Biology subjects

Ding, R.

Publications and source records attributed to Ding, R..

42 records · Page 3Linked to original sources

bioRxiv2021

Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1

The N-end rule pathway was one of the first ubiquitin (Ub)-dependent degradation pathways to be identified. Ubr1, a single-chain E3 ligase, targets proteins bearing a destabilizing residue at the N-terminus (N-degron) for rapid K48-linked ubiquitination and proteasome-dependent degradation. How Ubr1 catalyses the initiation of ubiquitination on the substrate and elongation of the Ub chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here, we report the cryo-electron microscopy structures of two complexes representing the initiation and elongation intermediates of Ubr1 captured using chemical approaches. In these two structures, Ubr1 adopts different conformations to facilitate the transfer of Ub from Ubc2 to either an N-degron peptide or a monoubiquitinated degron. These structures not only reveal the architecture of the Ubr1 complex but also provide mechanistic insights into the initiation and elongation steps of ubiquitination catalysed by Ubr1.

biophysics↗

bioRxiv2020

The expression of PDCD1 and CD274 in T cells and macrophages correlated positively with COVID-19 severity

The immune responses underlying the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unclear. To help understand the pathology of coronavirus disease 2019 (COVID-19) pandemics, public data were analyzed and the expression of PDCD1 (encoding PD-1) and CD274 (encoding PD-L1) in T cells and macrophages were identified to correlate positively with COVID-19 severity.

immunology↗

bioRxiv2020

Single-cell transcriptome analysis of the immunosuppressive effect of differential expression of tumor PD-L1 on responding TCR-T cells

PD-L1 expression levels in tumors do not consistently predict cancer patients response to PD-(L)1 inhibitors. We therefore evaluated how tumor PD-L1 levels affect the anti-PD-(L)1 efficacy and T cell function. We used MART-1-specific TCR-T cells (TCR-TMART-1) stimulated with MART-127-35 peptide-loaded MEL-526 tumor cells with different proportions of them expressing PD-L1 to perform cellular assays and high-throughput single-cell RNA sequencing. Compared to control T cells, TCR-TMART-1 were more sensitive to exhaustion and secreted lower pro-inflammatory but higher anti-inflammatory cytokines with increasing proportions of PD-L1+ tumor cells. The colocalization of T cells and tumor cells in gene clusters correlated negatively with the proportion of PD-L1+ tumor cells and positively with immune cell cytotoxicity. Moreover, elevated proportion of PD-L1+ tumor cells increased PD-L1 expression and decreased PD-1 expression on T cells and enhanced T cell death. The expression of PD-1 and PD-L1 in T cells and macrophages also correlated positively with COVID-19 severity.

immunology↗

bioRxiv2020

A quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children

Growing evidence suggests that autism spectrum disorder (ASD) is highly associated with dysbiosis in the gut microbiome. However, results of metagenome-based microbiome studies are not always consistent due to great individual diversity that overwhelms disease-associated alterations. Here, we proposed a novel analysis strategy--quasi-paired cohort and applied it to a metagenomic study of ASD microbiomes. By comparing the paired samples of ASD and neurotypical subjects, we identified significant deficiencies in ASD children in detoxifying enzymes and pathways, which showed strong correlations to mitochondrial damage. Diagnostic models with these detoxifying enzymes accurately discriminated ASD individuals from controls, and the dysfunction score inferred from the model increased with the clinical rating scores of ASD. Conclusively, our findings suggest a previously undiscovered mechanism in which impaired microbial detoxification leads to toxicant accumulation and mitochondrion damage contributes to the pathogenesis of ASD. This novel mechanism points to future therapeutic strategies of rebuilding microbial detoxification for ASD.

microbiology↗

bioRxiv2019

Selective targeting of an oncogenic KRAS mutant allele by CRISPR/Cas9 induces efficient tumor regression

BackgroundKRAS is one of the most frequently mutated oncogenes in human cancers, but its activating mutations have remained undruggable due to its picomolar affinity for GTP/GDP and its smooth protein structure resulting in the absence of known allosteric regulatory sites. ResultsWith the goal of treating mutated KRAS-driven cancers, two CRISPR systems, CRISPR-SpCas9 genome-editing system and transcription-regulating system dCas9-KRAB, were developed to directly deplete KRAS mutant allele or to repress its transcription in cancer cells, respectively, through guide RNA specifically targeting the mutant but not wild-type allele. The effect of in vitro proliferation and cell cycle on cancer cells as well as in vivo tumor growth was examined after delivery of Cas9 system. SpCas9 and dCas9-KRAB systems with sgRNA targeting the mutant allele both blocked the expression of mutant KRAS gene, leading to an inhibition of cancer cell proliferation. Local adenoviral injections using SpCas9 and dCas9-KRAB systems both suppressed tumor growth in vivo. The gene-depletion system (SpCas9) performed more effectively than the transcription-suppressing system (dCas9-KRAB) on tumor inhibition. Application of both Cas9 systems to wild-type KRAS tumor cells did not affect cell proliferation in vitro and in vivo. Furthermore, through bioinformatic analysis of 31555 SNP mutations of the top 20 cancer driver genes, we showed that our mutant-specific editing strategy could be extended to a list of oncogenic mutations with high editing potentials, and this pipeline can be applied to analyze the distribution of PAM sequence in the genome to survey the best targets for other editing purpose. ConclusionsWe successfully developed both gene-depletion and transcription-suppressing systems to specifically target an oncogenic mutant allele of KRAS which led to significant tumor regression. It provides a promising strategy for the treatment of tumors with driver gene mutations.

genetics↗

bioRxiv2019

Deficient stereopsis in the normal population revisited: why current clinical stereo tests may not be adequate

Significance statementApplied applications for occupational screening, clinical tests should assess sensitivity to the sign as well as the magnitude of disparity.\n\nPurposeTo determine why the high incidence of stereo anomaly found using laboratory tests with polarity-based increment judgements (i.e., depth sign) is not reflected in clinical measurements that involve single-polarity incremental judgements (i.e., depth magnitude).\n\nMethodsAn iPod-based measurement that involved the detection of an oriented shape defined by a single polarity-depth increment within a random dot display was used. A staircase procedure was used to gather sufficient trials to derive a meaningful measure of variance for the measurement of stereopsis over a large disparity range. Forty-five adults with normal binocular vision (20 - 65 years old) and normal or corrected-to-normal (0 logMAR or better) monocular vision participated in this study.\n\nResultsObservers stereo acuities ranged between 10 and 100 arc seconds, and were normally distributed on a log scale (p = 0.90, 2-tailed Shapiro-Wilk test). The present results using a single polarity depth increment task (i.e., depth magnitude) show a similar distribution to those using a similar task using the Randot preschool stereo test on individuals between the ages of 19-35 using either the 4-book test (n = 33) or the 3-book test (n = 40), but very different results when the iPod test involved a polarity-based increment judgement (i.e., depth sign).\n\nConclusionsThe present clinical stereo tests are based on magnitude judgements and are unable to detect the high percentage of stereo anomalous individuals in the normal population revealed using depth sign judgements.

neuroscience↗