1
|
Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Koval J, Weber CR, Rubin DT, Sogin M, Crosson S, Huang J, Fiebig A, Dalal S, Chang EB, Basu A, Pott S. Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients. medRxiv 2023:2023.11.11.23298309. [PMID: 38014192 PMCID: PMC10680893 DOI: 10.1101/2023.11.11.23298309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background & Aims Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard of care for patients with severe treatment resistant ulcerative colitis (UC). Despite improvements in patient outcomes, about 50% of patients will develop inflammation of the pouch within 1-2 years following surgery. Establishment of UC pouches is associated with profound histological changes of the mucosa. A detailed characterization of these changes on a cellular and molecular level is crucial for an improved understanding of pouch physiology and diseases management. Methods We generated cell-type-resolved transcriptional and epigenetic atlases of UC pouches using scRNA-seq and scATAC-seq data from paired biopsy samples from the ileal pouch and ileal segment above the pouch (pre-pouch) of UC-IPAA patients (n=6, female=2) without symptoms. We also collected data from paired biopsies of the terminal ileum (TI) and ascending colon (AC) from healthy controls (n=6, female=3). Results We identified novel populations of colon-like absorptive and secretory epithelial cells, constituting a significant proportion of the epithelial cell fraction in the pouch but not in matched pre-pouch samples. Pouch-specific enterocytes expressed colon-specific genes, including CEACAM5, CA2. However, in contrast to normal colonic epithelium, these cells also expressed a range of inflammatory and secretory genes, similar to previously detected gene expression signatures in IBD patients. Comparison to longitudinal bulk RNA-seq data from UC pouches demonstrated that colon-like epithelial cells are present early after pouch functionalization and independently of subsequent pouchitis. Finally, single cell chromatin accessibility revealed activation colonic transcriptional regulators, including CDX1, NFIA, and EHF. Conclusion UC pouches are characterized by partial colonic metaplasia of the epithelium. These data constitute a resource of transcriptomic and epigenetic signatures of cell populations in the pouch and provide an anchor for understanding the underlying molecular mechanisms of pouchitis.
Collapse
Affiliation(s)
- Yu Zhao
- University of Chicago, Pritzker School of Molecular Engineering, Chicago, IL
| | - Ran Zhou
- University of Chicago, Department of Medicine, Chicago, IL
| | - Bingqing Xie
- University of Chicago, Department of Medicine, Chicago, IL
| | - Cambrian Y Liu
- University of Chicago, Department of Medicine, Chicago, IL
| | - Martin Kalski
- University of Chicago, Department of Medicine, Chicago, IL
| | - Candace M Cham
- University of Chicago, Department of Medicine, Chicago, IL
| | - Jason Koval
- University of Chicago, Department of Medicine, Chicago, IL
| | | | - David T Rubin
- University of Chicago, Department of Medicine, Chicago, IL
- University of Chicago, Department of Pathology, Chicago, IL
| | - Mitch Sogin
- Marine Biological Laboratory, Woods Hole, MA
| | | | - Jun Huang
- University of Chicago, Pritzker School of Molecular Engineering, Chicago, IL
| | | | - Sushila Dalal
- University of Chicago, Department of Medicine, Chicago, IL
| | - Eugene B Chang
- University of Chicago, Department of Medicine, Chicago, IL
| | - Anindita Basu
- University of Chicago, Department of Medicine, Chicago, IL
| | - Sebastian Pott
- University of Chicago, Department of Medicine, Chicago, IL
| |
Collapse
|
2
|
Liu CY, Girish N, Gomez ML, Kalski M, Bernard JK, Simons BD, Polk DB. Wound-healing plasticity enables clonal expansion of founder progenitor cells in colitis. Dev Cell 2023; 58:2309-2325.e7. [PMID: 37652012 PMCID: PMC10872951 DOI: 10.1016/j.devcel.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/30/2023] [Accepted: 08/05/2023] [Indexed: 09/02/2023]
Abstract
Chronic colonic injury and inflammation pose high risks for field cancerization, wherein injury-associated mutations promote stem cell fitness and gradual clonal expansion. However, the long-term stability of some colitis-associated mutational fields could suggest alternate origins. Here, studies of acute murine colitis reveal a punctuated mechanism of massive, neutral clonal expansion during normal wound healing. Through three-dimensional (3D) imaging, quantitative fate mapping, and single-cell transcriptomics, we show that epithelial wound repair begins with the loss of structural constraints on regeneration, forming fused labyrinthine channels containing epithelial cells reprogrammed to a non-proliferative plastic state. A small but highly proliferative set of epithelial founder progenitor cells (FPCs) subsequently emerges and undergoes extensive cell division, enabling fluid-like lineage mixing and spreading across the colonic surface. Crypt budding restores the glandular organization, imprinting the pattern of clonal expansion. The emergence and functions of FPCs within a critical window of plasticity represent regenerative targets with implications for preneoplasia.
Collapse
Affiliation(s)
- Cambrian Y Liu
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
| | - Nandini Girish
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Marie L Gomez
- Program in Biomedical and Biological Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Martin Kalski
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica K Bernard
- Program in Craniofacial Biology, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA 90033, USA
| | - Benjamin D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, UK; Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - D Brent Polk
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Rady Children's Hospital, San Diego, CA 92123, USA.
| |
Collapse
|
3
|
Reedich EJ, Kalski M, Armijo N, Cox GA, DiDonato CJ. Spinal motor neuron loss occurs through a p53-and-p21-independent mechanism in the Smn 2B/- mouse model of spinal muscular atrophy. Exp Neurol 2020; 337:113587. [PMID: 33382987 DOI: 10.1016/j.expneurol.2020.113587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/12/2020] [Accepted: 12/23/2020] [Indexed: 12/22/2022]
Abstract
Spinal muscular atrophy (SMA) is a pediatric neuromuscular disease caused by genetic deficiency of the survival motor neuron (SMN) protein. Pathological hallmarks of SMA are spinal motor neuron loss and skeletal muscle atrophy. The molecular mechanisms that elicit and drive preferential motor neuron degeneration and death in SMA remain unclear. Transcriptomic studies consistently report p53 pathway activation in motor neurons and spinal cord tissue of SMA mice. Recent work has identified p53 as an inducer of spinal motor neuron loss in severe Δ7 SMA mice. Additionally, the cyclin-dependent kinase inhibitor P21 (Cdkn1a), an inducer of cell cycle arrest and mediator of skeletal muscle atrophy, is consistently increased in motor neurons, spinal cords, and other tissues of various SMA models. p21 is a p53 transcriptional target but can be independently induced by cellular stressors. To ascertain whether p53 and p21 signaling pathways mediate spinal motor neuron death in milder SMA mice, and how they affect the overall SMA phenotype, we introduced Trp53 and P21 null alleles onto the Smn2B/- background. We found that p53 and p21 depletion did not modulate the timing or degree of Smn2B/- motor neuron loss as evaluated using electrophysiological and immunohistochemical methods. Moreover, we determined that Trp53 and P21 knockout differentially affected Smn2B/- mouse lifespan: p53 ablation impaired survival while p21 ablation extended survival through Smn-independent mechanisms. These results demonstrate that p53 and p21 are not primary drivers of spinal motor neuron death in Smn2B/- mice, a milder SMA mouse model, as motor neuron loss is not alleviated by their ablation.
Collapse
Affiliation(s)
- Emily J Reedich
- Human Molecular Genetics and Physiology Program, Stanley Manne Children's Research Institute at Ann & Robert H. Lurie Children's Hospital, Chicago, IL, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martin Kalski
- Human Molecular Genetics and Physiology Program, Stanley Manne Children's Research Institute at Ann & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Nicholas Armijo
- Human Molecular Genetics and Physiology Program, Stanley Manne Children's Research Institute at Ann & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Gregory A Cox
- The Jackson Laboratory, Bar Harbor, ME, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | - Christine J DiDonato
- Human Molecular Genetics and Physiology Program, Stanley Manne Children's Research Institute at Ann & Robert H. Lurie Children's Hospital, Chicago, IL, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| |
Collapse
|