Publications by authors named "Bing Ren"

265 Publications

Improved epicardial cardiac fibroblast generation from iPSCs.

J Mol Cell Cardiol 2021 Nov 24;164:58-68. Epub 2021 Nov 24.

Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA. Electronic address:

Since the initial isolation of human embryonic stem cells and subsequent discovery of reprogramming methods for somatic cells, thousands of protocols have been developed to create each of the hundreds of cell types found in-vivo with significant focus on disease-prone systems, e.g., cardiovascular. Robust protocols exist for many of these cell types, except for cardiac fibroblasts (CF). Very recently, several competing methods have been developed to generate these cells through a developmentally conserved epicardial pathway. Such methods generate epicardial cells, but here we report that prolonged exposure to growth factors such as bFGF induces fibroblast spindle-like morphology and similar chromatin architecture to primary CFs. Media conditions for growth and assays are provided, as well as suggestions for seeding densities and timepoints for protein harvest of extracellular matrix. We demonstrate marker expression and matrix competency of resultant cells as shown next to primary human cardiac fibroblasts. These methods provide additional guidance to the original protocol and result in an increasingly stable phenotype.
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http://dx.doi.org/10.1016/j.yjmcc.2021.11.011DOI Listing
November 2021

Effects of transglutaminase cross-linking process on printability of gelatin microgel-gelatin solution composite bioink.

Biofabrication 2021 Nov 25. Epub 2021 Nov 25.

Mechanical and Aerospace Engineering, University of Florida, 230 MAE-B Building, PO Box 116250, Gainesville, Florida, 32611-7011, UNITED STATES.

Three-dimensional (3D) bioprinting has emerged as a powerful engineering approach for various tissue engineering applications, particularly for the development of 3D cellular structures with unique mechanical and/or biological properties. For the jammed gelatin microgel-gelatin solution composite bioink, comprising a discrete phase of microgels (enzymatically gelled gelatin microgels) and a cross-linkable continuous gelatin precursor solution-based phase containing transglutaminase (TG), its rheology properties and printability change gradually due to the TG enzyme-induced cross-linking process. The objective of this study is to establish a direct mapping between the printability of the gelatin microgel-gelatin solution based cross-linkable composite bioink and the TG concentration and cross-linking time, respectively. Due to the inclusion of TG in the composite bioink, the bioink starts cross-linking once prepared and is usually prepared right before a printing process. Herein, the bioink printability is evaluated based on the three metrics: injectability, feature formability, and process-induced cell injury. In this study, the rheology properties such as the storage modulus and viscosity have been first systematically investigated and predicted at different TG concentrations and times during the cross-linking process using the first-order cross-linking kinetics model. The storage modulus and viscosity have been satisfactorily modeled as exponential functions of the TG concentration and time with an experimentally calibrated cross-linking kinetic rate constant. Furthermore, the injectability, feature formability, and process-induced cell injury have been successfully correlated to the TG concentration and cross-linking time via the storage modulus, viscosity, and/or process-induced shear stress. By combing the good injectability, good feature formability, and satisfactory cell viability zones, a good printability zone (1.65, 0.61, and 0.31 hours for the composite bioinks with 1.00, 2.00, and 4.00% w/v TG, respectively) has been established during the printing of mouse fibroblast-based 2% gelatin B microgel-3% gelatin B solution composite bioink. This printability zone approach can be extended to the use of other cross-linkable bioinks for bioprinting applications.
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http://dx.doi.org/10.1088/1758-5090/ac3d75DOI Listing
November 2021

Evaluation of an Artificial Intelligence-Augmented Digital System for Histologic Classification of Colorectal Polyps.

JAMA Netw Open 2021 Nov 1;4(11):e2135271. Epub 2021 Nov 1.

Department of Biomedical Data Science, Geisel School of Medicine, Hanover, New Hampshire.

Importance: Colorectal polyps are common, and their histopathologic classification is used in the planning of follow-up surveillance. Substantial variation has been observed in pathologists' classification of colorectal polyps, and improved assessment by pathologists may be associated with reduced subsequent underuse and overuse of colonoscopy.

Objective: To compare standard microscopic assessment with an artificial intelligence (AI)-augmented digital system that annotates regions of interest within digitized polyp tissue and predicts polyp type using a deep learning model to assist pathologists in colorectal polyp classification.

Design, Setting, And Participants: In this diagnostic study conducted at a tertiary academic medical center and a community hospital in New Hampshire, 100 slides with colorectal polyp samples were read by 15 pathologists using a microscope and an AI-augmented digital system, with a washout period of at least 12 weeks between use of each modality. The study was conducted from February 10 to July 10, 2020.

Main Outcomes And Measures: Accuracy and time of evaluation were used to compare pathologists' performance when a microscope was used with their performance when the AI-augmented digital system was used. Outcomes were compared using paired t tests and mixed-effects models.

Results: In assessments of 100 slides with colorectal polyp specimens, use of the AI-augmented digital system significantly improved pathologists' classification accuracy compared with microscopic assessment from 73.9% (95% CI, 71.7%-76.2%) to 80.8% (95% CI, 78.8%-82.8%) (P < .001). The overall difference in the evaluation time per slide between the digital system (mean, 21.7 seconds; 95% CI, 20.8-22.7 seconds) and microscopic examination (mean, 13.0 seconds; 95% CI, 12.4-13.5 seconds) was -8.8 seconds (95% CI, -9.8 to -7.7 seconds), but this difference decreased as pathologists became more familiar and experienced with the digital system; the difference between the time of evaluation on the last set of 20 slides for all pathologists when using the microscope and the digital system was 4.8 seconds (95% CI, 3.0-6.5 seconds).

Conclusions And Relevance: In this diagnostic study, an AI-augmented digital system significantly improved the accuracy of pathologic interpretation of colorectal polyps compared with microscopic assessment. If applied broadly to clinical practice, this tool may be associated with decreases in subsequent overuse and underuse of colonoscopy and thus with improved patient outcomes and reduced health care costs.
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http://dx.doi.org/10.1001/jamanetworkopen.2021.35271DOI Listing
November 2021

Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.

Nat Commun 2021 11 17;12(1):6636. Epub 2021 Nov 17.

Department of Pediatrics, Pediatric Diabetes Research Center, University of California, La Jolla, San Diego, CA, 92093, USA.

FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.
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http://dx.doi.org/10.1038/s41467-021-26950-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8599738PMC
November 2021

A single-cell atlas of chromatin accessibility in the human genome.

Cell 2021 Nov 12;184(24):5985-6001.e19. Epub 2021 Nov 12.

Ludwig Institute for Cancer Research, La Jolla, CA, USA; Center for Epigenomics, University of California San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA. Electronic address:

Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of gene regulatory elements in diverse cell types and tissues in the human body, we applied single-cell chromatin accessibility assays to 30 adult human tissue types from multiple donors. We integrated these datasets with previous single-cell chromatin accessibility data from 15 fetal tissue types to reveal the status of open chromatin for ∼1.2 million candidate cis-regulatory elements (cCREs) in 222 distinct cell types comprised of >1.3 million nuclei. We used these chromatin accessibility maps to delineate cell-type-specificity of fetal and adult human cCREs and to systematically interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues, life stages, and organ systems.
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http://dx.doi.org/10.1016/j.cell.2021.10.024DOI Listing
November 2021

An atlas of gene regulatory elements in adult mouse cerebrum.

Nature 2021 10 6;598(7879):129-136. Epub 2021 Oct 6.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures. Recent surveys of mouse and human brains with single-cell transcriptomics and high-throughput imaging technologies have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.
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http://dx.doi.org/10.1038/s41586-021-03604-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494637PMC
October 2021

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.

Nature 2021 10 6;598(7879):103-110. Epub 2021 Oct 6.

Allen Institute for Brain Science, Seattle, WA, USA.

Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.
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http://dx.doi.org/10.1038/s41586-021-03500-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494649PMC
October 2021

Comparative cellular analysis of motor cortex in human, marmoset and mouse.

Nature 2021 10 6;598(7879):111-119. Epub 2021 Oct 6.

Allen Institute for Brain Science, Seattle, WA, USA.

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
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http://dx.doi.org/10.1038/s41586-021-03465-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494640PMC
October 2021

DNA methylation atlas of the mouse brain at single-cell resolution.

Nature 2021 10 6;598(7879):120-128. Epub 2021 Oct 6.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.

Mammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing to profile 103,982 nuclei (including 95,815 neurons and 8,167 non-neuronal cells) from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, we constructed an artificial neural network model that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data enabled prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum.
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http://dx.doi.org/10.1038/s41586-020-03182-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494641PMC
October 2021

SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data.

Nat Methods 2021 09 26;18(9):1056-1059. Epub 2021 Aug 26.

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.

Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for Hi-C (SnapHiC), a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. Using scHi-C data from 742 mouse embryonic stem cells, we benchmark SnapHiC against a number of computational tools developed for mapping chromatin loops and interactions from bulk Hi-C. We further demonstrate its use by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells, which uncovers cell type-specific chromatin loops and predicts putative target genes for noncoding sequence variants associated with neuropsychiatric disorders. Our results indicate that SnapHiC could facilitate the analysis of cell type-specific chromatin architecture and gene regulatory programs in complex tissues.
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http://dx.doi.org/10.1038/s41592-021-01231-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8440170PMC
September 2021

Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).

Methods Mol Biol 2021 ;2351:181-199

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Proximity ligation-assisted ChIP-Seq (PLAC-Seq), also known as HiChIP, is a method to detect and quantify chromatin contacts anchored at genomic regions bound by specific proteins or histone modifications. By combining in situ Hi-C and chromatin immunoprecipitation (ChIP) using antibodies against transcription factors (TFs) or histone marks of interest, the method achieves targeted interrogation of chromatin organization at a subset of genomic regions. PLAC-Seq is able to identify long-range chromatin interactions at kilobase-scale resolution with significantly reduced sequencing cost.
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http://dx.doi.org/10.1007/978-1-0716-1597-3_10DOI Listing
September 2021

Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING.

Cell Rep 2021 Jul;36(3):109412

Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.

In this study, we investigate mechanisms leading to inflammation and immunoreactivity in ovarian tumors with homologous recombination deficiency (HRD). BRCA1 loss is found to lead to transcriptional reprogramming in tumor cells and cell-intrinsic inflammation involving type I interferon (IFN) and stimulator of IFN genes (STING). BRCA1-mutated (BRCA1) tumors are thus T cell inflamed at baseline. Genetic deletion or methylation of DNA-sensing/IFN genes or CCL5 chemokine is identified as a potential mechanism to attenuate T cell inflammation. Alternatively, in BRCA1 cancers retaining inflammation, STING upregulates VEGF-A, mediating immune resistance and tumor progression. Tumor-intrinsic STING elimination reduces neoangiogenesis, increases CD8 T cell infiltration, and reverts therapeutic resistance to dual immune checkpoint blockade (ICB). VEGF-A blockade phenocopies genetic STING loss and synergizes with ICB and/or poly(ADP-ribose) polymerase (PARP) inhibitors to control the outgrowth of Trp53Brca1 but not Brca1 ovarian tumors in vivo, offering rational combinatorial therapies for HRD cancers.
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http://dx.doi.org/10.1016/j.celrep.2021.109412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371260PMC
July 2021

3D-printed titanium implant combined with interleukin 4 regulates ordered macrophage polarization to promote bone regeneration and angiogenesis.

Bone Joint Res 2021 Jul;10(7):411-424

Institute of Stomatology, Shandong University, Jinan, Shandong, China.

Aims: The use of 3D-printed titanium implant (DT) can effectively guide bone regeneration. DT triggers a continuous host immune reaction, including macrophage type 1 polarization, that resists osseointegration. Interleukin 4 (IL4) is a specific cytokine modulating osteogenic capability that switches macrophage polarization type 1 to type 2, and this switch favours bone regeneration.

Methods: IL4 at concentrations of 0, 30, and 100 ng/ml was used at day 3 to create a biomimetic environment for bone marrow mesenchymal stromal cell (BMMSC) osteogenesis and macrophage polarization on the DT. The osteogenic and immune responses of BMMSCs and macrophages were evaluated respectively.

Results: DT plus 30 ng/ml of IL4 (DT + 30 IL4) from day 3 to day 7 significantly (p < 0.01) enhanced macrophage type 2 polarization and BMMSC osteogenesis compared with the other groups. Local injection of IL4 enhanced new bone formation surrounding the DT.

Conclusion: DT + 30 IL4 may switch macrophage polarization at the appropriate timepoints to promote bone regeneration. Cite this article:  2021;10(7):411-424.
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http://dx.doi.org/10.1302/2046-3758.107.BJR-2020-0334.R4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8333031PMC
July 2021

Splenic-vasculature involvement is associated with poor prognosis in resected distal pancreatic cancer.

Gastroenterol Rep (Oxf) 2021 Apr 24;9(2):139-145. Epub 2020 Nov 24.

Department of Pathology, Immunology and Lab Medicine, University of Florida, Gainesville, FL, USA.

Background: Distal pancreatic carcinoma is one of the most lethal cancers largely due to its high incidence of distant metastasis. This study aims to assess the prognostic value of splenic-vasculature involvement in resected distal pancreatic carcinoma.

Methods: In this retrospective study, we collected the clinicopathologic information of 454 patients with pancreatic cancer and performed univariate and multivariate analyses to identify factors associated with progression-free survival (PFS) and overall survival (OS), with an emphasis on the prognostic value of splenic-artery and -vein involvement.

Results: Univariate analysis revealed that larger tumor size, non-intraductal papillary mucinous neoplasm (non-IPMN)-associated adenocarcinoma, poor differentiation, stage pT3, nodal metastasis, lymphovascular invasion, perineural invasion, and pathologic and radiographic evidence of splenic-vein invasion were significantly associated with shorter PFS and OS (all  < 0.05). Multivariate analysis confirmed non-IPMN-associated adenocarcinoma, stage pT3, stage pN1-2, and post-operative adjuvant chemotherapy as independent risk factors for both PFS and OS, and larger tumor size and radiographic evidence of splenic-artery invasion as predictors of PFS only.

Conclusion: Guidelines should be developed for a uniform approach with regard to the examination and reporting of the status of the splenic vasculature when dealing with distal-pancreatic-cancer specimens.
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http://dx.doi.org/10.1093/gastro/goaa084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8128010PMC
April 2021

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.

Nat Genet 2021 07 17;53(7):1064-1074. Epub 2021 May 17.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.
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http://dx.doi.org/10.1038/s41588-021-00863-6DOI Listing
July 2021

Cardiac cell type-specific gene regulatory programs and disease risk association.

Sci Adv 2021 May 14;7(20). Epub 2021 May 14.

Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.

Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease-associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type-specific gene regulation in human hearts during health and disease.
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http://dx.doi.org/10.1126/sciadv.abf1444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121433PMC
May 2021

Complaint of Testicular Discomfort in Patient with Esophageal Adenocarcinoma.

Case Rep Urol 2021 19;2021:6692578. Epub 2021 Apr 19.

Department of Surgery/Section of Urology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.

We report a case of esophageal cancer with solitary metastasis to the testicle in a 71-year-old man. The tumor was picked up on physical exam following new onset complaints of pain and swelling. While most testicular masses in older men are due to lymphoma, this case highlights the need to consider metastatic disease as a source of new symptoms in patients with a recent cancer diagnosis.
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http://dx.doi.org/10.1155/2021/6692578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8079193PMC
April 2021

Effect of high concentration of ammonium on production of n-caproate: Recovery of a high-value biochemical from food waste via lactate-driven chain elongation.

Waste Manag 2021 Jun 3;128:25-35. Epub 2021 May 3.

Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China.

Ammonium accumulation is inevitable during the fermentation of food waste (FW), challenging the application of chain elongation process upgrading FW into the high-value biochemical n-caproate, which is a medium chain carboxylate. This study is the first to investigate ammonium inhibition of lactate-driven chain elongation process. The short-term exposure of a Clostridium IV-dominated chain elongating reactor microbiome at an ammonium concentration of 1-4 g L linearly decreased n-caproate production by 25-80%. High levels of ammonium (≥5 g L) could cause failure of chain elongation, shifting the product from n-caproate to propionate. The involved mechanisms revealed that ammonium reshaped the microbial community from Clostridium IV domination to Clostridium IV and Propionibacterium co-domination (based on 16S rRNA sequencing) and reduced the activities of key enzymes involved in the reversed β-oxidization pathway. We propose an effective strategy from our study, which is the first one to do in our knowledge, to upgrade raw FW without dilution to n-caproate: lowering the ammonium accumulation to 1.0 g L at the setup phase for adaptation and prolonging the hydraulic retention time (10 days) during the operation phase for the colonization of chain-elongation bacteria. These findings lay a foundation for the implementation of the LCE process on FW, providing an alternative way to alleviate the global FW crisis.
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http://dx.doi.org/10.1016/j.wasman.2021.04.015DOI Listing
June 2021

Iterative single-cell multi-omic integration using online learning.

Nat Biotechnol 2021 08 19;39(8):1000-1007. Epub 2021 Apr 19.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for integrating large, diverse and continually arriving single-cell datasets. Our approach scales to arbitrarily large numbers of cells using fixed memory, iteratively incorporates new datasets as they are generated and allows many users to simultaneously analyze a single copy of a large dataset by streaming it over the internet. Iterative data addition can also be used to map new data to a reference dataset. Comparisons with previous methods indicate that the improvements in efficiency do not sacrifice dataset alignment and cluster preservation performance. We demonstrate the effectiveness of online iNMF by integrating more than 1 million cells on a standard laptop, integrating large single-cell RNA sequencing and spatial transcriptomic datasets, and iteratively constructing a single-cell multi-omic atlas of the mouse motor cortex.
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http://dx.doi.org/10.1038/s41587-021-00867-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8355612PMC
August 2021

Development and evaluation of a deep neural network for histologic classification of renal cell carcinoma on biopsy and surgical resection slides.

Sci Rep 2021 03 29;11(1):7080. Epub 2021 Mar 29.

Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.

Renal cell carcinoma (RCC) is the most common renal cancer in adults. The histopathologic classification of RCC is essential for diagnosis, prognosis, and management of patients. Reorganization and classification of complex histologic patterns of RCC on biopsy and surgical resection slides under a microscope remains a heavily specialized, error-prone, and time-consuming task for pathologists. In this study, we developed a deep neural network model that can accurately classify digitized surgical resection slides and biopsy slides into five related classes: clear cell RCC, papillary RCC, chromophobe RCC, renal oncocytoma, and normal. In addition to the whole-slide classification pipeline, we visualized the identified indicative regions and features on slides for classification by reprocessing patch-level classification results to ensure the explainability of our diagnostic model. We evaluated our model on independent test sets of 78 surgical resection whole slides and 79 biopsy slides from our tertiary medical institution, and 917 surgical resection slides from The Cancer Genome Atlas (TCGA) database. The average area under the curve (AUC) of our classifier on the internal resection slides, internal biopsy slides, and external TCGA slides is 0.98 (95% confidence interval (CI): 0.97-1.00), 0.98 (95% CI: 0.96-1.00) and 0.97 (95% CI: 0.96-0.98), respectively. Our results suggest that the high generalizability of our approach across different data sources and specimen types. More importantly, our model has the potential to assist pathologists by (1) automatically pre-screening slides to reduce false-negative cases, (2) highlighting regions of importance on digitized slides to accelerate diagnosis, and (3) providing objective and accurate diagnosis as the second opinion.
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http://dx.doi.org/10.1038/s41598-021-86540-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8007643PMC
March 2021

Comprehensive analysis of single cell ATAC-seq data with SnapATAC.

Nat Commun 2021 02 26;12(1):1337. Epub 2021 Feb 26.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.
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http://dx.doi.org/10.1038/s41467-021-21583-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910485PMC
February 2021

Joint profiling of histone modifications and transcriptome in single cells from mouse brain.

Nat Methods 2021 03 15;18(3):283-292. Epub 2021 Feb 15.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissues lack single-cell resolution. Here we describe an ultra-high-throughput method, Paired-Tag, for joint profiling of histone modifications and transcriptome in single cells to produce cell-type-resolved maps of chromatin state and transcriptome in complex tissues. We used this method to profile five histone modifications jointly with transcriptome in the adult mouse frontal cortex and hippocampus. Integrative analysis of the resulting maps identified distinct groups of genes subject to divergent epigenetic regulatory mechanisms. Our single-cell multiomics approach enables comprehensive analysis of chromatin state and gene regulation in complex tissues and characterization of gene regulatory programs in the constituent cell types.
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http://dx.doi.org/10.1038/s41592-021-01060-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954905PMC
March 2021

A β-catenin-driven switch in TCF/LEF transcription factor binding to DNA target sites promotes commitment of mammalian nephron progenitor cells.

Elife 2021 Feb 15;10. Epub 2021 Feb 15.

Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, United States.

The canonical Wnt pathway transcriptional co-activator β-catenin regulates self-renewal and differentiation of mammalian nephron progenitor cells (NPCs). We modulated β-catenin levels in NPC cultures using the GSK3 inhibitor CHIR99021 (CHIR) to examine opposing developmental actions of β-catenin. Low CHIR-mediated maintenance and expansion of NPCs are independent of direct engagement of TCF/LEF/β-catenin transcriptional complexes at low CHIR-dependent cell-cycle targets. In contrast, in high CHIR, TCF7/LEF1/β-catenin complexes replaced TCF7L1/TCF7L2 binding on enhancers of differentiation-promoting target genes. Chromosome confirmation studies showed pre-established promoter-enhancer connections to these target genes in NPCs. High CHIR-associated de novo looping was observed in positive transcriptional feedback regulation to the canonical Wnt pathway. Thus, β-catenin's direct transcriptional role is restricted to the induction of NPCs, where rising β-catenin levels switch inhibitory TCF7L1/TCF7L2 complexes to activating LEF1/TCF7 complexes at primed gene targets poised for rapid initiation of a nephrogenic program.
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http://dx.doi.org/10.7554/eLife.64444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924951PMC
February 2021

Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development.

Elife 2021 Feb 5;10. Epub 2021 Feb 5.

Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, San Diego, United States.

Genetic variants associated with type 2 diabetes (T2D) risk affect gene regulation in metabolically relevant tissues, such as pancreatic islets. Here, we investigated contributions of regulatory programs active during pancreatic development to T2D risk. Generation of chromatin maps from developmental precursors throughout pancreatic differentiation of human embryonic stem cells (hESCs) identifies enrichment of T2D variants in pancreatic progenitor-specific stretch enhancers that are not active in islets. Genes associated with progenitor-specific stretch enhancers are predicted to regulate developmental processes, most notably tissue morphogenesis. Through gene editing in hESCs, we demonstrate that progenitor-specific enhancers harboring T2D-associated variants regulate cell polarity genes and . Knockdown of or in zebrafish embryos causes a defect in pancreas morphogenesis and impairs islet cell development. Together, our findings reveal that a subset of T2D risk variants specifically affects pancreatic developmental programs, suggesting that dysregulation of developmental processes can predispose to T2D.
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http://dx.doi.org/10.7554/eLife.59067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864636PMC
February 2021

Systematic analysis of binding of transcription factors to noncoding variants.

Nature 2021 03 27;591(7848):147-151. Epub 2021 Jan 27.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Many sequence variants have been linked to complex human traits and diseases, but deciphering their biological functions remains challenging, as most of them reside in noncoding DNA. Here we have systematically assessed the binding of 270 human transcription factors to 95,886 noncoding variants in the human genome using an ultra-high-throughput multiplex protein-DNA binding assay, termed single-nucleotide polymorphism evaluation by systematic evolution of ligands by exponential enrichment (SNP-SELEX). The resulting 828 million measurements of transcription factor-DNA interactions enable estimation of the relative affinity of these transcription factors to each variant in vitro and evaluation of the current methods to predict the effects of noncoding variants on transcription factor binding. We show that the position weight matrices of most transcription factors lack sufficient predictive power, whereas the support vector machine combined with the gapped k-mer representation show much improved performance, when assessed on results from independent SNP-SELEX experiments involving a new set of 61,020 sequence variants. We report highly predictive models for 94 human transcription factors and demonstrate their utility in genome-wide association studies and understanding of the molecular pathways involved in diverse human traits and diseases.
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http://dx.doi.org/10.1038/s41586-021-03211-0DOI Listing
March 2021

FIREcaller: Detecting frequently interacting regions from Hi-C data.

Comput Struct Biotechnol J 2021 29;19:355-362. Epub 2020 Dec 29.

Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.

Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of -regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.
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http://dx.doi.org/10.1016/j.csbj.2020.12.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788093PMC
December 2020

The biomechanical effects of Ti versus PEEK used in the PLIF surgery on lumbar spine: a finite element analysis.

Comput Methods Biomech Biomed Engin 2021 Aug 11;24(10):1115-1124. Epub 2021 Jan 11.

Key Laboratory of High Efficiency and Clean Manufacturing, School of Mechanical Engineering, Shandong University, Jinan, China.

Titanium (Ti) and polyetheretherketone (PEEK) are commonly used in posterior lumbar interbody fusion (PLIF). The study investigated biomechanical effects of Ti versus PEEK used as materials of cage and rods on the lumbar spine. Four different configurations of PLIF were constituted. Stiff Ti rods provided satisfactory initial stability but increased the stress on rods significantly under simulated physiological load conditions. Ti cage increased the stress on bone endplates significantly. Materials of cage and rods had insignificant effects on the nucleus pressure and facet joint force of non-instrumented segments. Further clinical studies and follow-up observations are essential for corroborating these findings.
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http://dx.doi.org/10.1080/10255842.2020.1869219DOI Listing
August 2021
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