Xiling Shen

Overview:

Dr. Shen’s research interests lie at precision medicine and systems biology. His lab integrates engineering, computational and biological techniques to study cancer, stem cells, microbiota and the nervous system in the gut. This multidisciplinary work has been instrumental in initiating several translational clinical trials in precision therapy. He is the director of the Woo Center for Big Data and Precision Health (DAP) and a core member of the Center for Genomics and Computational Biology (GCB).

Positions:

Hawkins Family Associate Professor

Biomedical Engineering
Pratt School of Engineering

Associate Professor in the Department of Biomedical Engineering

Biomedical Engineering
Pratt School of Engineering

Associate Professor in the Department of Electrical and Computer Engineering

Electrical and Computer Engineering
Pratt School of Engineering

Associate Professor in Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Affiliate of the Regeneration Next Initiative

Regeneration Next Initiative
School of Medicine

Education:

B.Sc. 2001

Stanford University

M.Sc. 2001

Stanford University

Ph.D. 2008

Stanford University

Grants:

A comprehensive research resource to define mechanisms underlying microbial regulation of host metabolism in pediatric obesity and obesity-targeted therapeutics

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Co Investigator
Start Date
End Date

Epigenomic Reprogramming in Patient Derived Models of Colorectal Cancer

Administered By
Biomedical Engineering
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

EFRI CEE : Engineering Technologies to Determine Causal Relationships Between Chromatin Structure and Gene Regulation

Administered By
Biomedical Engineering
Awarded By
National Science Foundation
Role
Co-Principal Investigator
Start Date
End Date

An organotypic model recapitulating colon cancer microenvironment and metastasis

Administered By
Biomedical Engineering
Role
Principal Investigator
Start Date
End Date

Functional mapping of efferent gut neuroepithelial circuits

Administered By
Biomedical Engineering
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Publications:

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

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.
Authors
Altunel, E; Roghani, RS; Chen, K-Y; Kim, SY; McCall, S; Ware, KE; Shen, X; Somarelli, JA; Hsu, DS
MLA Citation
Altunel, Erdem, et al. “Development of a precision medicine pipeline to identify personalized treatments for colorectal cancer.Bmc Cancer, vol. 20, no. 1, June 2020, p. 592. Pubmed, doi:10.1186/s12885-020-07090-y.
URI
https://scholars.duke.edu/individual/pub1448846
PMID
32580713
Source
pubmed
Published In
Bmc Cancer
Volume
20
Published Date
Start Page
592
DOI
10.1186/s12885-020-07090-y

A Deep Learning Approach to Analysis of Kidney Transplant Frozen Sections

Authors
Davis, R; Lafata, K; Li, X; Souma, N; Howell, D; Shen, X; Barisoni, L
MLA Citation
Davis, Richard, et al. “A Deep Learning Approach to Analysis of Kidney Transplant Frozen Sections.” Laboratory Investigation, vol. 100, no. SUPPL 1, NATURE PUBLISHING GROUP, 2020, pp. 1573–1573.
URI
https://scholars.duke.edu/individual/pub1435322
Source
wos
Published In
Laboratory Investigation
Volume
100
Published Date
Start Page
1573
End Page
1573

A Deep Learning Approach to Analysis of Kidney Transplant Frozen Sections

Authors
Davis, R; Lafata, K; Li, X; Souma, N; Howell, D; Shen, X; Barisoni, L
MLA Citation
Davis, Richard, et al. “A Deep Learning Approach to Analysis of Kidney Transplant Frozen Sections.” Modern Pathology, vol. 33, no. SUPPL 2, NATURE PUBLISHING GROUP, 2020, pp. 1573–1573.
URI
https://scholars.duke.edu/individual/pub1435323
Source
wos
Published In
Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc
Volume
33
Published Date
Start Page
1573
End Page
1573

Electrical stimulation can delay fluid propulsion during motor complexes in mouse colon

Authors
Barth, BB; Travis, L; Shen, X; Grill, WM; Spencer, NJ
MLA Citation
Barth, Bradley B., et al. “Electrical stimulation can delay fluid propulsion during motor complexes in mouse colon.” Neurogastroenterology and Motility, vol. 32, WILEY, 2020.
URI
https://scholars.duke.edu/individual/pub1436762
Source
wos
Published In
Neurogastroenterology and Motility : the Official Journal of the European Gastrointestinal Motility Society
Volume
32
Published Date

Intravital imaging of mouse embryos.

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.
Authors
Huang, Q; Cohen, MA; Alsina, FC; Devlin, G; Garrett, A; McKey, J; Havlik, P; Rakhilin, N; Wang, E; Xiang, K; Mathews, P; Wang, L; Bock, C; Ruthig, V; Wang, Y; Negrete, M; Wong, CW; Murthy, PKL; Zhang, S; Daniel, AR; Kirsch, DG; Kang, Y; Capel, B; Asokan, A; Silver, DL; Jaenisch, R; Shen, X
MLA Citation
Huang, Qiang, et al. “Intravital imaging of mouse embryos.Science, vol. 368, no. 6487, Apr. 2020, pp. 181–86. Pubmed, doi:10.1126/science.aba0210.
URI
https://scholars.duke.edu/individual/pub1436476
PMID
32273467
Source
pubmed
Published In
Science
Volume
368
Published Date
Start Page
181
End Page
186
DOI
10.1126/science.aba0210