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Reyes RJ, Pham O, Fergusson R, Ceberio N, Clark C, Sarah Cohen C, Fuse M, Pennings P. SCIP: a self-paced, community-based summer coding program creates community and increases coding confidence, lessons learned from the pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.12.27.521952. [PMID: 36597523 PMCID: PMC9810221 DOI: 10.1101/2022.12.27.521952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In 2020, many students lost summer opportunities due to the COVID-19 pandemic. We wanted to offer students an opportunity to learn computational skills and be part of a community while they were stuck at home. Because the pandemic was very isolating, it was important to support students to learn and build community online. We used lessons learned from literature and our own experience to design, run and test an online program for students called the Science Coding Immersion Program (SCIP). In our program, students worked in small teams for 8 hours a week spread over the week, with one participant as the team leader and Zoom host. Teams worked on an online R or Python class at their own pace with support on Slack from the organizing team. For motivation and career advice, we hosted a weekly webinar with guest speakers. We used pre- and post-program surveys to determine how different aspects of the program impacted students. We were able to recruit a large and diverse group of participants who were happy with the program, found community in their team, and improved their coding confidence. We hope that our work will inspire others to start their own version of SCIP.
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Affiliation(s)
| | - Olivia Pham
- Biology Department, San Francisco State University, San Francisco, CA
| | - Ryan Fergusson
- Biology Department, San Francisco State University, San Francisco, CA
| | - Niquo Ceberio
- Biology Department, San Francisco State University, San Francisco, CA
| | - Candace Clark
- Biology Department, San Francisco State University, San Francisco, CA
| | - C Sarah Cohen
- Biology Department, San Francisco State University, San Francisco, CA
| | - Megumi Fuse
- Biology Department, San Francisco State University, San Francisco, CA
| | - Pleuni Pennings
- Biology Department, San Francisco State University, San Francisco, CA
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Carey GB, Ezelle HJ, Steinle N, Cao Q, Simington L, Matson C, Singh N, Jones L, Mohindra P, Cullen KJ, Giglio M, Parker E, Hassel BA. Robust Institutional Support and Collaboration Between Summer Training Programs in Cancer and Biomedicine Drive the Pivot to a Virtual Format in Response to the COVID Pandemic. JOURNAL OF CANCER EDUCATION : THE OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER EDUCATION 2022; 37:857-871. [PMID: 35098479 PMCID: PMC8801290 DOI: 10.1007/s13187-021-02124-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Summer internships serve important roles in training the next generation of biomedical researchers and healthcare providers through laboratory and clinical experiences that excite trainees about these fields and help them make informed decisions about career paths. The SARS-CoV-2 (COVID) pandemic and associated physical distancing restrictions precluded implementation of traditional in-person summer curricula and led to the cancellation of many internships across the USA. COVID-related disruptions also created opportunities for trainees to engage in remote research, become proficient in online learning platforms, and explore multidisciplinary topics. These skills are highly relevant to trainees as virtual interfaces occupy an increasingly mainstream role in their professional paths. The response to the COVID pandemic required real-time adaptations at all levels for major biomedical institutions including the University of Maryland Baltimore (UMB). Pivoting summer programs to a virtual format as part of this response provided a "teachable moment" to expose trainees to the innovation and resilience that are essential components of the biomedical profession. UMB summer programs, which span diverse biomedical disciplines from cancer research to diabetes, consolidated resources and identified mentors with online research projects to develop a robust virtual curriculum. Herein, data from a cancer-focused internship illustrate the collaborative adaptations to established components and creation of new learning modules in the transition to, and implementation of, online training. Outcomes are presented in the context of the COVID pandemic and significant societal issues that arose in the summer of 2020. The utility of virtual components and their impact on future programs is discussed.
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Affiliation(s)
- G B Carey
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Office of Student Research, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - H J Ezelle
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - N Steinle
- Department of Medicine, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Maryland VA Health Care System, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - Q Cao
- Office of Student Research, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - L Simington
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - C Matson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - N Singh
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - L Jones
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - P Mohindra
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
- Radiation Oncology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - K J Cullen
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - M Giglio
- Institute for Genome Science, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - E Parker
- Department of Physical Therapy and Rehabilitation Science, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA
| | - B A Hassel
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA.
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Sriramkumar S, Sood R, Huntington TD, Ghobashi AH, Vuong TT, Metcalfe TX, Wang W, Nephew KP, O'Hagan HM. Platinum-induced mitochondrial OXPHOS contributes to cancer stem cell enrichment in ovarian cancer. J Transl Med 2022; 20:246. [PMID: 35641987 PMCID: PMC9153190 DOI: 10.1186/s12967-022-03447-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/18/2022] [Indexed: 01/06/2023] Open
Abstract
Background Platinum based agents—cisplatin and carboplatin in combination with taxanes are used for the treatment of ovarian cancer (OC) patients. However, the majority of OC patients develop recurrent, platinum resistant disease that is uniformly fatal. Platinum treatment enriches for chemoresistant aldehyde dehydrogenase (ALDH) + ovarian cancer stem cells (OCSCs), which contribute to tumor recurrence and disease relapse. Acquired platinum resistance also includes metabolic reprograming and switching to oxidative phosphorylation (OXPHOS). Chemosensitive cells rely on glycolysis while chemoresistant cells have the ability to switch between glycolysis and OXPHOS, depending on which pathway drives a selective advantage for growth and chemoresistance. High expression of genes involved in OXPHOS and high production of mitochondrial ROS are characteristics of OCSCs, suggesting that OCSCs favor OXPHOS over glycolysis. Based on connections between OCSCs, chemoresistance and OXPHOS, we hypothesize that platinum treatment induces changes in metabolism that contribute to platinum-induced enrichment of OCSCs. Methods The effect of cisplatin on mitochondrial activity was assessed by JC1 staining and expression of OXPHOS genes by RT-qPCR. Cisplatin-induced changes in Sirtuin 1 (SIRT1) levels and activity were assessed by western blot. Small molecule inhibitors of mitochondrial complex I and SIRT1 were used to determine if their enzymatic activity contributes to the platinum-induced enrichment of OCSCs. The percentage of ALDH + OCSCs in OC cells and tumor tissue from xenograft models across different treatment conditions was analyzed using ALDEFLUOR assay and flow cytometry. Results We demonstrate that platinum treatment increases mitochondrial activity. Combined treatment of platinum agents and OXPHOS inhibitors blocks the platinum-induced enrichment of ALDH + OCSCs in vitro and in vivo. Furthermore, platinum treatment increases SIRT1 levels and subsequent deacetylase activity, which likely contributes to the increase in platinum-induced mitochondrial activity. Conclusions These findings on metabolic pathways altered by platinum-based chemotherapy have uncovered key targets that can be exploited therapeutically to block the platinum-induced enrichment of OCSCs, ultimately improving the survival of OC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03447-y.
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Affiliation(s)
- Shruthi Sriramkumar
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA
| | - Riddhi Sood
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Genome, Cell and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, IN, 47405, USA
| | - Thomas D Huntington
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA
| | - Ahmed H Ghobashi
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Genome, Cell and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, IN, 47405, USA
| | - Truc T Vuong
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA
| | - Tara X Metcalfe
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA
| | - Weini Wang
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA
| | - Kenneth P Nephew
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA.,Genome, Cell and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, IN, 47405, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA.,Department of Anatomy, Cell Biology and Physiology, Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Heather M O'Hagan
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA. .,Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN, 47405, USA. .,Genome, Cell and Developmental Biology, Department of Biology, Indiana University Bloomington, Bloomington, IN, 47405, USA. .,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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