Biology subjects

Lu, Q.

Publications and source records attributed to Lu, Q..

At least 109 records · Page 6Linked to original sources

bioRxiv2021

Estimating genetic correlation jointly using individual-level and summary-level GWAS data

With the increasing accessibility of individual-level data from genome wide association studies, it is now common for researchers to have individual-level data of some traits in one specific population. For some traits, we can only access public released summary-level data due to privacy and safety concerns. The current methods to estimate genetic correlation can only be applied when the input data type of the two traits of interest is either both individual-level or both summary-level. When researchers have access to individual-level data for one trait and summary-level data for the other, they have to transform the individual-level data to summary-level data first and then apply summary data-based methods to estimate the genetic correlation. This procedure is computationally and statistically inefficient and introduces information loss. We introduce GENJI (Genetic correlation EstimatioN Jointly using Individual-level and summary data), a method that can estimate within-population or transethnic genetic correlation based on individual-level data for one trait and summary-level data for another trait. Through extensive simulations and analyses of real data on within-population and transethnic genetic correlation estimation, we show that GENJI produces more reliable and efficient estimation than summary data-based methods. Besides, when individual-level data are available for both traits, GENJI can achieve comparable performance than individual-level data-based methods. Downstream applications of genetic correlation can benefit from more accurate estimates. In particular, we show that more accurate genetic correlation estimation facilitates the predictability of cross-population polygenic risk scores.

genetics↗

bioRxiv2021

TGF--dependent Lymphoid Tissue Residency of Stem-like T cells Limits the Response to Tumor Vaccine

Stem-like CD8+ T cells represent the key subset responding to multiple tumor immunotherapies, including tumor vaccination. However, the signals that control the differentiation of stem-like T cells are not entirely known. Most previous investigations on stem-like T cells are focused on tumor infiltrating T cells (TIL). The behavior of stem-like T cells in other tissues remains to be elucidated. Tissue-resident memory T cells (TRM) are often defined as a non-circulating T cell population residing in non-lymphoid tissues. TILs carrying TRM features are associated with better tumor control. Here, we found that stem-like CD8+ T cells differentiated into TRMs in a TGF-{beta} and tumor antigen dependent manner almost exclusively in tumor draining lymph node (TDLN). TDLN-resident stemlike T cells were negatively associated with the response to tumor vaccine. In other words, after tumor vaccine, TDLN stem-like T cells transiently lost TRM features, differentiated into migratory effectors and exerted tumor control.

immunology↗

bioRxiv2021

Interpreting Polygenic Score Effects in Sibling Analysis

Researchers often claim that sibling analysis can be used to separate causal genetic effects from the assortment of biases that contaminate most downstream genetic studies. Indeed, typical results from sibling models show large (>50%) attenuations in the associations between polygenic scores and phenotypes compared to non-sibling models, consistent with researchers expectations about bias reduction. This paper explores these expectations by using family (quad) data and simulations that include indirect genetic effect processes and evaluates the ability of sibling models to uncover direct genetic effects. We find that sibling models, in general, fail to uncover direct genetic effects; indeed, these models have both upward and downward biases that are difficult to sign in typical data. When genetic nurture effects exist, sibling models create "measurement error" that attenuate associations between polygenic scores and phenotypes. As the correlation between direct and indirect effect changes, this bias can increase or decrease. Our findings suggest that interpreting results from sibling analysis aimed at uncovering direct genetic effects should be treated with caution.

genetics↗

bioRxiv2021

Quantifying concordant genetic effects of de novo mutations on multiple disorders

Exome sequencing on tens of thousands of parent-proband trios has identified numerous deleterious de novo mutations (DNMs) and implicated risk genes for many disorders. Recent studies have suggested shared genes and pathways are enriched for DNMs across multiple disorders. However, existing analytic strategies only focus on genes that reach statistical significance for multiple disorders and require large trio samples in each study. As a result, these methods are not able to characterize the full landscape of genetic sharing due to polygenicity and incomplete penetrance. In this work, we introduce EncoreDNM, a novel statistical framework to quantify shared genetic effects between two disorders characterized by concordant enrichment of DNMs in the exome. EncoreDNM makes use of exome-wide, summary-level DNM data, including genes that do not reach statistical significance in single-disorder analysis, to evaluate the overall and annotation-partitioned genetic sharing between two disorders. Applying EncoreDNM to DNM data of nine disorders, we identified abundant pairwise enrichment correlations, especially in genes intolerant to pathogenic mutations and genes highly expressed in fetal tissues. These results suggest that EncoreDNM improves current analytic approaches and may have broad applications in DNM studies.

genetics↗

bioRxiv2021

Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation

Although most eukaryotic mRNAs require a 5'-cap for translation initiation, some can also be translated through a poorly studied cap-independent pathway. Here we developed a circRNA-based system and unbiasedly identified more than 10,000 sequences in the human transcriptome that contain Cap-independent Translation Initiators (CiTIs). Surprisingly, most of the identified CiTIs are located in 3'UTRs, which mainly promote translation initiation in mRNAs bearing highly structured 5'UTR. Mechanistically, CiTI recruits several translation initiation factors including eIF3 and DHX29, which in turn unwind 5'UTR structures and facilitate ribosome scanning. Functionally, we showed that the translation of HIF1A mRNA, an endogenous DHX29 target, is antagonistically regulated by its 5'UTR structure and a new 3'-CiTI in response to hypoxia. Therefore, deletion of 3'-CiTI suppresses cell growth in hypoxia and tumor progression in vivo. Collectively, our study uncovers a new regulatory mode for translation where the 3'UTR actively participate in the translation initiation.

molecular biology↗

bioRxiv2021

FIND-IT: Ultrafast mining of genome diversity

Novel crop improvement methodologies, including the exploitation of natural genetic variation, are urgently required to feed our rapidly growing human population in the context of global climate change. Here we describe a Fast Identification of Nucleotide variants by DigITal PCR (FIND-IT) method for the rapid identification of pre-targeted genetic variants or rare alleles in large genomic populations. Libraries of 500,000 individuals can be screened and desired variants isolated within two weeks. FIND-IT is widely applicable for mining valuable diversity in any genomic population, including elite breeding and wild germplasm collections. The method provides single nucleotide resolution that has been validated by identifying and isolating knockout lines, non-synonymous codon changes and variants of miRNA and transcription factor binding sites in the agronomically important crop barley. In contrast to existing methods, FIND-IT does not require transformation, cloning or enzymatic steps, and is exempt from GMO regulations. Thus, FIND-IT can be applied immediately to elite crop cultivars and can be tailored to minimize or eliminate time-consuming backcrossing requirements.

genetics↗

bioRxiv2021

A Modified Comprehensive Grading System for Murine Knee Osteoarthritis: Scoring the Whole Joint as an Organ

ObjectiveThis study aimed to develop a comprehensive but easy to apply histologic grading system to score osteoarthritic changes in the whole knee joint for both spontaneous and posttraumatic osteoarthritis (OA) mouse models. MethodsThe new OA grading scheme was developed based on extensive literature review and the authors experience in mouse OA models with relatively long periods of observation (up to 24 months of age or 24-week post-surgery). Semi-quantitative assessments of the histopathologic OA changes were applied to all four quadrants of the knee. Grading elements per quadrant were defined as follows: cartilage (0-7) including three new grading elements for early- and late-stage OA, respectively; osteophyte (0-2) covering chondro-osteophytes in both outer and inner joint margins; subchondral bone (0-2) containing subchondral bone thickening and destruction; synovitis (0-2) comprised of both synovial plica and intercondylar notch; and peri-articular tissues (0-2) highlighting ectopic chondrogenesis and ossification in the knee capsule, ligament, and musculature. ResultsStatistical analyses showed that the new grading system had high intra- and inter-observer reproducibility (Pearsons correlation coefficients r >0.9) for both experienced and novice scorers. Sensitivity and reliability analyses confirmed the ability of the new system to detect minimal OA progression between two timepoints with a two-week interval and to accurately identify tissue-specific OA severity within the knee joint. ConclusionsThe comprehensive histologic grading system presented here covers all-stage osteoarthritic changes in all major knee joint tissues of mice, which enable us to score OA severity for the whole joint reproducibly and accurately without software-assisted time-consuming measurements.

pathology↗

bioRxiv2021

A quantile integral linear model to quantify genetic effects on phenotypic variability

Detecting genetic variants associated with the variance of complex traits, i.e. variance quantitative trait loci (vQTL), can provide crucial insights into the interplay between genes and environments and how they jointly shape human phenotypes in the population. We propose a quantile integral linear model (QUAIL) to estimate genetic effects on trait variability. Through extensive simulations and analyses of real data, we demonstrate that QUAIL provides computationally efficient and statistically powerful vQTL mapping that is robust to non-Gaussian phenotypes and confounding effects on phenotypic variability. Applied to UK Biobank (N=375,791), QUAIL identified 11 novel vQTL for body mass index (BMI). Top vQTL findings showed substantial enrichment for interactions with physical activities and sedentary behavior. Further, variance polygenic scores (vPGS) based on QUAIL effect estimates showed superior predictive performance on both population-level and within-individual BMI variability compared to existing approaches. Overall, QUAIL is a unified framework to quantify genetic effects on the phenotypic variability at both single-variant and vPGS levels. It addresses critical limitations in existing approaches and may have broad applications in future gene-environment interaction studies.

genetics↗

bioRxiv2021

Genomics-informed insights into microbial degradation of N,N-dimethylformamide

Effective degradation of N,N-Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to be capable of degrading DMF. Aerobic remediation of DMF has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include methane as a byproduct. Here, we analyzed 20,762 complete genomes and 28 constructed draft genomes for the genes associated with DMF degradation. We identified 952 genomes that harbor genes involved in DMF degradation, expanding the known diversity of prokaryotes with these metabolic capabilities. Our findings suggest acquisition of DMF-degrading gene via plasmids are important in the order Rhizobiales and genus Paracoccus, but not in most other lineages. Degradation pathway analysis reveals that most putative DMF degraders using aerobic Pathway I will accumulate methylamine intermediate, while members of Paracoccus, Rhodococcus, Achromobacter, and Pseudomonas could potentially mineralize DMF completely under aerobic conditions. The aerobic DMF degradation via Pathway II is more common than thought and is primarily present in -and {beta}-Proteobacteria and Actinobacteria. Most putative DMF degraders could grow with nitrate anaerobically (Pathway III), however, genes for the use of methyl-CoM to produce methane were not found. These analyses suggest that microbial consortia could be more advantageous in DMF degradation than pure culture, particularly for methane production under the anaerobic condition. The identified genomes and plasmids form an important foundation for optimizing bioremediation of DMF-containing wastewaters. ImportanceDMF is extensively used as a solvent in industries, and is classified as a probable carcinogen. DMF is a refractory compound resistant to degradation, and until now, only few bacterial isolates have been reported to degrade DMF. To achieve effective microbial degradation of DMF from wastewater, it is necessary to identify genomic diversity with the potential to degrade DMF and characterize the genes involved in two aerobic degradation pathways and potential anaerobic degradation for methane production. A wide diversity of organisms has the potential to degrade DMF. Plasmid-mediated degradation of DMF is important for Rhizobiales and Paracoccus. Most DMF degraders could grow anaerobically with nitrate as electron acceptor, while co-cultures are required to complete intermediate methanogenesis for methane production. This is the first genomics-based global investigation into DMF degradation pathways. The genomic database generated by this study provides an important foundation for the bioremediation of DMF in industrial waste waters. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/435917v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e46e1dorg.highwire.dtl.DTLVardef@f93887org.highwire.dtl.DTLVardef@1ee5ce8org.highwire.dtl.DTLVardef@15a529_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Butyryl/Caproyl-CoA:Acetate CoA-Transferase: Cloning, Expression and Characterization of the Key Enzyme Involved in Medium-Chain Fatty Acid Biosynthesis

Coenzyme A transferases (CoATs) are important enzymes involved in carbon chain elongation contributing to medium-chain fatty acid (MCFA) biosynthesis. For example, butyryl-CoA:acetate CoA transferase (BCoAT) is responsible for the final step of butyrate synthesis from butyryl-CoA. However, little is known about caproyl-CoA:acetate CoA-transferase (CCoAT), which is responsible for the final step of caproate synthesis from caproyl-CoA. In this study, two CoAT genes from Ruminococcaceae bacterium CPB6 and Clostridium tyrobutyricum BEY8 were identified by gene cloning and expression analysis. The enzyme assays and kinetic studies were carried out using butyryl-CoA or caproyl-CoA as the substrate. CPB6-CoAT can catalyze the conversion of both butyryl-CoA to butyrate and caproyl-CoA to caproate, but its catalytic efficiency with caproyl-CoA as the substrate was 3.8 times higher than that with butyryl-CoA. In contrast, BEY8-CoAT had only BCoAT activity, not CCoAT activity. This demonstrated the existence of a specific CCoAT involved in chain elongation via the reverse {beta}-oxidation pathway. Comparative bioinformatics analysis showed the presence of a highly conserved motif (GGQXDFXXGAXX) in CoATs, which is predicted to be the active center of CoATs. Single point mutations in the conserved motif of CPB6-CoAT (Asp346 and Ala351) led to marked decreases in the activity for butyryl-CoA and caproyl-CoA, indicating that the conserved motif is the active center of CPB6-CoAT, and sites Asp346 and Ala351 were critical residues that affect enzymatic activity. This work provides insight into the function of CCoAT in caproic acid biosynthesis and improves the understanding of the chain elongation pathway for MCFA production.

biochemistry↗

bioRxiv2021

Aberrant Temporal-spatial Patterns to Sad expressions in Major Depressive Disorders via Hidden Markov Model

BackgroundThe pathological mechanisms of Major depressive disorders (MDD) is associated with over-expressing of negative emotions, and the overall temporal-spatial patterns underlying over-representation in depression still remained to be revealed to date. We hypothesized that the aberrant spatio-temporal attributes of the process of sad expressions relate to MDD and help to detect depression severity. MethodsWe enrolled a total of 96 subjects including 47 MDDs and 49 healthy controls (HCs), and recorded their Magnetoencephalography data under a sad expressions recognition task. A hidden Markov model (HMM) was applied to separate the whole neural activity into several brain states, then to characterize the dynamics. To find the disrupted spatial-temporal features, power estimations and fractional occupancy of each state were contrasted between MDDs and HCs. ResultsThree states were found over the period of emotional stimuli processing procedure. The visual state was mainly distributed in early stage (0 - 270ms) and the limbic state in middle and later stage (270ms - 600ms) of the task, while the fronto-parietal state remained a steady proportion across the whole period. MDDs activated statistically more in limbic system during limbic state (p = 0.0045) and less in frontoparietal control network during fronto-parietal state (p = 5.38*10-5) relative to HCs. Hamilton-Depression-Rating Scale scores was significantly correlated with the predicted severity value using the state descriptors (p = 0.0062, r = 0.3933). DiscussionAs human brain exhibited varied activation patterns under the negative stimuli, MDDs expressed disrupted temporal-spatial activated patterns across varied stages involving the primary visual perception and emotional contents processing compared to HCs, indicting disordered regulation of brain functions. Furthermore, descriptors built by HMM could be potential biomarkers for identifying the severity of depression disorders.

neuroscience↗

bioRxiv2021

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

microbiology↗

bioRxiv2021

A ciliopathy complex builds distal appendages to initiate ciliogenesis

Cells inherit two centrioles, the older of which is uniquely capable of generating a cilium. Using proteomics and super-resolved imaging, we identified a module which we term DISCO (DIStal centriole COmplex). DISCO components CEP90, MNR and OFD1 underlie human ciliopathies. This complex localized to both distal centrioles and centriolar satellites, proteinaceous granules surrounding centrioles. Cells and mice lacking CEP90 or MNR did not generate cilia, failed to assemble distal appendages, and did not transduce Hedgehog signals. Disrupting the satellite pools did not affect distal appendage assembly, indicating that it is the centriolar populations of MNR and CEP90 that are critical for ciliogenesis. CEP90 recruited the most proximal known distal appendage component, CEP83, to root distal appendages formation, an early step in ciliogenesis. In addition, MNR, but not CEP90, restricted centriolar length by recruiting OFD1. We conclude that DISCO acts at the distal centriole to support ciliogenesis by restraining centriole length and assembling distal appendages, defects in which cause human ciliopathies. eTOC summaryKumar et al. identifies a multi-protein complex called DISCO (DIStal centriole COmplex) required to nucleate distal appendages and restrain centriole elongation, essential for the initiation of cilium assembly. Without DISCO, cells fail to ciliate and transduce Hedgehog signals, critical for mammalian development.

cell biology↗

bioRxiv2021

Spontaneous Facet Joint Osteoarthritis in NFAT1-Mutant Mice

ObjectivesAlthough rodent models of traumatically or chemically induced intervertebral facet joint osteoarthritis (FJOA) were previously described, the characteristics of spontaneous FJOA animal models have not been documented. This study aimed to identify the characteristics of a murine model of spontaneous FJOA and its underlying mechanisms. MethodsThe lumbar facet joints of mutant mice carrying a disrupted NFAT1 (nuclear factor of activated T cells 1) allele and of wild-type control mice were examined by histochemistry, quantitative gene expression analysis, immunohistochemistry, and histomorphometry using a novel FJOA scoring system at 2, 6, 12, and 18 months of age. The reproducibility of the FJOA scoring system was analyzed by inter-observer and intra-observer variability tests. Tissue-specific histomorphometric and gene expression changes were statistically analyzed. ResultsNFAT1-mutant facet joints displayed dysfunction of articular chondrocytes and synovial cells with aberrant gene and protein expression in cartilage and synovium as early as 2 months, followed by osteoarthritic structural changes such as articular surface fissuring and chondro-osteophyte formation at 6 months. Deeper cartilage lesions, synovitis, separation of cartilage from thickened subchondral bone, and tissue-specific molecular and cellular alterations in NFAT1-mutant facet joints became evident at 12 and 18 months. Osteoarthritic structural changes were not detected in wild-type facet joints at any ages, though age-related cartilage degeneration was observed at 18 months. ConclusionsUsing NFAT1-mutant mice, this study has identified for the first time an animal model of spontaneous FJOA with age-dependent osteoarthritic characteristics, developed the first FJOA scoring system, and elucidated the molecular mechanisms of NFAT1 mutation-mediated FJOA.

molecular biology↗

bioRxiv2021

CSF metabolites associate with CSF tau and improve prediction of Alzheimer's disease status

INTRODUCTIONCerebrospinal fluid (CSF) total tau (t-tau) and phosphorylated tau (p-tau) are biomarkers of Alzheimers disease (AD), yet much is unknown about AD-associated changes in tau metabolism and tau tangle etiology. METHODSWe assessed the variation of t-tau and p-tau explained by 38 previously identified CSF metabolites using linear regression models in middle-age controls from the Wisconsin Alzheimers Disease Research Center, and predicted AD/mild cognitive impairment (MCI) vs. an independent set of older controls using metabolites selected by the least absolute shrinkage and selection operator (LASSO). RESULTSThe 38 CSF metabolites explained 70.3% and 75.7% of the variance in t-tau and p-tau. Of these, 7 LASSO-selected metabolites improved the prediction ability of AD/MCI vs. older controls (AUC score increased from 0.92 to 0.97 and 0.78 to 0.93) compared to the base model. DISCUSSIONThese tau-correlated CSF metabolites increase AD/MCI prediction accuracy and may provide insight into tau tangle etiology.

molecular biology↗

bioRxiv2020

Learning to use episodic memory for event prediction

Recent human behavioral and neuroimaging results suggest that people are selective in when they encode and retrieve episodic memories. To explain these findings, we trained a memory-augmented neural network to use its episodic memory to support prediction of upcoming states in an environment where past situations sometimes reoccur. We found that the network learned to retrieve selectively as a function of several factors, including its uncertainty about the upcoming state. Additionally, we found that selectively encoding episodic memories at the end of an event (but not mid-event) led to better subsequent prediction performance. In all of these cases, the benefits of selective retrieval and encoding can be explained in terms of reducing the risk of retrieving irrelevant memories. Overall, these modeling results provide a resource-rational account of why episodic retrieval and encoding should be selective and lead to several testable predictions.

neuroscience↗

bioRxiv2020

Gamete simulation improves polygenic transmission disequilibrium analysis

Polygenic risk scores (PRS) derived from summary statistics of genome-wide association studies (GWAS) have enjoyed great popularity in human genetics research. Applied to population cohorts, PRS can effectively stratify individuals by risk group and has promising applications in early diagnosis and clinical intervention. However, our understanding of within-family polygenic risk is incomplete, in part because the small samples per family significantly limits power. Here, to address this challenge, we introduce ORIGAMI, a computational framework that uses parental genotype data to simulate offspring genomes. ORIGAMI uses state-of-the-art genetic maps to simulate realistic recombination events on phased parental genomes and allows quantifying the prospective PRS variability within each family. We quantify and showcase the substantially reduced yet highly heterogeneous PRS variation within families for numerous complex traits. Further, we incorporate within-family PRS variability to improve polygenic transmission disequilibrium test (pTDT). Through simulations, we demonstrate that modeling within-family risk substantially improves the statistical power of pTDT. Applied to 7,805 trios of autism spectrum disorder (ASD) probands and healthy parents, we successfully replicated previously reported over-transmission of ASD, educational attainment, and schizophrenia risk, and identified multiple novel traits with significant transmission disequilibrium. These results provided novel etiologic insights into the shared genetic basis of various complex traits and ASD.

genetics↗

bioRxiv2020

Biofilm Formation and Virulence of Shigella flexneri is Modulated by pH of Gastrointestinal Tract

Shigella infections remain a major public health issue in developing countries. One model of Shigella pathogenesis suggests that the microfold epithelial cells in the small intestine are the preferred initial site of infection. However, a growing body of evidence supports an alternative model whereby Shigella primarily infects a much wider range of epithelial cells that reside primarily within the colon. Here, we investigated whether the luminal pH difference between the small intestine and colon could provide evidence in support of either model of Shigella flexneri pathogenesis. As virulence factors leading to cellular invasion are linked to biofilms in S. flexneri, we examined the effect of pH on S. flexneris ability to form and maintain adherent biofilms when induced by deoxycholate. We showed that a basic pH inhibited formation and dispersed pre-assembled mature biofilms while an acidic pH (similar to the colonic environment) did not have either of these effects. To further elucidate this phenomenon at the molecular level, we probed the transcriptomes of biofilms and S. flexneri grown in different pH conditions. We identified specific amino acid metabolic pathways (cysteine and arginine) that were enriched in the bacteria that formed the biofilms, but decreased upon pH increase. We then utilized a type III secretion system reporter strain to show that increasing pH reduced deoxycholate-induced virulence of S. flexneri in a dose dependent manner. Taken together, these experiments support a model whereby Shigella infection is favored in the colon because of the local pH differences in these organs.

microbiology↗