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Pike CM, Zwarycz B, McQueen BE, Castillo M, Barron C, Morowitz JM, Levi JA, Phadke D, Balik-Meisner M, Mav D, Shah R, Cunningham Glasspoole DL, Laetham R, Thelin W, Bunger MK, Boazak EM. Characterization and optimization of variability in a human colonic epithelium culture model. ALTEX 2024. [PMID: 38641922 DOI: 10.14573/altex.2309221] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Animal models have historically been poor preclinical predictors of gastrointestinal (GI) directed therapeutic efficacy and drug-induced GI toxicity. Human stem and primary cell-derived culture systems are a major focus of efforts to create biologically relevant models that enhance preclinical predictive value of intestinal efficacy and toxicity. The inherent variability in stem-cell-based cultures makes development of useful models a challenge; the stochastic nature of stem-cell differentiation interferes with the ability to build and validate reproducible assays that query drug responses and pharmacokinetics. In this study, we aimed to characterize and reduce sources of variability in a complex stem cell-derived intestinal epithelium model, termed RepliGut® Planar, across cells from multiple human donors, cell lots, and passage numbers. Assessment criteria included barrier formation and integrity, gene expression, and cytokine responses. Gene expression and culture metric analyses revealed that controlling cell passage number reduces variability and maximizes physiological relevance of the model. In a case study where passage number was optimized, distinct cytokine responses were observed among four human donors, indicating that biological variability can be detected in cell cultures originating from diverse human sources. These findings highlight key considerations for designing assays that can be applied to additional primary-cell derived systems, as well as establish utility of the RepliGut® Planar platform for robust development of human-predictive drug-response assays.
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Southerland KW, Xu Y, Peters DT, Lin X, Wei X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y. Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. Genome Med 2023; 15:95. [PMID: 37950327 PMCID: PMC10636829 DOI: 10.1186/s13073-023-01250-y] [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: 04/11/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Chronic limb-threatening ischemia (CLTI), a severe manifestation of peripheral arterial disease (PAD), is associated with a 1-year limb amputation rate of approximately 15-20% and substantial mortality. A key feature of CLTI is the compromised regenerative ability of skeletal muscle; however, the mechanisms responsible for this impairment are not yet fully understood. In this study, we aim to delineate pathological changes at both the cellular and transcriptomic levels, as well as in cell-cell signaling pathways, associated with compromised muscle regeneration in limb ischemia in both human tissue samples and murine models of CLTI. METHODS We performed single-cell transcriptome analysis of ischemic and non-ischemic muscle from the same CLTI patients and from a murine model of CLTI. In both datasets, we analyzed gene expression changes in macrophage and muscle satellite cell (MuSC) populations as well as differential cell-cell signaling interactions and differentiation trajectories. RESULTS Single-cell transcriptomic profiling and immunofluorescence analysis of CLTI patient skeletal muscle demonstrated that ischemic-damaged tissue displays a pro-inflammatory macrophage signature. Comparable results were observed in a murine CLTI model. Moreover, integrated analyses of both human and murine datasets revealed premature differentiation of MuSCs to be a key feature of failed muscle regeneration in the ischemic limb. Furthermore, in silico inferences of intercellular communication and in vitro assays highlight the importance of macrophage-MuSC signaling in ischemia induced muscle injuries. CONCLUSIONS Collectively, our research provides the first single-cell transcriptome atlases of skeletal muscle from CLTI patients and a murine CLTI model, emphasizing the crucial role of macrophages and inflammation in regulating muscle regeneration in CLTI through interactions with MuSCs.
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Affiliation(s)
- Kevin W Southerland
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Yueyuan Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Derek T Peters
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Xin Lin
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Xiaolin Wei
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Kaileen Fei
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke University School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Lindsey A Olivere
- Division of Vascular Surgery, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15217, USA
| | - Jeremy M Morowitz
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Development and Stem Cell Biology Program, Duke University, Durham, NC, 27710, USA
| | - James Otto
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Qunsheng Dai
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Christopher D Kontos
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA.
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.
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Pike CM, Zwarycz B, McQueen BE, Castillo M, Barron C, Morowitz JM, Levi JA, Phadke D, Balik-Meisner M, Mav D, Shah R, Glasspoole DLC, Laetham R, Thelin W, Bunger MK, Boazak EM. Characterization and optimization of variability in a human colonic epithelium culture model. bioRxiv 2023:2023.09.22.559007. [PMID: 37790345 PMCID: PMC10542543 DOI: 10.1101/2023.09.22.559007] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Animal models have historically been poor preclinical predictors of gastrointestinal (GI) directed therapeutic efficacy and drug-induced GI toxicity. Human stem and primary cell-derived culture systems are a major focus of efforts to create biologically relevant models that enhance preclinical predictive value of intestinal efficacy and toxicity. The inherent variability in stem-cell-based complex cultures makes development of useful models a challenge; the stochastic nature of stem-cell differentiation interferes with the ability to build and validate robust, reproducible assays that query drug responses and pharmacokinetics. In this study, we aimed to characterize and reduce potential sources of variability in a complex stem cell-derived intestinal epithelium model, termed RepliGut® Planar, across cells from multiple human donors, cell lots, and passage numbers. Assessment criteria included barrier formation and integrity, gene expression, and cytokine responses. Gene expression and culture metric analyses revealed that controlling for stem/progenitor-cell passage number reduces variability and maximizes physiological relevance of the model. After optimizing passage number, donor-specific differences in cytokine responses were observed in a case study, suggesting biologic variability is observable in cell cultures derived from multiple human sources. Our findings highlight key considerations for designing assays that can be applied to additional primary-cell derived systems, as well as establish utility of the RepliGut® Planar platform for robust development of human-predictive drug-response assays.
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Southerland KW, Xu Y, Peters DT, Wei X, Lin X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y. Pro-inflammatory macrophages impair skeletal muscle regeneration in ischemic-damaged limbs by inducing precocious differentiation of satellite cells. bioRxiv 2023:2023.04.01.535211. [PMID: 37066299 PMCID: PMC10103943 DOI: 10.1101/2023.04.01.535211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Chronic limb-threatening ischemia (CLTI), representing the end-stage of peripheral arterial disease (PAD), is associated with a one-year limb amputation rate of ∼15-20% and significant mortality. A key characteristic of CLTI is the failure of the innate regenerative capacity of skeletal muscle, though the underlying mechanisms remain unclear. Here, single-cell transcriptome analysis of ischemic and non-ischemic muscle from the same CLTI patients demonstrated that ischemic-damaged tissue is enriched with pro-inflammatory macrophages. Comparable results were also observed in a murine CLTI model. Importantly, integrated analyses of both human and murine data revealed premature differentiation of muscle satellite cells (MuSCs) in damaged tissue and indications of defects in intercellular signaling communication between MuSCs and their inflammatory niche. Collectively, our research provides the first single-cell transcriptome atlases of skeletal muscle from CLTI patients and murine models, emphasizing the crucial role of macrophages and inflammation in regulating muscle regeneration in CLTI through interactions with MuSCs.
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Tse LV, Meganck RM, Araba KC, Yount BL, Shaffer KM, Hou YJ, Munt JE, Adams LE, Wykoff JA, Morowitz JM, Dong S, Magness ST, Marzluff WF, Gonzalez LM, Ehre C, Baric RS. Genomewide CRISPR knockout screen identified PLAC8 as an essential factor for SADS-CoVs infection. Proc Natl Acad Sci U S A 2022; 119:e2118126119. [PMID: 35476513 PMCID: PMC9170153 DOI: 10.1073/pnas.2118126119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/16/2022] [Indexed: 01/27/2023] Open
Abstract
Zoonotic transmission of coronaviruses poses an ongoing threat to human populations. Endemic outbreaks of swine acute diarrhea syndrome coronavirus (SADS-CoV) have caused severe economic losses in the pig industry and have the potential to cause human outbreaks. Currently, there are no vaccines or specific antivirals against SADS-CoV, and our limited understanding of SADS-CoV host entry factors could hinder prompt responses to a potential human outbreak. Using a genomewide CRISPR knockout screen, we identified placenta-associated 8 protein (PLAC8) as an essential host factor for SADS-CoV infection. Knockout of PLAC8 abolished SADS-CoV infection, which was restored by complementing PLAC8 from multiple species, including human, rhesus macaques, mouse, pig, pangolin, and bat, suggesting a conserved infection pathway and susceptibility of SADS-CoV among mammals. Mechanistically, PLAC8 knockout does not affect viral entry; rather, knockout cells displayed a delay and reduction in viral subgenomic RNA expression. In a swine primary intestinal epithelial culture (IEC) infection model, differentiated cultures have high levels of PLAC8 expression and support SADS-CoV replication. In contrast, expanding IECs have low levels of PLAC8 expression and are resistant to SADS-CoV infection. PLAC8 expression patterns translate in vivo; the immunohistochemistry of swine ileal tissue revealed high levels of PLAC8 protein in neonatal compared to adult tissue, mirroring the known SADS-CoV pathogenesis in neonatal piglets. Overall, PLAC8 is an essential factor for SADS-CoV infection and may serve as a promising target for antiviral development for potential pandemic SADS-CoV.
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Affiliation(s)
- Longping V. Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Rita M. Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Kenza C. Araba
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Boyd L. Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Kendall M. Shaffer
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Yixuan J. Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Jennifer E. Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Lily E. Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Jason A. Wykoff
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Jeremy M. Morowitz
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Scott T. Magness
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, NC 27514
| | - William F. Marzluff
- Integrated Program for Biological and Genome Sciences, Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Liara M. Gonzalez
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606
| | - Camille Ehre
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514
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Morowitz JM, Pogson KB, Roque DA, Church FC. Role of SARS-CoV-2 in Modifying Neurodegenerative Processes in Parkinson's Disease: A Narrative Review. Brain Sci 2022; 12:536. [PMID: 35624923 PMCID: PMC9139310 DOI: 10.3390/brainsci12050536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, continues to impact global health regarding both morbidity and mortality. Although SARS-CoV-2 primarily causes acute respiratory distress syndrome (ARDS), the virus interacts with and influences other organs and tissues, including blood vessel endothelium, heart, gastrointestinal tract, and brain. We are learning much about the pathophysiology of SARS-CoV-2 infection; however, we are just beginning to study and understand the long-term and chronic health consequences. Since the pandemic's beginning in late 2019, older adults, those with pre-existing illnesses, or both, have an increased risk of contracting COVID-19 and developing severe COVID-19. Furthermore, older adults are also more likely to develop the neurodegenerative disorder Parkinson's disease (PD), with advanced age as the most significant risk factor. Thus, does SARS-CoV-2 potentially influence, promote, or accelerate the development of PD in older adults? Our initial focus was aimed at understanding SARS-CoV-2 pathophysiology and the connection to neurodegenerative disorders. We then completed a literature review to assess the relationship between PD and COVID-19. We described potential molecular and cellular pathways that indicate dopaminergic neurons are susceptible, both directly and indirectly, to SARS-CoV-2 infection. We concluded that under certain pathological circumstances, in vulnerable persons-with-Parkinson's disease (PwP), SARS-CoV-2 acts as a neurodegenerative enhancer to potentially support the development or progression of PD and its related motor and non-motor symptoms.
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Affiliation(s)
- Jeremy M. Morowitz
- Developmental and Stem Cell Biology Program, Duke University, Durham, NC 27708, USA;
| | - Kaylyn B. Pogson
- School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Daniel A. Roque
- Department of Neurology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA;
| | - Frank C. Church
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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Raab JR, Tulasi DY, Wager KE, Morowitz JM, Magness ST, Gracz AD. Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation. Development 2020; 147:dev.181966. [PMID: 31862843 DOI: 10.1242/dev.181966] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/25/2019] [Accepted: 11/27/2019] [Indexed: 12/26/2022]
Abstract
Intestinal stem cell (ISC) plasticity is thought to be regulated by broadly permissive chromatin shared between ISCs and their progeny. Here, we have used a Sox9EGFP reporter to examine chromatin across ISC differentiation. We find that open chromatin regions (OCRs) can be defined as broadly permissive or dynamic in a locus-specific manner, with dynamic OCRs found primarily in loci consistent with distal enhancers. By integrating gene expression with chromatin accessibility at transcription factor (TF) motifs in the context of Sox9EGFP populations, we classify broadly permissive and dynamic chromatin relative to TF usage. These analyses identify known and potential regulators of ISC differentiation via association with dynamic changes in chromatin. Consistent with computational predictions, Id3-null mice exhibit increased numbers of cells expressing the ISC-specific biomarker OLFM4. Finally, we examine the relationship between gene expression and 5-hydroxymethylcytosine (5hmC) in Sox9EGFP populations, which reveals 5hmC enrichment in absorptive lineage-specific genes. Our data demonstrate that intestinal chromatin dynamics can be quantitatively defined in a locus-specific manner, identify novel potential regulators of ISC differentiation and provide a chromatin roadmap for further dissecting cis regulation of cell fate in the intestine.
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Affiliation(s)
- Jesse R Raab
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Deepthi Y Tulasi
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Kortney E Wager
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Jeremy M Morowitz
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Scott T Magness
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, NC 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, NC 27599, USA.,Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, NC 27599, USA
| | - Adam D Gracz
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA .,Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, NC 27599, USA
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