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Gardner AL, Jost TA, Brock A. Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596337. [PMID: 38854060 PMCID: PMC11160629 DOI: 10.1101/2024.05.28.596337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Intratumor heterogeneity reduces treatment efficacy and complicates our understanding of tumor progression. There is a pressing need to understand the functions of heterogeneous tumor cell subpopulations within a tumor, yet biological systems to study these processes in vitro are limited. With the advent of single-cell RNA sequencing (scRNA-seq), it has become clear that some cancer cell line models include distinct subpopulations. Heterogeneous cell lines offer a unique opportunity to study the dynamics and evolution of genetically similar cancer cell subpopulations in controlled experimental settings. Here, we present clusterCleaver, a computational package that uses metrics of statistical distance to identify candidate surface markers maximally unique to transcriptomic subpopulations in scRNA-seq which may be used for FACS isolation. clusterCleaver was experimentally validated using the MDA-MB-231 and MDA-MB-436 breast cancer cell lines. ESAM and BST2/tetherin were experimentally confirmed as surface markers which identify and separate major transcriptomic subpopulations within MDA-MB-231 and MDA-MB-436 cells, respectively. clusterCleaver is a computationally efficient and experimentally validated workflow for identification and enrichment of distinct subpopulations within cell lines which paves the way for studies on the coexistence of cancer cell subpopulations in well-defined in vitro systems.
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Affiliation(s)
- Andrea L. Gardner
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Tyler A. Jost
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin
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Petersen C, Mucke L, Corces MR. CHOIR improves significance-based detection of cell types and states from single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576317. [PMID: 38328105 PMCID: PMC10849522 DOI: 10.1101/2024.01.18.576317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Clustering is a critical step in the analysis of single-cell data, as it enables the discovery and characterization of putative cell types and states. However, most popular clustering tools do not subject clustering results to statistical inference testing, leading to risks of overclustering or underclustering data and often resulting in ineffective identification of cell types with widely differing prevalence. To address these challenges, we present CHOIR (clustering hierarchy optimization by iterative random forests), which applies a framework of random forest classifiers and permutation tests across a hierarchical clustering tree to statistically determine which clusters represent distinct populations. We demonstrate the enhanced performance of CHOIR through extensive benchmarking against 14 existing clustering methods across 100 simulated and 4 real single-cell RNA-seq, ATAC-seq, spatial transcriptomic, and multi-omic datasets. CHOIR can be applied to any single-cell data type and provides a flexible, scalable, and robust solution to the important challenge of identifying biologically relevant cell groupings within heterogeneous single-cell data.
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Affiliation(s)
- Cathrine Petersen
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - M. Ryan Corces
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
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Lee CM, Hwang Y, Jeong JW, Kim M, Lee J, Bae SJ, Ahn SG, Fang S. BRCA1 mutation promotes sprouting angiogenesis in inflammatory cancer-associated fibroblast of triple-negative breast cancer. Cell Death Discov 2024; 10:5. [PMID: 38182557 PMCID: PMC10770063 DOI: 10.1038/s41420-023-01768-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with inferior outcomes owing to its low treatment response and high invasiveness. Based on abundant cancer-associated fibroblasts (CAFs) and frequent mutation of breast cancer-associated 1 (BRCA1) in TNBC, the characteristics of CAFs in TNBC patients with BRCA1 mutation compared to wild-type were investigated using single-cell analysis. Intriguingly, we observed that characteristics of inflammatory CAFs (iCAFs) were enriched in patients with BRCA1 mutation compared to the wild-type. iCAFs in patients with BRCA1 mutation exhibited outgoing signals to endothelial cells (ECs) clusters, including chemokine (C-X-C motif) ligand (CXCL) and vascular endothelial growth factor (VEGF). During CXCL signaling, the atypical chemokine receptor 1 (ACKR1) mainly interacts with CXCL family members in tumor endothelial cells (TECs). ACKR1-high TECs also showed high expression levels of angiogenesis-related genes, such as ANGPT2, MMP1, and SELE, which might lead to EC migration. Furthermore, iCAFs showed VEGF signals for FLT1 and KDR in TECs, which showed high co-expression with tip cell marker genes, including ZEB1 and MAFF, involved in sprouting angiogenesis. Moreover, BRCA1 mutation patients with relatively abundant iCAFs and tip cell gene expression exhibited a limited response to neoadjuvant chemotherapy, including cisplatin and bevacizumab. Importantly, our study observed the intricate link between iCAFs-mediated angiogenesis and chemoresistance in TNBC with BRCA1 mutation.
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Affiliation(s)
- Chae Min Lee
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Yeseong Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jae Woong Jeong
- Department of Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Minki Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Janghee Lee
- Department of Surgery, Sacred Heart Hospital, Hallym University, Dongtan, 18450, Republic of Korea
- Department of Medicine, Yonsei University Graduate School, Seoul, 03722, Republic of Korea
| | - Soong June Bae
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
| | - Sung Gwe Ahn
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.
- Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Chronic Intractable Disease for Systems Medicine Research Center, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Severance Institute for Vascular and Metabolic Research, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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Wang H, Huang R, Nelson J, Gao C, Tran M, Yeaton A, Felt K, Pfaff KL, Bowman T, Rodig SJ, Wei K, Goods BA, Farhi SL. Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570603. [PMID: 38106230 PMCID: PMC10723440 DOI: 10.1101/2023.12.07.570603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmarked the performance of three commercial iST platforms on serial sections from tissue microarrays (TMAs) containing 23 tumor and normal tissue types for both relative technical and biological performance. On matched genes, we found that 10x Xenium shows higher transcript counts per gene without sacrificing specificity, but that all three platforms concord to orthogonal RNA-seq datasets and can perform spatially resolved cell typing, albeit with different false discovery rates, cell segmentation error frequencies, and with varying degrees of sub-clustering for downstream biological analyses. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.
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Affiliation(s)
- Huan Wang
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Ruixu Huang
- Thayer School of Engineering, Molecular and Systems Biology, and Program in Quantitative Biomedical Sciences at Dartmouth College, Hanover, NH 03755, USA
| | - Jack Nelson
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Ce Gao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Miles Tran
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Anna Yeaton
- Present affiliation: Immunai, New York, NY 10016, USA
| | - Kristen Felt
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Tissue Biomarker Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Teri Bowman
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Scott J. Rodig
- Center for Immuno-Oncology, Tissue Biomarker Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Brittany A. Goods
- Thayer School of Engineering, Molecular and Systems Biology, and Program in Quantitative Biomedical Sciences at Dartmouth College, Hanover, NH 03755, USA
| | - Samouil L. Farhi
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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Kang K, Wu Y, Han C, Wang L, Wang Z, Zhao A. Homologous recombination deficiency in triple-negative breast cancer: Multi-scale transcriptomics reveals distinct tumor microenvironments and limitations in predicting immunotherapy response. Comput Biol Med 2023; 158:106836. [PMID: 37031511 DOI: 10.1016/j.compbiomed.2023.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/17/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and has the highest proportion of homologous recombination deficiency (HRD). HRD has been considered a biomarker of response to immune checkpoint inhibitors (ICIs), but the reality is more complicated. A comprehensive comparison of the tumor microenvironment (TME) in HRD and non-HRD TNBC samples may be helpful. METHODS Datasets from single-cell, spatial, and bulk RNA-sequencing were collected to explore the role of HRD in the development of TME at multiple scales. Based on the findings in the TME, machine learning algorithms were used to construct a response prediction model in eleven ICI therapy cohorts. RESULTS A more exhausted phenotype of T cells and a more tolerogenic phenotype of dendritic cells were found in the non-HRD group. HRD reprograms the predominant phenotype of cancer-associated fibroblasts (CAFs) from myofibroblastic CAFs to inflammatory-like CAFs. As interactions between myofibroblastic CAFs and other cells, DPP4-chemokines associated with reduced immune cell recruitment were unique in the non-HRD group. The prediction model based on DPP4-related genes had acceptable performance in predicting response, prognosis, and immune cell content. Higher HRD scores in bulk RNA-sequencing samples indicated more activated immune cell function, but not higher immune cell content, which may be affected by factors such as antigen-presenting capacity. CONCLUSIONS Based on multi-scale transcriptomics, our findings comprehensively reveal differences in the TME between HRD and non-HRD samples. Combining HRD with the prediction model or other methods for assessing immune cell content, may better predict response to ICIs in TNBC.
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Affiliation(s)
- Kai Kang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yijun Wu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chang Han
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhile Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ailin Zhao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China.
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