Biology subjects

Pan, C.

Publications and source records attributed to Pan, C..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

Glucocorticoid signaling delays castration-induced regression in murine models of prostate cancer

Androgen deprivation therapy (ADT) induces regression of recurrent and advanced prostate cancer (PrCa), but many tumors recur. To understand the response to ADT, changes in tumor volume were imaged after castration of murine PrCa models. While mouse (non-tumor) prostate begins to regress within two days of castration, murine PrCa regresses after a delay of 3-14 days in two distinct mouse models. Intra-tumoral androgens are undetectable after castration, but tumor cells proliferate during this period. Intratumoral glucocorticoids and glucocorticoid receptor (GR) protein increase, as does GR mRNA and a set of GR-regulated genes specifically in tumor epithelial cells identified using scRNAseq. A selective GR antagonist (CORT125281, relacorilant), in clinical trials for late-state PrCa, eliminates the delayed regression phenotype in both models. Thus, activated GR signaling and murine tumor proliferation following castration resembles the GR-dependent escape mechanism of castrate resistant PrCa. These results suggest simultaneous inhibition of GR and androgen receptor signaling could improve PrCa therapy. In briefAndrogen deprivation therapy for high risk and recurrent prostate cancers is initially effective, but ultimately fails; better understanding the mechanisms should improve therapy. In two murine prostate cancer models, GR signaling is activated immediately following castration, substituting for the acute reduction in AR signaling, and allowing for continued tumor growth. This continued growth is blocked by relacorilant, selective GR antagonist in clinical trials for late-state PrCa. HighlightsO_LIAndrogen deprivation therapy induces regression of prostate cancer, but tumors recur C_LIO_LIMurine PrCa continues to proliferate for 3-14 days in two distinct mouse prostate cancer models C_LIO_LITumor cells proliferate during this period, and intratumoral glucocorticoids and glucocorticoid receptor (GR) protein increase, as does GR mRNA and a set of GR-regulated genes C_LIO_LIRelacorilant, a selective GR antagonist in clinical trials for late-state PrCa, eliminates the delayed regression C_LI

cancer biology↗

bioRxiv2021

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing

DNA is a promising next-generation data storage medium, but the recording latency and synthesis cost of oligos using the four natural nucleotides remain high. Here, we describe an improved DNA-based storage system that uses an extended 11-letter molecular alphabet combining natural and chemically modified nucleotides. Our extended-alphabet molecular storage paradigm offers a nearly two-fold increase in storage density and potentially the same order of reduction in the recording time. Experimental results involving a library of 77 custom-designed hybrid sequences reveal that one can readily detect and discriminate different combinations and orders of monomers via MspA nanopores. Furthermore, a neural network architecture designed to classify raw current signals generated by Oxford Nanopore Technologies sequencing ensures an average accuracy exceeding 60%, which is 39 times higher than that of random guessing. Molecular dynamics simulations reveal that the majority of modified nucleotides do not induce dramatic disruption of the DNA double helix, making the extended alphabet system potentially compatible with PCR-based random access data retrieval. The methodologies proposed provide a forward path for new implementations of molecular recorders.

synthetic biology↗

bioRxiv2021

Plant-based biosensors for detecting CRISPR-mediated genome engineering

CRISPR/Cas has recently emerged as the most reliable system for genome engineering in various species. However, concerns about risks associated with CRISPR/Cas9 technology are increasing on potential unintended DNA changes that might accidentally arise from CRISPR gene editing. Developing a system that can detect and report the presence of active CRIPSR/Cas tools in biological systems is therefore very necessary. Here, we developed the real-time detection systems that can spontaneously indicate CRISPR-Cas tools for genome editing and gene regulation including CRISPR/Cas9 nuclease, base editing, prime editing and CRISPRa in plants. Using the fluorescence-based molecular biosensors, we demonstrated that the activities of CRISPR/Cas9 nuclease, base editing, prime editing and CRIPSRa can be effectively detected in transient expression via protoplast transformation and leaf infiltration (in Arabidopsis, poplar, and tobacco) and stable transformation in Arabidopsis.

plant biology↗

bioRxiv2021

Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes

Transcriptome-wide association studies (TWAS) explore genetic variants affecting gene expression for association with a trait. Here we studied coronary artery disease (CAD) using this approach by first determining genotype-regulated expression levels in nine CAD relevant tissues by EpiXcan in two genetics-of-gene-expression panels, the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) and the Genotype-Tissue Expression (GTEx). Based on these data we next imputed gene expression in respective nine tissues from individual level genotype data on 37,997 CAD cases and 42,854 controls for a subsequent gene-trait association analysis. Transcriptome-wide significant association (P < 3.85e-6) was observed for 114 genes, which by genetic means were differentially expressed predominately in arterial, liver, and fat tissues. Of these, 96 resided within previously identified GWAS risk loci and 18 were novel (CAND1, EGFLAM, EZR, FAM114A1, FOCAD, GAS8, HOMER3, KPTN, MGP, NLRC4, RGS19, SDCCAG3, STX4, TSPAN11, TXNRD3, UFL1, WASF1, and WWP2). Gene set analyses showed that TWAS genes were strongly enriched in CAD-related pathways and risk traits. Associations with CAD or related traits were also observed for damaging mutations in 67 of these TWAS genes (11 novel) in whole-exome sequencing data of UK Biobank. Association studies in human genotype data of UK Biobank and expression-trait association statistics of atherosclerosis mouse models suggested that newly identified genes predominantly affect lipid metabolism, a classic risk factor for CAD. Finally, CRISPR/Cas9-based gene knockdown of RGS19 and KPTN in a human hepatocyte cell line resulted in reduced secretion of APOB100 and lipids in the cell culture medium. Taken together, our TWAS approach was able to i) prioritize genes at known GWAS risk loci and ii) identify novel genes which are associated with CAD.

genetics↗

bioRxiv2021

Structural and mechanistic insight into CRISPR-Cas9 inhibition by anti-CRISPR protein AcrIIC4

Phages, plasmids, and other mobile genetic elements express inhibitors of CRISPR-Cas immune systems, known as anti-CRISPR proteins, to protect themselves from targeted destruction. These anti-CRISPRs have been shown to function through very diverse mechanisms. In this work we investigate the activity of an anti-CRISPR isolated from a prophage in Haemophilus parainfluenzae that blocks CRISPR-Cas9 DNA cleavage activity. We determine the three-dimensional crystal struture of AcrIIC4 and show that it binds to the Cas9 Recognition Domain. This binding does not prevent the Cas9-anti-CRISPR complex from interacting with target DNA but does inhibit DNA cleavage. AcrIIC4 likely acts by blocking the conformational changes that allow the HNH and RuvC endonuclease domains to contact the DNA sites to be nicked.

biochemistry↗

bioRxiv2021

A Chromosome-level Assembly of a Wild Castor Genome Provides New Insights into the Adaptive Evolution in a Tropical Desert

Wild castor grows in the high-altitude tropical desert of the African Plateau, a region known for high ultraviolet radiations, strong lights and extremely dry conditions. To investigate the potential genetic basis of adaptation to both highland and tropical deserts, we generated a chromosome-level genome sequence of the wild castor accession WT05, with genome size of 316 Mb and scaffold and contig N50 sizes of 31.93 Mb and 8.96 Mb, respectively. Compared with cultivated castor and other Euphorbiaceae species, the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair, photosynthesis and abiotic stress responses. Genetic variations associated with positive selection were identified in several key genes, such as LIG1, DDB2, and RECG1, involved in nucleotide excision repair. Moreover, a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments. The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.

genomics↗

bioRxiv2021

Rewritable Two-Dimensional DNA-Based Data Storage with Machine Learning Reconstruction

DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores high-density images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.

synthetic biology↗

bioRxiv2021

All-Flesh Tomato Regulated by Reduced Dosage of AFF Provides New Insights into Berry Fruit Evolution

The formation of locule gel is not only an important developmental process in tomato but also a typical characteristic of berry fruit. In this study, we collected a tomato material that produces all-flesh fruits (AFF), whose locule tissue remains in a solid state during fruit development. We built genetic populations to fine map the causal gene of AFF trait, investigate the function of AFF gene, and identified it as the causal locus conferring the locule gel formation. We determined the causal mutation as a 416-bp deletion that occurred in the promoter region of AFF, which reduces the expression dosage of AFF. The 416-bp deleted sequence has a high level of conservation among closely related Solanaceae species, as well as in the tomato population. The activity of the 416-bp deletion in down-regulating gene expression was further verified by the relative activity in a luciferase experiment. Furthermore, with the BC6 NIL materials, we reveal that the reduced expression dosage of AFF does not impact the normal development of seeds, while produces non-liquefied locule tissue, which is distinct from that of the normal tomatoes in terms of metabolic components. Based on these findings, we propose that the AFF gene is the core node in locule tissue liquefaction, whose function cannot be compensated by its paralogs TAG1, TAGL1, or TAGL11. Our findings provide clues to investigate fruit type differentiation among Solanaceae crops, and also contributes to the breeding application of all flesh fruit tomatoes for the tomato processing industry. One Sentence SummaryThe sequence deletion that occurred in the cis-regulatory region of AFF--the core node of locule tissue liquefaction determined here--reduced its expression dosage, and produced all flesh fruit tomato.

plant biology↗

bioRxiv2020

An Engineered Genetic Circuit for Lactose Intolerance Alleviation Coupled with Gut Microbiota Recovery

BackgroundLactose malabsorption occurs in around 68% of the world populations, causing lactose intolerance (LI) symptoms such as abdominal pain, bloating and diarrhoea. To alleviate LI, previous studies mainly focused on strengthening intestinal {beta}-galactosidase activity but neglected the inconspicuous colon pH drop caused by gut microbes fermentation on non-hydrolysed lactose. The colon pH drop will reduce intestinal {beta}-galactosidase activity and influence the intestinal homeostasis. ResultsHere, we synthesized a tri-stable-switch circuit equipped with high {beta}-galactosidase activity and pH rescue ability. This circuit can switch in functionality between expression of {beta}-galactosidase and expression of l-lactate dehydrogenase in respond to intestinal lactose signal and intestinal pH signal. We confirmed the circuit functionality was efficient using 12-hrs in vitro culture at a range of pH levels, as well as 6-hrs in vivo simulations in mice colon. Moreover, another 21-days mice trial indicated that this circuit can recover lactose-effected gut microbiota of mice to the status (enterotypes) similar to that of mice without lactose intake. ConclusionsTaken together, the tri-stable-switch circuit can serve as a promising prototype for LI symptoms relief, especially by flexibly adapting to environmental variation, stabilizing colon pH and restoring gut microbiota.

bioengineering↗

bioRxiv2020

Long-term survival of salmon-attached SARS-CoV-2 at 4 degree as a potential source of transmission in seafood markets

Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. Here we showed that salmon-attached SARS-CoV-2 at 4{degrees}C could remain infectious for more than one week, suggesting that fish-attached SARS-CoV-2 may be a source of transmission.

microbiology↗

bioRxiv2020

Machine learning reveals time-varying microbial predictors with complex effects on glucose regulation

The incidence of type 2 diabetes (T2D) has been increasing globally and a growing body of evidence links type 2 diabetes with altered microbiota composition. Type 2 diabetes is preceded by a long pre-diabetic state characterized by changes in various metabolic parameters. We tested whether the gut microbiome could have predictive potential for T2D development during the healthy and pre-diabetic disease stages. We used prospective data of 608 well-phenotyped Finnish men collected from the population-based Metabolic Syndrome In Men (METSIM) study to build machine learning models for predicting continuous glucose and insulin measures in a shorter (1.5 year) and longer (4.5 year) period. Our results show that the inclusion of gut microbiome improves prediction accuracy for modelling T2D associated parameters such as glycosylated hemoglobin and insulin measures. We identified novel microbial biomarkers and described their effects on the predictions using interpretable machine learning techniques, which revealed complex linear and non-linear associations. Additionally, the modelling strategy carried out allowed us to compare the stability of model performances and biomarker selection, also revealing differences in short-term and long-term predictions. The identified microbiome biomarkers provide a predictive measure for various metabolic traits related to T2D, thus providing an additional parameter for personal risk assessment. Our work also highlights the need for robust modelling strategies and the value of interpretable machine learning. ImportanceRecent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent. In order to consider microbiome as a factor in disease risk assessment, prospective studies are needed. Our study is the first study that assesses the gut microbiome as a predictive measure for several type 2 diabetes associated parameters in a longitudinal study setting. Our results revealed a number of novel microbial biomarkers that can improve the prediction accuracy for continuous insulin measures and glycosylated hemoglobin levels. These results make the prospect of using microbiome in personalized medicine promising.

microbiology↗

bioRxiv2020

Actinobacillus utilizes a binding-protein dependent ABC transporter to acquire Vitamin B6

Bacteria require high efficiency uptake systems to survive and proliferate in nutrient limiting environments, such as those found in the host. The ABC transporters at the bacterial plasma membrane provide a mechanism for transport of many substrates. We recently demonstrated that an AfuABC operon, previously annotated as encoding a ferrous iron uptake system, is in fact a cyclic hexose/heptose-phosphate transporter with high selectivity and specificity for these metabolites. In this study, we examine a second operon containing a periplasmic binding protein discovered in Actinobacillus for its potential role in nutrient acquisition. Using electron density obtained from the crystal structure of the periplasmic binding protein we modeled a pyridoxal-5-phosphate (P5P/PLP/Vitamin B6) ligand into the atomic resolution electron density map. The identity of the Vitamin B6 bound to this periplasmic binding protein was verified by isothermal titration calorimetry, microscale thermophoresis, and mass spectrometry, leading us to name the protein P5PA and the operon P5PAB. To illustrate the functional utility of this uptake system, we introduced the P5PAB operon from A. pleuropneumoniae into an E. coli K-12 strain that was devoid of a key enzyme required for Vitamin B6 synthesis. The growth of this strain at low levels of Vitamin B6 supports the role of this newly identify operon in Vitamin B6 uptake.

biochemistry↗

bioRxiv2020

Targeted delivery of acid alpha-glucosidase corrects skeletal muscle phenotypes in Pompe disease mice

Lysosomal diseases are a class of genetic disorders predominantly caused by loss of lysosomal hydrolases, leading to lysosomal and cellular dysfunction. Enzyme Replacement Therapy (ERT), where recombinant enzyme is given intravenously, internalized by cells, and trafficked to the lysosome, has been applied to treat several lysosomal diseases. However, current ERT regimens do not correct disease phenotypes in all affected organs because the biodistribution of enzyme uptake does not match that of the affected cells and tissues that require the enzyme. We present here targeted ERT, an approach that utilizes antibody-enzyme fusion proteins to target the enzyme to specific tissues. The antibody moiety recognizes transmembrane proteins involved in lysosomal trafficking and that are also preferentially expressed in those cells most affected in disease. Using Pompe disease (PD) as an example, we show that targeted ERT is superior to ERT in treating the skeletal muscle phenotypes of PD mice.

bioengineering↗

bioRxiv2020

Effects of rhein on bile acid homeostasis in rats

Rhein, the active ingredient of rhubarb, a medicinal and edible plant, is widely used in clinical practice. In this work, we investigated the alterations of 14 bile acids and hepatic transporters after rats were administered rhein for 5 consecutive weeks. There was no obvious injury to the liver and kidney, and there were no significant changes in biochemical indicators. However, 1,000 mg/kg rhein increased the liver total bile acid (TBA) levels, especially taurine-conjugated bile acids (t-CBAs), inhibited the expression of Farnesoid X receptor (FXR) and (bile salt export pump) BSEP mRNA, and upregulated the expression of (cholesterol 7-hydroxylase) CYP7A1 mRNA. Rhein close to the clinical dose reduced the amounts of TBAs, especially unconjugated bile acids (UCBAs), and elevated the expression of FXR and multidrug resistance-associated protein 3 (Mrp3) mRNA. These results denote that rhein is not toxic and is safe to use at a reasonable dose and timing.

pharmacology and toxicology↗

bioRxiv2020

Measuring genetic variation in the multi-ethnic Million Veteran Program (MVP)

The Million Veteran Program (MVP), initiated by the Department of Veterans Affairs (VA), aims to collect consented biosamples from at least one million Veterans. Presently, blood samples have been collected from over 800,000 enrolled participants. The size and diversity of the MVP cohort, as well as the availability of extensive VA electronic health records make it a promising resource for precision medicine. MVP is conducting array-based genotyping to provide genome-wide scan of the entire cohort, in parallel with whole genome sequencing, methylation, and other omics assays. Here, we present the design and performance of MVP 1.0 custom Axiom(R) array, which was designed and developed as a single assay to be used across the multi-ethnic MVP cohort. A unified genetic quality control analysis was developed and conducted on an initial tranche of 485,856 individuals leading to a high-quality dataset of 459,777 unique individuals. 668,418 genetic markers passed quality control and showed high quality genotypes not only on common variants but also on rare variants. We confirmed the substantial ancestral diversity of MVP with nearly 30% non-European individuals, surpassing other large biobanks. We also demonstrated the quality of the MVP dataset by replicating established genetic associations with height in European Americans and African Americans ancestries. This current data set has been made available to approved MVP researchers for genome-wide association studies and other downstream analyses. Further data releases will be available for analysis as recruitment at the VA continues and the cohort expands both in size and diversity.

genetics↗

bioRxiv2019

Image Processing in DNA

The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain both individual oligo (fragment) symbol errors as well as missing DNA oligo errors, with rates that exceed those of modern storage systems by orders of magnitude. These errors can be corrected either through the use of a large number of redundant oligos or through cycles of writing, reading, and rewriting of information that eliminate the errors. Both approaches add to the overall storage cost and are hence undesirable. Here we propose the first method for storing quantized images in DNA that uses signal processing and machine learning techniques to deal with error and cost issues without resorting to the use of redundant oligos or rewriting. Our methods rely on decoupling the RGB channels of images, performing specialized quantization and compression on the individual color channels, and using new discoloration detection and image inpainting techniques. We demonstrate the performance of our approach experimentally on a collection of movie posters stored in DNA.

bioinformatics↗

bioRxiv2019

Large-scale Genetic Analysis Identifies 66 Novel Loci for Asthma

We carried out a genome-wide association study (GWAS) for asthma in UK Biobank, followed by a meta-analysis with results from the Trans-National Asthma Genetic Consortium (TAGC). 66 novel genomic regions were identified, bringing the number of known asthma susceptibility loci to 211. Significant gene-sex interactions were also observed where susceptibility alleles, either individually or as a function of polygenic risk scores, increased asthma risk to a greater extent in men than women. Bioinformatics analyses demonstrated that asthma-associated variants were enriched for colocalizing to regions of open chromatic in immune cells and identified candidate causal genes at 52 of the novel loci, including CD52. An anti-CD52 (-CD52) antibody mimicked the immune cell-depleting effects of an FDA-approved human -CD52 antibody and reduced allergen-induced airway hyperreactivity in mice. These results further elucidate the genetic architecture of asthma, provide evidence that the immune system plays a prominent role in its pathogenesis, and suggest that CD52 represents a potentially novel therapeutic target for treating asthma.

genetics↗

bioRxiv2019

Deep learning reveals cancer metastasis and therapeutic antibody targeting in whole body

Reliable detection of disseminated tumor cells and of the biodistribution of tumor-targeting therapeutic antibodies within the entire body has long been needed to better understand and treat cancer metastasis. Here, we developed an integrated pipeline for automated quantification of cancer metastases and therapeutic antibody targeting, named DeepMACT. First, we enhanced the fluorescent signal of tumor cells more than 100-fold by applying the vDISCO method to image single cancer cells in intact transparent mice. Second, we developed deep learning algorithms for automated quantification of metastases with an accuracy matching human expert manual annotation. Deep learning-based quantifications in a model of spontaneous metastasis using human breast cancer cells allowed us to systematically analyze clinically relevant features such as size, shape, spatial distribution, and the degree to which metastases are targeted by a therapeutic monoclonal antibody in whole mice. DeepMACT can thus considerably improve the discovery of effective therapeutic strategies for metastatic cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/541862v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@ffe1b9org.highwire.dtl.DTLVardef@13c55eborg.highwire.dtl.DTLVardef@2ccb6corg.highwire.dtl.DTLVardef@df55e9_HPS_FORMAT_FIGEXP M_FIG C_FIG Supplementary Movies and deep learning algorithms of DeepMACT are available at http://discotechnologies.org/DeepMACT/

cancer biology↗