Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 919 records · Page 51Linked to original sources

bioRxiv2020

Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning：esophageal cancer as an example

BackgroundCancer is an important public health problem worldwide and its early diagnosis and effective prognosis are critical for its treatment. In recent years, as a good material for cancer liquid biopsy, plasma cell-free DNA (cfDNA) has been widely analyzed by next generation sequencing (NGS) for finding new molecular markers for cancer diagnosis such as size, methylation and end coordinate. However, the current studies did not still involve esophageal cancer (ESCA), a main cancer that seriously threatens human health and life in China. Here we therefore tried to find new biomarkers for this cancer from cfDNA. Materials & methodsThirty cfDNA samples from 26 ESCA patients and 4 healthy people were used to construct the NGS libraries and sequenced by using SALP-seq. The sequencing data were analyzed with variant bioinformatics methods for finding ESCA molecular biomarkers. Results & conclusionWe identified 103 epigenetic markers (including 54 genome-wide and 49 promoter markers) and 37 genetic markers for ESCA. These markers provide new molecular biomarkers for ESCA diagnosis, prognosis and therapy. Importantly, this study provides a new pipeline for finding new molecular markers for cancers from cfDNA by combining SALP-seq and machine learning. Finally, by finding new molecular markers for ESCA from cfDNA, this study sheds important new insights on the clinical worth of cfDNA.

cancer biology↗

bioRxiv2020

Quantitative Analysis of Tissue Secretome Reveals the Diagnostic and Prognostic Value of Carbonic Anhydrase II in Hepatocellular Carcinoma

Early detection and intervention are key strategies to reduce mortality, increase long-term survival and improve the therapeutic effects of hepatocellular carcinoma (HCC) patients. Herein, the isobaric tag for relative and absolute quantitation (iTRAQ) quantitative proteomic strategy was used to study the secretome in conditioned media from HCC cancerous tissues, surrounding noncancerous and distal noncancerous tissues to identify diagnostic and prognostic biomarkers for HCC. In total, 22 and 49 secretory proteins were identified to be dysregulated in the cancerous and surrounding noncancerous tissues compared with the distal noncancerous tissues. Among these proteins, carbonic anhydrase II (CA2) was identified to be significantly upregulated in the secretome of cancerous tissues; correspondingly, the serum concentrations of CA2 were remarkably increased in HCC patients than that in normal populations. Interestingly, a significant increase of serum CA2 in recurrent HCC patients after radical resection was also confirmed compared with HCC patients without recurrence, and the serum level of CA2 could act as an independent prognostic factor for time to recurrence (TTR) and overall survival (OS). Regarding the mechanism, the secreted CA2 enhances the migration and invasion of HCC cells by activating the epithelial mesenchymal transition (EMT) pathway. Taken together, this study identified a novel biomarker for HCC diagnosis and prognosis and provides a valuable resource of the HCC secretome for investigating serological biomarkers.

cancer biology↗

bioRxiv2020

Composition and Abundance of Drifting Fish Eggs on the Upper Reaches of Xijiang River, China, after the Formation of the Cascade Reservoirs

To develop effective management actions of riverine fisheries, it is important to monitor how fish resources (i.e., eggs) are recruited in the upper reaches of natural rivers, particularly where dams have been constructed, which potentially hinder life-history strategies. Here, we aimed to determine the State of drifting fish eggs resources, and the underlying environmental factors regulating the presence of fish eggs in the upper reaches of a river (Laibin section of Xijiang River, China). Based on surveys conducted over one spawning period (2016), we set out to: (1) describe the composition and abundance of drifting fish eggs in the 150 km Lainbin section under a dam control, and (2) analyze how the composition and distribution of fish eggs was correlated with environmental factors. A total of 15157 eggs belonging to two orders, four families, and 18 species were collected. Comparison of these data with historical records in the same area showed that the community structure of drifting eggs has changed considerably. Previously, the community was dominated by larger-bodied species, rather than the smaller species documented in 2016. Eggs were primarily detected between May and August. In the natural channel, the greatest abundance of eggs occurred during May and June. In comparison, the greatest abundance of eggs downstream of the dam was detected in July. The results of this study provide important information for water conservancy institutions towards managing regions containing dams to maintain the ecology of rivers and protect important fish resources.

ecology↗

bioRxiv2020

Regulating AMPK and insulin level by Vinegar, Swimming and Refeeding on High-Fat Diet Rats to Rebuild Lipid Homeostasis

Our aims were to explore the effects of dietary and behavior interventions on lipometabolism caused by unhealthy high-fat diet and the best method to rebuild lipid homeostasis of this lifestyle. Apart from normal diet rats, 34 rats were fed with high-fat emulsion for 4 weeks before being divided into 4 groups and intervened for another 4 weeks. 8 of them were classified into high-fat control group and 9 were sorted into high-fat diet with rice vinegar group. Meanwhile, 10 were put into high-fat diet with swimming group and 7 were just for refeeding normal diet group. Then the data of body weight was recorded and analyzed. Serum, pancreas, liver, cardiac tissues and epididymis adipose were sampled as required. Indexes of serum were tested by kits. AMPK, HNF1, CTRP6 from tissues were detected by western blot. According to our experiments, Swimming and refeeding groups reflected a better regulation on lipid homeostasis mainly by up-regulating the expression of pancreas AMPK. To be more specific, the refeeding rats showed lower T-CHO (P<0.001) and LDL-C (P<0.05), but higher weight gain (P<0.001),insulin level (P<0.01)and pancreas AMPK (P<0.01)than high-fat control rats. Compared with rats experimented by swimming or rice vinegar, they showed higher weight gain (P<0.001),insulin level (P<0.01)and HNF1, but lower of CTRP6. In summary, refeeding diet functioned better in regulating the lipometabolic level after high-fat diet. Whatever approach mentioned above we adopted to intervene, the best policy to keep the balance of lipid homeostasis is to maintain a healthy diet.

molecular biology↗

bioRxiv2020

Individual variability in functional organization of the human and monkey auditory cortex

Accumulating evidence shows that auditory cortex (AC) of humans, and other primates, is involved in more complex cognitive processes than feature segregation only, which are shaped by experience-dependent plasticity and thus likely show substantial individual variability. However, thus far, individual variability of ACs has been considered a methodological impediment rather than a phenomenon of theoretical importance. Here, we examined the variability of ACs using intrinsic functional connectivity patterns in humans and macaques. Our results demonstrate that in humans, functional variability is 1) greater near the non-primary than primary ACs, 2) greater in ACs than comparable visual areas, and 3) greater in the left than right ACs. Remarkably similar modality differences and lateralization of variability were observed in macaques. These connectivity-based findings are consistent with a confirmatory task-based fMRI analysis. The quantitative proof of the exceptional variability of ACs has implications for understanding the evolution of advanced auditory functions in humans.

neuroscience↗

bioRxiv2020

Dscam gene triplication causes neocortical overinhibition in Down syndrome

A growing number of molecules have been identified as regulators of inhibitory synapse development, but whether dysregulated expression of these molecules contribute to brain disorders is poorly understood. Here we show that Down syndrome cell adhesion molecule (Dscam) regulates the inhibition of neocortical pyramidal neurons (PyNs) in a level-dependent fashion. Loss of Dscam impairs inhibitory neuron development and function. In the Ts65Dn mouse model for Down syndrome, where Dscam is overexpressed, GABAergic innervation of cortical PyNs by chandelier and basket cells is increased. Genetic normalization of Dscam expression rescues the excessive GABAergic innervation and the increased inhibition of PyNs. These findings demonstrate excessive GABAergic innervation and inhibition in the neocortex of Down syndrome mouse model and identify Dscam overexpression as the cause. They also implicate dysregulated Dscam levels as a potential pathogenic driver in related neurological disorders.

neuroscience↗

bioRxiv2019

Estimating allele-specific expression of SNVs from 10x Genomics Single-Cell RNA-Sequencing Data

With the recent advances in single-cell RNA-sequencing (scRNA-seq) technologies, estimation of allele expression from single cells is becoming increasingly reliable. Allele expression is both quantitative and dynamic and is an essential component of the genomic interactome. Here, we systematically estimate allele expression from heterozygous single nucleotide variant (SNV) loci using scRNA-seq data generated on the 10x Genomics platform. We include in the analysis 26,640 human adipose-derived mesenchymal stem cells (from three healthy donors), with an average sequencing reads over 120K/cell (more than 4 billion scRNA-seq reads total). High quality SNV calls assessed in our study contained approximately 15% exonic and >50% intronic loci. To analyze the allele expression, we estimate the expressed Variant Allele Fraction (VAFRNA) from SNV-aware alignments and analyze its variance and distribution (mono- and bi-allelic) at different cutoffs for required minimal number of sequencing reads. Our analysis shows that when assessing SNV loci covered by a minimum of 3 unique sequencing reads, over 50% of the heterozygous SNVs show bi-allelic expression, while at minimum of 10 reads, nearly 90% of the SNVs are bi-allelic. Consistent with single cell studies on RNA velocity and models of transcriptional burst kinetics, we observe a substantially higher rate of monoallelic expression among intronic SNVs, signifying the usefulness of scVAFRNA to assess dynamic cellular processes. Our analysis demonstrates the feasibility of scVAFRNA estimation from current scRNA-seq datasets and shows that the 3-based library generation protocol of 10x Genomics scRNA-seq data can be highly informative in SNV-based analyses.

genomics↗

bioRxiv2019

Genome-wide CRISPR screens identify essential cell growth mediators in BRAF-inhibitor resistant melanoma

BRAF is a serine-threonine kinase that harbors activating mutations in [~]7% of human malignancies and [~]60% of melanomas. Despite initial clinical responses to BRAF inhibitors (BRAFi), patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAFi-resistant melanoma, we conducted CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAFi. The screens identified pathways and genes critical for BRAFi resistance in melanoma cells. To investigate the mechanisms and pathways enabling resistance to BRAFi in melanomas, we integrated expression data, ATAC-seq, and CRISPR screen results. We identified the JUN family of transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6 that enabled resistance to BRAFi in melanoma cells. Our findings reveal genes whose loss of function conferred resistance to a selective BRAF inhibitor, providing new insight into signaling pathways that contribute to acquired resistance in melanoma.

cancer biology↗

bioRxiv2019

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

Single-cell technologies enable measure of unique cellular signatures, but are typically limited to a single modality. Computational approaches allow integration of diverse single-cell datasets, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells in tissues, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied it to post-mortem human frontal cortex tissue. We developed a computational framework to validate fine-grained cell types using multi-modal information and assessed the effectiveness of computational integration methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling prediction of cell types with causal roles in disease.

genomics↗

bioRxiv2019

Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 100 pounds). To date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2,822 and 2,034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch- and sucrose metabolism, photosynthesis and others. The copy number of several starch synthesis related genes were found increased in jackfruit and breadfruit compared to closely related species, and the tissue specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

genomics↗

bioRxiv2019

Distinct architecture and composition of mouse axonemal radial spoke head revealed by cryo-EM

The radial spoke (RS) transmits mechanochemical signals from the central pair apparatus (CP) to axonemal dynein arms to coordinate ciliary motility. The RS head, directly contacting with CP, differs dramatically in morphology between protozoan and mammal. Here we show the murine RS head is compositionally distinct from the Chlamydomonas one. Our reconstituted murine RS head core complex consists of Rsph1, Rsph3b, Rsph4a, and Rsph9, lacking Rsph6a whose orthologue exists in the Chlamydomonas RS head. We present the unprecedented cryo-EM structure of RS head core complex at 4.5-[A] resolution and identified the subunit location and their interaction network. In this complex, Rsph3b, Rsph4a, and Rsph9 forms a compact body with Rsph4a serving possibly as an assembly scaffold and Rsph3b in a location that might link the head with stalk. Interestingly, two Rsph1 subunits constitute the two stretching-arms possibly for optimized RS-CP interaction. We also propose a sawtooth model for the RS-CP interaction. Our study suggests that the RS head experiences profound remodeling to probably comply with both structural and functional alterations of the axoneme during evolution.

cell biology↗

bioRxiv2019

Elucidation of the determinant for orchestration of solo unisexual cycle in an important human fungal pathogen

In fungi, the sex-determination program universally directs sexual development and syngamy (the fusion of gametes) that underlies pre-meiotic diploidization. However, the contribution of sex-determination to syngamy-independent sexual cycle, which requires autopolyploidization as an alternative approach to elevate ploidy before meiosis, remains unclear in fungi and other eukaryotes. The human fungal pathogen Cryptococcus neoformans, as a model organism for studying fungal sexual reproduction, can undergo syngamy-dependent bisexual and syngamy-independent solo unisexual reproduction, in which endoreplication is considered to enable pre-meiotic self-diploidization. Here, by characterizing a mutant lacking all the core sex-determination factors, we show that sex-determination plays a central role in bisexual syngamy but is not strictly required for unisexual development and self-diploidization. This implies an unknown circuit, rather than the sex-determination program, for specifically coordinating Cryptococcus unisexual cycle. We reveal that syngamy and self-diploidization are both governed by the Qsp1-directed paracrine system via two regulatory branches, Vea2 and Cqs2. Vea2 directs bisexual syngamy through the sex-determination program; conversely, Cqs2 is dispensable for bisexual syngamy but activates unisexual endoreplication. Through functional profiling of 41 transcription factors documented to regulate Cryptococcus sexual development, we reveal that only Cqs2 can drive and integrate all unisexual phases and ensure the production of meiospore progenies. Furthermore, ChIP-seq analysis together with genetic evaluation indicate that Cqs2 induces unisexual self-diploidization through its direct control of PUM1, whose expression is sufficient to drive autopolyploidization. Therefore, Cqs2 serves as the critical determinant that orchestrates Cryptococcus multistage unisexual cycle that does not strictly require the sexual-determination program.

microbiology↗

bioRxiv2019

GHSR-1a is not Required for Ghrelin's Anti-inflammatory and Fat-sparing Effects in Cancer Cachexia

Adipose tissue (AT) atrophy is a hallmark of cancer cachexia contributing to increased morbidity/mortality. Ghrelin has been proposed as a treatment for cancer cachexia partly by preventing AT atrophy. However, the mechanisms mediating ghrelins effects are incompletely understood, including the extent to which its only known receptor, GHSR-1a, is required for these effects. This study characterizes the pathways involved in AT atrophy in the Lewis Lung Carcinoma (LLC)-induced cachexia model and those mediating the effects of ghrelin in Ghsr+/+ and Ghsr-/- mice. We show that LLC causes AT atrophy by inducing anorexia, and increasing AT inflammation, thermogenesis and energy expenditure. These changes were greater in Ghsr-/-. Ghrelin administration prevented LLC-induced anorexia only in Ghsr+/+, but prevented WAT inflammation and atrophy in both genotypes, although its effects were greater in Ghsr+/+. LLC-induced increases in BAT inflammation, WAT and BAT thermogenesis, and energy expenditure were not affected by ghrelin. In conclusion, ghrelin ameliorates WAT inflammation, fat atrophy and anorexia in LLC-induced cachexia. GHSR-1a is required for ghrelins orexigenic effect but not for its anti-inflammatory or fat-sparing effects.

cancer biology↗

bioRxiv2019

Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning

Nanopore sequencing has enabled sequencing of native RNA molecules without conversion to cDNA, thus opening the gates to a new era for the unbiased study of RNA biology. However, a formal barcoding protocol for direct sequencing of native RNA molecules is currently lacking, limiting the efficient processing of multiple samples in the same flowcell. A major limitation for the development of barcoding protocols for direct RNA sequencing is the error rate introduced during the base-calling process, especially towards the 5 and 3 ends of reads, which complicates sequence-based barcode demultiplexing. Here, we propose a novel strategy to barcode and demultiplex direct RNA sequencing nanopore data, which does not rely on base-calling or additional library preparation steps. Specifically, custom DNA oligonucleotides are ligated to RNA transcripts during library preparation. Then, raw current signal corresponding to the DNA barcode is extracted and transformed into an array of pixels, which is used to determine the underlying barcode using a deep convolutional neural network classifier. Our method, DeePlexiCon, implements a 20-layer residual neural network model that can demultiplex 93% of the reads with 95.1% specificity, or 60% of reads with 99.9% specificity. The availability of an efficient and simple barcoding strategy for native RNA sequencing will enhance the use of direct RNA sequencing by making it more cost-effective to the entire community. Moreover, it will facilitate the applicability of direct RNA sequencing to samples where the RNA amounts are limited, such as patient-derived samples.

genomics↗

bioRxiv2019

Hypoxia on vhl-deficient cells to obtain hif related genes through bioinformatics analysis.

Vhl is responsible for degrading the transcription factor hif-1. Hif-1 transcription factors drive changes in hypoxic gene expression to adapt cells to exposure to hypoxic environments. This study hopes to analyze the effect of hypoxia on the vhl-deficient cells to obtain hif regulated genes through bioinformatics analysis. The top ten genes evaluated by connectivity degree in the PPI network were identified. CDK1, CTNNB1, NHP2, CCNA2, CTNNB1, MRPL16, CCND1 were down-regulated. CDK1, RPL12, RPL17, RPL27, RPS10 were up-regulated.

cell biology↗

bioRxiv2019

Phase separation-aided compartmentalization of protein-protein interactions in cells

Protein-protein interactions (PPIs) are of great significance in many biological activities and diseases. It is essential to distinguish between direct, indirect and false PPIs in order to accurately understand their biological functions. Here we report a method based on phase separation-aided compartmentalization of protein-protein interactions in cells (PACPIC), which is tailored for identification of direct and indirect PPIs in cells, using recruitment as the readout.

cell biology↗

bioRxiv2019

Slicing the genome of star-fruit (Averrhoa carambola L.)

The Averrhoa carambola is commonly known as star fruit because of its peculiar shape and its fruit is a rich source of minerals and vitamins. It is also used in traditional medicines in countries like India, China, the Philippines, and Brazil for treating various ailments such as fever, diarrhea, vomiting, and skin disease. Here we present the first draft genome of the Oxalidaceae family with an assembled genome size of 470.51 Mb. In total, 24,726 protein-coding genes were identified and 16,490 genes were annotated using various well-known databases. The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family. Based on the gene functional annotations, we also discovered the enzymes possibly involved in the important nutritional pathways in star fruit genome. Overall, being the first sequenced genome in the Oxalidaceae family, the data provides an essential resource for the nutritional, medicinal, and cultivational studies for this economically important star-fruit plant.

genomics↗

bioRxiv2019

Abnormal nitration and S-sulfhydration of Sp1-CSE-H2S pathway contribute to the progress of HHcy

Sp1 (Specificity protein 1)-CSE (cystathionine-{gamma}-lyase)-H2S (hydrogen sulfide) pathway plays an important role in homocysteine-metabolism, whose disorder can result in hyperhomocysteinemia. The deficiency of plasma H2S in patients and animal models with hyperhomocysteinemia has been reported but it is unclear whether this deficiency plays a role in the progress of hyperhomocysteinemia. Furthermore, it remains unknown whether the post-translational modification of Sp1 or CSE mediated by hyperhomocysteinemia itself can in turn affect the development of hyperhomocysteinemia. By both in vivo and in vitro studies, we conducted immunoprecipitation and maleimide assays to detect the post-translational modification of Sp1-CSE-H2S pathway and revealed four major findings: (1) the accumulation of homocysteine augmented the nitration of CSE, thus blunted its bio-activity and caused H2S deficiency. (2) H2S deficiency lowered the S-sulfhydration of Sp1 and inhibited its transcriptional activity, resulted in lower expression of CSE. CSE deficiency decreased the H2S level further, which in turn lowered the S-sulfhydration level of CSE. (3) CSE was S-sulfhydrated at Cys84, Cys109, Cys172, Cys229, Cys252, Cys307 and Cys310 under physiological conditions, mutation of Cys84, Cys109, Cys229, Cys252 and Cys307 decreased its S-sulfhydration level and bio-activity. (4) H2S deficiency could trap hyperhomocysteinemia into a progressive vicious circle and trigger a rapid increase of homocysteine, while blocking nitration or restoring S-sulfhydration could break this circle. In conclusion, this study reveals a novel mechanism involved in the disorder of homocysteine-metabolism, which may provide a candidate therapeutic strategy for hyperhomocysteinemia.

pathology↗