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Zhang W, Maeser D, Lee A, Huang Y, Gruener RF, Abdelbar IG, Jena S, Patel AG, Huang RS. Integration of Pan-Cancer Cell Line and Single-Cell Transcriptomic Profiles Enables Inference of Therapeutic Vulnerabilities in Heterogeneous Tumors. Cancer Res 2024; 84:2021-2033. [PMID: 38581448 PMCID: PMC11178452 DOI: 10.1158/0008-5472.can-23-3005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/18/2023] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) greatly advanced the understanding of intratumoral heterogeneity by identifying distinct cancer cell subpopulations. However, translating biological differences into treatment strategies is challenging due to a lack of tools to facilitate efficient drug discovery that tackles heterogeneous tumors. Developing such approaches requires accurate prediction of drug response at the single-cell level to offer therapeutic options to specific cell subpopulations. Here, we developed a transparent computational framework (nicknamed scIDUC) to predict therapeutic efficacies on an individual cell basis by integrating single-cell transcriptomic profiles with large, data-rich pan-cancer cell line screening data sets. This method achieved high accuracy in separating cells into their correct cellular drug response statuses. In three distinct prospective tests covering different diseases (rhabdomyosarcoma, pancreatic ductal adenocarcinoma, and castration-resistant prostate cancer), the predicted results using scIDUC were accurate and mirrored biological expectations. In the first two tests, the framework identified drugs for cell subpopulations that were resistant to standard-of-care (SOC) therapies due to intrinsic resistance or tumor microenvironmental effects, and the results showed high consistency with experimental findings from the original studies. In the third test using newly generated SOC therapy-resistant cell lines, scIDUC identified efficacious drugs for the resistant line, and the predictions were validated with in vitro experiments. Together, this study demonstrates the potential of scIDUC to quickly translate scRNA-seq data into drug responses for individual cells, displaying the potential as a tool to improve the treatment of heterogenous tumors. SIGNIFICANCE A versatile method that infers cell-level drug response in scRNA-seq data facilitates the development of therapeutic strategies to target heterogeneous subpopulations within a tumor and address issues such as treatment failure and resistance.
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Affiliation(s)
- Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Danielle Maeser
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Adam Lee
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Yingbo Huang
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Robert F. Gruener
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Israa G. Abdelbar
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
- Clinical Pharmacy Practice Department, The British University in Egypt, El Sherouk, 11837, Egypt
| | - Sampreeti Jena
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Anand G. Patel
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - R. Stephanie Huang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
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Maeser D, Zhang W, Huang Y, Huang RS. A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data. Curr Opin Struct Biol 2024; 84:102745. [PMID: 38109840 PMCID: PMC10922290 DOI: 10.1016/j.sbi.2023.102745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Cancer treatment failure is often attributed to tumor heterogeneity, where diverse malignant cell clones exist within a patient. Despite a growing understanding of heterogeneous tumor cells depicted by single-cell RNA sequencing (scRNA-seq), there is still a gap in the translation of such knowledge into treatment strategies tackling the pervasive issue of therapy resistance. In this review, we survey methods leveraging large-scale drug screens to generate cellular sensitivities to various therapeutics. These methods enable efficient drug screens in scRNA-seq data and serve as the bedrock of drug discovery for specific cancer cell groups. We envision that they will become an indispensable tool for tailoring patient care in the era of heterogeneity-aware precision medicine.
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Affiliation(s)
- Danielle Maeser
- Department of Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States; Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, United States
| | - Weijie Zhang
- Department of Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States; Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, United States
| | - Yingbo Huang
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, United States
| | - R Stephanie Huang
- Department of Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States; Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, United States.
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Yan N, Xie W, Wang D, Fang Q, Guo J, Chen Y, Li X, Gong L, Wang J, Guo W, Zhang X, Zhang Y, Gu J, Li C. Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors. Genome Med 2024; 16:2. [PMID: 38167466 PMCID: PMC10759356 DOI: 10.1186/s13073-023-01267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Pituitary neuroendocrine tumors (PitNETs) are one of the most common types of intracranial tumors. Currently, the cellular characteristics of normal pituitary and various other types of PitNETs are still not completely understood. METHODS We performed single-cell RNA sequencing (scRNA-seq) on 4 normal samples and 24 PitNET samples for comprehensive bioinformatics analysis. Findings regarding the function of PBK in the aggressive tumor cells were validated by siRNA knockdown, overexpression, and transwell experiments. RESULTS We first constructed a reference cell atlas of the human pituitary. Subsequent scRNA-seq analysis of PitNET samples, representing major tumor subtypes, shed light on the intrinsic cellular heterogeneities of the tumor cells and tumor microenvironment (TME). We found that the expression of hormone-encoding genes defined the major variations of the PIT1-lineage tumor cell transcriptomic heterogeneities. A sub-population of TPIT-lineage tumor cells highly expressing GZMK suggested a novel subtype of corticotroph tumors. In immune cells, we found two clusters of tumor-associated macrophages, which were both highly enriched in PitNETs but with distinct functional characteristics. In PitNETs, the stress response pathway was significantly activated in T cells. While a majority of these tumors are benign, our study unveils a common existence of aggressive tumor cells in the studied samples, which highly express a set of malignant signature genes. The following functional experiments confirmed the oncogenic role of selected up-regulated genes. The over-expression of PBK could promote both tumor cell proliferation and migration, and it was also significantly associated with poor prognosis in PitNET patients. CONCLUSIONS Our data and analysis manifested the basic cell types in the normal pituitary and inherent heterogeneity of PitNETs, identified several features of the tumor immune microenvironments, and found a novel epithelial cell sub-population with aggressive signatures across all the studied cases.
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Affiliation(s)
- Nan Yan
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Weiyan Xie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Dongfang Wang
- Biomedical Pioneering Innovative Center, Peking University, Beijing, 100871, China
| | - Qiuyue Fang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Yiyuan Chen
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Xinqi Li
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Lei Gong
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Jialin Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Wenbo Guo
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, 100070, China.
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China.
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, 100070, China.
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Zhang W, Maeser D, Lee A, Huang Y, Gruener RF, Abdelbar IG, Jena S, Patel AG, Huang RS. Inferring therapeutic vulnerability within tumors through integration of pan-cancer cell line and single-cell transcriptomic profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564598. [PMID: 37961545 PMCID: PMC10634928 DOI: 10.1101/2023.10.29.564598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Single-cell RNA sequencing greatly advanced our understanding of intratumoral heterogeneity through identifying tumor subpopulations with distinct biologies. However, translating biological differences into treatment strategies is challenging, as we still lack tools to facilitate efficient drug discovery that tackles heterogeneous tumors. One key component of such approaches tackles accurate prediction of drug response at the single-cell level to offer therapeutic options to specific cell subpopulations. Here, we present a transparent computational framework (nicknamed scIDUC) to predict therapeutic efficacies on an individual-cell basis by integrating single-cell transcriptomic profiles with large, data-rich pan-cancer cell line screening datasets. Our method achieves high accuracy, with predicted sensitivities easily able to separate cells into their true cellular drug resistance status as measured by effect size (Cohen's d > 1.0). More importantly, we examine our method's utility with three distinct prospective tests covering different diseases (rhabdomyosarcoma, pancreatic ductal adenocarcinoma, and castration-resistant prostate cancer), and in each our predicted results are accurate and mirrored biological expectations. In the first two, we identified drugs for cell subpopulations that are resistant to standard-of-care (SOC) therapies due to intrinsic resistance or effects of tumor microenvironments. Our results showed high consistency with experimental findings from the original studies. In the third test, we generated SOC therapy resistant cell lines, used scIDUC to identify efficacious drugs for the resistant line, and validated the predictions with in-vitro experiments. Together, scIDUC quickly translates scRNA-seq data into drug response for individual cells, displaying the potential as a first-line tool for nuanced and heterogeneity-aware drug discovery.
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Affiliation(s)
- Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Danielle Maeser
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Adam Lee
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Yingbo Huang
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Robert F Gruener
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Israa G Abdelbar
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
- Clinical Pharmacy Practice Department, The British University in Egypt, El Sherouk, 11837, Egypt
| | - Sampreeti Jena
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - R Stephanie Huang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
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McKinley S, Taylor A, Peeples C, Jacob M, Khaparde G, Walter Y, Ekpenyong A. Simulated Microgravity-Induced Changes to Drug Response in Cancer Cells Quantified Using Fluorescence Morphometry. Life (Basel) 2023; 13:1683. [PMID: 37629540 PMCID: PMC10455503 DOI: 10.3390/life13081683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Unlike plants that have special gravity-sensing cells, such special cells in animals are yet to be discovered. However, microgravity, the condition of apparent weightlessness, causes bone, muscular and immune system dysfunctions in astronauts following spaceflights. Decades of investigations show correlations between these organ and system-level dysfunctions with changes induced at the cellular level both by simulated microgravity as well as microgravity conditions in outer space. Changes in single bone, muscle and immune cells include morphological abnormalities, altered gene expression, protein expression, metabolic pathways and signaling pathways. These suggest that human cells mount some response to microgravity. However, the implications of such adjustments on many cellular functions and responses are not clear. Here, we addressed the question whether microgravity induces alterations to drug response in cancer cells. We used both adherent cancer cells (T98G) and cancer cells in suspension (K562) to confirm the known effects of simulated microgravity and then treated the K562 cells with common cancer drugs (hydroxyurea and paclitaxel) following 48 h of exposure to simulated microgravity via a NASA-developed rotary cell culture system. Through fluorescence-guided morphometry, we found that microgravity abolished a significant reduction (p < 0.01) in the nuclear-to-cytoplasm ratio of cancer cells treated with hydroxyurea. Our results call for more studies on the impact of microgravity on cellular drug response, in light of the growing need for space medicine, as space exploration grows.
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Affiliation(s)
- Spencer McKinley
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Adam Taylor
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Conner Peeples
- Physics Department, Creighton University, Omaha, NE 68178, USA; (C.P.); (Y.W.)
| | - Megha Jacob
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Gargee Khaparde
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Yohan Walter
- Physics Department, Creighton University, Omaha, NE 68178, USA; (C.P.); (Y.W.)
| | - Andrew Ekpenyong
- Physics Department, Creighton University, Omaha, NE 68178, USA; (C.P.); (Y.W.)
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