells emerge in some patient-derived cultured CTCs. C_LIO_LIDTX-tolerant persisters restrict endoreduplication and polyploidy through CDKN1 (p27kip1). C_LIO_LIDTX exposure induces CDKN1B stabilization through AKT mediated phosphorylation at serine 10. C_LIO_LISuppression of polyploidy underlies a drug tolerant persister state specific to mitotic inhibitors. C_LI

cancer biology↗

bioRxiv2021

Pose-gait analysis for cetaceans with biologging tags

Biologging tags are a key enabling tool for investigating cetacean behavior and locomotion in their natural habitat. Identifying and then parameterizing gait from movement sensor data is critical for these investigations. But how best to characterize gait from tag data remains an open question. Further, the location and orientation of the tag on an animal in the field are variable and can change multiple times during deployment. As a result, the relative orientation of the tag with respect to (wrt) the animal must be determined before a wide variety of further analyses. Currently, custom scripts that involve specific manual heuristics methods tend to be used in the literature. These methods require a level of knowledge and experience that can affect the reliability and repeatability of the analysis. The authors of this work argue that an animals gait is composed of a sequence of body poses observed by the tag, demonstrating a specific spatial pattern in the data that can be utilized for different purposes. This work presents an automated data processing pipeline (and software) that takes advantage of the common characteristics of pose and gait of the animal to 1) Identify time instances associated with occurrences of relative motion between the tag and animal; 2) Identify the relative orientation of tag wrt the animals body for a given data segment; and 3) Extract gait parameters that are invariant to pose and tag orientation. The authors included biologging tag data from bottlenose dolphins, humpback whales, and beluga whales in this work to validate and demonstrate the approach. Results show that the average relative orientation error of the tag wrt the dolphins body after processing was within 11 degrees in roll, pitch, and yaw directions. The average precision and recall for identifying relative tag motion were 0.87 and 0.89, respectively. Examples of the resulting pose and gait analysis demonstrate the potential of this approach to enhance studies that use tag data to investigate movement and behavior. MATLAB source code and data presented in the paper were made available to the public (https://github.com/ding-z/cetacean-pose-gait-analysis.git), with suggestions related to tag data processing practices provided in this paper. The proposed analysis approach will facilitate the use of biologging tags to study cetacean locomotion and behavior.

animal behavior and cognition↗

bioRxiv2020

Cdc42 GTPase Activating Proteins (GAPs) Maintain Generational Inheritance of Cell Polarity and Cell Shape in Fission Yeast

The highly conserved small GTPase Cdc42 regulates polarized cell growth and morphogenesis from yeast to humans. We previously reported that Cdc42 activation exhibits oscillatory dynamics in Schizosaccharomyces pombe cells. Mathematical modeling suggests that this dynamic behavior enables a variety of symmetric and asymmetric Cdc42 distributions to coexist in cell populations. For individual wild type cells, however, growth follows a stereotypical pattern where Cdc42 distribution is initially asymmetrical in young daughter cells and becomes more symmetrical as cell volume increases, enabling bipolar growth activation. To explore whether different states of Cdc42 activation are possible in a biological context, we examined S. pombe rga4{Delta} mutant cells, lacking the Cdc42 GTPase activating protein (GAP) Rga4. We found that monopolar rga4{Delta} mother cells divide asymmetrically leading to the emergence of both symmetric and asymmetric Cdc42 distributions in rga4{Delta} daughter cells. Using genetic screening approaches to identify mutants that alter the rga4{Delta} phenotype, we tested the predictions of different computational models that reproduce the unequal fate of daughter cells. We found experimentally that the unequal distribution of active Cdc42 GTPase in daughter cells is consistent with an unequal inheritance of another Cdc42 GAP, Rga6, in the two daughter cells. Our findings highlight the crucial role of Cdc42 GAP protein localization in determining the morphological fate of cell progeny and ensuring consistent Cdc42 activation and growth patterns across generations.

cell biology↗