Publications by authors named "Xiling Shen"

75 Publications

Living fabrication of functional semi-interpenetrating polymeric materials.

Nat Commun 2021 06 8;12(1):3422. Epub 2021 Jun 8.

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

Cell-mediated living fabrication has great promise for generating materials with versatile, programmable functions. Here, we demonstrate the engineering of living materials consisting of semi-interpenetrating polymer networks (sIPN). The fabrication process is driven by the engineered bacteria encapsulated in a polymeric microcapsule, which serves as the initial scaffold. The bacteria grow and undergo programmed lysis in a density-dependent manner, releasing protein monomers decorated with reactive tags. Those protein monomers polymerize with each other to form the second polymeric component that is interlaced with the initial crosslinked polymeric scaffold. The formation of sIPN serves the dual purposes of enhancing the mechanical property of the living materials and anchoring effector proteins for diverse applications. The material is resilient to perturbations because of the continual assembly of the protein mesh from the monomers released by the engineered bacteria. We demonstrate the adoption of the platform to protect gut microbiota in animals from antibiotic-mediated perturbations. Our work lays the foundation for programming functional living materials for diverse applications.
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http://dx.doi.org/10.1038/s41467-021-23812-7DOI Listing
June 2021

An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility.

Genome Med 2021 05 17;13(1):83. Epub 2021 May 17.

Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA.

Background: While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysiology remains an important challenge. Methods are needed to systematically bridge this crucial gap to facilitate experimental testing of hypotheses and translation to clinical utility.

Results: Here, we leveraged cross-phenotype associations to identify traits with shared genetic architecture, using linkage disequilibrium (LD) information to accurately capture shared SNPs by proxy, and calculate significance of enrichment. This shared genetic architecture was examined across differing biological scales through incorporating data from catalogs of clinical, cellular, and molecular GWAS. We have created an interactive web database (interactive Cross-Phenotype Analysis of GWAS database (iCPAGdb)) to facilitate exploration and allow rapid analysis of user-uploaded GWAS summary statistics. This database revealed well-known relationships among phenotypes, as well as the generation of novel hypotheses to explain the pathophysiology of common diseases. Application of iCPAGdb to a recent GWAS of severe COVID-19 demonstrated unexpected overlap of GWAS signals between COVID-19 and human diseases, including with idiopathic pulmonary fibrosis driven by the DPP9 locus. Transcriptomics from peripheral blood of COVID-19 patients demonstrated that DPP9 was induced in SARS-CoV-2 compared to healthy controls or those with bacterial infection. Further investigation of cross-phenotype SNPs associated with both severe COVID-19 and other human traits demonstrated colocalization of the GWAS signal at the ABO locus with plasma protein levels of a reported receptor of SARS-CoV-2, CD209 (DC-SIGN). This finding points to a possible mechanism whereby glycosylation of CD209 by ABO may regulate COVID-19 disease severity.

Conclusions: Thus, connecting genetically related traits across phenotypic scales links human diseases to molecular and cellular measurements that can reveal mechanisms and lead to novel biomarkers and therapeutic approaches. The iCPAGdb web portal is accessible at http://cpag.oit.duke.edu and the software code at https://github.com/tbalmat/iCPAGdb .
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http://dx.doi.org/10.1186/s13073-021-00904-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127495PMC
May 2021

Mapping the peripheral nervous system in the whole mouse via compressed sensing tractography.

J Neural Eng 2021 Jun 8;18(4). Epub 2021 Jun 8.

Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States of America.

The peripheral nervous system (PNS) connects the central nervous system with the rest of the body to regulate many physiological functions and is therapeutically targeted to treat diseases such as epilepsy, depression, intestinal dysmotility, chronic pain, and more. However, we still lack understanding of PNS innervation in most organs because the large span, diffuse nature, and small terminal nerve bundle fibers have precluded whole-organism, high resolution mapping of the PNS. We sought to produce a comprehensive peripheral nerve atlas for use in future interrogation of neural circuitry and selection of targets for neuromodulation.We used diffusion tensor magnetic resonance imaging (DT-MRI) with high-speed compressed sensing to generate a tractogram of the whole mouse PNS. The tractography generated from the DT-MRI data is validated using lightsheet microscopy on optically cleared, antibody stained tissue.Herein we demonstrate the first comprehensive PNS tractography in a whole mouse. Using this technique, we scanned the whole mouse in 28 h and mapped PNS innervation and fiber network in multiple organs including heart, lung, liver, kidneys, stomach, intestines, and bladder at 70m resolution. This whole-body PNS tractography map has provided unparalleled information; for example, it delineates the innervation along the gastrointestinal tract by multiple sacral levels and by the vagal nerves. The map enabled a quantitative tractogram that revealed relative innervation of the major organs by each vertebral foramen as well as the vagus nerve.This novel high-resolution nerve atlas provides a potential roadmap for future neuromodulation therapies and other investigations into the neural circuits which drive homeostasis and disease throughout the body.
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http://dx.doi.org/10.1088/1741-2552/ac0089DOI Listing
June 2021

Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19.

Med (N Y) 2021 Apr 13. Epub 2021 Apr 13.

Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA.

Sexual dimorphisms in immune responses contribute to coronavirus disease 2019 (COVID-19) outcomes, yet the mechanisms governing this disparity remain incompletely understood. We carried out sex-balanced sampling of peripheral blood mononuclear cells from confirmed COVID-19 inpatients and outpatients, uninfected close contacts, and healthy controls for 36-color flow cytometry and single cell RNA-sequencing. Our results revealed a pronounced reduction of circulating mucosal associated invariant T (MAIT) cells in infected females. Integration of published COVID-19 airway tissue datasets implicate that this reduction represented a major wave of MAIT cell extravasation during early infection in females. Moreover, female MAIT cells possessed an immunologically active gene signature, whereas male counterparts were pro-apoptotic. Collectively, our findings uncover a female-specific protective MAIT profile, potentially shedding light on reduced COVID-19 susceptibility in females.
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http://dx.doi.org/10.1016/j.medj.2021.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043578PMC
April 2021

The frontier of live tissue imaging across space and time.

Cell Stem Cell 2021 04;28(4):603-622

Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA. Electronic address:

What you see is what you get-imaging techniques have long been essential for visualization and understanding of tissue development, homeostasis, and regeneration, which are driven by stem cell self-renewal and differentiation. Advances in molecular and tissue modeling techniques in the last decade are providing new imaging modalities to explore tissue heterogeneity and plasticity. Here we describe current state-of-the-art imaging modalities for tissue research at multiple scales, with a focus on explaining key tradeoffs such as spatial resolution, penetration depth, capture time/frequency, and moieties. We explore emerging tissue modeling and molecular tools that improve resolution, specificity, and throughput.
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http://dx.doi.org/10.1016/j.stem.2021.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034393PMC
April 2021

Dysregulated transcriptional responses to SARS-CoV-2 in the periphery.

Nat Commun 2021 02 17;12(1):1079. Epub 2021 Feb 17.

Durham Veterans Affairs Medical Center, Durham, NC, USA.

SARS-CoV-2 infection has been shown to trigger a wide spectrum of immune responses and clinical manifestations in human hosts. Here, we sought to elucidate novel aspects of the host response to SARS-CoV-2 infection through RNA sequencing of peripheral blood samples from 46 subjects with COVID-19 and directly comparing them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. Early SARS-CoV-2 infection triggers a powerful transcriptomic response in peripheral blood with conserved components that are heavily interferon-driven but also marked by indicators of early B-cell activation and antibody production. Interferon responses during SARS-CoV-2 infection demonstrate unique patterns of dysregulated expression compared to other infectious and healthy states. Heterogeneous activation of coagulation and fibrinolytic pathways are present in early COVID-19, as are IL1 and JAK/STAT signaling pathways, which persist into late disease. Classifiers based on differentially expressed genes accurately distinguished SARS-CoV-2 infection from other acute illnesses (auROC 0.95 [95% CI 0.92-0.98]). The transcriptome in peripheral blood reveals both diverse and conserved components of the immune response in COVID-19 and provides for potential biomarker-based approaches to diagnosis.
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http://dx.doi.org/10.1038/s41467-021-21289-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889643PMC
February 2021

Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity.

Nat Commun 2021 01 11;12(1):262. Epub 2021 Jan 11.

Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA.

The pathogenesis of ulcerative colitis (UC), a major type of inflammatory bowel disease, remains unknown. No model exists that adequately recapitulates the complexity of clinical UC. Here, we take advantage of induced pluripotent stem cells (iPSCs) to develop an induced human UC-derived organoid (iHUCO) model and compared it with the induced human normal organoid model (iHNO). Notably, iHUCOs recapitulated histological and functional features of primary colitic tissues, including the absence of acidic mucus secretion and aberrant adherens junctions in the epithelial barrier both in vitro and in vivo. We demonstrate that the CXCL8/CXCR1 axis was overexpressed in iHUCO but not in iHNO. As proof-of-principle, we show that inhibition of CXCL8 receptor by the small-molecule non-competitive inhibitor repertaxin attenuated the progression of UC phenotypes in vitro and in vivo. This patient-derived organoid model, containing both epithelial and stromal compartments, will generate new insights into the underlying pathogenesis of UC while offering opportunities to tailor interventions to the individual patient.
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http://dx.doi.org/10.1038/s41467-020-20351-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801686PMC
January 2021

An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility.

medRxiv 2020 Dec 22. Epub 2020 Dec 22.

Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA.

While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysiology remains an important challenge. Methods are needed to systematically bridge this crucial gap to facilitate experimental testing of hypotheses and translation to clinical utility. Here, we leveraged cross-phenotype associations to identify traits with shared genetic architecture, using linkage disequilibrium (LD) information to accurately capture shared SNPs by proxy, and calculate significance of enrichment. This shared genetic architecture was examined across differing biological scales through incorporating data from catalogs of clinical, cellular, and molecular GWAS. We have created an interactive web database (interactive Cross-Phenotype Analysis of GWAS database (iCPAGdb); http://cpag.oit.duke.edu ) to facilitate exploration and allow rapid analysis of user-uploaded GWAS summary statistics. This database revealed well-known relationships among phenotypes, as well as the generation of novel hypotheses to explain the pathophysiology of common diseases. Application of iCPAGdb to a recent GWAS of severe COVID-19 demonstrated unexpected overlap of GWAS signals between COVID-19 and human diseases, including with idiopathic pulmonary fibrosis driven by the locus. Transcriptomics from peripheral blood of COVID-19 patients demonstrated that was induced in SARS-CoV-2 compared to healthy controls or those with bacterial infection. Further investigation of cross-phenotype SNPs with severe COVID-19 demonstrated colocalization of the GWAS signal of the locus with plasma protein levels of a reported receptor of SARS-CoV-2, CD209 (DC-SIGN), pointing to a possible mechanism whereby glycosylation of CD209 by may regulate COVID-19 disease severity. Thus, connecting genetically related traits across phenotypic scales links human diseases to molecular and cellular measurements that can reveal mechanisms and lead to novel biomarkers and therapeutic approaches.
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http://dx.doi.org/10.1101/2020.12.20.20248572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781346PMC
December 2020

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants.

Cell Host Microbe 2021 02 6;29(2):281-298.e5. Epub 2021 Jan 6.

Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA. Electronic address:

Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated by original matched TCGA samples. Gene copies and nucleotide variants can further distinguish mixed-evidence species. We, thus, present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to the discovery of prognostic species and blood signatures of mucosal barrier injuries and enabled systematic matched microbe-host multi-omic analyses, which will help guide future studies of the microbiome's role in human health and disease.
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http://dx.doi.org/10.1016/j.chom.2020.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878430PMC
February 2021

Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity.

bioRxiv 2020 Dec 5. Epub 2020 Dec 5.

SARS-CoV-2 infection triggers highly variable host responses and causes varying degrees of illness in humans. We sought to harness the peripheral blood mononuclear cell (PBMC) response over the course of illness to provide insight into COVID-19 physiology. We analyzed PBMCs from subjects with variable symptom severity at different stages of clinical illness before and after IgG seroconversion to SARS-CoV-2. Prior to seroconversion, PBMC transcriptomes did not distinguish symptom severity. In contrast, changes in chromatin accessibility were associated with symptom severity. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif occupancy for individual PBMC cell types. The most extensive remodeling occurred in CD14+ monocytes where sub-populations with distinct chromatin accessibility profiles were associated with disease severity. Our findings indicate that pre-seroconversion chromatin remodeling in certain innate immune populations is associated with divergence in symptom severity, and the identified transcription factors, regulatory elements, and downstream pathways provide potential prognostic markers for COVID-19 subjects.
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http://dx.doi.org/10.1101/2020.12.04.412155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724678PMC
December 2020

Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration.

JCI Insight 2020 11 19;5(22). Epub 2020 Nov 19.

Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA.

Adult liver has enormous regenerative capacity; it can regenerate after losing two-thirds of its mass while sustaining essential metabolic functions. How the liver balances dual demands for increased proliferative activity with maintenance of organ function is unknown but essential to prevent liver failure. Using partial hepatectomy (PHx) in mice to model liver regeneration, we integrated single-cell RNA- and ATAC-Seq to map state transitions in approximately 13,000 hepatocytes at single-cell resolution as livers regenerated, and validated key findings with IHC, to uncover how the organ regenerates hepatocytes while simultaneously fulfilling its vital tissue-specific functions. After PHx, hepatocytes rapidly and transiently diversified into multiple distinct populations with distinct functional bifurcation: some retained the chromatin landscapes and transcriptomes of hepatocytes in undamaged adult livers, whereas others transitioned to acquire chromatin landscapes and transcriptomes of fetal hepatocytes. Injury-related signaling pathways known to be critical for regeneration were activated in transitioning hepatocytes, and the most fetal-like hepatocytes exhibited chromatin landscapes that were enriched with transcription factors regulated by those pathways.
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http://dx.doi.org/10.1172/jci.insight.141024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710279PMC
November 2020

A Tissue Engineering Approach to Metastatic Colon Cancer.

iScience 2020 Nov 20;23(11):101719. Epub 2020 Oct 20.

Department of Cancer Biology, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA.

Colon cancer remains the third most common cause of cancer in the US, and the third most common cause of cancer death. Worldwide, colon cancer is the second most common cause of cancer and cancer deaths. At least 25% of patients still present with metastatic disease, and at least 25-30% will develop metastatic colon cancer in the course of their disease. While chemotherapy and surgery remain the mainstay of treatment, understanding the fundamental cellular niche and mechanical properties that result in metastases would facilitate both prevention and cure. Advances in biomaterials, novel 3D primary human cells, modelling using microfluidics and the ability to alter the physical environment, now offers a unique opportunity to develop and test impactful treatment.
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http://dx.doi.org/10.1016/j.isci.2020.101719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653071PMC
November 2020

A Precision Medicine Drug Discovery Pipeline Identifies Combined CDK2 and 9 Inhibition as a Novel Therapeutic Strategy in Colorectal Cancer.

Mol Cancer Ther 2020 12 6;19(12):2516-2527. Epub 2020 Nov 6.

Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina.

Colorectal cancer is the third most common cancer in the United States and responsible for over 50,000 deaths each year. Therapeutic options for advanced colorectal cancer are limited, and there remains an unmet clinical need to identify new treatments for this deadly disease. To address this need, we developed a precision medicine pipeline that integrates high-throughput chemical screens with matched patient-derived cell lines and patient-derived xenografts (PDX) to identify new treatments for colorectal cancer. High-throughput screens of 2,100 compounds were performed across six low-passage, patient-derived colorectal cancer cell lines. These screens identified the CDK inhibitor drug class among the most effective cytotoxic compounds across six colorectal cancer lines. Among this class, combined targeting of CDK1, 2, and 9 was the most effective, with ICs ranging from 110 nmol/L to 1.2 μmol/L. Knockdown of CDK9 in the presence of a CDK2 inhibitor (CVT-313) showed that CDK9 knockdown acted synergistically with CDK2 inhibition. Mechanistically, dual CDK2/9 inhibition induced significant G-M arrest and anaphase catastrophe. Combined CDK2/9 inhibition synergistically reduced PDX tumor growth. Our precision medicine pipeline provides a robust screening and validation platform to identify promising new cancer therapies. Application of this platform to colorectal cancer pinpointed CDK2/9 dual inhibition as a novel combinatorial therapy to treat colorectal cancer.
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http://dx.doi.org/10.1158/1535-7163.MCT-20-0454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7718319PMC
December 2020

The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress.

Nat Commun 2020 10 9;11(1):5117. Epub 2020 Oct 9.

Institute of Molecular Cancer Research, University of Zurich, 8057, Zurich, Switzerland.

Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double strand breaks. Here, we show that H. pylori-induced DNA damage occurs co-transcriptionally in S-phase cells that activate NF-κB signaling upon innate immune recognition of the lipopolysaccharide biosynthetic intermediate β-ADP-heptose by the ALPK1/TIFA signaling pathway. DNA damage depends on the bi-functional RfaE enzyme and the Cag pathogenicity island of H. pylori, is accompanied by replication fork stalling and can be observed also in primary cells derived from gastric organoids. Importantly, H. pylori-induced replication stress and DNA damage depend on the presence of co-transcriptional RNA/DNA hybrids (R-loops) that form in infected cells during S-phase as a consequence of β-ADP-heptose/ ALPK1/TIFA/NF-κB signaling. H. pylori resides in close proximity to S-phase cells in the gastric mucosa of gastritis patients. Taken together, our results link bacterial infection and NF-κB-driven innate immune responses to R-loop-dependent replication stress and DNA damage.
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http://dx.doi.org/10.1038/s41467-020-18857-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7547021PMC
October 2020

Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection.

JCI Insight 2020 10 15;5(20). Epub 2020 Oct 15.

Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.

Myeloid cells are increasingly recognized as major players in transplant rejection. Here, we used a murine kidney transplantation model and single cell transcriptomics to dissect the contribution of myeloid cell subsets and their potential signaling pathways to kidney transplant rejection. Using a variety of bioinformatic techniques, including machine learning, we demonstrate that kidney allograft-infiltrating myeloid cells followed a trajectory of differentiation from monocytes to proinflammatory macrophages, and they exhibited distinct interactions with kidney allograft parenchymal cells. While this process correlated with a unique pattern of myeloid cell transcripts, a top gene identified was Axl, a member of the receptor tyrosine kinase family Tyro3/Axl/Mertk (TAM). Using kidney transplant recipients with Axl gene deficiency, we further demonstrate that Axl augmented intragraft differentiation of proinflammatory macrophages, likely via its effect on the transcription factor Cebpb. This, in turn, promoted intragraft recruitment, differentiation, and proliferation of donor-specific T cells, and it enhanced early allograft inflammation evidenced by histology. We conclude that myeloid cell Axl expression identified by single cell transcriptomics of kidney allografts in our study plays a major role in promoting intragraft myeloid cell and T cell differentiation, and it presents a potentially novel therapeutic target for controlling kidney allograft rejection and improving kidney allograft survival.
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http://dx.doi.org/10.1172/jci.insight.141321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605544PMC
October 2020

Development of a precision medicine pipeline to identify personalized treatments for colorectal cancer.

BMC Cancer 2020 Jun 24;20(1):592. Epub 2020 Jun 24.

Department of Medicine, Division of Medical Oncology, Duke University Medical Center, 3008 Snyderman Building, 905 S. LaSalle St., Durham, NC, 27710, USA.

Background: Metastatic colorectal cancer (CRC) continues to be a major health problem, and current treatments are primarily for disease control and palliation of symptoms. In this study, we developed a precision medicine strategy to discover novel therapeutics for patients with CRC.

Methods: Six matched low-passage cell lines and patient-derived xenografts (PDX) were established from CRC patients undergoing resection of their cancer. High-throughput drug screens using a 119 FDA-approved oncology drug library were performed on these cell lines, which were then validated in vivo in matched PDXs. RNA-Seq analysis was then performed to identify predictors of response.

Results: Our study revealed marked differences in response to standard-of-care agents across patients and pinpointed druggable pathways to treat CRC. Among these pathways co-targeting of fibroblast growth factor receptor (FGFR), SRC, platelet derived growth factor receptor (PDGFR), or vascular endothelial growth factor receptor (VEGFR) signaling was found to be an effective strategy. Molecular analyses revealed potential predictors of response to these druggable pathways.

Conclusions: Our data suggests that the use of matched low-passage cell lines and PDXs is a promising strategy to identify new therapies and pathways to treat metastatic CRC.
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http://dx.doi.org/10.1186/s12885-020-07090-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313200PMC
June 2020

Intravital imaging of mouse embryos.

Science 2020 04;368(6487):181-186

Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.

Embryonic development is a complex process that is unamenable to direct observation. In this study, we implanted a window to the mouse uterus to visualize the developing embryo from embryonic day 9.5 to birth. This removable intravital window allowed manipulation and high-resolution imaging. In live mouse embryos, we observed transient neurotransmission and early vascularization of neural crest cell (NCC)-derived perivascular cells in the brain, autophagy in the retina, viral gene delivery, and chemical diffusion through the placenta. We combined the imaging window with in utero electroporation to label and track cell division and movement within embryos and observed that clusters of mouse NCC-derived cells expanded in interspecies chimeras, whereas adjacent human donor NCC-derived cells shrank. This technique can be combined with various tissue manipulation and microscopy methods to study the processes of development at unprecedented spatiotemporal resolution.
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http://dx.doi.org/10.1126/science.aba0210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7646360PMC
April 2020

An imprecise path to precision medicine.

Authors:
Xiling Shen

Nat Med 2020 01;26(1):14

Department of Biomedical Engineering, Woo Center for Big Data and Precision Health, Duke University, Durham, NC, USA.

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http://dx.doi.org/10.1038/s41591-019-0718-6DOI Listing
January 2020

An intravital window to image the colon in real time.

Nat Commun 2019 12 11;10(1):5647. Epub 2019 Dec 11.

Department of Biomedical Engineering, Duke University, Durham, NC, 27710, USA.

Intravital microscopy is a powerful technique to observe dynamic processes with single-cell resolution in live animals. No intravital window has been developed for imaging the colon due to its anatomic location and motility, although the colon is a key organ where the majority of microbiota reside and common diseases such as inflammatory bowel disease, functional gastrointestinal disorders, and colon cancer occur. Here we describe an intravital murine colonic window with a stabilizing ferromagnetic scaffold for chronic imaging, minimizing motion artifacts while maximizing long-term survival by preventing colonic obstruction. Using this setup, we image fluorescently-labeled stem cells, bacteria, and immune cells in live animal colons. Furthermore, we image nerve activity via calcium imaging in real time to demonstrate that electrical sacral nerve stimulation can activate colonic enteric neurons. The simple implantable apparatus enables visualization of live processes in the colon, which will open the window to a broad range of studies.
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http://dx.doi.org/10.1038/s41467-019-13699-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6906443PMC
December 2019

Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance.

Genes Dis 2021 Mar 29;8(2):203-214. Epub 2019 Oct 29.

Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA.

Colorectal cancer is a leading cause of cancer deaths. Most colorectal cancer patients eventually develop chemoresistance to the current standard-of-care therapies. Here, we used patient-derived colorectal cancer organoids to demonstrate that resistant tumor cells undergo significant chromatin changes in response to oxaliplatin treatment. Integrated transcriptomic and chromatin accessibility analyses using ATAC-Seq and RNA-Seq identified a group of genes associated with significantly increased chromatin accessibility and upregulated gene expression. CRISPR/Cas9 silencing of fibroblast growth factor receptor 1 (FGFR1) and oxytocin receptor (OXTR) helped overcome oxaliplatin resistance. Similarly, treatment with oxaliplatin in combination with an FGFR1 inhibitor (PD166866) or an antagonist of OXTR (L-368,899) suppressed chemoresistant organoids. However, oxaliplatin treatment did not activate either FGFR1 or OXTR expression in another resistant organoid, suggesting that chromatin accessibility changes are patient-specific. The use of patient-derived cancer organoids in combination with transcriptomic and chromatin profiling may lead to precision treatments to overcome chemoresistance in colorectal cancer.
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http://dx.doi.org/10.1016/j.gendis.2019.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099686PMC
March 2021

Author Correction: Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging.

Sci Rep 2019 Sep 30;9(1):13992. Epub 2019 Sep 30.

Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, 14853, USA.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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http://dx.doi.org/10.1038/s41598-019-43805-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768855PMC
September 2019

Author Correction: A recellularized human colon model identifies cancer driver genes.

Nat Biotechnol 2019 Jul;37(7):820

Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41587-019-0163-6DOI Listing
July 2019

Novel Three-Dimensional Cultures of Patient-Derived Cancer and Tumor Immune Cells.

Gastroenterology 2019 07 25;157(1):260-261. Epub 2019 May 25.

Department of Biomedical Engineering, Duke University, Durham, North Carolina.

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http://dx.doi.org/10.1053/j.gastro.2019.05.036DOI Listing
July 2019

Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche.

Methods Mol Biol 2019 ;1975:3-35

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

Agent-based modelling (ABM) offers a framework to realistically couple subcellular signaling pathways to cellular behavior and macroscopic tissue organization. However, these models have been previously inaccessible to many systems biologists due to the difficulties with formulating and simulating multi-scale behavior. In this chapter, a review of the Compucell3D framework is presented along with a general workflow for transitioning from a well-mixed ODE model to an ABM. These techniques are demonstrated through a case study on the simulation of a Notch-Delta Positive Feedback, Lateral Inhibition (PFLI) gene circuit in the intestinal crypts. Specifically, techniques for gene circuit-driven hypothesis formation, geometry construction, selection of simulation parameters, and simulation quantification are presented.
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http://dx.doi.org/10.1007/978-1-4939-9224-9_1DOI Listing
September 2019

Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference.

Exp Biol Med (Maywood) 2019 04 16;244(6):445-458. Epub 2019 Mar 16.

Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA.

Impact Statement: This review provides a comprehensive description of experimental and statistical tools used for network analyses of the human gut microbiome. Understanding the system dynamics of microbial interactions may lead to the improvement of therapeutic approaches for managing microbiome-associated diseases. Microbiome network inference tools have been developed and applied to both cross-sectional and longitudinal experimental designs, as well as to multi-omic datasets, with the goal of untangling the complex web of microbe-host, microbe-environmental, and metabolism-mediated microbial interactions. The characterization of these interaction networks may lead to a better understanding of the systems dynamics of the human gut microbiome, augmenting our knowledge of the microbiome's role in human health, and guiding the optimization of effective, precise, and rational therapeutic strategies for managing microbiome-associated disease.
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http://dx.doi.org/10.1177/1535370219836771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547001PMC
April 2019

A SIMPLE ASPECT RATIO DEPENDENT METHOD OF PATTERNING MICROWELLS FOR SELECTIVE CELL ATTACHMENT.

2018 Des Med Devices Conf (2018) 2018 Apr;2018

Department of Biomedical Engineering, Duke University Durham, NC, United States.

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http://dx.doi.org/10.1115/DMD2018-6811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408146PMC
April 2018

TOWARD A MICROFLUIDIC IMPLEMENTATION OF A DIGITAL POTENTIOMETER.

2018 Des Med Devices Conf (2018) 2018 Apr;2018

Department of Biomedical Engineering Duke University, Durham, NC, United States.

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http://dx.doi.org/10.1115/DMD2018-6812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407897PMC
April 2018

SENP3-mediated host defense response contains HBV replication and restores protein synthesis.

PLoS One 2019 14;14(1):e0209179. Epub 2019 Jan 14.

Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, United States of America.

Certain organs are capable of containing the replication of various types of viruses. In the liver, infection of Hepatitis B virus (HBV), the etiological factor of Hepatitis B and hepatocellular carcinoma (HCC), often remains asymptomatic and leads to a chronic carrier state. Here we investigated how hepatocytes contain HBV replication and promote their own survival by orchestrating a translational defense mechanism via the stress-sensitive SUMO-2/3-specific peptidase SENP3. We found that SENP3 expression level decreased in HBV-infected hepatocytes in various models including HepG2-NTCP cell lines and a humanized mouse model. Downregulation of SENP3 reduced HBV replication and boosted host protein translation. We also discovered that IQGAP2, a Ras GTPase-activating-like protein, is a key substrate for SENP3-mediated de-SUMOylation. Downregulation of SENP3 in HBV infected cells facilitated IQGAP2 SUMOylation and degradation, which leads to suppression of HBV gene expression and restoration of global translation of host genes via modulation of AKT phosphorylation. Thus, The SENP3-IQGAP2 de-SUMOylation axis is a host defense mechanism of hepatocytes that restores host protein translation and suppresses HBV gene expression.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0209179PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331149PMC
September 2019

is a microRNA safeguard for -induced inflammatory colon oncogenesis.

Elife 2018 12 13;7. Epub 2018 Dec 13.

Center for Genomics and Computational Biology, Duke University, Durham, United States.

Inflammation often induces regeneration to repair the tissue damage. However, chronic inflammation can transform temporary hyperplasia into a fertile ground for tumorigenesis. Here, we demonstrate that the microRNA acts as a central safeguard to protect the inflammatory stem cell niche and reparative regeneration. Although playing little role in regular homeostasis, deficiency leads to colon tumorigenesis after infection. targets both immune and epithelial cells to restrain inflammation-induced stem cell proliferation. targets Interleukin six receptor (IL-6R) and Interleukin 23 receptor (IL-23R) to suppress T helper 17 (Th17) cell differentiation and expansion, targets chemokine CCL22 to hinder Th17 cell recruitment to the colon epithelium, and targets an orphan receptor Interleukin 17 receptor D (IL-17RD) to inhibit IL-17-induced stem cell proliferation. Our study highlights the importance of microRNAs in protecting the stem cell niche during inflammation despite their lack of function in regular tissue homeostasis.
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http://dx.doi.org/10.7554/eLife.39479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314783PMC
December 2018

Exploitation of Synthetic mRNA To Drive Immune Effector Cell Recruitment and Functional Reprogramming In Vivo.

J Immunol 2019 01 12;202(2):608-617. Epub 2018 Dec 12.

Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853;

Therapeutic strategies based on in vitro-transcribed mRNA (IVT) are attractive because they avoid the permanent signature of genomic integration that is associated with DNA-based therapy and result in the transient production of proteins of interest. To date, IVT has mainly been used in vaccination protocols to generate immune responses to foreign Ags. In this "proof-of-principle" study, we explore a strategy of combinatorial IVT to recruit and reprogram immune effector cells to acquire divergent biological functions in mice in vivo. First, we demonstrate that synthetic mRNA encoding CCL3 is able to recruit murine monocytes in a nonprogrammed state, exhibiting neither bactericidal nor tissue-repairing properties. However, upon addition of either mRNA or mRNA, we successfully polarized these cells to adopt either M1 or M2 macrophage activation phenotypes. This cellular reprogramming was demonstrated through increased expression of known surface markers and through the differential modulation of NADPH oxidase activity, or the superoxide burst. Our study demonstrates how IVT strategies can be combined to recruit and reprogram immune effector cells that have the capacity to fulfill complex biological tasks in vivo.
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http://dx.doi.org/10.4049/jimmunol.1800924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325005PMC
January 2019