1
|
Zikry TM, Wolff SC, Ranek JS, Davis HM, Naugle A, Luthra N, Whitman AA, Kedziora KM, Stallaert W, Kosorok MR, Spanheimer PM, Purvis JE. Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells. Proc Natl Acad Sci U S A 2024; 121:e2309261121. [PMID: 38324568 PMCID: PMC10873600 DOI: 10.1073/pnas.2309261121] [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: 06/06/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage of tumor cells continues to divide in the presence of palbociclib-a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcomes. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant cells in both cultured and primary breast tumor samples resected from patients. Resistant cells showed premature accumulation of multiple G1 regulators including E2F1, retinoblastoma protein, and CDK2, as well as enhanced sensitivity to pharmacological inhibition of CDK2 activity. Using trajectory inference approaches, we show how plasticity among cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.
Collapse
Affiliation(s)
- Tarek M. Zikry
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC27599
| | - Samuel C. Wolff
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jolene S. Ranek
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Harris M. Davis
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Ander Naugle
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Namit Luthra
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Austin A. Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Katarzyna M. Kedziora
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburg, Pittsburgh, PA15620
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburg, Pittsburgh, PA15620
| | - Michael R. Kosorok
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC27599
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jeremy E. Purvis
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| |
Collapse
|
2
|
Kahkoska AR, Freeman NLB, Jones EP, Shirazi D, Browder S, Page A, Sperger J, Zikry TM, Yu F, Busby-Whitehead J, Kosorok MR, Batsis JA. Individualized interventions and precision health: Lessons learned from a systematic review and implications for analytics-driven geriatric research. J Am Geriatr Soc 2023; 71:383-393. [PMID: 36524627 PMCID: PMC10037848 DOI: 10.1111/jgs.18141] [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: 05/24/2022] [Revised: 09/16/2022] [Accepted: 10/22/2022] [Indexed: 12/23/2022]
Abstract
Older adults are characterized by profound clinical heterogeneity. When designing and delivering interventions, there exist multiple approaches to account for heterogeneity. We present the results of a systematic review of data-driven, personalized interventions in older adults, which serves as a use case to distinguish the conceptual and methodologic differences between individualized intervention delivery and precision health-derived interventions. We define individualized interventions as those where all participants received the same parent intervention, modified on a case-by-case basis and using an evidence-based protocol, supplemented by clinical judgment as appropriate, while precision health-derived interventions are those that tailor care to individuals whereby the strategy for how to tailor care was determined through data-driven, precision health analytics. We discuss how their integration may offer new opportunities for analytics-based geriatric medicine that accommodates individual heterogeneity but allows for more flexible and resource-efficient population-level scaling.
Collapse
Affiliation(s)
- Anna R. Kahkoska
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nikki L. B. Freeman
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emily P. Jones
- Health Sciences Library, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniela Shirazi
- Department of Medicine, California University of Science and Medicine, Colton, California, USA
| | - Sydney Browder
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annie Page
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John Sperger
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tarek M. Zikry
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fei Yu
- School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jan Busby-Whitehead
- Division of Geriatric Medicine, Department of Medicine, Center for Aging and Health, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael R. Kosorok
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - John A. Batsis
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Geriatric Medicine, Department of Medicine, Center for Aging and Health, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| |
Collapse
|
3
|
Kim S, Cho H, Bang D, De Marchi D, El-Zaatari H, Shah KS, Valancius M, Zikry TM, Kosorok MR. Discussion of ‘Estimating time-varying causal excursion effects in mobile health with binary outcomes’. Biometrika 2021. [DOI: 10.1093/biomet/asaa094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Summary
In this discussion, we examine the contributions of Qian et al. (2021) and potential applications of the newly developed estimator for the causal excursion effect in binary outcome data. Specifically, we consider extension of their method to count outcomes and observational data, propose an alternative use of their method for analysing excursion effect trajectories and discuss ways of improving estimator efficiency.
Collapse
Affiliation(s)
- S Kim
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - H Cho
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - D Bang
- Ancestry, 153 Townsend St, San Francisco, California 94129, U.S.A
| | - D De Marchi
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - H El-Zaatari
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - K S Shah
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - M Valancius
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - T M Zikry
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| | - M R Kosorok
- Department of Biostatistics, University of North Carolina, Chapel Hill, 3101 McGavran-Greenberg Hall, Chapel Hill, North Carolina 27599, U.S.A
| |
Collapse
|
4
|
Freeman NLB, Sperger J, El-Zaatari H, Kahkoska AR, Lu M, Valancius M, Virkud AV, Zikry TM, Kosorok MR. Beyond Two Cultures: Cultural Infrastructure for Data-driven Decision Support. Obs Stud 2021; 7:77-94. [PMID: 35106520 PMCID: PMC8802367 DOI: 10.1353/obs.2021.0024] [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: 06/14/2023]
Abstract
In the twenty years since Dr. Leo Breiman's incendiary paper Statistical Modeling: The Two Cultures was first published, algorithmic modeling techniques have gone from controversial to commonplace in the statistical community. While the widespread adoption of these methods as part of the contemporary statistician's toolkit is a testament to Dr. Breiman's vision, the number of high-profile failures of algorithmic models suggests that Dr. Breiman's final remark that "the emphasis needs to be on the problem and the data" has been less widely heeded. In the spirit of Dr. Breiman, we detail an emerging research community in statistics - data-driven decision support. We assert that to realize the full potential of decision support, broadly and in the context of precision health, will require a culture of social awareness and accountability, in addition to ongoing attention towards complex technical challenges.
Collapse
Affiliation(s)
- Nikki L B Freeman
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - John Sperger
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Helal El-Zaatari
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Anna R Kahkoska
- Department of Nutrition, University of North Carolina School of Medicine
| | - Minxin Lu
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Michael Valancius
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Arti V Virkud
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Tarek M Zikry
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Michael R Kosorok
- Department of Biostatistics, University of North Carolina at Chapel Hill
| |
Collapse
|
5
|
Martin CL, Ward-Caviness CK, Dhingra R, Zikry TM, Galea S, Wildman DE, Koenen KC, Uddin M, Aiello AE. Neighborhood environment, social cohesion, and epigenetic aging. Aging (Albany NY) 2021; 13:7883-7899. [PMID: 33714950 PMCID: PMC8034890 DOI: 10.18632/aging.202814] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/16/2021] [Indexed: 12/30/2022]
Abstract
Living in adverse neighborhood environments has been linked to risk of aging-related diseases and mortality; however, the biological mechanisms explaining this observation remain poorly understood. DNA methylation (DNAm), a proposed mechanism and biomarker of biological aging responsive to environmental stressors, offers promising insight into potential molecular pathways. We examined associations between three neighborhood social environment measures (poverty, quality, and social cohesion) and three epigenetic clocks (Horvath, Hannum, and PhenoAge) using data from the Detroit Neighborhood Health Study (n=158). Using linear regression models, we evaluated associations in the total sample and stratified by sex and social cohesion. Neighborhood quality was associated with accelerated DNAm aging for Horvath age acceleration (β = 1.8; 95% CI: 0.4, 3.1), Hannum age acceleration (β = 1.7; 95% CI: 0.4, 3.0), and PhenoAge acceleration (β = 2.1; 95% CI: 0.4, 3.8). In models stratified on social cohesion, associations of neighborhood poverty and quality with accelerated DNAm aging remained elevated for residents living in neighborhoods with lower social cohesion, but were null for those living in neighborhoods with higher social cohesion. Our study suggests that living in adverse neighborhood environments can speed up epigenetic aging, while positive neighborhood attributes may buffer effects.
Collapse
Affiliation(s)
- Chantel L. Martin
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cavin K. Ward-Caviness
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Durham, NC 27709, USA
| | - Radhika Dhingra
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Institute of Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tarek M. Zikry
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sandro Galea
- School of Public Health, Boston University, Boston, MA 02118, USA
| | - Derek E. Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Karestan C. Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Allison E Aiello
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
6
|
Martin CL, Vladutiu CJ, Zikry TM, Grace MR, Siega-Riz AM. Maternal lipid levels during pregnancy and child weight status at 3 years of age. Pediatr Obes 2019; 14:e12485. [PMID: 30516000 PMCID: PMC6545288 DOI: 10.1111/ijpo.12485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/16/2018] [Revised: 08/21/2018] [Accepted: 09/30/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND The intrauterine environment is critical in the development of child obesity. OBJECTIVE To investigate the association between maternal lipid levels during pregnancy and child weight status. METHODS Maternal lipid levels (total cholesterol, high-density and low-density lipoprotein cholesterol, triglycerides) collected from fasting blood samples collected at less than 20 and 24-29 weeks' gestation and child weight status at age 3 were examined prospectively among 183 mother-child dyads enrolled in the Pregnancy, Infection, and Nutrition. Measured height and weight at 3 years were used to calculate age- and sex-specific body mass index z-scores. Child risk of overweight/obesity was defined as body mass index greater than or equal to 85th percentile for age and sex. Regression models estimated the association between maternal lipid levels and child body mass index z-score and risk of being affected by overweight/obesity, respectively. RESULTS Higher triglyceride levels at less than 20 and 24-29 weeks of pregnancy were associated with higher body mass index z-scores (β = 0.23; 95% CI: 0.07-0.38 and β = 0.15; 95% CI: 0.01-0.29; respectively) after adjusting for confounders. There was no evidence of an association between total or low-density lipoprotein cholesterol and child weight status at age 3. CONCLUSIONS Early childhood body mass index may be influenced by maternal triglyceride levels during pregnancy.
Collapse
Affiliation(s)
- Chantel L. Martin
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC
| | - Catherine J. Vladutiu
- Department of Obstetrics & Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
- Maternal and Child Health Bureau, Health Resources and Services Administration, Rockville, Maryland
| | - Tarek M. Zikry
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC
| | - Matthew R. Grace
- Department of Obstetrics & Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
- Department of Obstetric and Gynecology, University of Tennessee Health Sciences Center College of Medicine, Nashville, TN
| | - Anna Maria Siega-Riz
- School of Nursing and Departments of Public Health Sciences and Obstetrics & Gynecology, University of Virginia School of Medicine, Charlottesville, VA
| |
Collapse
|
7
|
Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE. Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. Mol Syst Biol 2018; 14:e8140. [PMID: 30177503 PMCID: PMC6120590 DOI: 10.15252/msb.20178140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 01/24/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that clonal cells can make different fate decisions, but it is unclear whether these decisions are determined during, or before, a cell's own lifetime. Here, we engineered an endogenous fluorescent reporter for the pluripotency factor OCT4 to study the timing of differentiation decisions in human embryonic stem cells. By tracking single-cell OCT4 levels over multiple cell cycle generations, we found that the decision to differentiate is largely determined before the differentiation stimulus is presented and can be predicted by a cell's preexisting OCT4 signaling patterns. We further quantified how maternal OCT4 levels were transmitted to, and distributed between, daughter cells. As mother cells underwent division, newly established OCT4 levels in daughter cells rapidly became more predictive of final OCT4 expression status. These results imply that the choice between developmental cell fates can be largely predetermined at the time of cell birth through inheritance of a pluripotency factor.
Collapse
Affiliation(s)
- Samuel C Wolff
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Raluca Dumitru
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Cierra D Dungee
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Tarek M Zikry
- Department of Biostatistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Rachel A Haggerty
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - JrGang Cheng
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Margaret A Redick
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|