Biology subjects

Ma, N.

Publications and source records attributed to Ma, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Task Activation Results in Regional 13C-Lactate Signal Increase in the Human Brain

Hyperpolarized-13C magnetic resonance imaging (HP-13C MRI) was used to image changes in 13C-lactate signal during a visual stimulus condition in comparison to an eyes-closed control condition. Whole-brain 13C-pyruvate, 13C-lactate and 13C-bicarbonate production was imaged in healthy volunteers (N=6, ages 24-33) for the two conditions using two separate hyperpolarized 13C-pyruvate injections. BOLD-fMRI scans were used to delineate regions of functional activation. 13C-metabolite signal was normalized by 13C-metabolite signal from the brainstem and the percentage change in 13C-metabolite signal conditions was calculated. A one-way Wilcoxon signed-rank test showed a significant increase in 13C-lactate in regions of activation when compared to the remainder of the brain (p = 0.02, V = 21). No significant increase was observed in 13C-pyruvate (p = 0.11, V = 17) or 13C-bicarbonate (p = 0.95, V = 3) signal. The results show an increase in 13C-lactate production in the activated region that is measurable with HP-13C MRI.

neuroscience↗

bioRxiv2023

Cellular Lipids Regulate the Conformational Ensembles of the Disordered Intracellular Loop 3 in beta-2 Adrenergic Receptor

The structurally disordered intracellular loops (ICLs) of G protein-coupled receptors (GPCRs) play a critical role in G protein coupling. In our previous work, we used a combination of FRET-based and computational methodologies to show that the third intracellular loop (ICL3) modulates the activity and G protein coupling selectivity in GPCRs. In the current study, we have uncovered the role of several lipid components in modulating the conformational ensemble of ICL3 of the {beta}2-adrenergic receptor ({beta}2AR). Our findings indicate that phosphatidylinositol 4,5-bisphosphate (PIP2) in the inner leaflet of the membrane bilayer acts as a stabilizing anchor for ICL3, opening the intracellular cavity to facilitate G protein coupling. This interaction between PIP2 and ICL3 causes tilting of {beta}2AR within the cellular membrane. Notably, this tilting of the receptor is supported by ganglioside GM3 stabilizing the extracellular loops on the outer leaflet of the bilayer, thereby exerting an allosteric effect on the orthosteric ligand binding pocket. Our results underscore the significance of lipids in modulating GPCR activity, proposing an allosteric mechanism that occurs through the receptors orientation within the membrane.

biophysics↗

bioRxiv2023

Engineered odorant receptors illuminate structural principles of odor discrimination

A central challenge in olfaction is understanding how the olfactory system detects and distinguishes odorants with diverse physicochemical properties and molecular configurations. Vertebrate animals perceive odors via G protein-coupled odorant receptors (ORs). In humans, [~]400 ORs enable the sense of smell. The OR family is composed of two major classes: Class I ORs are tuned to carboxylic acids while Class II ORs, representing the vast majority of the human repertoire, respond to a wide variety of odorants. How ORs recognize chemically diverse odorants remains poorly understood. A fundamental bottleneck is the inability to visualize odorant binding to ORs. Here, we uncover fundamental molecular properties of odorant-OR interactions by employing engineered ORs crafted using a consensus protein design strategy. Because such consensus ORs (consORs) are derived from the 17 major subfamilies of human ORs, they provide a template for modeling individual native ORs with high sequence and structural homology. The biochemical tractability of consORs enabled four cryoEM structures of distinct consORs with unique ligand recognition properties. The structure of a Class I consOR, consOR51, showed high structural similarity to the native human receptor OR51E2 and yielded a homology model of a related member of the human OR51 family with high predictive power. Structures of three Class II consORs revealed distinct modes of odorant-binding and activation mechanisms between Class I and Class II ORs. Thus, the structures of consORs lay the groundwork for understanding molecular recognition of odorants by the OR superfamily.

neuroscience↗

bioRxiv2023

Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling

Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior of interface interactions and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces it is challenging to determine which amino acid pair interactions are cooperative. In this work we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with G proteins. Our results reveal a strong co-dependency in the formation of interface GPCR:G protein contacts. This observation indicates that cooperativity of GPCR:G protein interactions is necessary for the coupling and selectivity of G proteins and is thus critical for receptor function. We have identified subnetworks containing polar and hydrophobic interactions that are common among multiple GPCRs coupling to different G protein subtypes (Gs, Gi and Gq). These common subnetworks along with G protein-specific subnetworks together confer selectivity to the G protein coupling. This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.

biophysics↗

bioRxiv2023

Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain

Multivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employed an icosahedral DNA origami (ICO) as a display particle for SARS-CoV-2 RBD nanovaccines. The morphology and diameter of the particles were close to those of the virus (91 {+/-} 11 nm). The surface addressability of the DNA origami permitted facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using an in vitro screening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoked stronger and more enduring humoral and T cell immune responses in mouse models compared to soluble RBD antigens. Our vaccines activated similar humoral immunity and slightly stronger cellular immunity compared to mRNA vaccines. These results provide reference principles for the rational design of nanovaccines and exemplify the utility of DNA origami as a display platform for vaccines against infectious disease.

bioengineering↗

bioRxiv2023

Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f

There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein Gs and bound to the odorant N,N-dimethylcyclohexylamine (DMCH) to an overall resolution of 2.9 [A]. DMCH is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the {beta}-adrenoceptors, with the significant difference that DMCH interacts directly with one of the main activation microswitch residues.

molecular biology↗

bioRxiv2023

Haplotype-resolve genome assembly and resequencing provide insights into the origin and domestication of modern rose

Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here, we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida Samantha and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. The two subgenomes of Samantha show no significant global bias in gene loss but substantial expression bias, and homoeologous exchanges are frequently observed between subgenomes. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses, and highlight that R. odorata and its derived cultivars contribute more to modern roses than R. chinensis Old Blush. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous flowering, floral organ identity, flower senescence, and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.

genomics↗

bioRxiv2023

Single-cell Spatial Metabolic and Immune Phenotyping of Head and Neck Cancer Tissues Identifies Tissue Signatures of Response and Resistance to Immunotherapy

Head and neck squamous cell carcinomas (HNSCC) are the seventh most common cancer and represent a global health burden. Immune checkpoint inhibitors (ICIs) have shown promise in treating recurrent/metastatic cases, with durable benefit in [~]30% of patients. Current biomarkers for head and neck tumors are limited in their dynamic ability to capture tumor microenvironment (TME) features, with an increasing need for deeper tissue characterization. Therefore, new biomarkers are needed to accurately stratify patients and predict responses to therapy. Here, we have optimized and applied an ultra-high plex, single-cell spatial protein analysis in HNSCC. Tissues were simultaneously analyzed with a panel of 101 antibodies that targeted biomarkers related to tumor immune, metabolic and stress microenvironments. Our data uncovered a high degree of intra-tumoral heterogeneity intrinsic to head and neck tumors and provided unique insights into the biology of the tumor. In particular, a cellular neighborhood analysis revealed the presence of 6 unique spatial tumor-immune neighborhoods enriched in functionally specialized immune cell subsets across the patient tissue. Additionally, functional phenotyping based on key metabolic and stress markers identified four distinct tumor regions with differential protein signatures. One tumor region was marked by infiltration of CD8+ cytotoxic T cells and overexpression of BAK, a proapoptotic regulator, suggesting strong immune activation and stress. Another adjacent region within the same tumor had high expression of G6PD and MMP9, known drivers of tumor resistance and invasion respectively. This dichotomy of immune activation-induced death and tumor progression in the same sample demonstrates the heterogenous niches and competing microenvironments that underpin clinical responses of therapeutic resistance. Our data integrate single-cell ultra-high plex spatial information with the functional state of the tumor microenvironment to provide insights into a partial response to immune checkpoint inhibitor therapy in HNSCC. We believe that the approach outlined in this study will pave the way towards a new understanding of TME features associated with response and sensitivity to ICI therapies.

cancer biology↗

bioRxiv2023

Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling

Initiation of B-cell receptor (BCR)1 signaling, and subsequent antigen-encounter in germinal centers2,3 represent milestones of B-lymphocyte development that are both marked by sharp increases of CD25 surface-expression. Oncogenic signaling in B-cell leukemia (B-ALL)4 and lymphoma5 also induced CD25-surface expression. While CD25 is known as an IL2-receptor chain on T- and NK-cells6-9, the significance of its expression on B-cells was unclear. Our experiments based on genetic mouse models and engineered patient-derived xenografts revealed that, rather than functioning as an IL2-receptor chain, CD25 expressed on B-cells assembled an inhibitory complex including PKC{delta} and SHIP1 and SHP1 phosphatases for feedback control of BCR-signaling or its oncogenic mimics. Recapitulating phenotypes of genetic ablation of PKC{delta}10-12, SHIP113,14 and SHP114, 15,16, conditional CD25-deletion decimated early B-cell subsets but expanded mature B-cell populations and induced autoimmunity. In B-cell malignancies arising from early (B-ALL) and late (lymphoma) stages of B-cell development, CD25-loss induced cell death in the former and accelerated proliferation in the latter. Clinical outcome annotations mirrored opposite effects of CD25-deletion: high CD25 expression levels predicted poor clinical outcomes for patients with B-ALL, in contrast to favorable outcomes for lymphoma-patients. Biochemical and interactome studies revealed a critical role of CD25 in BCR-feedback regulation: BCR-signaling induced PKC{delta}-mediated phosphorylation of CD25 on its cytoplasmic tail (S268). Genetic rescue experiments identified CD25-S268 tail-phosphorylation as central structural requirement to recruit SHIP1 and SHP1 phosphatases to curb BCR-signaling. A single point mutation CD25S268A abolished recruitment and activation of SHIP1 and SHP1 to limit duration and strength of BCR-signaling. Loss of phosphatase-function, autonomous BCR-signaling and Ca2+-oscillations induced anergy and negative selection during early B-cell development, as opposed to excessive proliferation and autoantibody production in mature B-cells. These findings highlight the previously unrecognized role of CD25 in assembling inhibitory phosphatases to control oncogenic signaling in B-cell malignancies and negative selection to prevent autoimmune disease.

immunology↗

bioRxiv2023

A deep population reference panel of tandem repeat variation

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3,550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

genomics↗

bioRxiv2023

Evidence of Lactate Shuttling in the Human Brain using Hyperpolarized 13C-MRI

PurposeTo test the hypothesis that lactate shuttling contributes to the 13C-lactate and 13C-bicarbonate signal observed in the awake human brain using hyperpolarized 13C MRI. MethodsHealthy human volunteers (n = 6) were scanned twice using hyperpolarized 13C-MRI, with reduced radiofrequency saturation of 13C-lactate on one set of scans. 13C-lactate, 13C-bicarbonate, and 13C-pyruvate signals for 132 brain regions across each set of scans were compared using a clustered Wilcoxon sum rank test. ResultsReduced 13C-lactate radiofrequency saturation resulted in a significantly greater 13C-bicarbonate signal (p = 0.04). These changes were observed across the majority of brain regions. ConclusionRadiofrequency saturation of 13C-lactate leads to a decrease in 13C-bicarbonate signal, demonstrating that the 13C-lactate generated from the injected 13C-pyruvate is being converted back to 13C-pyruvate and oxidized throughout the human brain.

neuroscience↗

bioRxiv2022

Structural basis of odorant recognition by a human odorant receptor

Our sense of smell enables us to navigate a vast space of chemically diverse odor molecules. This task is accomplished by the combinatorial activation of approximately 400 olfactory G protein-coupled receptors (GPCRs) encoded in the human genome1-3. How odorants are recognized by olfactory receptors (ORs) remains mysterious. Here we provide mechanistic insight into how an odorant binds a human olfactory receptor. Using cryogenic electron microscopy (cryo-EM), we determined the structure of active human OR51E2 bound to the fatty acid propionate. Propionate is bound within an occluded pocket in OR51E2 and makes specific contacts critical to receptor activation. Mutation of the odorant binding pocket in OR51E2 alters the recognition spectrum for fatty acids of varying chain length, suggesting that odorant selectivity is controlled by tight packing interactions between an odorant and an olfactory receptor. Molecular dynamics simulations demonstrate propionate-induced conformational changes in extracellular loop 3 to activate OR51E2. Together, our studies provide a high-resolution view of chemical recognition of an odorant by a vertebrate OR, providing insight into how this large family of GPCRs enables our olfactory sense.

biochemistry↗

bioRxiv2022

A novel cuproptosis-related long non-coding RNAs model that effectively predicts prognosis in hepatocellular carcinoma

BackgroundCuproptosis has recently been considered a novel form of programmed cell death. To date, factors crucial to the regulation of this process remain unelucidated. Here, we aimed to identify long-chain non-coding RNAs (lncRNAs) associated with cuproptosis in order to predict the prognosis of patients with hepatocellular carcinoma (HCC). MethodsUsing RNA sequence data from The Cancer Genome Atlas Live Hepatocellular Carcinoma (TCGA-LIHC), a co-expression network of cuproptosis-related mRNAs and lncRNAs was constructed. For HCC prognosis, we developed a cuproptosis-related lncRNA signature (CupRLSig) using univariate Cox, lasso, and multivariate Cox regression analyses. Kaplan-Meier analysis was used to compare overall survival among high- and low-risk groups stratified by median CupRLSig score. Furthermore, comparisons of functional annotation, immune infiltration, somatic mutation, TMB (tumor mutation burden), and pharmacologic options were made between high- and low-risk groups. ResultsOur prognostic risk model was constructed using the cuproptosis-related PICSAR, FOXD2-AS1, and AP001065.1 lncRNAs. The CupRLSig high-risk group was associated with poor overall survival (hazard ratio = 1.162, 95% CI = 1.063- 1.270; p < 0.001). Model accuracy was further supported by receiver operating characteristic and principal component analysis as well as internal validation cohorts. A prognostic nomogram developed considering CupRLSig data and a number of clinical characteristics were found to exhibit adequate performance in survival risk stratification. Mutation analysis revealed that high-risk combinations with high TMB carried worse prognoses. Finally, differences in immune checkpoint expression and responses to chemotherapy as well as in targeted therapy among CupRLSig stratified high- and low-risk groups were explored. ConclusionsThe lncRNA signature constructed in this study is valuable in prognostic estimation in the setting of HCC.

bioinformatics↗

bioRxiv2022

Private and sub-family specific mutations of founder haplotypes in the BXD family reveal phenotypic consequences relevant to health and disease

The BXD family of recombinant inbred mice were developed by crossing and inbreeding progeny of C57BL/6J and DBA/2J strains. This family is the largest and most extensively phenotyped mammalian experimental genetic resource. Although used in genetics for 52 years, we do not yet have comprehensive data on DNA variants segregating in the BXDs. Using linked-read whole-genome sequencing, we sequenced 152 members of the family at about 40X coverage and quantified most variants. We identified 6.25 million polymorphism segregating at a near-optimal minor allele frequency of 0.42. We also defined two other major variants: strain-specific de novo singleton mutations and epoch-specific de novo polymorphism shared among subfamilies of BXDs. We quantified per-generation mutation rates of de novo variants and demonstrate how founder-derived, strain-specific, and epoch-specific variants can be analyzed jointly to model genome-phenome causality. This integration enables forward and reverse genetics at scale, rapid production of any of more than 10,000 diallel F1 hybrid progeny to test predictions across diverse environments or treatments. Combined with five decades of phenome data, the BXD family and F1 hybrids are a major resource for systems genetics and experimental precision medicine.

genomics↗

bioRxiv2022

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice

Short tandem repeats (STRs) are a class of rapidly mutating genetic elements characterized by repeated units of 1 or more nucleotides. We leveraged whole genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family derived from C57BL/6J and DBA/2J mice to study the effects of genetic background on genome-wide patterns of new mutations at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and identified a locus on chromosome 13 associated with the propensity of STRs to expand. Several dozen genes lie in the QTL region, including Msh3, a known modifier of STR stability at pathogenic repeat expansions in mice and humans. Detailed analysis of the locus revealed a cluster of variants near the 5 end of Msh3, including multiple protein-coding variants within the DNA mismatch recognition domain of MSH3, and a retrotransposon insertion overlapping an annotated exon. Additionally, gene expression analysis demonstrates co-localization of this QTL with expression QTLs for multiple nearby genes, including Msh3. Our results suggest a novel role for Msh3 in regulating genome-wide patterns of germline STR mutations and demonstrate that inherited genetic variation can contribute to variability in accumulation of new mutations across individuals.

genomics↗

bioRxiv2021

Optogenetic operated probiotics to regulate host metabolism by mimicking enteroendocrine

The enteroendocrine system plays an important role in metabolism. The gut microbiome regulates enteroendocrine in an extensive way, arousing attention in biomedicine. However, conventional strategies of enteroendocrine regulation via gut microbiome are usually non-specific or imprecise. Here, an optogenetic operated probiotics system was developed combining synthetic biology and flexible electronics to achieve in situ controllable secretion to mimic enteroendocrine. Firstly, optogenetic engineered Lactococcus lactis (L. lactis) were administrated in the intestinal tract. A wearable optogenetic device was designed to control optical signals remotely. Then, L. lactis could secrete enteroendocrine hormone according to optical signals. As an example, optogenetic L. lactis could secrete glucagon-like peptide-1(GLP-1) under the control of the wearable optogenetic device. To improve the half-life of GLP-1 in vivo, the Fc domain from immunoglobulin was fused. Treated with this strategy, blood glucose, weight and other features were relatively well controlled in rats and mice models. Furthermore, up-conversion microcapsules were introduced to increase the excitation wavelength of the optogenetic system for better penetrability. This strategy has biomedical potential in metabolic diseases therapy by mimicking enteroendocrine.

bioengineering↗

bioRxiv2021

Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions

Cell-cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit (IFC) that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell-cell interactions. The temporal variations in natural killer (NK) - triple-negative breast cancer (TNBC) cell distances were tracked and compared with terminally profiled cellular transcriptomes. The results showed the time-bound activities of regulatory modules and alluded to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live cell interactions at doublet resolution, which can be applied across different cancers and cell types.

cancer biology↗

bioRxiv2020

A novel deep-sea bacterial threonine dehydratase drives cysteine desulfuration and hydrogen sulfide production

Cysteine desulfuration is one of the main ways for hydrogen sulfide (H2S) generation in cells and is usually conducted by cystathionine {gamma}-lyase. Herein, we describe a newly discovered deep-sea bacterial threonine dehydratase (psTD), which is surprisingly discovered to drive L-cysteine desulfuration. The mechanisms of psTD catalyzing cysteine desulfuration towards H2S production are first clarified in vitro and in vivo through a combination of genetic and biochemical methods. Furthermore, based on the solved structures of psTD and its various mutants, two or three pockets are found in the active site of psTD, and switch states between inward and outward orientation of a key amino acid R77 determine the open or close status of Pocket III for small molecule exchanges, which further facilitates cysteine desulfuration. Our results reveal the functional diversity and structural specificity of psTD towards L-cysteine desulfuration and H2S formation. Given the broad distribution of psTD homologs in different bacteria, we speculate that some threonine dehydratases have evolved a novel function towards cysteine desulfuration, which benefits the producer to utilize cysteine as a sulfur source for better adapting external environments.

microbiology↗