Biology subjects

Jeong, H.

Publications and source records attributed to Jeong, H..

82 records · Page 5Linked to original sources

bioRxiv2020

PRIME: a probabilistic imputation method to reduce dropouteffects in single cell RNA sequencing

Single-cell RNA sequencing technology provides a novel means to analyze the transcriptomic profiles of individual cells. The technique is vulnerable, however, to a type of noise called dropout effects, which lead to zero-inflated distributions in the transcriptome profile and reduce the reliability of the results. Single-cell RNA sequencing data therefore need to be carefully processed before in-depth analysis. Here we describe a novel imputation method that reduces dropout effects in single-cell sequencing. We construct a cell correspondence network and adjust gene expression estimates based on transcriptome profiles for the local community of cells of the same type. We comprehensively evaluated this method, called PRIME (PRobabilistic IMputation to reduce dropout effects in Expression profiles of single cell sequencing), on six datasets and verified that it improves the quality of visualization and accuracy of clustering analysis and can discover gene expression patterns hidden by noise.

bioinformatics↗

bioRxiv2019

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

Structural variation (SV), where rearrangements delete, duplicate, invert or translocate DNA segments, is a major source of somatic cell variation. It can arise in rapid bursts, mediate genetic heterogenity, and dysregulate cancer-related pathways. The challenge to systematically discover SVs in single cells remains unsolved, with copy-neutral and complex variants typically escaping detection. We developed single cell tri-channel-processing (scTRIP), a computational framework that jointly integrates read depth, template strand and haplotype phase to comprehensively discover SVs in single cells. We surveyed SV landscapes of 565 single cell genomes, including transformed epithelial cells and patient-derived leukemic samples, and discovered abundant SV classes including inversions, translocations and large-scale genomic rearrangements mediating oncogenic dysregulation. We dissected the molecular karyotype of the leukemic samples and examined their clonal structure. Different from prior methods, scTRIP also enabled direct detection and discrimination of SV mutational processes in individual cells, including breakage-fusion-bridge cycles. scTRIP will facilitate studies of clonal evolution, genetic mosaicism and somatic SV formation, and could improve disease classification for precision medicine.

genomics↗

bioRxiv2019

Phenylpropionc acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity

ABSTRACTAcetaminophen (APAP) overdose causes hepatic injury and is major contributor to acute liver injury cases. To investigate potential roles of gut microbiota in APAP-induced liver injury, C57BL/6 mice from Jackson (JAX) or Taconic (TAC) were challenged with APAP. TAC mice were more susceptible to APAP toxicity, and this disappeared upon co-housing of JAX and TAC mice. When the cecum contents from JAX and TAC mice were transplanted to germ-free mice, the mice that received TAC gut microbiota exhibited more significant hepatotoxicity after APAP administration. Non-targeted metabolomic analysis using portal vein serum and liver tissue of the mice led to identification of 19 metabolites the levels of which are associated with JAX or TAC gut microbiota. A gut bacteria-derived metabolite phenylpropionic acid (PPA) levels in cecum contents and blood were higher in mice harboring JAX gut microbiota. PPA supplementation in drinking water alleviated APAP-induced hepatotoxicity in TAC mice. This was accompanied by reduced hepatic protein levels of cytochrome P450 (CYP) 2E1, the enzyme responsible for APAP bioactivation to a toxic metabolite. This illustrates a gut microbe-liver interaction mediated by a gut bacteria-derived metabolite in modulating drug-induced liver injury.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pharmacology and toxicology↗

bioRxiv2019

Living cell-only bioink and photocurable supporting medium for printing and generation of engineered tissues with complex geometries

Scaffold-free engineering of three-dimensional (3D) tissue has focused on building sophisticated structures to achieve functional constructs. Although the development of advanced manufacturing techniques such as 3D printing has brought remarkable capabilities to the field of tissue engineering, technology to create and culture individual cell only-based high-resolution tissues, without an intervening biomaterial scaffold to maintain construct shape and architecture, has been unachievable to date. In this report, we introduce a cell printing platform which addresses the aforementioned challenge and permits 3D printing and long-term culture of a living cell-only bioink lacking a biomaterial carrier for functional tissue formation. A biodegradable and photocrosslinkable microgel supporting bath serves initially as a fluid, allowing free movement of the printing nozzle for high-resolution cell extrusion, while also presenting solid-like properties to sustain the structure of the printed constructs. The printed human stem cells, which are the only component of the bioink, couple together via transmembrane adhesion proteins and differentiate down tissue-specific lineages while being cultured in a further photocrosslinked supporting bath to form bone and cartilage tissue with precisely controlled structure. Collectively, this system, which is applicable to general 3D printing strategies, is paradigm shifting for printing of scaffold-free individual cells, cellular condensations and organoids, and may have far reaching impact in the fields of regenerative medicine, drug screening, and developmental biology.

bioengineering↗

bioRxiv2019

Cell-type specific epigenetic links to schizophrenia risk in brain

The importance of cell-type specific epigenetic variation of non-coding regions in neuropsychiatric disorders is increasingly appreciated, yet data from disease brains are conspicuously lacking. We generated cell-type specific whole-genome methylomes (N=95) and transcriptomes (N=89) from neurons and oligodendrocytes from brains of schizophrenia and matched controls. The methylomes of these two cell-types are highly distinct, with the majority of differential DNA methylation occurring in non-coding regions. DNA methylation difference between control and schizophrenia brains is subtle compared to cell-type difference, yet robust against permuted data and validated in targeted deep-sequencing analyses. Differential DNA methylation between control and schizophrenia tends to occur in cell-type differentially methylated sites, highlighting the significance of cell-type specific epigenetic dysregulation in a complex neuropsychiatric disorder. Our resource provides novel and comprehensive methylome and transcriptome data from distinct cell populations from schizophrenia brains, further revealing reduced cell-type epigenetic distinction in schizophrenia.

genomics↗

bioRxiv2019

Prior physical synchrony enhances rapport and inter-brain synchronization during subsequent educational communication

Physical synchrony has been suggested to have positive effects on not only concurrent but also subsequent communication, but the underlying neural processes are unclear. Using functional near-infrared spectroscopy (fNIRS) hyperscanning, we tested the effects of preceding physical synchrony on subsequent dyadic teaching-learning communication. Thirty-two pairs of participants performed two experimental sessions. In each session, they underwent a rhythmic arm movement block with synchronous or asynchronous conditions, and then taught/learned unknown words to/from each other according to a given scenario. Neural activities in their medial and left lateral prefrontal cortex (PFC) were measured and inter-brain synchronization (IBS) during the teaching-learning blocks was evaluated. Participants rated their subjective rapport during the teaching-learning blocks, and took a word memory test. The analyses revealed that (1) prior physical synchrony enhanced teacher-learner rapport; (2) prior physical synchrony also enhanced IBS in the lateral PFC; and (3) IBS changes correlated positively with rapport changes. Physical synchrony did however not affect word memory performance. These results suggest that IBS can be useful to measure the effects of social-bonding facilitation activities for educational communication.

neuroscience↗

bioRxiv2018

Prevalence, Characteristics, and Clinical Significance of Concomitant Cardiomyopathies in Subjects with Bicuspid Aortic Valve

BackgroundIn this study, the prevalence, characteristics, and clinical significance of concomitant specific cardiomyopathies were investigated in subjects with bicuspid aortic valve (BAV).\n\nMethodsWe retrospectively evaluated 1,186 adults with BAV (850 males, mean age 56 {+/-} 14 years). Left ventricular non-compaction, hypertrophic cardiomyopathy, and idiopathic dilated cardiomyopathy were diagnosed when patients fulfilled current clinical and echocardiographic criteria. Clinical and echocardiographic characteristics including comorbidities, heart failure presentation, BAV morphology, function, and aorta phenotypes in BAV subjects with or without specific cardiomyopathies were compared.\n\nResultsOverall, 67 subjects (5.6 %) had concomitant cardiomyopathies: 40 (3.4%) patients with left ventricular non-compaction, 17 (1.4%) with hypertrophic cardiomyopathy, and 10 (0.8%) with dilated cardiomyopathy. BAV subjects with hypertrophic cardiomyopathy had a higher prevalence of diabetes mellitus, heart failure with preserved ejection fraction, and tended to have type 0 phenotype, while BAV subjects with dilated cardiomyopathy showed a higher prevalence of chronic kidney disease and heart failure with reduced ejection fraction. BAV subjects with left ventricular non-compaction were significantly younger, predominantly male, and had greater BAV dysfunction and a higher prevalence of normal aorta shape. In multiple regression analysis, presence of cardiomyopathy was independently associated with heart failure (odds ratio 2.866, 95% confidential interval 1.652-4.974, p < 0.001) even after controlling confounding factors.\n\nConclusionConcomitant cardiomyopathies were observed in 5.6% of subjects with BAV. A few clinical and echocardiographic characteristics including comorbidities, heart failure presentation, BAV morphology, function, and presence of aortopathy were found. The presence of cardiomyopathy was independently associated with heart failure.

epidemiology↗

bioRxiv2018

Commensal gut bacteria convert the immunosuppressant tacrolimus to less potent metabolites

Tacrolimus exhibits low and variable drug exposure after oral dosing, but the contributing factors remain unclear. Based on our recent report showing a positive correlation between fecal abundance of Faecalibacterium prausnitzii and oral tacrolimus dose in kidney transplant patients, we tested whether F. prausnitzii and other gut abundant bacteria are capable of metabolizing tacrolimus. Incubation of F. prausnitzii with tacrolimus led to production of two compounds (the major one named M1), which was not observed upon tacrolimus incubation with hepatic microsomes. Isolation, purification, and structure elucidation using mass spectrometry and nuclear magnetic resonance spectroscopy indicated that M1 is a C-9 keto-reduction product of tacrolimus. Pharmacological activity testing using human peripheral blood mononuclear cells demonstrated that M1 is 15-fold less potent than tacrolimus as an immunosuppressant. Screening of 22 gut bacteria species revealed that most Clostridiales bacteria are extensive tacrolimus metabolizers. Tacrolimus conversion to M1 was verified in fresh stool samples from two healthy adults. M1 was also detected in the stool samples from kidney transplant recipients who had been taking tacrolimus orally. Together, this study presents gut bacteria metabolism as a previously unrecognized elimination route of tacrolimus, potentially contributing to the low and variable tacrolimus exposure after oral dosing.

pharmacology and toxicology↗

bioRxiv2018

Conversion of a soluble protein into a potent chaperone in vivo

Protein-folding assistance and aggregation inhibition by cellular factors are largely understood in the context of molecular chaperones. As an alternative and complementary model, we previously proposed that, in general, soluble cellular macromolecules including chaperones with large excluded volume and surface charges exhibit the intrinsic chaperone activity to prevent aggregation of their connected polypeptides, irrespective of the connection types, and thus to aid productive protein folding. As a proof of concept, we here demonstrated that a model soluble protein with an inactive protease domain robustly exerted chaperone activity toward various proteins harboring a short protease-recognition tag of 7 residues in Escherichia coli. The chaperone activity of this protein was similar or even superior to that of representative E. coli chaperones in vivo. Furthermore, in vitro refolding experiments confirmed the in vivo results. Our findings revealed that a soluble protein exhibits the intrinsic chaperone activity, which is manifested, upon binding to aggregation-prone proteins. This study gives new insights into the ubiquitous chaperoning role of cellular macromolecules in protein-folding assistance and aggregation inhibition underlying the maintenance of protein solubility and proteostasis in vivo.

biochemistry↗

bioRxiv2016

Contamination as a major factor in poor Illumina assembly of microbial isolate genomes

The nonhybrid hierarchical assembly of PacBio long reads is becoming the most preferred method for obtaining genomes for microbial isolates. On the other hand, among massive numbers of Illumina sequencing reads produced, there is a slim chance of re-evaluating failed microbial genome assembly (high contig number, large total contig size, and/or the presence of low-depth contigs). We generated Illumina-type test datasets with various levels of sequencing error, pretreatment (trimming and error correction), repetitive sequences, contamination, and ploidy from both simulated and real sequencing data and applied k-mer abundance analysis to quickly detect possible diagnostic signatures of poor assemblies. Contamination was the only factor leading to poor assemblies for the test dataset derived from haploid microbial genomes, resulting in an extraordinary peak within low-frequency k-mer range. When thirteen Illumina sequencing reads of microbes belonging to genera Bacillus or Paenibacillus from a single multiplexed run were subjected to a k-mer abundance analysis, all three samples leading to poor assemblies showed peculiar patterns of contamination. Read depth distribution along the contig length indicated that all problematic assemblies suffered from too many contigs with low average read coverage, where 1% to 15% of total reads were mapped to low-coverage contigs. We found that subsampling or filtering out reads having rare k-mers could efficiently remove low-level contaminants and greatly improve the de novo assemblies. An analysis of 16S rRNA genes recruited from reads or contigs and the application of read classification tools originally designed for metagenome analyses can help identify the source of a contamination. The unexpected presence of proteobacterial reads across multiple samples, which had no relevance to our lab environment, implies that such prevalent contamination might have occurred after the DNA preparation step, probably at the place where sequencing service was provided.

genomics↗