1
|
Activation of RAS Signalling is Associated with Altered Cell Adhesion in Phaeochromocytoma. Int J Mol Sci 2020; 21:ijms21218072. [PMID: 33138083 PMCID: PMC7663737 DOI: 10.3390/ijms21218072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
Phaeochromocytomas and paragangliomas (PPGLs) are neuroendocrine catecholamine-producing tumours that may progress into inoperable metastatic disease. Treatment options for metastatic disease are limited, indicating a need for functional studies to identify pharmacologically targetable pathophysiological mechanisms, which require biologically relevant experimental models. Recently, a human progenitor phaeochromocytoma cell line named “hPheo1” was established, but its genotype has not been characterised. Performing exome sequencing analysis, we identified a KIF1B T827I mutation, and the oncogenic NRAS Q61K mutation. While KIF1B mutations are recurring somatic events in PPGLs, NRAS mutations have hitherto not been detected in PPGLs. Therefore, we aimed to assess its implications for the hPheo1 cell line, and possible relevance for the pathophysiology of PPGLs. We found that transient downregulation of NRAS in hPheo1 led to elevated expression of genes associated with cell adhesion, and enhanced adhesion to hPheo1 cells’ extracellular matrix. Analyses of previously published mRNA data from two independent PPGL patient cohorts (212 tissue samples) revealed a subcluster of PPGLs featuring hyperactivated RAS pathway-signalling and under-expression of cell adhesion-related gene expression programs. Thus, we conclude that NRAS activity in hPheo1 decreases adhesion to their own extracellular matrix and mirrors a transcriptomic RAS-signalling-related phenomenon in PPGLs.
Collapse
|
2
|
Liu J, Banerjee A, Herring CA, Attalla J, Hu R, Xu Y, Shao Q, Simmons AJ, Dadi PK, Wang S, Jacobson DA, Liu B, Hodges E, Lau KS, Gu G. Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity. Dev Cell 2019; 48:49-63.e7. [PMID: 30620902 PMCID: PMC6327977 DOI: 10.1016/j.devcel.2018.11.048] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 08/26/2018] [Accepted: 11/29/2018] [Indexed: 12/15/2022]
Abstract
In the developing pancreas, transient Neurog3-expressing progenitors give rise to four major islet cell types: α, β, δ, and γ; when and how the Neurog3+ cells choose cell fate is unknown. Using single-cell RNA-seq, trajectory analysis, and combinatorial lineage tracing, we showed here that the Neurog3+ cells co-expressing Myt1 (i.e., Myt1+Neurog3+) were biased toward β cell fate, while those not simultaneously expressing Myt1 (Myt1-Neurog3+) favored α fate. Myt1 manipulation only marginally affected α versus β cell specification, suggesting Myt1 as a marker but not determinant for islet-cell-type specification. The Myt1+Neurog3+ cells displayed higher Dnmt1 expression and enhancer methylation at Arx, an α-fate-promoting gene. Inhibiting Dnmts in pancreatic progenitors promoted α cell specification, while Dnmt1 overexpression or Arx enhancer hypermethylation favored β cell production. Moreover, the pancreatic progenitors contained distinct Arx enhancer methylation states without transcriptionally definable sub-populations, a phenotype independent of Neurog3 activity. These data suggest that Neurog3-independent methylation on fate-determining gene enhancers specifies distinct endocrine-cell programs.
Collapse
Affiliation(s)
- Jing Liu
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Amrita Banerjee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles A Herring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jonathan Attalla
- Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry and the Vanderbilt Genetic Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Ruiying Hu
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yanwen Xu
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qiujia Shao
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA
| | - Alan J Simmons
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Prasanna K Dadi
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Sui Wang
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - David A Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Bindong Liu
- Center for AIDS Health Disparities Research, Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA
| | - Emily Hodges
- Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry and the Vanderbilt Genetic Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Guoqiang Gu
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Program in Developmental Biology and Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
3
|
Lyons J, Ghazi PC, Starchenko A, Tovaglieri A, Baldwin KR, Poulin EJ, Gierut JJ, Genetti C, Yajnik V, Breault DT, Lauffenburger DA, Haigis KM. The colonic epithelium plays an active role in promoting colitis by shaping the tissue cytokine profile. PLoS Biol 2018; 16:e2002417. [PMID: 29596476 PMCID: PMC5892915 DOI: 10.1371/journal.pbio.2002417] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/10/2018] [Accepted: 03/02/2018] [Indexed: 12/15/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic condition driven by loss of homeostasis between the mucosal immune system, the commensal gut microbiota, and the intestinal epithelium. Our goal is to understand how these components of the intestinal ecosystem cooperate to control homeostasis. By combining quantitative measures of epithelial hyperplasia and immune infiltration with multivariate analysis of inter- and intracellular signaling, we identified epithelial mammalian target of rapamycin (mTOR) signaling as a potential driver of inflammation in a mouse model of colitis. A kinetic analysis of mTOR inhibition revealed that the pathway regulates epithelial differentiation, which in turn controls the cytokine milieu of the colon. Consistent with our in vivo analysis, we found that cytokine expression of organoids grown ex vivo, in the absence of bacteria and immune cells, was dependent on differentiation state. Our study suggests that proper differentiation of epithelial cells is an important feature of colonic homeostasis because of its effect on the secretion of inflammatory cytokines.
Collapse
Affiliation(s)
- Jesse Lyons
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Phaedra C. Ghazi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alina Starchenko
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alessio Tovaglieri
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Katherine R. Baldwin
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Emily J. Poulin
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jessica J. Gierut
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Casie Genetti
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vijay Yajnik
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - David T. Breault
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- Harvard Digestive Disease Center, Boston, Massachusetts, United States of America
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kevin M. Haigis
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Digestive Disease Center, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
4
|
Herring CA, Banerjee A, McKinley ET, Simmons AJ, Ping J, Roland JT, Franklin JL, Liu Q, Gerdes MJ, Coffey RJ, Lau KS. Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. Cell Syst 2017; 6:37-51.e9. [PMID: 29153838 DOI: 10.1016/j.cels.2017.10.012] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/17/2017] [Accepted: 10/13/2017] [Indexed: 12/19/2022]
Abstract
Modern single-cell technologies allow multiplexed sampling of cellular states within a tissue. However, computational tools that can infer developmental cell-state transitions reproducibly from such single-cell data are lacking. Here, we introduce p-Creode, an unsupervised algorithm that produces multi-branching graphs from single-cell data, compares graphs with differing topologies, and infers a statistically robust hierarchy of cell-state transitions that define developmental trajectories. We have applied p-Creode to mass cytometry, multiplex immunofluorescence, and single-cell RNA-seq data. As a test case, we validate cell-state-transition trajectories predicted by p-Creode for intestinal tuft cells, a rare, chemosensory cell type. We clarify that tuft cells are specified outside of the Atoh1-dependent secretory lineage in the small intestine. However, p-Creode also predicts, and we confirm, that tuft cells arise from an alternative, Atoh1-driven developmental program in the colon. These studies introduce p-Creode as a reliable method for analyzing large datasets that depict branching transition trajectories.
Collapse
Affiliation(s)
- Charles A Herring
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Amrita Banerjee
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jie Ping
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA
| | - Jeffrey L Franklin
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael J Gerdes
- Life Sciences Division, GE Global Research, Niskayuna, NY 12309, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN 37232, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, 2213 Garland Avenue, 10475 MRB IV, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
5
|
Kim SW, Ehrman J, Ahn MR, Kondo J, Lopez AAM, Oh YS, Kim XH, Crawley SW, Goldenring JR, Tyska MJ, Rericha EC, Lau KS. Shear stress induces noncanonical autophagy in intestinal epithelial monolayers. Mol Biol Cell 2017; 28:3043-3056. [PMID: 28855375 PMCID: PMC5662261 DOI: 10.1091/mbc.e17-01-0021] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/04/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Shear stress applied on the apical side of polarizing intestinal cells induces vacuole formation via the autophagy machinery. This response is relayed through apical microvilli that act as mechanosensors linking the physical environment to the intracellular trafficking pathways. Flow of fluids through the gut, such as milk from a neonatal diet, generates a shear stress on the unilaminar epithelium lining the lumen. We report that exposure to physiological levels of fluid shear stress leads to the formation of large vacuoles, containing extracellular contents within polarizing intestinal epithelial cell monolayers. These observations lead to two questions: how can cells lacking primary cilia transduce shear stress, and what molecular pathways support the formation of vacuoles that can exceed 80% of the cell volume? We find that shear forces are sensed by actin-rich microvilli that eventually generate the apical brush border, providing evidence that these structures possess mechanosensing ability. Importantly, we identified the molecular pathway that regulates large vacuole formation downstream from mechanostimulation to involve central components of the autophagy pathway, including ATG5 and LC3, but not Beclin. Together our results establish a novel link between the actin-rich microvilli, the macroscopic transport of fluids across cells, and the noncanonical autophagy pathway in organized epithelial monolayers.
Collapse
Affiliation(s)
- Sun Wook Kim
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jonathan Ehrman
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235
| | - Mok-Ryeon Ahn
- Department of Food Science and Nutrition, Dong-A University, Busan 604-714, Republic of Korea
| | - Jumpei Kondo
- Department of Biochemistry, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Andrea A Mancheno Lopez
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Yun Sik Oh
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Xander H Kim
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Scott W Crawley
- Department of Biological Sciences, University of Toledo, Toledo, OH 43606
| | - James R Goldenring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232.,Nashville VA Medical Center, Nashville, TN 37212
| | - Matthew J Tyska
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Erin C Rericha
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232 .,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| |
Collapse
|
6
|
Simmons AJ, Lau KS. Deciphering tumor heterogeneity from FFPE tissues: Its promise and challenges. Mol Cell Oncol 2016; 4:e1260191. [PMID: 28197533 DOI: 10.1080/23723556.2016.1260191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 12/27/2022]
Abstract
An impediment to the understanding of cancer is the heterogeneous nature of cell populations within a tumor microenvironment. We reported a method to query protein signaling in single epithelial cells from formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues. Here, we discuss the feasibility and limitations of this approach for investigating signaling state heterogeneity.
Collapse
Affiliation(s)
- Alan J Simmons
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine , Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine , Nashville, TN, USA
| |
Collapse
|
7
|
Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS. Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. Sci Signal 2016; 9:rs11. [PMID: 27729552 DOI: 10.1126/scisignal.aah4413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cellular heterogeneity poses a substantial challenge to understanding tissue-level phenotypes and confounds conventional bulk analyses. To analyze signaling at the single-cell level in human tissues, we applied mass cytometry using cytometry time of flight to formalin-fixed, paraffin-embedded (FFPE) normal and diseased intestinal specimens. This technique, called FFPE-DISSECT (disaggregation for intracellular signaling in single epithelial cells from tissue), is a single-cell approach to characterizing signaling states in embedded tissue samples. We applied FFPE-DISSECT coupled to mass cytometry and found differential signaling by tumor necrosis factor-α in intestinal enterocytes, goblet cells, and enteroendocrine cells, implicating the downstream RAS-RAF-MEK pathway in determining goblet cell identity. Application of this technique and computational analyses to human colon specimens confirmed the reduced differentiation in colorectal cancer (CRC) compared to normal colon and revealed increased intratissue and intertissue heterogeneity in CRC with quantitative changes in the regulation of signaling pathways. Specifically, coregulation of the kinases p38 and ERK, the translation regulator 4EBP1, and the transcription factor CREB in proliferating normal colon cells was lost in CRC. Our data suggest that this single-cell approach, applied in conjunction with genomic annotation, enables the rapid and detailed characterization of cellular heterogeneity from clinical repositories of embedded human tissues. This technique can be used to derive cellular landscapes from archived patient samples (beyond CRC) and as a high-resolution tool for disease characterization and subtyping.
Collapse
Affiliation(s)
- Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Cherié R Scurrah
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles A Herring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Chemical and Physical Biology Program, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan M Irish
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN 37232, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Chemical and Physical Biology Program, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| |
Collapse
|
8
|
Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) 2016; 7:740-57. [PMID: 26040649 DOI: 10.1039/c5ib00030k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When functioning properly, the intestine is one of the key interfaces between the human body and its environment. It is responsible for extracting nutrients from our food and excreting our waste products. It provides an environment for a host of healthful microbes and serves as a first defense against pathogenic ones. These processes require tight homeostatic controls, which are provided by the interactions of a complex mix of epithelial, stromal, neural and immune cells, as well as the resident microflora. This homeostasis can be disrupted by invasive microbes, genetic lesions, and carcinogens, resulting in diseases such Clostridium difficile infection, inflammatory bowel disease (IBD) and cancer. Enormous strides have been made in understanding how this important organ functions in health and disease using everything from cell culture systems to animal models to human tissue samples. This has resulted in better therapies for all of these diseases, but there is still significant room for improvement. In the United States alone, 14,000 people per year die of C. difficile, up to 1.6 million people suffer from IBD, and more than 50,000 people die every year from colon cancer. Because these and other intestinal diseases arise from complex interactions between the different components of the gut ecosystem, we propose that systems approaches that address this complexity in an integrative manner may eventually lead to improved therapeutics that deliver lasting cures. This review will discuss the use of systems biology for studying intestinal diseases in vivo with particular emphasis on mouse models. Additionally, it will focus on established experimental techniques that have been used to drive this systems-level analysis, and emerging techniques that will push this field forward in the future.
Collapse
Affiliation(s)
- Jesse Lyons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | |
Collapse
|
9
|
Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo. Mol Syst Biol 2015; 11:835. [PMID: 26519361 PMCID: PMC4631206 DOI: 10.15252/msb.20156282] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Understanding heterogeneous cellular behaviors in a complex tissue requires the evaluation of signaling networks at single-cell resolution. However, probing signaling in epithelial tissues using cytometry-based single-cell analysis has been confounded by the necessity of single-cell dissociation, where disrupting cell-to-cell connections inherently perturbs native cell signaling states. Here, we demonstrate a novel strategy (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue-DISSECT) that preserves native signaling for Cytometry Time-of-Flight (CyTOF) and fluorescent flow cytometry applications. A 21-plex CyTOF analysis encompassing core signaling and cell-identity markers was performed on the small intestinal epithelium after systemic tumor necrosis factor-alpha (TNF-α) stimulation. Unsupervised and supervised analyses robustly selected signaling features that identify a unique subset of epithelial cells that are sensitized to TNF-α-induced apoptosis in the seemingly homogeneous enterocyte population. Specifically, p-ERK and apoptosis are divergently regulated in neighboring enterocytes within the epithelium, suggesting a mechanism of contact-dependent survival. Our novel single-cell approach can broadly be applied, using both CyTOF and multi-parameter flow cytometry, for investigating normal and diseased cell states in a wide range of epithelial tissues.
Collapse
Affiliation(s)
- Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amrita Banerjee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cherie' R Scurrah
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Charles A Herring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leslie S Gewin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Ryota Masuzaki
- The Transplant Center and Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth J Karp
- The Transplant Center and Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey L Franklin
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Jonathan M Irish
- Departments of Cancer Biology, and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA Department of Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
10
|
Birse K, Arnold KB, Novak RM, McCorrister S, Shaw S, Westmacott GR, Ball TB, Lauffenburger DA, Burgener A. Molecular Signatures of Immune Activation and Epithelial Barrier Remodeling Are Enhanced during the Luteal Phase of the Menstrual Cycle: Implications for HIV Susceptibility. J Virol 2015; 89:8793-805. [PMID: 26085144 PMCID: PMC4524071 DOI: 10.1128/jvi.00756-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/03/2015] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED The variable infectivity and transmissibility of HIV/SHIV has been recently associated with the menstrual cycle, with particular susceptibility observed during the luteal phase in nonhuman primate models and ex vivo human explant cultures, but the mechanism is poorly understood. Here, we performed an unbiased, mass spectrometry-based proteomic analysis to better understand the mucosal immunological processes underpinning this observed susceptibility to HIV infection. Cervicovaginal lavage samples (n = 19) were collected, characterized as follicular or luteal phase using days since last menstrual period, and analyzed by tandem mass spectrometry. Biological insights from these data were gained using a spectrum of computational methods, including hierarchical clustering, pathway analysis, gene set enrichment analysis, and partial least-squares discriminant analysis with LASSO feature selection. Of the 384 proteins identified, 43 were differentially abundant between phases (P < 0.05, ≥2-fold change). Cell-cell adhesion proteins and antiproteases were reduced, and leukocyte recruitment (interleukin-8 pathway, P = 1.41E-5) and extravasation proteins (P = 5.62E-4) were elevated during the luteal phase. LASSO/PLSDA identified a minimal profile of 18 proteins that best distinguished the luteal phase. This profile included cytoskeletal elements and proteases known to be involved in cellular movement. Gene set enrichment analysis associated CD4(+) T cell and neutrophil gene set signatures with the luteal phase (P < 0.05). Taken together, our findings indicate a strong association between proteins involved in tissue remodeling and leukocyte infiltration with the luteal phase, which may represent potential hormone-associated mechanisms of increased susceptibility to HIV. IMPORTANCE Recent studies have discovered an enhanced susceptibility to HIV infection during the progesterone-dominant luteal phase of the menstrual cycle. However, the mechanism responsible for this enhanced susceptibility has not yet been determined. Understanding the source of this vulnerability will be important for designing efficacious HIV prevention technologies for women. Furthermore, these findings may also be extrapolated to better understand the impact of exogenous hormone application, such as the use of hormonal contraceptives, on HIV acquisition risk. Hormonal contraceptives are the most widely used contraceptive method in sub-Saharan Africa, the most HIV-burdened area of the world. For this reason, research conducted to better understand how hormones impact host immunity and susceptibility factors important for HIV infection is a global health priority.
Collapse
Affiliation(s)
- Kenzie Birse
- National Lab for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kelly B Arnold
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard M Novak
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stuart McCorrister
- Mass Spectrometry Core Facility, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Souradet Shaw
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Garrett R Westmacott
- Mass Spectrometry Core Facility, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Terry B Ball
- National Lab for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada Department of Medical Microbiology, University of Nairobi, Department of Medical Microbiology, Nairobi, Kenya
| | - Douglas A Lauffenburger
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Adam Burgener
- National Lab for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|