1
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Schaff DL, Fasse AJ, White PE, Vander Velde RJ, Shaffer SM. Clonal differences underlie variable responses to sequential and prolonged treatment. Cell Syst 2024; 15:213-226.e9. [PMID: 38401539 PMCID: PMC11003565 DOI: 10.1016/j.cels.2024.01.011] [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: 03/31/2023] [Revised: 11/14/2023] [Accepted: 01/29/2024] [Indexed: 02/26/2024]
Abstract
Cancer cells exhibit dramatic differences in gene expression at the single-cell level, which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Dylan L Schaff
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Aria J Fasse
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19146, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Phoebe E White
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Robert J Vander Velde
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19146, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Sydney M Shaffer
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19146, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA.
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2
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Ouellet M, Kim JZ, Guillaume H, Shaffer SM, Bassett LC, Bassett DS. Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems. New J Phys 2024; 26:023006. [PMID: 38327877 PMCID: PMC10845163 DOI: 10.1088/1367-2630/ad1bdd] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
In interacting dynamical systems, specific local interaction rules for system components give rise to diverse and complex global dynamics. Long dynamical cycles are a key feature of many natural interacting systems, especially in biology. Examples of dynamical cycles range from circadian rhythms regulating sleep to cell cycles regulating reproductive behavior. Despite the crucial role of cycles in nature, the properties of network structure that give rise to cycles still need to be better understood. Here, we use a Boolean interaction network model to study the relationships between network structure and cyclic dynamics. We identify particular structural motifs that support cycles, and other motifs that suppress them. More generally, we show that the presence of dynamical reflection symmetry in the interaction network enhances cyclic behavior. In simulating an artificial evolutionary process, we find that motifs that break reflection symmetry are discarded. We further show that dynamical reflection symmetries are over-represented in Boolean models of natural biological systems. Altogether, our results demonstrate a link between symmetry and functionality for interacting dynamical systems, and they provide evidence for symmetry's causal role in evolving dynamical functionality.
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Affiliation(s)
- Mathieu Ouellet
- Department of Electrical & Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Jason Z Kim
- Department of Bioengineering, School of Engineering & Applied Science, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Harmange Guillaume
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Cell and Molecular Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Sydney M Shaffer
- Cell and Molecular Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Biological Engineering, School of Engineering & Applied Science, University of Pennsylvania, Philadelphia, PA 19104, United States of America
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Lee C Bassett
- Department of Electrical & Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Dani S Bassett
- Department of Electrical & Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, United States of America
- Department of Biological Engineering, School of Engineering & Applied Science, University of Pennsylvania, Philadelphia, PA 19104, United States of America
- Department of Physics & Astronomy, College of Arts & Sciences, University of Pennsylvania, Philadelphia, PA 19104, United States of America
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
- Santa Fe Institute, Santa Fe, NM 87501, United States of America
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3
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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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Harmange G, Hueros RAR, Schaff DL, Emert B, Saint-Antoine M, Kim LC, Niu Z, Nellore S, Fane ME, Alicea GM, Weeraratna AT, Simon MC, Singh A, Shaffer SM. Disrupting cellular memory to overcome drug resistance. Nat Commun 2023; 14:7130. [PMID: 37932277 PMCID: PMC10628298 DOI: 10.1038/s41467-023-41811-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/03/2022] [Accepted: 09/15/2023] [Indexed: 11/08/2023] Open
Abstract
Gene expression states persist for varying lengths of time at the single-cell level, a phenomenon known as gene expression memory. When cells switch states, losing memory of their prior state, this transition can occur in the absence of genetic changes. However, we lack robust methods to find regulators of memory or track state switching. Here, we develop a lineage tracing-based technique to quantify memory and identify cells that switch states. Applied to melanoma cells without therapy, we quantify long-lived fluctuations in gene expression that are predictive of later resistance to targeted therapy. We also identify the PI3K and TGF-β pathways as state switching modulators. We propose a pretreatment model, first applying a PI3K inhibitor to modulate gene expression states, then applying targeted therapy, which leads to less resistance than targeted therapy alone. Together, we present a method for finding modulators of gene expression memory and their associated cell fates.
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Affiliation(s)
- Guillaume Harmange
- Cellular and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Raúl A Reyes Hueros
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dylan L Schaff
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Michael Saint-Antoine
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Laura C Kim
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zijian Niu
- Department of Chemistry, College of the Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics, College of the Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Shivani Nellore
- Department of Biology, College of the Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell E Fane
- Cancer Signaling and Microenvironment Research Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Gretchen M Alicea
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sydney M Shaffer
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Song H, Tomasevich A, Acheampong KK, Schaff DL, Shaffer SM, Dolle JP, Johnson VE, Mikytuck B, Lee EB, Nolan A, Keene CD, Weiss SR, Stewart W, Smith DH. Detection of blood-brain barrier disruption in brains of patients with COVID-19, but no evidence of brain penetration by SARS-CoV-2. Acta Neuropathol 2023; 146:771-775. [PMID: 37624381 PMCID: PMC10592095 DOI: 10.1007/s00401-023-02624-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Affiliation(s)
- Hailong Song
- Department of Neurosurgery, Center for Brain Injury and Repair, University of Pennsylvania, 3320 Smith Walk, 105 Hayden Hall, Philadelphia, PA, 19104, USA
| | - Alexandra Tomasevich
- Department of Neurosurgery, Center for Brain Injury and Repair, University of Pennsylvania, 3320 Smith Walk, 105 Hayden Hall, Philadelphia, PA, 19104, USA
| | - Kofi K Acheampong
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Dylan L Schaff
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, USA
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, USA
| | - Jean-Pierre Dolle
- Department of Neurosurgery, Center for Brain Injury and Repair, University of Pennsylvania, 3320 Smith Walk, 105 Hayden Hall, Philadelphia, PA, 19104, USA
| | - Victoria E Johnson
- Department of Neurosurgery, Center for Brain Injury and Repair, University of Pennsylvania, 3320 Smith Walk, 105 Hayden Hall, Philadelphia, PA, 19104, USA
| | - Bailey Mikytuck
- Translational Neuropathology Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Amber Nolan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Susan R Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - William Stewart
- School of Neuroscience and Psychology, University of Glasgow, Glasgow, G51 4TF, UK
- Department of Neuropathology, Queen Elizabeth University Hospital, Glasgow, G12 8QQ, UK
| | - Douglas H Smith
- Department of Neurosurgery, Center for Brain Injury and Repair, University of Pennsylvania, 3320 Smith Walk, 105 Hayden Hall, Philadelphia, PA, 19104, USA.
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6
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Ng RWS, Shaffer SM. Patterns of tumour transcriptional variability. Nature 2023; 618:464-465. [PMID: 37258729 DOI: 10.1038/d41586-023-01744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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7
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Schaff DL, Fasse AJ, White PE, Vander Velde RJ, Shaffer SM. Clonal differences underlie variable responses to sequential and prolonged treatment. bioRxiv 2023:2023.03.24.534152. [PMID: 36993721 PMCID: PMC10055379 DOI: 10.1101/2023.03.24.534152] [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
Cancer cells exhibit dramatic differences in gene expression at the single-cell level which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA-sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor.
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8
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Gier RA, Hueros RAR, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM. Clonal cell states link Barrett's esophagus and esophageal adenocarcinoma. bioRxiv 2023:2023.01.26.525564. [PMID: 36747708 PMCID: PMC9900873 DOI: 10.1101/2023.01.26.525564] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett's esophagus have not been resolved in humans. To address this, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis revealed discrete lineages in Barrett's esophagus, normal esophagus, and gastric cardia. Transitional basal progenitor cells of the gastroesophageal junction were unexpectedly related to both esophagus and gastric cardia cells. Barrett's esophagus was polyclonal, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic foci were initiated by the expansion of a single molecularly aberrant Barrett's esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the full disease trajectory, from its origin to cancer.
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Affiliation(s)
- Rodrigo A. Gier
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Raúl A. Reyes Hueros
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiazhen Rong
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maureen DeMarshall
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tatiana A. Karakasheva
- Gastrointestinal Epithelium Modeling Program, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amanda B. Muir
- Gastrointestinal Epithelium Modeling Program, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gary W. Falk
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy R. Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M. Shaffer
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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9
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Varella MH, Andrade OA, Shaffer SM, Castro G, Rodriguez P, Barengo NC, Acuna JM. E-cigarette use and respiratory symptoms in residents of the United States: A BRFSS report. PLoS One 2022; 17:e0269760. [PMID: 36454742 PMCID: PMC9714717 DOI: 10.1371/journal.pone.0269760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
PURPOSE E-cigarettes are the most common type of electronic nicotine delivery system in the United States. E-cigarettes contain numerous toxic compounds that has been shown to induce severe structural damage to the airways. The objective of this study is to assess if there is an association between e-cigarette use and respiratory symptoms in adults in the US as reported in the BRFSS. METHODS We analyzed data from 18,079 adults, 18-44 years, who participated at the Behavioral Risk Factor Surveillance System (BRFSS) in the year 2017. E-cigarette smoking status was categorized as current everyday user, current some days user, former smoker, and never smoker. The frequency of any respiratory symptoms (cough, phlegm, or shortness of breath) was compared. Unadjusted and adjusted logistic regression analysis were used to calculate odds ratios (OR) and 95% confidence intervals (CI). RESULTS The BRFSS reported prevalence of smoking e-cigarettes was 6%. About 28% of the participants reported any of the respiratory symptoms assessed. The frequency of reported respiratory symptoms was highest among current some days e-cigarette users (45%). After adjusting for selected participant's demographic, socio-economic, and behavioral characteristics, and asthma and COPD status, the odds of reporting respiratory symptoms increased by 49% among those who use e-cigarettes some days (OR 1.49; 95% CI: 1.06-2.11), and by 29% among those who were former users (OR 1.29; 95% CI: 1.07-1.55) compared with those who never used e-cigarettes. No statistically significant association was found for those who used e-cigarettes every day (OR 1.41; 95% CI 0.96-2.08). CONCLUSION E-cigarettes cannot be considered as a safe alternative to aid quitting use of combustible traditional cigarettes. Cohort studies may shed more evidence on the association between e-cigarette use and respiratory diseases.
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Affiliation(s)
- Marcia H. Varella
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States of America
| | - Olyn A. Andrade
- American University of Antigua College of Medicine, United States of America
| | - Sydney M. Shaffer
- American University of Antigua College of Medicine, United States of America
| | - Grettel Castro
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States of America
| | - Pura Rodriguez
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States of America
| | - Noël C. Barengo
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States of America
- Department of Health Policy and Management, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, United States of America
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juan M. Acuna
- Department of Epidemiology and Aw 8474000331 R-DISC, Khalifa University, Abu Dhabi, United Arab Emirates
- CRUSADA, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, United States of America
- * E-mail:
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10
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Fasse AJ, Schaff DL, Shaffer SM. Abstract B019: Does order matter? Dissecting the single-cell differences underlying resistance to sequential drug treatment. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-b019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Most cancer patients are given multiple different drugs during the course of their cancer treatment. An important but outstanding question is the role that drug order plays in the development of resistance to sequential drug treatment– that is, if cells that develop resistance to a certain first and second-line therapy are similar to cells that develop resistance to the same drugs given in the opposite order. During treatment with a first drug, both selection and transcriptional reprogramming events alter the cells within a tumor. As such, surviving cells may exhibit increased sensitivity or increased resistance to future drug therapies. Here, we zoom in to the single-cell level using cell barcoding and sequencing and explicitly test whether the order of treatment leads to different populations of cells developing resistance to a panel of different therapies. As the initial application of drug therapy changes a tumor in multiple ways, it is currently unclear which changes are most influential in the overall modification of a tumor’s sensitivity to a second-line therapy. One hypothesis is that changes in sensitivity are due to specific drug-induced modifications in the characteristics of cells that survived the first-line therapy, in which case order may matter. An alternative hypothesis is that changes in sensitivity are simply the result of a decrease in clonal diversity within the tumor, where the ability of individual subpopulations to survive the second-line therapy is unchanged by the first-line treatment, in which case order may not matter. To distinguish between these hypotheses, we have combined single-cell RNA sequencing with cellular barcoding to assess both the survival and transcriptome of cells from over 100,000 cells over the course of treatment with multiple stressors. These stressors include a combination of targeted inhibitors (Dabrafenib and Trametinib), chemotherapy (Cisplatin), and hypoxic stress (CoCl2). Through analysis of the transcriptome of cells within the same lineage after surviving each therapy in the sequential treatment scheme, we are now working to determine whether development of resistance to a first-line therapy causes individual cells within a lineage to change in ways that alter their sensitivity to subsequent therapies. Should we find that developing resistance to first-line therapy does increase resistance to specific second-line therapies, we will use our sequencing data to identify specific transcriptomic changes which lead to this induced resistance. We will then look to block this induced resistance through either small-molecule inhibitors (if available) or CRISPR-mediated knockout of genes that promote resistance to second-line therapies. Overall, this study will provide two methods for increasing the efficacy of sequential drug treatment through both the identification of ideal drug ordering and the targeting of changes that promote induced resistance, thus leading to resistance-free treatment strategies.
Citation Format: Aria J. Fasse, Dylan L. Schaff, Sydney M. Shaffer. Does order matter? Dissecting the single-cell differences underlying resistance to sequential drug treatment [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B019.
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11
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Schaff DL, Fasse AJ, Shaffer SM. Abstract B013: Dissecting cell states that enable multi-stressor resistance in cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-b013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In this work, we investigate how single-cell differences in melanoma lead to resistance to multiple diverse and therapeutically relevant stressors. Targeted small-molecule inhibitors and immunotherapy have shown incredible success in the clinic. However, most patients still only partially respond to a given treatment, succumbing to recurrent, treatment-resistant tumors. As a result, oncologists must resort to sequentially treating tumors with new drugs or co-treating with multiple drugs from the beginning. Despite such a complex clinical paradigm, researchers are still studying the root of treatment resistance one drug at a time. We believe that by more broadly studying how certain cells adapt to and survive a multitude of stressful conditions, we can identify treatment strategies that more effectively overcome many resistant behaviors at once. Here, we use lentiviral cell barcoding to simultaneously trace cells that survive stress from microenvironmental factors (extracellular acidosis and hypoxia), inhibition of specific signaling pathways (with Dabrafenib and Trametinib), and chemotherapy (Cisplatin and Doxorubicin) back to their cells of origin and characterize them by scRNA-seq. Strikingly, we have found that there is a rare population of stress-naïve cells that is resistant to our entire panel of stressors. We are exploring two complementary approaches for overcoming this multi-stressor resistance. First, we have combined cell barcoding and scRNA-seq to identify the initial differences in gene expression that allow certain lineages of cells to survive across stressful conditions. Our goal is to use small-molecule inhibitors and genetic knockouts to target these differences in gene expression in stress-naïve cells, eliminating multi-stressor resistance at its source. Second, we are tracking lineages of cells as they undergo a series of cellular changes needed to ultimately survive our panel of stressors. Using scRNA-seq and cell barcoding, we are identifying these crucial changes as cells reprogram into full resistance. We will look to prevent this reprogramming by simultaneously stressing cells and targeting core reprogramming genes and pathways. Overall, this work uncovers single-cell gene expression differences that allow cancer cells to survive under many stressful conditions. We will work to overcome this resistance by directly eliminating the multi-stressor resistant cells and disrupting their ability to reprogram.
Citation Format: Dylan L. Schaff, Aria J. Fasse, Sydney M. Shaffer. Dissecting cell states that enable multi-stressor resistance in cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B013.
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12
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Acheampong KK, Schaff DL, Emert BL, Lake J, Reffsin S, Shea EK, Comar CE, Litzky LA, Khurram NA, Linn RL, Feldman M, Weiss SR, Montone KT, Cherry S, Shaffer SM. Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization. bioRxiv 2021:2021.08.11.455959. [PMID: 34401878 PMCID: PMC8366794 DOI: 10.1101/2021.08.11.455959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA FISH with amplification by hybridization chain reaction (HCR). We developed probe sets that target different regions of SARS-CoV-2 (including ORF1a and N) as well as probe sets that specifically target SARS-CoV-2 subgenomic mRNAs. We validated these probe sets in cell culture and tissues (lung, lymph node, and placenta) from infected patients. Using this technology, we observe distinct subcellular localization patterns of the ORF1a and N regions, with the ORF1a concentrated around the nucleus and the N showing a diffuse distribution across the cytoplasm. In human lung tissue, we performed multiplexed RNA FISH HCR for SARS-CoV-2 and cell-type specific marker genes. We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene (SFTPC) and the alveolar macrophage marker gene (MARCO), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene (AGER). Moreover, we observed distinct subcellular localization patterns of viral RNA in AT2 cells and alveolar macrophages, consistent with phagocytosis of infected cells. In sum, we demonstrate the use of RNA FISH HCR for visualizing different RNA species from SARS-CoV-2 in cell lines and FFPE autopsy specimens. Furthermore, we multiplex this assay with probes for cellular genes to determine what cell-types are infected within the lung. We anticipate that this platform could be broadly useful for studying SARS-CoV-2 pathology in tissues as well as extended for other applications including investigating the viral life cycle, viral diagnostics, and drug screening.
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Affiliation(s)
- Kofi K Acheampong
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Dylan L Schaff
- Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia, PA
| | - Benjamin L Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jonathan Lake
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sam Reffsin
- Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia, PA
| | - Emily K Shea
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Courtney E Comar
- Department of Microbiology, University of Pennsylvania, Philadelphia PA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia, PA
| | - Leslie A Litzky
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nigar A Khurram
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Susan R Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia PA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia, PA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia, PA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia, PA
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Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM, Raj A. Variability within rare cell states enables multiple paths toward drug resistance. Nat Biotechnol 2021; 39:865-876. [PMID: 33619394 PMCID: PMC8277666 DOI: 10.1038/s41587-021-00837-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/18/2021] [Indexed: 01/07/2023]
Abstract
Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA FISH to directly capture rare cells that give rise to cellular behaviors of interest. Applied to BRAFV600E melanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of ~1:1000–1:10,000 cells) and relative persistence of MAP-kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences between several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones following drug treatment. Our results reveal hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure. A new methodology, Rewind, traces vemurafenib-resistant melanoma back to their initial cell state before drug treatment, creating, effectively, a cellular time machine.
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Affiliation(s)
- Benjamin L Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher J Cote
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Eduardo A Torre
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Connie L Jiang
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Naveen Jain
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M Shaffer
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arjun Raj
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
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Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A. Genetic screening for single-cell variability modulators driving therapy resistance. Nat Genet 2021; 53:76-85. [PMID: 33398196 PMCID: PMC7796998 DOI: 10.1038/s41588-020-00749-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Cellular plasticity describes the ability of cells to transition from one set of phenotypes to another. In melanoma, transient fluctuations in the molecular state of tumor cells mark the formation of rare cells primed to survive BRAF inhibition and reprogram into a stably drug-resistant fate. However, the biological processes governing cellular priming remain unknown. We used CRISPR-Cas9 genetic screens to identify genes that affect cell fate decisions by altering cellular plasticity. We found that many factors can independently affect cellular priming and fate decisions. We discovered a new plasticity-based mode of increasing resistance to BRAF inhibition that pushes cells towards a more differentiated state. Manipulating cellular plasticity through inhibition of DOT1L before the addition of the BRAF inhibitor resulted in more therapy resistance than concurrent administration. Our results indicate that modulating cellular plasticity can alter cell fate decisions and may prove useful for treating drug resistance in other cancers.
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Affiliation(s)
- Eduardo A Torre
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eri Arai
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sareh Bayatpour
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Connie L Jiang
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren E Beck
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin L Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M Shaffer
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Mellis
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell E Fane
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Gretchen M Alicea
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Krista A Budinich
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Shaffer SM, Emert BL, Reyes Hueros RA, Cote C, Harmange G, Schaff DL, Sizemore AE, Gupte R, Torre E, Singh A, Bassett DS, Raj A. Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. Cell 2020; 182:947-959.e17. [PMID: 32735851 PMCID: PMC7496637 DOI: 10.1016/j.cell.2020.07.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [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: 12/23/2019] [Revised: 05/04/2020] [Accepted: 07/01/2020] [Indexed: 01/25/2023]
Abstract
Non-genetic factors can cause individual cells to fluctuate substantially in gene expression levels over time. It remains unclear whether these fluctuations can persist for much longer than the time of one cell division. Current methods for measuring gene expression in single cells mostly rely on single time point measurements, making the duration of gene expression fluctuations or cellular memory difficult to measure. Here, we combined Luria and Delbrück's fluctuation analysis with population-based RNA sequencing (MemorySeq) for identifying genes transcriptome-wide whose fluctuations persist for several divisions. MemorySeq revealed multiple gene modules that expressed together in rare cells within otherwise homogeneous clonal populations. These rare cell subpopulations were associated with biologically distinct behaviors like proliferation in the face of anti-cancer therapeutics. The identification of non-genetic, multigenerational fluctuations can reveal new forms of biological memory in single cells and suggests that non-genetic heritability of cellular state may be a quantitative property.
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Affiliation(s)
- Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin L Emert
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Raúl A Reyes Hueros
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Cote
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guillaume Harmange
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Cell and Molecular Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dylan L Schaff
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Ann E Sizemore
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Rohit Gupte
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Eduardo Torre
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Danielle S Bassett
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA; Department of Physics and Astronomy, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Department of Electrical and Systems Engineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Santa Fe Institute, Santa Fe, NM, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Shaffer SM, Pear WS, Vahedi G, Faryabi RB. TooManyCells identifies and visualizes relationships of single-cell clades. Nat Methods 2020; 17:405-413. [PMID: 32123397 PMCID: PMC7439807 DOI: 10.1038/s41592-020-0748-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/15/2020] [Indexed: 01/24/2023]
Abstract
Identifying and visualizing transcriptionally similar cells is instrumental for accurate exploration of the cellular diversity revealed by single-cell transcriptomics. However, widely used clustering and visualization algorithms produce a fixed number of cell clusters. A fixed clustering 'resolution' hampers our ability to identify and visualize echelons of cell states. We developed TooManyCells, a suite of graph-based algorithms for efficient and unbiased identification and visualization of cell clades. TooManyCells introduces a visualization model built on a concept intentionally orthogonal to dimensionality-reduction methods. TooManyCells is also equipped with an efficient matrix-free divisive hierarchical spectral clustering different from prevalent single-resolution clustering methods. TooManyCells enables multiresolution and multifaceted exploration of single-cell clades. An advantage of this paradigm is the immediate detection of rare and common populations that outperforms popular clustering and visualization algorithms, as demonstrated using existing single-cell transcriptomic data sets and new data modeling drug-resistance acquisition in leukemic T cells.
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Affiliation(s)
- Gregory W Schwartz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Fasolino
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature 2017; 546:431-435. [PMID: 28607484 PMCID: PMC5542814 DOI: 10.1038/nature22794] [Citation(s) in RCA: 684] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 04/25/2017] [Indexed: 12/18/2022]
Abstract
Therapies targeting signaling molecules mutated in cancers can often have striking short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures1,2. Resistance can result from a secondary mutations3,4, but other times there is no clear genetic cause, raising the possibility of non-genetic rare cell variability5–11. Here, we show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug treatment. This variability involves infrequent, semi-coordinated transcription of a number of resistance markers at high levels in a very small percentage of cells. The addition of drug then induces epigenetic reprogramming in these cells, converting the transient transcriptional state to a stably resistant state. This reprogramming begins with a loss of SOX10-mediated differentiation followed by activation of new signaling pathways, partially mediated by activity of Jun-AP-1 and TEAD. Our work reveals the multistage nature of the acquisition of drug resistance and provides a framework for understanding resistance dynamics in single cells. We find that other cell types also exhibit sporadic expression of many of these same marker genes, suggesting the existence of a general rare-cell expression program.
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Affiliation(s)
- Sydney M Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Margaret C Dunagin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Stefan R Torborg
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eduardo A Torre
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Benjamin Emert
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Genomics and Computational Biology Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Clemens Krepler
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, Pennsylvania 19104, USA
| | - Marilda Beqiri
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, Pennsylvania 19104, USA
| | - Katrin Sproesser
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, Pennsylvania 19104, USA
| | - Patricia A Brafford
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, Pennsylvania 19104, USA
| | - Min Xiao
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, Pennsylvania 19104, USA
| | - Elliott Eggan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ioannis N Anastopoulos
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Cesar A Vargas-Garcia
- Electrical and Computer Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Abhyudai Singh
- Electrical and Computer Engineering, University of Delaware, Newark, Delaware 19716, USA.,Biomedical Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Katherine L Nathanson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Meenhard Herlyn
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, Pennsylvania 19104, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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18
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Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS. Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels. PLoS One 2016; 11:e0158298. [PMID: 27467384 PMCID: PMC4965078 DOI: 10.1371/journal.pone.0158298] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/13/2016] [Indexed: 11/18/2022] Open
Abstract
Recent analysis demonstrates that the HIV-1 Long Terminal Repeat (HIV LTR) promoter exhibits a range of possible transcriptional burst sizes and frequencies for any mean-expression level. However, these results have also been interpreted as demonstrating that cell-to-cell expression variability (noise) and mean are uncorrelated, a significant deviation from previous results. Here, we re-examine the available mRNA and protein abundance data for the HIV LTR and find that noise in mRNA and protein expression scales inversely with the mean along analytically predicted transcriptional burst-size manifolds. We then experimentally perturb transcriptional activity to test a prediction of the multiple burst-size model: that increasing burst frequency will cause mRNA noise to decrease along given burst-size lines as mRNA levels increase. The data show that mRNA and protein noise decrease as mean expression increases, supporting the canonical inverse correlation between noise and mean.
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Affiliation(s)
- Roy D. Dar
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Sydney M. Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, United States of America
| | | | - Michael L. Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Leor S. Weinberger
- Gladstone Institute (Virology and Immunology), San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
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19
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Shaffer SM, Joshi RP, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE, Issadore D, Raj A. Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. Lab Chip 2015; 15:3170-82. [PMID: 26113495 PMCID: PMC4670042 DOI: 10.1039/c5lc00459d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Viral infections are a major cause of human disease, but many require molecular assays for conclusive diagnosis. Current assays typically rely on RT-PCR or ELISA; however, these tests often have limited speed, sensitivity or specificity. Here, we demonstrate that rapid RNA FISH is a viable alternative method that could improve upon these limitations. We describe a platform beginning with software to generate RNA FISH probes both for distinguishing related strains of virus (even those different by a single base) and for capturing large numbers of strains simultaneously. Next, we present a simple fluidic device for reliably performing RNA FISH assays in an automated fashion. Finally, we describe an automated image processing pipeline to robustly identify uninfected and infected samples. Together, our results establish RNA FISH as a methodology with potential for viral point-of-care diagnostics.
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Affiliation(s)
- Sydney M Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, USA.
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Jamiolkowski RM, Guo LY, Li YR, Shaffer SM, Naji A. Islet transplantation in type I diabetes mellitus. Yale J Biol Med 2012; 85:37-43. [PMID: 22461742 PMCID: PMC3313538] [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] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
For most patients with type I diabetes, insulin therapy and glucose monitoring are sufficient to maintain glycemic control. However, hypoglycemia is a potentially lethal side effect of insulin treatment in patients who are glycemically labile or have hypoglycemia-associated autonomic failure [1]. For those patients, an alternative therapy is beta cell replacement via pancreas or islet transplantation. Pancreas transplants using cadaveric donor organs reduce insulin dependence but carry risks involved in major surgery and chronic immunosuppression. Islet transplantation, in which islets are isolated from donor pancreases and intravenously infused, require no surgery and can utilize islets isolated from pancreases unsuitable for whole organ transplantation. However, islet transplantation also requires immunosuppression, and standard steroid regimens may be toxic to beta cells [2]. The 2000 Edmonton Trial demonstrated the first long-term successful islet transplantation by using a glucocorticoid-free immunosuppressive regimen (sirolimus and tacrolimus). The Clinical Islet Transplantation (CIT) Consortium seeks to improve upon the Edmonton Protocol by using anti-thymocyte globulin (ATG) and TNFα antagonist (etanercept). The trials currently in progress, in addition to research efforts to find new sources of islet cells, reflect enormous potential for islet transplantation in treatment of type I diabetes.
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Affiliation(s)
- Ryan M. Jamiolkowski
- Medical Scientist Training Program, Perelman School of
Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lucie Y. Guo
- Medical Scientist Training Program, Perelman School of
Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yun Rose Li
- Medical Scientist Training Program, Perelman School of
Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sydney M. Shaffer
- Medical Scientist Training Program, Perelman School of
Medicine at University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ali Naji
- University of Pennsylvania Medical Center,
Transplantation Department, Philadelphia, Pennsylvania,To whom all correspondence should be
addressed: Ali Naji, MD, PhD, Professor of Surgery, University of Pennsylvania
Medical Center, 3400 Spruce Street, 1 Founders, Transplantation Department,
Philadelphia, PA 19104; Tele: 215-662-2066; Fax: 215-615-4900;
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McAuley E, Shaffer SM, Rudolph D. Affective responses to acute exercise in elderly impaired males: the moderating effects of self-efficacy and age. Int J Aging Hum Dev 1995; 41:13-27. [PMID: 8530191 DOI: 10.2190/kak1-01xj-clbl-t1ej] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The purpose of the present study was to examine the relationships between perceptions of personal efficacy and affective responsibility to acute exercise in elderly male in-patients and outpatients at a Veterans Administration Medical Center. Participants completed self-efficacy measures prior to and following upper body ergometry exercise. Multidimensional affect was assessed prior to and following activity and in-task affect was assessed by retrospective recall. A significant change in feelings of fatigue was revealed over time but exercise effects on affect were shown to be moderated by perceptions of efficacy and age. Specifically, more efficacious individuals reported significantly more positive well-being and less psychological distress during and following exercise. Older individuals were less efficacious and experienced more negative responses to exercise. Finally, participants who experienced less psychological distress and more positive well-being during activity were more efficacious post-exercise. The results are discussed with respect to the role played by self-efficacy and age in the generation of affective responses to exercise.
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Affiliation(s)
- E McAuley
- University of Illinois at Urbana-Champaign, USA
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Deckert BK, Dempsey WE, Shaffer SM. Maintaining wartime medical readiness in the peacetime Air Force. J Am Optom Assoc 1995; 66:208-12. [PMID: 7751536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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