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Biology subjects

Shang, K.

Publications and source records attributed to Shang, K..

6 recordsLinked to original sources

Cortical Organoid Model of PPP2R5D Genetic Intellectual Disability Models Disease Severity Phenotype

Jordans Syndrome (JS) is a rare, neurodevelopmental disorder caused by de novo missense mutations in protein phosphatase 2 regulatory subunit Bdelta (PPP2R5D). JS is characterized by severe neurological impairments starting in early life. PPP2R5D encodes for B56{delta}, one of the regulatory subunits of protein phosphatase 2A (PP2A). PP2A is a heterotrimeric protein serine/threonine phosphatase that is highly expressed in the brain and the liver. Past studies have focused on PP2As role in liver and little is known about the holoenzymes behavior in neuronal cells. Although B56{delta} is known to play an important role in the substrate specificity of PP2A, the identification of validated downstream substrates in JS remains unclear. To better understand how the mutations affect neuronal cells, we developed cerebral cortical-like organoids from an engineered allele series of the most common JS mutations to characterize the physiological changes throughout different stages of neurodevelopment. Organoids were assessed for transcriptomic, protein, and electrophysiological changes utilizing bulk RNA sequencing, immunocytochemistry, Western Blot, and high-density MicroElectrode Array. The results identify differentially expressed genes and translated proteins, potential neuronal substrates, and significant electrophysiological signatures that suggest mutations in B56{delta} lead to variant-specific dysfunction of PP2A. Overexpression of PPP2R5D through AAV transduction of organoids rescued several phenotypes in the variants, suggesting different pathogenetic etiology underneath. Our findings successfully characterized cerebral cortical-like organoids in JS cell lines and demonstrated its potential as a model for studying neurodevelopmental disorder and for screening therapeutic approaches.

cell biology↗

Suaeda Salsa Hyperspectral Index (SSHI) for mapping S. salsa in coastal wetlands using hyperspectral satellite imagery

Suaeda Salsa (S. salsa), a pioneer species with short and red-purplish plants in the intertidal zones, has significant ecological, economic, recreational and tourism values. Timely monitoring of S. salsa is crucial for understanding its dynamics and sustainable management of coastal wetlands. Hyperspectral satellite offers valuable opportunities due to its detailed spectral information. This study proposed a Suaeda Salsa Hyperspectral Index (SSHI) for S. salsa mapping based on hyperspectral satellite imagery. The SSHI was developed by considering the large within-class spectral variations of cover types at coastal wetlands, accounting for the spectral correlations in hyperspectral data, and employing dynamic band selection on a per-pixel basis to optimize the separation of S. salsa from other land covers. [Formula] (1+ L), where i[isin][499nm, 611nm], j[isin][628nm, 851nm], L= 0.5. We applied SSHI on ZY1-02D/E AHSI images over Yellow River Delta (YRD) and Liao River Delta (LRD), China during 2021 to 2023. Based on SSHI, a simple thresholding method and a random forest (RF) model were used to map S. salsa. Our results showed that the overall accuracies of S. salsa maps achieved 87.96%[~]89.43% (YRD) and 92.03%[~]93.36% (LRD) using thresholds, and 92.62%[~]94.05% (YRD) and 94.74%[~]94.79% (LRD) using RF. For RF, incorporating SSHI improves S. salsa producers accuracies (users accuracies) by 1.02%[~]6.85% (2.26%[~]6.25%) compared to those without SSHI, proving the effectiveness of SSHI. The S. salsa maps reveal notable temporal variations, reflecting the impacts of climate change and human activities. SSHI is also applicable to other hyperspectral imagery, such as GF-5B and PRISMA.

ecology↗

Architecture of a pentameric assembly of the tail tube protein in SPR phages

The majority of phages, viruses that infect prokaryotes, deliver their genomic material into host cells via a tail structure. Previous research has established that the central tube of these phages, composed of tail tube protein (TTP), is structurally conserved, typically forming either hexameric or trimeric rings. In this study, we revealed a novel pentameric assembly of TTP and present two cryo-EM structures at resolutions of 3.5 [A] and 3.7 [A], respectively. Our detailed structural analysis demonstrates that the inner surface of the pentameric tube is highly negatively charged. Critical residues located on the loop between {beta}3 and {beta}4 play pivotal roles in the formation of the pentameric rings, and mismatches of the interactions between the stacked layers can induce the curvature of the tube. The cryo-EM structure of the TTP polymer at the tubes end uncovered that the {beta}-strands that span amino acids 27-65 move towards the central tunnel, potentially blocking the tunnel through which the phage genome is released. Our study provides new structural insights into a novel assembly of TTP, which will extend the understanding of phage assembly.

biophysics↗

Multi-omics investigation of spontaneous T2DM macaque reveals gut microbiota promote T2DM by up-regulating the absorption of excess palmitic acid

Although gut microbiota and lipid metabolites have been suggested to be closely associated with type 2 diabetes mellitus (T2DM), the interactions between gut microbiota, lipid metabolites and the host in T2DM development remains unclear. Rhesus macaques may be the best animal model to investigate these relationships given their spontaneous development of T2DM. We identified eight spontaneous T2DM macaques and conducted a comprehensive study investigating the relationships using multi-omics sequencing technology. Our results from 16S rRNA, metagenome, metabolome and transcriptome analyses identified that gut microbiota imbalance, tryptophan metabolism and fatty acid {beta} oxidation disorders, long-chain fatty acid (LCFA) accumulation, and inflammation occurred in T2DM macaques. We verified the accumulation of palmitic acid (PA) and activation of inflammation in T2DM macaques. Importantly, mice transplanted with spontaneous T2DM macaque fecal microbiota and fed a high PA diet developed prediabetes within 120 days. We determined that gut microbiota mediated the absorption of excess PA in the ileum, resulting in the accumulation of PA in the serum consequently leading to T2DM in mice. In particular, we demonstrated that the specific microbiota composition was probably involved in the process. This study provides new insight into interactions between microbiota and metabolites and confirms causative effect of gut microbiota on T2DM development.

microbiology↗

Balancing activation and costimulation of CAR tunes signaling dynamics and enhances therapeutic potency

BackgroundPrimary human T cells engineered with chimeric antigen receptors (CARs) ex vivo can be adoptively transferred to treat cancer. CD19-targeting CAR with CD28 costimulatory domain and CD3{zeta} activation domain have been approved by the US FDA for treating B cell malignancies. MethodsHere we generated mutation of immunorecpetor tyrosine-based activation motifs (ITAMs) in CD3{zeta}, namely 1XX CAR, which altered the balance of activation and costimulation. Next we investigated whether 1XX design could enhance therapeutic potency against solid tumors. We constructed both CD19- and AXL-specific 1XX CARs and compared their in vitro and in vivo functions with their WT counterparts. ResultsEven though 1XX CARs decreased cytotoxicity against tumor cells in vitro, they showed better anti-tumor efficacy in both pancreatic and melanoma mouse models. Detailed analysis revealed that 1XX CAR-T cells proliferated more in response to antigen stimulation in vitro, persisted longer in vivo and had higher percentage of central memory cells. As 1XX modification directly calibrates CAR activation potential, we utilized fluorescence resonance energy transfer (FRET)-based biosensor to monitor signaling dynamics downstream of CARs. Decreased ITAM numbers in 1XX resulted in similar ZAP70 activation, while 1XX induced higher Ca2+ elevation and faster Erk activation than WT CAR, which may contribute to the better therapeutic potency of 1XX. ConclusionsOur results established the surpiosity of 1XX against two targets in different solid tumor models and shed light on the underlying molecular mechanism of CAR signaling, paving the way for the clinical application of 1XX CARs against solid tumors.

immunology↗

Cas9-cleavage sequences in minimal plasmids enhance non-viral genome targeting of CARs in primary human T cells

T cell genome editing holds great promise to advance a range of immunotherapies but is encumbered by the dependence on difficult-to-produce and expensive viral vectors. Here we have designed small double-stranded plasmid DNA modified to mediate high-efficiency homologous recombination. The resulting chimeric antigen receptor (CAR)-T cells display a similar phenotype, transcriptional profile and in vivo potency as CAR-T cells generated using adeno-associated viral (AAV) vector. This method should simplify and accelerate the use of precision engineering to produce edited T cells for research and clinical purposes.

bioengineering↗