Biology subjects

Huang, Y.

Publications and source records attributed to Huang, Y..

At least 595 records · Page 33Linked to original sources

bioRxiv2023

CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data

Five-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing transcription start sites (TSS) has not been fully utilised. Here, we present a computational method suite, CamoTSS, to precisely identify TSS and quantify its expression by leveraging the cDNA on read 1, which enables effective detection of alternative TSS usage. With various experimental data sets, we have demonstrated that CamoTSS can accurately identify TSS and the detected alternative TSS usages showed strong specificity in different biological processes, including cell types across human organs, the development of human thymus, and cancer conditions. As evidenced in nasopharyngeal cancer, alternative TSS usage can also reveal regulatory patterns including systematic TSS dysregulations.

bioinformatics↗

bioRxiv2023

Stray cats and dogs carrying zoonotic Enterocytozoon bieneusi genotype D in China: a public health concern

Enterocytozoon bieneusi is reported to be a common microsporidian of humans and animals in various countries. However, scarce information on E. bieneusi has been recorded in cats (Felis catus) and dogs (Canis familiaris) in China. As such, we undertook molecular epidemiological investigation of E. bieneusi in cats and dogs in Shanghai, China. A total of 359 genomic DNAs were extracted from individual faecal samples from cats (n = 59) and dogs (n = 300), and then tested using a nested PCR-based sequencing approach employing internal transcribed spacer (ITS) of nuclear ribosomal DNA as the genetic marker. Enterocytozoon bieneusi was detected in 34 of all 359 (9.5%) faecal samples from cats (32.2%; 19/59) and dogs (5.0%; 15/300), including 24 stray cats and dogs (22.6%; 24/106), as well as ten household/raised cats and dogs (4.0%; 10/253). Correlation analyses revealed that E. bieneusi positive rates were significantly associated with stray cats and dogs (P < 0.05). The analysis of ITS sequence data revealed the presentation of five known genotypes CD7, CHN-HD2, D, PtEb IX and Type IV and two novel genotypes D-like1 and PtEb IX-like1. Zoonotic genotype D was the predominant type with percentage of 61.8 (21/34). Phylogenetic analysis of ITS sequence data sets showed that genotypes D, D-like1 and Type IV clustered within Group 1, showing zoonotic potential. The others were assigned into Group 10 with host specificity. These findings suggested that cats and dogs in Shanghai harbor zoonotic genotype D of E. bieneusi and may have a significant risk for zoonotic transmission. Further insight into the epidemiology of E. bieneusi in animals, water and the environment from other areas in China will be important to have an informed position on the public health significance of microsporidiosis caused by this microbe.

genetics↗

bioRxiv2023

The genomic landscape of adaptation to a new host plant

Adaptation to novel ecological niches is known to be rapid. However, how the loci underlying ecological divergence are coupled to traits reproductively isolating populations, ultimately enabling the formation of persistent species, remains a consequential question in speciation research. Here, we investigated the genomic differences underpinning colonization of a new niche and formation of two partly sympatric host races of Tephritis conura peacock flies. We took advantage of two independent sympatric zones west and east of the Baltic Sea, where host plant specialists using the thistle species Cirsium heterophyllum and C. oleraceum co-occur, and address what regions of the genome maintain the host races in parallel. Using genome-wide association, differentiation and divergence statistics, we identified a large, highly divergent region associated with host use among western and eastern populations. Within this region, we identified unique haplotypes associated with each host race, indicative of a large inversion, adding to the growing body of evidence that structural changes to the genome are important for adaptations to persist in the face of gene flow. We further showed strong signatures of selection in this region, especially in populations of the derived C. oleraceum specialist host race. The region also had reduced introgression, especially in western populations, while the rest of the genome showed signs of extensive gene flow. Genes within highly differentiated windows within the putative inversion were not only enriched for functions involved in host adaptation, including phenology and metabolic responses to different metabolites in the two host plants, but also enriched for gametogenesis, fertilization and embryological development, all of which suggest sequence divergence could have large consequences on reproductive isolation between the host races. In conclusion, this study suggests that structural changes in the genome may facilitate the formation of persistent host races, and ultimately speciation, in face of gene flow.

evolutionary biology↗

bioRxiv2023

Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells

Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remained unknown. We mapped genome-wide chromatin contacts and TF binding profiles in HSPC subsets (HSC, CMP, GMP, MEP) and found that heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific heptad-TF combinations play critical roles in regulating hematopoietic differentiation and provide a valuable resource for development of targeted therapies to manipulate specific HSPC subsets.

developmental biology↗

bioRxiv2023

Transcriptomic profiling of nuclei from PFA-fixed and FFPE brain tissues

Formalin-fixed and paraffin-embedded (FFPE) tissue archives are the largest repository of clinically annotated specimens, and FFPE-compatible single cell gene expression workflow had been developed and applied recently. However, for tissues where cells are hard to dissociate or brains with complex neuronal cells, nuclear transcriptomic profiling are desirable. Moreover, the effects of standard pathological practice on the transcriptome of samples obtained from such archived specimens was also largely anecdotal. Here, we performed RNA-seq of nuclei from hippocampal of mice that underwent freezing, paraformaldehyde (PFA) fixation, and paraffin embedding. Then, we comprehensively evaluated the parameters affecting mRNA quality, transcription patterns, functional level and cell states of nuclei, including PFA fixation time and storage time of FFPE tissues. The results showed that the transcriptome signatures of nuclei isolated from fresh PFA-fixed and fresh FFPE tissues were more similar to matched frozen samples. By contrast, the brain fixed for more than 3 days had prominent impacts on the sequencing data, such as the numbers and biotypes of gene, GC content and ratio of reads interval. Commensurately, prolonged fixation time will result in more differentially expressed genes, especially those enriched in spliceosome and synaptic related pathways, affecting the analysis of gene splicing and neuron cells. MuSiC deconvolution results revealed that PFA infiltrating brains for 3 days will destroy the real cell states, and the proportion of neuron, endothelial and oligodendrocytes diminished while that of microglia was reversed. Yet the effect of storage time on cell composition was more neglectable for FFPE samples. In addition, oligodendrocyte precursor cells were most affected in all fixed samples, and their destruction was independent of fixation time and preservation time. The comprehensive results highlighted that fixation time had much more influences on the nuclear transcriptomic profiles than FFPE retention time, and the cliff-like effects appeared to occur over a fixed period of 1-3 days, with no more differences from additional fixation durations.

molecular biology↗

bioRxiv2023

Arl3 regulates ODA16-mediated intraflagellar transport in motile cilia biogenesis

Arl13b and Arl3 are ciliary GTPases implicated in human Joubert Syndrome, affecting ciliary membrane and axoneme organization. Although the mechanism of Arl13b as a guanine nucleotide exchange factor (GEF) of Arl3 and the function of Arl13b and Arl3 in ciliary membrane protein transport are well established, their role in axoneme biogenesis is unclear. In Trypanosoma brucei, TbArl13 acts as a GEF for two distinct TbArl3 proteins, TbArl3A and TbArl3C. Here, we identified the T. brucei homolog of ODA16, a cargo adapter facilitating intraflagellar transport (IFT) of motile ciliary components, as an effector of both TbArl3A and TbArl3C. Depletion of TbArl3 GTPases stabilized TbODA16 interaction with IFT, while active TbArl3 variants displaced TbODA16 from IFT, demonstrating a mechanism of TbArl3 in motile ciliary cargo transport. One-sentence summaryArl3 acts as a displacement factor and releases ODA16 from IFT

cell biology↗

bioRxiv2023

RTEL1 is required for silencing and epigenome stability

Transcriptional silencing is an essential mechanism for controlling the expression of genes, transgenes and heterochromatic repeats through specific epigenetic marks on chromatin that are maintained during DNA replication. In Arabidopsis, silenced transgenes and heterochromatic sequences are typically associated with high levels of DNA methylation, while silenced genes are enriched in H3K27me3. Reactivation of these loci is often correlated with decreased levels of these repressive epigenetic marks. Here, we report that the DNA helicase REGULATOR OF TELOMERE ELONGATION 1 (RTEL1) is required for transcriptional silencing. RTEL1 deficiency causes upregulation of many genes enriched in H3K27me3 accompanied by a moderate decrease in this mark, but no loss of DNA methylation at reactivated heterochromatic loci. Instead, heterochromatin exhibits DNA hypermethylation and increased H3K27me3 in rtel1. We further find that loss of RTEL1 suppresses the release of heterochromatin silencing caused by the absence of the MOM1 silencing factor. RTEL1 is conserved among eukaryotes and plays a key role in resolving DNA secondary structures during DNA replication. Inducing such aberrant DNA structures using DNA cross-linking agents also results in a loss of transcriptional silencing. These findings uncover unappreciated roles for RTEL1 in transcriptional silencing and in stabilizing DNA methylation and H3K27me3 patterns.

genomics↗

bioRxiv2023

Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking

SARS-CoV-2 continues to evolve and evade most existing neutralizing antibodies, including all clinically authorized antibodies. We have isolated and characterized two human monoclonal antibodies, 12-16 and 12-19, which exhibited neutralizing activities against all SARS-CoV-2 variants tested, including BQ.1.1 and XBB.1.5. They also blocked infection in hamsters challenged with Omicron BA.1 intranasally. Structural analyses revealed both antibodies targeted a conserved quaternary epitope located at the interface between the N-terminal domain and subdomain 1, revealing a previously unrecognized site of vulnerability on SARS-CoV-2 spike. These antibodies prevent viral receptor engagement by locking the receptor-binding domain of spike in the down conformation, revealing a novel mechanism of virus neutralization for non-RBD antibodies. Deep mutational scanning showed that SARS-CoV-2 could mutate to escape 12-19, but the responsible mutations are rarely found in circulating viruses. Antibodies 12-16 and 12-19 hold promise as prophylactic agents for immunocompromised persons who do not respond robustly to COVID-19 vaccines.

microbiology↗

bioRxiv2023

SpotLight proteomics identifies variable sequences of blood antibodies specific against deamidated human serum albumin

Spontaneous deamidation of asparaginyl residues in proteins, if not repaired or cleared, can set in motion a cascade that leads to deteriorated health. Previously, we have discovered that deamidated human serum albumin (HSA) is elevated in blood of patients with Alzheimers disease and other neurodegenerative diseases, while the level of endogenous antibodies against deamidated HSA is significantly diminished, creating an imbalance between the risk factor and the defense against it. Endogenous antibodies against deamidated proteins are still unexplored. In the current study, we employed the SpotLight proteomics approach to identify novel amino acid sequences in antibodies specific to deamidated HSA. The results provide new insights into the clearance mechanism of deamidated proteins, a possible avenue for prevention of neurodegeneration.

immunology↗

bioRxiv2023

The central nervous system is a potential reservoir and possible origin of drug resistance in HBV

The significance of HBV in cerebrospinal fluid (CSF) is unclear. In the present study, synchronous serum and CSF samples were collected from 13 patients. HBV-DNA, full-length genome, quasispecies, phylogenetic tree, compartmentalization and mutation of reverse transcriptase (RT) region analyses were performed based on PCR and sequencing methods. We found HBV-DNA was detected in the CSF of 3 antiviral-naive patients and one patient after successful antiviral therapy. Complete full-length HBV genomes were isolated from the CSF of 5 patients, including 2 patients with undetectable serum HBV-DNA. Ten patients exhibited distinct CSF-serum quasispecies, 8 harbored independent CSF-serum genetic compartmentalization and phylogenetic trees, and 5 patients presented lamivudine/entecavir-associated resistance mutations in only the CSF. The frequencies of rtL180M and rtM204I/V mutations in both serum and CSF were higher in HIV/HBV-coinfected patients than in HBV-monoinfected patients (serum: rtL180M: 3.9% vs. 0, P = 0.004; rtM204I/V: 21.3% vs. 0, P < 0.001; CSF: rtL180M: 7.6% vs. 0, P = 0.026; rtM204I/V 7.6% vs. 1.6%, P = 0.097). Our data suggested CSF is a potential HBV reservoir, and HBV in CSF harbors distinct evolution and mutation models from that in serum. HIV infection increases the possibility of HBV rtL180M and rtM204I/V mutations in both serum and CSF.

evolutionary biology↗

bioRxiv2023

XClone: detection of allele-specific subclonal copy number variations from single-cell transcriptomic data

Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of such data makes it challenging to identify allele-specific CNAs, particularly in complex clonal structures. In this study, we present a statistical method, XClone, that strengthens the signals of read depth and allelic imbalance by effective smoothing on cell neighborhood and gene coordinate graphs to detect haplotype-aware CNAs from scRNA-seq data. By applying XClone to multiple datasets with challenging compositions, we demonstrated its ability to robustly detect different types of allele-specific CNAs and potentially indicate whole genome duplication, therefore enabling the discovery of corresponding subclones and the dissection of their phenotypic impacts.

bioinformatics↗

bioRxiv2023

RNA landscapes of brain tissue and brain tissue-derived extracellular vesicles in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology

IntroductionAntiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Brain tissue-derived extracellular vesicles (bdEVs) act locally in the source tissue and may indicate molecular mechanisms in HIV CNS pathology. Regulatory RNAs from EVs have emerged as important participants in HIV disease pathogenesis. Using brain tissue and bdEVs from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation. MethodsPostmortem occipital cortex tissue were collected from pigtailed macaques: uninfected controls and SIV-infected subjects (acute phase and chronic phase with or without CNS pathology). bdEVs were separated and characterized in accordance with international consensus standards. RNAs from bdEVs and source tissue were used for sequencing and qPCR to detect mRNA, miRNA, and circRNA levels ResultsMultiple dysregulated bdEV RNAs, including mRNAs, miRNAs, and circRNAs, were identified in acute infection and chronic infection with pathology. Most dysregulated mRNAs in bdEVs reflected dysregulation in their source tissues. These mRNAs are disproportionately involved in inflammation and immune responses, especially interferon pathways. For miRNAs, qPCR assays confirmed differential abundance of miR-19a-3p, let-7a-5p, and miR-29a-3p (acute SIV infection), and miR- 146a-5p and miR-449a-5p (chronic with pathology) in bdEVs. In addition, target prediction suggested that several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in small RNA levels in bdEVs during SIV infection. ConclusionsRNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.

neuroscience↗

bioRxiv2023

Transcriptional Biomarker Discovery Towards Building A Load Stress Reporting System for Engineered Escherichia coli Strains

Foreign proteins are produced by inserting synthetic constructs into host bacteria in biotechnology applications. This process can cause resource competition between synthetic circuits and host cells, placing a metabolic burden on the host cells which may result load stress and detrimental physiological changes. Consequently, the host bacteria can experience slow growth, while the synthetic system may suffer from suboptimal function and reduced productivity. To address this issue, we developed machine learning strategies to select a minimal number of genes that could serve as biomarkers for the design of load stress reporters. We identified pairs of biomarkers that showed discriminative capacity to detect the load stress states induced in 41 engineered E. coli strains. These biomarker genes are mainly involved in Envelope stress response, Ion transport, Energy production and conversion.

synthetic biology↗

bioRxiv2023

Modeling, dissecting, and subtyping of E-Cadherin inactivation-associated diffuse-type gastric adenocarcinoma

This study investigates diffuse-type gastric adenocarcinoma (DGAC), a deadly and treatment-resistant cancer. It reveals that CDH1 inactivation occurs in a subset of DGAC patient tumors, leading to the identification of two distinct DGAC subtypes. The findings emphasize the importance of understanding DGACs molecular diversity for personalized medicine in patients with CDH1 inactivation.

cancer biology↗

bioRxiv2023

HCC-1 accelerates atherosclerosis by inducing endothelial cells and macrophages pyroptosis and serves as an early diagnostic biomarker

BACKGROUNDHCC-1 (Hemofiltrate CC chemokine-1), a CC-type chemokine, exerts function to change intracellular calcium concentration, induce leukocyte and manipulate enzyme release especially in monocytes. It has been reported that HCC-1 could predict the persistent acute kidney injury (AKI) or suppress hepatocellular carcinoma (HCC) by modulating cell cycle and promoting apoptosis, but the effect of HCC-1 on atherosclerosis is poorly understood. Here, we aimed to clarify the function and mechanism of HCC-1 in atherosclerosis and whether it could serve as a novel biomarker for the diagnosis of atherosclerosis. METHODSHCC-1 expression in serum, atherosclerotic plaques and normal arterial tissue from patients with atherosclerosis and control group was assessed by enzyme-linked immunosorbent assay, immunohistochemistry and con-focal microscope. The atherosclerotic model of HCC-1 overexpressing mice and control mice were generated by infection of AAV9-HCC-1 on an ApoE-/- background. Cell adhesion, polarization and pyroptosis were evaluated in vitro. The relationship between HCC-1 concentration in serum and atherosclerosis was analyzed in patients with atherosclerosis. RESULTSHCC-1 expression increased in patients with atherosclerosis both in serum and atherosclerotic plaque. HCC-1 overexpression mice had an enhancement in macrophage accumulation in plaque, higher levels of inflammatory factors, increased pyroptotic rate in ECs and Macrophages in plaque and decreased atherosclerotic plaque stability. In vitro, HCC-1 promoted monocytes to adhere to endothelial cells and M1 polarization, induced inflammation and pyroptosis both in ECs and Macrophages. CONCLUSIONSHCC-1 expression markedly increased in patients with atherosclerosis and HCC-1 overexpression accelerated atherosclerotic burden via an enhancement in monocytes recruitment, M1 polarization and pyroptosis both in ECs and Macrophages. Our findings suggested that HCC-1 may serve as an early biomarker for the diagnosis of atherosclerosis, with the capacity to reflect the degree of stenosis. GRAPHIC ABSTRACTA graphic abstract is available for this article.

cell biology↗

bioRxiv2023

Plastome-based Phylogenomic analyses provide insights into the germplasm resource diversity of Cibotium in China

Germplasm resource is the source of herbal medicine production. Cultivation of superior germplasm resources helps to resolve the serious conflict between long-term population persistence and growing market demand by producing materials with high quality consistently. Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness of lower extremity. Long-history use of Cibotium has rendered wild populations of this species declined seriously in China. Without sufficient understanding of species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone selecting high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic difference distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense, a cryptic species endemic to NW Yunnan and adjacent region of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed in the east and west side of a classic phylogeographic boundary that probably shaped by monsoons and landforms in China. We also evaluated the resolution of nine traditional barcode loci, and designed five new DNA barcodes based on the plastome data which can discriminate all these species and lineages of Chinese Cibotium accurately. These novel findings integrated genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit germplasm resources of Cibotium in China.

evolutionary biology↗

bioRxiv2023

Integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression

Transposable elements (TEs) can influence human diseases by disrupting genome integrity, yet their quantification has been challenging due to the repetitive nature of these sequences across the genome. We developed LocusMasterTE, a method that integrates long-read with short-read RNA-seq to increase the accuracy of TE expression quantification. By incorporating fractional transcript per million (TPM) values from long-read sequencing data into an expectation-maximization (EM) algorithm, LocusMasterTE reassigns multi-mapped reads, enhancing accuracy in short-read-based TE quantification. Validated with simulated and human datasets, LocusMasterTE holds promise for revealing new insights into TE functions through precise quantification.

genomics↗

bioRxiv2023

Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution

The canonical ion channels gated by chemical ligands use the free energy of agonist binding to open the channel pore, returning to a closed state upon agonist departure. A unique class of ion channels, known as channel-enzymes (chanzymes), possess additional enzymatic activity that is directly or indirectly linked to their channel function. Here we investigated a TRPM2 chanzyme from choanoflagellates, an evolutionary ancestor of all metazoan TRPM channels, which integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP ribose (ADPR) with high open probability and an enzyme module (NUDT9-H domain) consuming ADPR at a remarkably slow rate. Using time-resolved cryo- electron microscopy (cryo-EM), we captured a complete series of structural snapshots of the gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. Our results showed that the slow kinetics of the NUDT9-H enzyme module confers a novel self-regulatory mechanism, whereby the enzyme module modulates channel gating in a binary manner. Binding of ADPR to NUDT9-H first triggers tetramerization of the enzyme modules, promoting channel opening, while the subsequent hydrolysis reaction reduces local ADPR availability, inducing channel closure. This coupling enables the ion-conducting pore to alternate rapidly between open and closed states, avoiding Mg2+ and Ca2+ overload. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADPR hydrolase module in early species TRPM2 to a fully integrated component of a gating ring essential for channel activation in advanced species TRPM2. Our study demonstrated an example of how organisms can adapt to their environments at the molecular level.

biophysics↗