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Parham LR, Williams PA, Katada K, Nettleford SK, Chatterji P, Acheampong KK, Danan CH, Ma X, Simon LA, Naughton KE, Mizuno R, Karakasheva T, McMillan EA, Whelan KA, Brady DC, Shaffer SM, Hamilton KE. IGF2BP1/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B. Cell Mol Gastroenterol Hepatol 2023; 17:439-451. [PMID: 38081361 PMCID: PMC10835461 DOI: 10.1016/j.jcmgh.2023.12.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/02/2024]
Abstract
BACKGROUND & AIMS The intestinal epithelium interfaces with a diverse milieu of luminal contents while maintaining robust digestive and barrier functions. Facultative intestinal stem cells are cells that survive tissue injury and divide to re-establish the epithelium. Prior studies have shown autophagic state as functional marker of facultative intestinal stem cells, but regulatory mechanisms are not known. The current study evaluated a post-transcriptional regulation of autophagy as an important factor for facultative stem cell state and tissue regeneration. METHODS We evaluated stem cell composition, autophagic vesicle content, organoid formation, and in vivo regeneration in mice with intestinal epithelial deletion of the RNA binding protein IGF2 messenger RNA binding protein 1 (IMP1). The contribution of autophagy to resulting in vitro and in vivo phenotypes was evaluated via genetic inactivation of Atg7. Molecular analyses of IMP1 modulation of autophagy at the protein and transcript localization levels were performed using IMP1 mutant studies and single-molecule fluorescent in situ hybridization. RESULTS Epithelial Imp1 deletion reduced leucine rich repeat containing G protein coupled receptor 5 cell frequency but enhanced both organoid formation efficiency and in vivo regeneration after irradiation. We confirmed prior studies showing increased autophagy with IMP1 deletion. Deletion of Atg7 reversed the enhanced regeneration observed with Imp1 deletion. IMP1 deletion or mutation of IMP1 phosphorylation sites enhanced expression of essential autophagy protein microtubule-associated protein 1 light chain 3β. Furthermore, immunofluorescence imaging coupled with single-molecule fluorescent in situ hybridization showed IMP1 colocalization with MAP1LC3B transcripts at homeostasis. Stress induction led to decreased colocalization. CONCLUSIONS Depletion of IMP1 enhances autophagy, which promotes intestinal regeneration via expansion of facultative intestinal stem cells.
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Affiliation(s)
- Louis R Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Patrick A Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shaneice K Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Priya Chatterji
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kofi K Acheampong
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Charles H Danan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lauren A Simon
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kaitlyn E Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Rei Mizuno
- Department of Surgery, Uji-Tokushukai Medical Center, Uji, Kyoto, Japan
| | - Tatiana Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Emily A McMillan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kelly A Whelan
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania; Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Donita C Brady
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
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2
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Danan CH, Naughton KE, Hayer KE, Vellappan S, McMillan EA, Zhou Y, Matsuda R, Nettleford SK, Katada K, Parham LR, Ma X, Chowdhury A, Wilkins BJ, Shah P, Weitzman MD, Hamilton KE. Intestinal transit-amplifying cells require METTL3 for growth factor signaling and cell survival. JCI Insight 2023; 8:e171657. [PMID: 37883185 PMCID: PMC10795831 DOI: 10.1172/jci.insight.171657] [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: 04/24/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023] Open
Abstract
Intestinal epithelial transit-amplifying cells are essential stem progenitors required for intestinal homeostasis, but their rapid proliferation renders them vulnerable to DNA damage from radiation and chemotherapy. Despite these cells' critical roles in intestinal homeostasis and disease, few studies have described genes that are essential to transit-amplifying cell function. We report that RNA methyltransferase-like 3 (METTL3) is required for survival of transit-amplifying cells in the murine small intestine. Transit-amplifying cell death after METTL3 deletion was associated with crypt and villus atrophy, loss of absorptive enterocytes, and uniform wasting and death in METTL3-depleted mice. Sequencing of polysome-bound and methylated RNAs in enteroids and in vivo demonstrated decreased translation of hundreds of methylated transcripts after METTL3 deletion, particularly transcripts involved in growth factor signal transduction such as Kras. Further investigation verified a relationship between METTL3 and Kras methylation and protein levels in vivo. Our study identifies METTL3 as an essential factor supporting the homeostasis of small intestinal tissue via direct maintenance of transit-amplifying cell survival. We highlight the crucial role of RNA modifications in regulating growth factor signaling in the intestine with important implications for both homeostatic tissue renewal and epithelial regeneration.
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Affiliation(s)
- Charles H. Danan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Medical Scientist Training Program, Perelman School of Medicine; and
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kaitlyn E. Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sangeevan Vellappan
- Waksman Institute of Microbiology and
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
| | - Emily A. McMillan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rina Matsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathobiology, School of Veterinary Medicine, and
| | - Shaneice K. Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louis R. Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Afrah Chowdhury
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
| | - Matthew D. Weitzman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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Williams PA, Naughton KE, Simon LA, Soto GE, Parham LR, Ma X, Danan CH, Hu W, Friedman ES, McMillan EA, Mehta H, Stoltz MA, Ocaña JS, Zackular JP, Bittinger K, Whelan KA, Karakasheva TA, Hamilton KE. Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. Am J Physiol Gastrointest Liver Physiol 2023; 324:G354-G368. [PMID: 36852920 PMCID: PMC10069975 DOI: 10.1152/ajpgi.00248.2022] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
Calorie restriction can enhance the regenerative capacity of the injured intestinal epithelium. Among other metabolic changes, calorie restriction can activate the autophagy pathway. Although independent studies have attributed the regenerative benefit of calorie restriction to downregulation of mTORC1, it is not known whether autophagy itself is required for the regenerative benefit of calorie restriction. We used mouse and organoid models with autophagy gene deletion to evaluate the contribution of autophagy to intestinal epithelial regeneration following calorie restriction. In the absence of injury, mice with intestinal epithelial-specific deletion of autophagy gene Atg7 (Atg7ΔIEC) exhibit weight loss and histological changes similar to wild-type mice following calorie restriction. Conversely, calorie-restricted Atg7ΔIEC mice displayed a significant reduction in regenerative crypt foci after irradiation compared with calorie-restricted wild-type mice. Targeted analyses of tissue metabolites in calorie-restricted mice revealed an association between calorie restriction and reduced glycocholic acid (GCA) in wild-type mice but not in Atg7ΔIEC mice. To evaluate whether GCA can directly modulate epithelial stem cell self-renewal, we performed enteroid formation assays with or without GCA. Wild-type enteroids exhibited reduced enteroid formation efficiency in response to GCA treatment, suggesting that reduced availability of GCA during calorie restriction may be one mechanism by which calorie restriction favors epithelial regeneration in a manner dependent upon epithelial autophagy. Taken together, our data support the premise that intestinal epithelial Atg7 is required for the regenerative benefit of calorie restriction, due in part to its role in modulating luminal GCA with direct effects on epithelial stem cell self-renewal.NEW & NOTEWORTHY Calorie restriction is associated with enhanced intestinal regeneration after irradiation, but the requirement of autophagy for this process is not known. Our data support the premise that intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. We also report that luminal levels of primary bile acid glycocholic acid are modulated by epithelial cell autophagy during calorie restriction with direct effects on epithelial stem cell function.
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Affiliation(s)
- Patrick A Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kaitlyn E Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Lauren A Simon
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Gloria E Soto
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Louis R Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Charles H Danan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Elliot S Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Emily A McMillan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Hritik Mehta
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Madison A Stoltz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Joshua Soto Ocaña
- Division of Protective Immunity, Children's Hospital of Philadelphia, Pennsylvania United States
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Pennsylvania United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kelly A Whelan
- Department of Pathology & Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States
- Fels Institute for Cancer Research & Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States
| | - Tatiana A Karakasheva
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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4
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Danan CH, Naughton KE, Hayer KE, Vellappan S, McMillan EA, Zhou Y, Matsuda R, Nettleford SK, Katada K, Parham LR, Ma X, Chowdhury A, Wilkins BJ, Shah P, Weitzman MD, Hamilton KE. Intestinal transit amplifying cells require METTL3 for growth factor signaling, KRAS expression, and cell survival. bioRxiv 2023:2023.04.06.535853. [PMID: 37066277 PMCID: PMC10104132 DOI: 10.1101/2023.04.06.535853] [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: 04/18/2023]
Abstract
Intestinal epithelial transit amplifying cells are essential stem progenitors required for intestinal homeostasis, but their rapid proliferation renders them vulnerable to DNA damage from radiation and chemotherapy. Despite their critical roles in intestinal homeostasis and disease, few studies have described genes that are essential to transit amplifying cell function. We report that the RNA methyltransferase, METTL3, is required for survival of transit amplifying cells in the murine small intestine. Transit amplifying cell death after METTL3 deletion was associated with crypt and villus atrophy, loss of absorptive enterocytes, and uniform wasting and death in METTL3-depleted mice. Ribosome profiling and sequencing of methylated RNAs in enteroids and in vivo demonstrated decreased translation of hundreds of unique methylated transcripts after METTL3 deletion, particularly transcripts involved in growth factor signal transduction such as Kras. Further investigation confirmed a novel relationship between METTL3 and Kras methylation and protein levels in vivo. Our study identifies METTL3 as an essential factor supporting the homeostasis of small intestinal tissue via direct maintenance of transit amplifying cell survival. We highlight the crucial role of RNA modifications in regulating growth factor signaling in the intestine, with important implications for both homeostatic tissue renewal and epithelial regeneration.
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Affiliation(s)
- Charles H. Danan
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kaitlyn E. Naughton
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sangeevan Vellappan
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ, 08854, USA
| | - Emily A. McMillan
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Rina Matsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shaneice K. Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis R. Parham
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Afrah Chowdhury
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ, 08854, USA
| | - Matthew D. Weitzman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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5
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Johnson NM, Parham LR, Na J, Monaghan KE, Kolev HM, Klochkova A, Kim MS, Danan CH, Cramer Z, Simon LA, Naughton KE, Adams‐Tzivelekidis S, Tian Y, Williams PA, Leu NA, Sidoli S, Whelan KA, Li N, Lengner CJ, Hamilton KE. Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium. EMBO Rep 2022; 23:e55209. [PMID: 36120829 PMCID: PMC9638868 DOI: 10.15252/embr.202255209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/08/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/25/2023] Open
Abstract
The intestinal epithelium exhibits a rapid and efficient regenerative response to injury. Emerging evidence supports a model where plasticity of differentiated cells, particularly those in the secretory lineages, contributes to epithelial regeneration upon ablation of injury-sensitive stem cells. However, such facultative stem cell activity is rare within secretory populations. Here, we ask whether specific functional properties predict facultative stem cell activity. We utilize in vivo labeling combined with ex vivo organoid formation assays to evaluate how cell age and autophagic state contribute to facultative stem cell activity within secretory lineages. Strikingly, we find that cell age (time elapsed since cell cycle exit) does not correlate with secretory cell plasticity. Instead, high autophagic vesicle content predicts plasticity and resistance to DNA damaging injury independently of cell lineage. Our findings indicate that autophagic status prior to injury serves as a lineage-agnostic marker for the prospective identification of facultative stem cells.
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Affiliation(s)
- Nicolette M Johnson
- Medical Scientist Training Program, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Louis R Parham
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Division of Gastroenterology, Hepatology, and NutritionChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Jeeyoon Na
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Keara E Monaghan
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Hannah M Kolev
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Alena Klochkova
- Fels Institute for Cancer Research & Molecular BiologyLewis Katz School of Medicine at Temple UniversityPhiladelphiaPennsylvaniaUSA
| | - Melissa S Kim
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Charles H Danan
- Medical Scientist Training Program, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Division of Gastroenterology, Hepatology, and NutritionChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Zvi Cramer
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Lauren A Simon
- Division of Gastroenterology, Hepatology, and NutritionChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Kaitlyn E Naughton
- Division of Gastroenterology, Hepatology, and NutritionChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Stephanie Adams‐Tzivelekidis
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Yuhua Tian
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Patrick A Williams
- Division of Gastroenterology, Hepatology, and NutritionChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - N Adrian Leu
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Simone Sidoli
- Department of BiochemistryAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Kelly A Whelan
- Fels Institute for Cancer Research & Molecular BiologyLewis Katz School of Medicine at Temple UniversityPhiladelphiaPennsylvaniaUSA
- Department of Pathology & Laboratory MedicineLewis Katz School of Medicine at Temple UniversityPhiladelphiaPennsylvaniaUSA
| | - Ning Li
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Regenerative MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Regenerative MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Cell & Developmental Biology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Kathryn E Hamilton
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Division of Gastroenterology, Hepatology, and NutritionChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Institute for Regenerative MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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