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Das P, San Martin R, Hong T, McCord RP. Rearrangement of 3D genome organization in breast cancer epithelial - mesenchymal transition and metastasis organotropism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609227. [PMID: 39229150 PMCID: PMC11370564 DOI: 10.1101/2024.08.23.609227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Breast cancer cells exhibit organotropism during metastasis, showing preferential homing to certain organs such as bone, lung, liver, and brain. One potential explanation for this organotropic behavior is that cancer cells gain properties that enable thriving in certain microenvironments. Such specific metastatic traits may arise from gene regulation at the primary tumor site. Spatial genome organization plays a crucial role in oncogenic transformation and progression, but the extent to which chromosome architecture contributes to organ-specific metastatic traits is unclear. This work characterizes chromosome architecture changes associated with organotropic metastatic traits. By comparing a collection of genomic data from different subtypes of localized and lung metastatic breast cancer cells with both normal and cancerous lung cells, we find important trends of genomic reorganization. The most striking differences in 3D genome compartments segregate cell types according to their epithelial vs. mesenchymal status. This EMT compartment signature occurs at genomic regions distinct from transcription-defined EMT signatures, suggesting a separate layer of regulation. Specifically querying organotropism, we find 3D genome changes consistent with adaptations needed to survive in a new microenvironment, with lung metastatic breast cells exhibiting compartment switch signatures that shift the genome architecture to a lung cell-like conformation and brain metastatic prostate cancer cells showing compartment shifts toward a brain-like state. TCGA patient data reveals gene expression changes concordant with these organ-permissive compartment changes. These results suggest that genome architecture provides an additional level of cell fate specification informing organotropism and enabling survival at the metastatic site.
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Xiong X, Wang X, Liu CC, Shao ZM, Yu KD. Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era. Biomark Res 2024; 12:107. [PMID: 39294728 PMCID: PMC11411917 DOI: 10.1186/s40364-024-00654-1] [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: 06/28/2024] [Accepted: 09/10/2024] [Indexed: 09/21/2024] Open
Abstract
As one of the most common tumors in women, the pathogenesis and tumor heterogeneity of breast cancer have long been the focal point of research, with the emergence of tumor metastasis and drug resistance posing persistent clinical challenges. The emergence of single-cell sequencing (SCS) technology has introduced novel approaches for gaining comprehensive insights into the biological behavior of malignant tumors. SCS is a high-throughput technology that has rapidly developed in the past decade, providing high-throughput molecular insights at the individual cell level. Furthermore, the advent of multitemporal point sampling and spatial omics also greatly enhances our understanding of cellular dynamics at both temporal and spatial levels. The paper provides a comprehensive overview of the historical development of SCS, and highlights the most recent advancements in utilizing SCS and spatial omics for breast cancer research. The findings from these studies will serve as valuable references for future advancements in basic research, clinical diagnosis, and treatment of breast cancer.
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Affiliation(s)
- Xin Xiong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xin Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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3
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Chen H, Lee YJ, Ovando-Ricardez JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J. Recovering single-cell expression profiles from spatial transcriptomics with scResolve. CELL REPORTS METHODS 2024:100864. [PMID: 39326411 DOI: 10.1016/j.crmeth.2024.100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/14/2024] [Accepted: 08/30/2024] [Indexed: 09/28/2024]
Abstract
Many popular spatial transcriptomics techniques lack single-cell resolution. Instead, these methods measure the collective gene expression for each location from a mixture of cells, potentially containing multiple cell types. Here, we developed scResolve, a method for recovering single-cell expression profiles from spatial transcriptomics measurements at multi-cellular resolution. scResolve accurately restores expression profiles of individual cells at their locations, which is unattainable with cell type deconvolution. Applications of scResolve on human breast cancer data and human lung disease data demonstrate that scResolve enables cell-type-specific differential gene expression analysis between different tissue contexts and accurate identification of rare cell populations. The spatially resolved cellular-level expression profiles obtained through scResolve facilitate more flexible and precise spatial analysis that complements raw multi-cellular level analysis.
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Affiliation(s)
- Hao Chen
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Young Je Lee
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jose A Ovando-Ricardez
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Lorena Rosas
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mauricio Rojas
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Ana L Mora
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Ziv Bar-Joseph
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jose Lugo-Martinez
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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Zhao G, Zhang X, Meng L, Dong K, Shang S, Jiang T, Liu Z, Gao H. Single-cell RNA-sequencing reveals a unique landscape of the tumor microenvironment in obesity-associated breast cancer. Oncogene 2024:10.1038/s41388-024-03161-7. [PMID: 39300255 DOI: 10.1038/s41388-024-03161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024]
Abstract
As two diseases with rapidly increasing incidence, the molecular linkages between obesity and breast cancer (BC) are intriguing. Overall, obesity may be a negative prognostic factor for BC. Single-cell RNA-sequencing (scRNA-seq) was performed on tumor tissues from 6 obese and non-obese BC patients. With 48,033 cells analyzed, we found heterogeneous tumor epithelium and microenvironment in these obese and lean BC patients. Interestingly, the obesity-associated epithelial cells exhibited specific expression signatures which linked tumor growth and hormone metabolism in BC. Notably, one population of obesity-specific macrophage up-regulated the nuclear receptor subfamily 1 group H member 3 (NR1H3), which acted a transcription factor and regulated FABP4 expression through its interaction with the DNA of SREBP1, and further increased the proliferation of tumor cells in BC. Using single-cell signatures, our study illustrate cell diversity and transcriptomic differences in tumors from obese and non-obese BC patients, and sheds light on potential molecular link between lipid metabolism and BC.
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Affiliation(s)
- Guanghui Zhao
- Peking University People's Hospital, Qingdao; Women and Children's Hospital, QINGDAO UNIVERSITY, Qingdao, 266111, China
| | - Xiaodong Zhang
- Medical Laboratory Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
| | - Liying Meng
- Medical Laboratory Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
| | - Ke Dong
- Department of Breast Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
| | - Shipeng Shang
- School of Basic Medicine, Qingdao University, Qingdao, 266035, China
| | - Tengfei Jiang
- Medical Laboratory Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
| | - Ziqian Liu
- Medical Laboratory Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China
| | - Haidong Gao
- Department of Breast Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China.
- Oncology Laboratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, China.
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5
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Wang K, Yan Y, Elgamal H, Li J, Tang C, Bai S, Xiao Z, Sei E, Lin Y, Wang J, Montalvan J, Nagi C, Thompson AM, Navin N. Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611519. [PMID: 39314325 PMCID: PMC11418942 DOI: 10.1101/2024.09.06.611519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Understanding the impact of genetic alterations on epigenomic phenotypes during breast cancer progression is challenging with unimodal measurements. Here, we report wellDA-seq, the first high-genomic resolution, high-throughput method that can simultaneously measure the whole genome and chromatin accessibility profiles of thousands of single cells. Using wellDA-seq, we profiled 22,123 single cells from 2 normal and 9 tumors breast tissues. By directly mapping the epigenomic phenotypes to genetic lineages across cancer subclones, we found evidence of both genetic hardwiring and epigenetic plasticity. In 6 estrogen-receptor positive breast cancers, we directly identified the ancestral cancer cells, and found that their epithelial cell-of-origin was Luminal Hormone Responsive cells. We also identified cell types with copy number aberrations (CNA) in normal breast tissues and discovered non-epithelial cell types in the microenvironment with CNAs in breast cancers. These data provide insights into the complex relationship between genetic alterations and epigenomic phenotypes during breast tumor evolution.
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Sundaram L, Kumar A, Zatzman M, Salcedo A, Ravindra N, Shams S, Louie BH, Bagdatli ST, Myers MA, Sarmashghi S, Choi HY, Choi WY, Yost KE, Zhao Y, Granja JM, Hinoue T, Hayes DN, Cherniack A, Felau I, Choudhry H, Zenklusen JC, Farh KKH, McPherson A, Curtis C, Laird PW, Demchok JA, Yang L, Tarnuzzer R, Caesar-Johnson SJ, Wang Z, Doane AS, Khurana E, Castro MAA, Lazar AJ, Broom BM, Weinstein JN, Akbani R, Kumar SV, Raphael BJ, Wong CK, Stuart JM, Safavi R, Benz CC, Johnson BK, Kyi C, Shen H, Corces MR, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. Science 2024; 385:eadk9217. [PMID: 39236169 DOI: 10.1126/science.adk9217] [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: 09/19/2023] [Accepted: 07/03/2024] [Indexed: 09/07/2024]
Abstract
To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin accessibility is strongly influenced by copy number alterations that can be used to identify subclones, yet underlying cis-regulatory landscapes retain cancer type-specific features. Using organ-matched healthy tissues, we identified the "nearest healthy" cell types in diverse cancers, demonstrating that the chromatin signature of basal-like-subtype breast cancer is most similar to secretory-type luminal epithelial cells. Neural network models trained to learn regulatory programs in cancer revealed enrichment of model-prioritized somatic noncoding mutations near cancer-associated genes, suggesting that dispersed, nonrecurrent, noncoding mutations in cancer are functional. Overall, these data and interpretable gene regulatory models for cancer and healthy tissue provide a framework for understanding cancer-specific gene regulation.
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Affiliation(s)
- Laksshman Sundaram
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Illumina AI laboratory, Illumina Inc, Foster City, CA, USA
- NVIDIA Bio Research, NVIDIA, Santa Clara, CA, USA
| | - Arvind Kumar
- Illumina AI laboratory, Illumina Inc, Foster City, CA, USA
| | - Matthew Zatzman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Neal Ravindra
- Illumina AI laboratory, Illumina Inc, Foster City, CA, USA
| | - Shadi Shams
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bryan H Louie
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Matthew A Myers
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hyo Young Choi
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Won-Young Choi
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kathryn E Yost
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Yanding Zhao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toshinori Hinoue
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - D Neil Hayes
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Ina Felau
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean C Zenklusen
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina Curtis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - John A Demchok
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Liming Yang
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roy Tarnuzzer
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Zhining Wang
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Ashley S Doane
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bradley M Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shwetha V Kumar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08540
| | - Christopher K Wong
- Biomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joshua M Stuart
- Biomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rojin Safavi
- Biomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Benjamin K Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Cindy Kyi
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - M Ryan Corces
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
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7
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Yang T, Dong Y, Wang G, Guan X. SOX13-mediated transcription of LRP11 enhances malignant properties of tumor cells and CD8 + T cell inactivation in breast cancer through the β-catenin/PD-L1 axis. Cell Signal 2024; 124:111383. [PMID: 39243917 DOI: 10.1016/j.cellsig.2024.111383] [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: 05/14/2024] [Revised: 08/22/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND High expression of low-density lipoprotein receptor related protein 11 (LRP11) has been associated with unfavorable prognosis of breast cancer (BC). This study explores the exact roles of LRP11 in BC progression and investigates the associated mechanism. METHODS LRP11 expression in BC tissues and cells was determined by immunohistochemistry or RT-qPCR. LRP11 upregulation was induced in two human BC cell lines to investigate its impact on cell proliferation, migration, and invasion. Its regulation on immune activity was assessed by detecting PD-L1 protein levels and generating a co-culture system of cancer cells and CD8+ T cells. Mouse allograft tumor models were generated to analyze the function of LRP11 in tumorigenesis and immune activity in vivo. Gain-of-function assays of SRY-box transcription factor 13 (SOX13) were performed to investigate its function in development and immunosuppression of BC. RESULTS LRP11 was found to be highly expressed in BC tissues and cells, presenting an association with unfavorable prognosis of patients. Artificial upregulation of LRP11 in BC cells triggered malignant properties of cells, enhancing β-catenin-mediated transcriptional activation of PD-L1, thus decreasing immune activity of the co-cultured CD8+ T cells. Consistently, LRP11 upregulation in mouse 4 T1 cells and promoted tumorigenesis and immune evasion in mice. SOX13 was found to bind the LRP11 promoter for transcriptional activation. Upregulation of SOX13 similarly promoted growth of BC cells and immunosuppression, with its oncogenic effects blocked by the additional LRP11 knockdown. CONCLUSION This study demonstrates that SOX13 is responsible for LRP11 transcription activation, leading to increased malignant phenotype of BC cells and diminished activity CD8+ T cells. This evidence highlights SOX13 and LRP11 as promising novel therapeutic targets to reduce malignant phenotype of BC cells and overcome immunosuppression.
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Affiliation(s)
- Tingting Yang
- Cancer Center, The First Hospital of Jilin University, Changchun 130021, Jilin, PR China
| | - Yi Dong
- The Second Breast Surgery Department, Jilin Cancer Hospital, Changchun 130012, Jilin, PR China
| | - Guoxiang Wang
- Cancer Center, The First Hospital of Jilin University, Changchun 130021, Jilin, PR China
| | - Xin Guan
- Breast Surgery Department, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, Jilin, PR China.
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Jena SG, Verma A, Engelhardt BE. Answering open questions in biology using spatial genomics and structured methods. BMC Bioinformatics 2024; 25:291. [PMID: 39232666 PMCID: PMC11375982 DOI: 10.1186/s12859-024-05912-5] [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: 10/10/2023] [Accepted: 08/22/2024] [Indexed: 09/06/2024] Open
Abstract
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shapes, relative locations, movement, and interactions of cells in space. Spatial technologies that collect genomic or epigenomic data while preserving spatial information have begun to overcome these limitations. These new data promise a deeper understanding of the factors that affect cellular behavior, and in particular the ability to directly test existing theories about cell state and variation in the context of morphology, location, motility, and signaling that could not be tested before. Rapid advancements in resolution, ease-of-use, and scale of spatial genomics technologies to address these questions also require an updated toolkit of statistical methods with which to interrogate these data. We present a framework to respond to this new avenue of research: four open biological questions that can now be answered using spatial genomics data paired with methods for analysis. We outline spatial data modalities for each open question that may yield specific insights, discuss how conflicting theories may be tested by comparing the data to conceptual models of biological behavior, and highlight statistical and machine learning-based tools that may prove particularly helpful to recover biological understanding.
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Affiliation(s)
- Siddhartha G Jena
- Department of Stem Cell and Regenerative Biology, Harvard, 7 Divinity Ave, Cambridge, MA, USA
| | - Archit Verma
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA, 94158, USA
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9
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Li Y, Long W, Zhou H, Tan T, Xie H. Revolutionizing breast cancer Ki-67 diagnosis: ultrasound radiomics and fully connected neural networks (FCNN) combination method. Breast Cancer Res Treat 2024; 207:453-468. [PMID: 38853220 DOI: 10.1007/s10549-024-07375-x] [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: 12/28/2023] [Accepted: 05/14/2024] [Indexed: 06/11/2024]
Abstract
PURPOSE This study aims to assess the diagnostic value of ultrasound habitat sub-region radiomics feature parameters using a fully connected neural networks (FCNN) combination method L2,1-norm in relation to breast cancer Ki-67 status. METHODS Ultrasound images from 528 cases of female breast cancer at the Affiliated Hospital of Xiangnan University and 232 cases of female breast cancer at the Affiliated Rehabilitation Hospital of Xiangnan University were selected for this study. We utilized deep learning methods to automatically outline the gross tumor volume and perform habitat clustering. Subsequently, habitat sub-regions were extracted to identify radiomics features and underwent feature engineering using the L1,2-norm. A prediction model for the Ki-67 status of breast cancer patients was then developed using a FCNN. The model's performance was evaluated using accuracy, area under the curve (AUC), specificity (Spe), positive predictive value (PPV), negative predictive value (NPV), Recall, and F1. In addition, calibration curves and clinical decision curves were plotted for the test set to visually assess the predictive accuracy and clinical benefit of the models. RESULT Based on the feature engineering using the L1,2-norm, a total of 9 core features were identified. The predictive model, constructed by the FCNN model based on these 9 features, achieved the following scores: ACC 0.856, AUC 0.915, Spe 0.843, PPV 0.920, NPV 0.747, Recall 0.974, and F1 0.890. Furthermore, calibration curves and clinical decision curves of the validation set demonstrated a high level of confidence in the model's performance and its clinical benefit. CONCLUSION Habitat clustering of ultrasound images of breast cancer is effectively supported by the combined implementation of the L1,2-norm and FCNN algorithms, allowing for the accurate classification of the Ki-67 status in breast cancer patients.
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Affiliation(s)
- Yanfeng Li
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Wengxing Long
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Hongda Zhou
- Department of Oncology, Affiliated Hospital of Xiangnan University, Chenzhou, 423000, Hunan, People's Republic of China
| | - Tao Tan
- Faulty of Applied Sciences, Macao Polytechnic University, Macao, 999078, People's Republic of China
| | - Hui Xie
- Department of Oncology, Affiliated Hospital of Xiangnan University, Chenzhou, 423000, Hunan, People's Republic of China.
- Faulty of Applied Sciences, Macao Polytechnic University, Macao, 999078, People's Republic of China.
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China.
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10
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Zakic T, Pekovic-Vaughan V, Cvoro A, Korac A, Jankovic A, Korac B. Redox and metabolic reprogramming in breast cancer and cancer-associated adipose tissue. FEBS Lett 2024; 598:2106-2134. [PMID: 38140817 DOI: 10.1002/1873-3468.14794] [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: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Redox and metabolic processes are tightly coupled in both physiological and pathological conditions. In cancer, their integration occurs at multiple levels and is characterized by synchronized reprogramming both in the tumor tissue and its specific but heterogeneous microenvironment. In breast cancer, the principal microenvironment is the cancer-associated adipose tissue (CAAT). Understanding how the redox-metabolic reprogramming becomes coordinated in human breast cancer is imperative both for cancer prevention and for the establishment of new therapeutic approaches. This review aims to provide an overview of the current knowledge of the redox profiles and regulation of intermediary metabolism in breast cancer while considering the tumor and CAAT of breast cancer as a unique Warburg's pseudo-organ. As cancer is now recognized as a systemic metabolic disease, we have paid particular attention to the cell-specific redox-metabolic reprogramming and the roles of estrogen receptors and circadian rhythms, as well as their crosstalk in the development, growth, progression, and prognosis of breast cancer.
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Affiliation(s)
- Tamara Zakic
- Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, Serbia
| | - Vanja Pekovic-Vaughan
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, William Henry Duncan Building, University of Liverpool, UK
| | | | | | - Aleksandra Jankovic
- Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, Serbia
| | - Bato Korac
- Institute for Biological Research "Sinisa Stankovic"-National Institute of Republic of Serbia, University of Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Serbia
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11
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WalyEldeen AA, Sabet S, Anis SE, Stein T, Ibrahim AM. FBLN2 is associated with basal cell markers Krt14 and ITGB1 in mouse mammary epithelial cells and has a preferential expression in molecular subtypes of human breast cancer. Breast Cancer Res Treat 2024:10.1007/s10549-024-07447-y. [PMID: 39110274 DOI: 10.1007/s10549-024-07447-y] [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: 04/05/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
Abstract
BACKGROUND Fibulin-2 (FBLN2) is a secreted extracellular matrix (ECM) glycoprotein and has been identified in the mouse mammary gland, in cap cells of terminal end buds (TEBs) during puberty, and around myoepithelial cells during early pregnancy. It is required for basement membrane (BM) integrity in mammary epithelium, and its loss has been associated with human breast cancer invasion. Herein, we attempted to confirm the relevance of FBLN2 to myoepithelial phenotype in mammary epithelium and to assess its expression in molecular subtypes of human breast cancer. METHODS The relationship between FBLN2 expression and epithelial markers was investigated in pubertal mouse mammary glands and the EpH4 mouse mammary epithelial cell line using immunohistochemistry, immunocytochemistry, and immunoblotting. Human breast cancer mRNA data from the METABRIC and TCGA datasets from Bioportal were analyzed to assess the association of Fbln2 expression with epithelial markers, and with molecular subtypes. Survival curves were generated using data from the METABRIC dataset and the KM databases. RESULTS FBLN2 knockdown in mouse mammary epithelial cells was associated with a reduction in KRT14 and an increase in KRT18. Further, TGFβ3 treatment resulted in the upregulation of FBLN2 in vitro. Meta-analyses of human breast cancer datasets from Bioportal showed a higher expression of Fbln2 mRNA in claudin-low, LumA, and normal-like breast cancers compared to LumB, Her2 +, and Basal-like subgroups. Fbln2 mRNA levels were positively associated with mesenchymal markers, myoepithelial markers, and markers of epithelial-mesenchymal transition. Higher expression of Fbln2 mRNA was associated with better prognosis in less advanced breast cancer and this pattern was reversed in more advanced lesions. CONCLUSION With further validation, these observations may offer a molecular prognostic tool for human breast cancer for more personalized therapeutic approaches.
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Affiliation(s)
| | - Salwa Sabet
- Department of Zoology, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Shady E Anis
- Department of Pathology, Faculty of Medicine, Cairo University, Cairo, 11562, Egypt
| | - Torsten Stein
- Institute of Veterinary Biochemistry, Freie Universität Berlin, 14163, Berlin, Germany
- Institute of Cancer Sciences, College of MVLS, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Ayman M Ibrahim
- Department of Zoology, Faculty of Science, Cairo University, Giza, 12613, Egypt.
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt.
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12
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Harris MA, Savas P, Virassamy B, O'Malley MMR, Kay J, Mueller SN, Mackay LK, Salgado R, Loi S. Towards targeting the breast cancer immune microenvironment. Nat Rev Cancer 2024; 24:554-577. [PMID: 38969810 DOI: 10.1038/s41568-024-00714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
The tumour immune microenvironment is shaped by the crosstalk between cancer cells, immune cells, fibroblasts, endothelial cells and other stromal components. Although the immune tumour microenvironment (TME) serves as a source of therapeutic targets, it is also considered a friend or foe to tumour-directed therapies. This is readily illustrated by the importance of T cells in triple-negative breast cancer (TNBC), culminating in the advent of immune checkpoint therapy in combination with cytotoxic chemotherapy as standard of care for both early and advanced-stage TNBC, as well as recent promising signs of efficacy in a subset of hormone receptor-positive disease. In this Review, we discuss the various components of the immune TME in breast cancer and therapies that target or impact the immune TME, as well as the complexity of host physiology.
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Affiliation(s)
- Michael A Harris
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Peter Savas
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Balaji Virassamy
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Megan M R O'Malley
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jasmine Kay
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Roberto Salgado
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Pathology, ZAS Ziekenhuizen, Antwerp, Belgium
| | - Sherene Loi
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
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13
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Shah OS, Nasrazadani A, Foldi J, Atkinson JM, Kleer CG, McAuliffe PF, Johnston TJ, Stallaert W, da Silva EM, Selenica P, Dopeso H, Pareja F, Mandelker D, Weigelt B, Reis-Filho JS, Bhargava R, Lucas PC, Lee AV, Oesterreich S. Spatial molecular profiling of mixed invasive ductal and lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations. Proc Natl Acad Sci U S A 2024; 121:e2322068121. [PMID: 39042692 PMCID: PMC11295029 DOI: 10.1073/pnas.2322068121] [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: 12/28/2023] [Accepted: 06/13/2024] [Indexed: 07/25/2024] Open
Abstract
Mixed invasive ductal and lobular carcinoma (MDLC) is a rare histologic subtype of breast cancer displaying both E-cadherin positive ductal and E-cadherin negative lobular morphologies within the same tumor, posing challenges with regard to anticipated clinical management. It remains unclear whether these distinct morphologies also have distinct biology and risk of recurrence. Our spatially resolved transcriptomic, genomic, and single-cell profiling revealed clinically significant differences between ductal and lobular tumor regions including distinct intrinsic subtype heterogeneity - e.g., MDLC with triple-negative breast cancer (TNBC) or basal ductal and estrogen receptor positive (ER+) luminal lobular regions, distinct enrichment of cell cycle arrest/senescence and oncogenic (ER and MYC) signatures, genetic and epigenetic CDH1 inactivation in lobular but not ductal regions, and single-cell ductal and lobular subpopulations with unique oncogenic signatures further highlighting intraregional heterogeneity. Altogether, we demonstrated that the intratumoral morphological/histological heterogeneity within MDLC is underpinned by intrinsic subtype and oncogenic heterogeneity which may result in prognostic uncertainty and therapeutic dilemma.
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MESH Headings
- Humans
- Female
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/pathology
- Carcinoma, Lobular/metabolism
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/metabolism
- Mutation
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/metabolism
- Breast Neoplasms/classification
- Cadherins/genetics
- Cadherins/metabolism
- Gene Expression Regulation, Neoplastic
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/pathology
- Triple Negative Breast Neoplasms/metabolism
- Transcriptome
- Gene Expression Profiling/methods
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Affiliation(s)
- Osama Shiraz Shah
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, PittsburghPA15260
| | - Azadeh Nasrazadani
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Julia Foldi
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15260
| | - Jennifer M. Atkinson
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA15260
| | - Celina G. Kleer
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
| | - Priscilla F. McAuliffe
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA15232
| | - Tyler J. Johnston
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Edaise M. da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Rohit Bhargava
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Peter C. Lucas
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Rochester, MN55902
| | - Adrian V. Lee
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA15260
| | - Steffi Oesterreich
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA15260
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14
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Hou J, Liu W, Yan M, Ren Y, Qian C, Fu Y, Wang H, Li Z. Unveiling heterogeneity and prognostic markers in ductal breast cancer through single-cell RNA-seq. Cancer Cell Int 2024; 24:266. [PMID: 39068476 PMCID: PMC11282761 DOI: 10.1186/s12935-024-03325-1] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is a heterogeneous disease, with the ductal subtype exhibiting significant cellular diversity that influences prognosis and response to treatment. Single-cell RNA sequencing data from the GEO database were utilized in this study to investigate the underlying mechanisms of cellular heterogeneity and to identify potential prognostic markers and therapeutic targets. METHODS Bioinformatics analysis was conducted using R packages to analyze the single-cell sequencing data. The presence of highly variable genes and differences in malignant potency within the same BC samples were examined. Differential gene expression and biological function between Type 1 and Type 2 ductal epithelial cells were identified. Lasso regression and Cox proportional hazards regression analyses were employed to identify genes associated with patient prognosis. Experimental validation was performed in vitro and in vivo to confirm the functional relevance of the identified genes. RESULTS The analysis revealed notable heterogeneity among BC cells, with the presence of highly variable genes and differences in malignant behavior within the same samples. Significant disparities in gene expression and biological function were identified between Type 1 and Type 2 ductal epithelial cells. Through regression analyses, CYP24A1 and TFPI2 were identified as pivotal genes associated with patient prognosis. Kaplan-Meier curves demonstrated their prognostic significance, and experimental validation confirmed their inhibitory effects on malignant behaviors of ductal BC cells. CONCLUSION This study highlights the cellular heterogeneity in ductal subtype breast cancer and delineates the differential gene expressions and biological functions between Type 1 and Type 2 ductal epithelial cells. The genes CYP24A1 and TFPI2 emerged as promising prognostic markers and therapeutic targets, exhibiting inhibitory effects on BC cell malignancy in vitro and in vivo. These findings offer the potential for improved BC management and the development of targeted treatment strategies.
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Affiliation(s)
- Jianxun Hou
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, P. R. China
| | - Meihong Yan
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Yanlv Ren
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Cheng Qian
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Yingqiang Fu
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Hongbin Wang
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China.
| | - Zhigao Li
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China.
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15
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Lane AN, Higashi RM, Fan TWM. Challenges of Spatially Resolved Metabolism in Cancer Research. Metabolites 2024; 14:383. [PMID: 39057706 PMCID: PMC11278851 DOI: 10.3390/metabo14070383] [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: 05/26/2024] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Stable isotope-resolved metabolomics comprises a critical set of technologies that can be applied to a wide variety of systems, from isolated cells to whole organisms, to define metabolic pathway usage and responses to perturbations such as drugs or mutations, as well as providing the basis for flux analysis. As the diversity of stable isotope-enriched compounds is very high, and with newer approaches to multiplexing, the coverage of metabolism is now very extensive. However, as the complexity of the model increases, including more kinds of interacting cell types and interorgan communication, the analytical complexity also increases. Further, as studies move further into spatially resolved biology, new technical problems have to be overcome owing to the small number of analytes present in the confines of a single cell or cell compartment. Here, we review the overall goals and solutions made possible by stable isotope tracing and their applications to models of increasing complexity. Finally, we discuss progress and outstanding difficulties in high-resolution spatially resolved tracer-based metabolic studies.
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Affiliation(s)
- Andrew N. Lane
- Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, USA; (R.M.H.); (T.W.-M.F.)
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16
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Vattulainen M, Smits JGA, Arts JA, Lima Cunha D, Ilmarinen T, Skottman H, Zhou H. Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA sequencing. Stem Cell Reports 2024; 19:1010-1023. [PMID: 38942029 PMCID: PMC11252539 DOI: 10.1016/j.stemcr.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/30/2024] Open
Abstract
A comprehensive understanding of the human pluripotent stem cell (hPSC) differentiation process stands as a prerequisite for the development of hPSC-based therapeutics. In this study, single-cell RNA sequencing (scRNA-seq) was performed to decipher the heterogeneity during differentiation of three hPSC lines toward corneal limbal stem cells (LSCs). The scRNA-seq data revealed nine clusters encompassing the entire differentiation process, among which five followed the anticipated differentiation path of LSCs. The remaining four clusters were previously undescribed cell states that were annotated as either mesodermal-like or undifferentiated subpopulations, and their prevalence was hPSC line dependent. Distinct cluster-specific marker genes identified in this study were confirmed by immunofluorescence analysis and employed to purify hPSC-derived LSCs, which effectively minimized the variation in the line-dependent differentiation efficiency. In summary, scRNA-seq offered molecular insights into the heterogeneity of hPSC-LSC differentiation, allowing a data-driven strategy for consistent and robust generation of LSCs, essential for future advancement toward clinical translation.
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Affiliation(s)
- Meri Vattulainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jos G A Smits
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Julian A Arts
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Dulce Lima Cunha
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Tanja Ilmarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heli Skottman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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17
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Fu Y, Tao J, Liu T, Liu Y, Qiu J, Su D, Wang R, Luo W, Cao Z, Weng G, Zhang T, Zhao Y. Unbiasedly decoding the tumor microenvironment with single-cell multiomics analysis in pancreatic cancer. Mol Cancer 2024; 23:140. [PMID: 38982491 PMCID: PMC11232163 DOI: 10.1186/s12943-024-02050-7] [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: 05/07/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a poor prognosis and limited therapeutic options. Research on the tumor microenvironment (TME) of PDAC has propelled the development of immunotherapeutic and targeted therapeutic strategies with a promising future. The emergence of single-cell sequencing and mass spectrometry technologies, coupled with spatial omics, has collectively revealed the heterogeneity of the TME from a multiomics perspective, outlined the development trajectories of cell lineages, and revealed important functions of previously underrated myeloid cells and tumor stroma cells. Concurrently, these findings necessitated more refined annotations of biological functions at the cell cluster or single-cell level. Precise identification of all cell clusters is urgently needed to determine whether they have been investigated adequately and to identify target cell clusters with antitumor potential, design compatible treatment strategies, and determine treatment resistance. Here, we summarize recent research on the PDAC TME at the single-cell multiomics level, with an unbiased focus on the functions and potential classification bases of every cellular component within the TME, and look forward to the prospects of integrating single-cell multiomics data and retrospectively reusing bulk sequencing data, hoping to provide new insights into the PDAC TME.
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Affiliation(s)
- Yifan Fu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Tao Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhe Cao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guihu Weng
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Yupei Zhao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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18
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Mazzucchelli S, Signati L, Messa L, Franceschini A, Bonizzi A, Castagnoli L, Gasparini P, Consolandi C, Mangano E, Pelucchi P, Cifola I, Camboni T, Severgnini M, Villani L, Tagliaferri B, Carelli S, Pupa SM, Cereda C, Corsi F. Breast cancer patient-derived organoids for the investigation of patient-specific tumour evolution. Cancer Cell Int 2024; 24:220. [PMID: 38926706 PMCID: PMC11210105 DOI: 10.1186/s12935-024-03375-5] [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: 12/14/2023] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND A reliable preclinical model of patient-derived organoids (PDOs) was developed in a case study of a 69-year-old woman diagnosed with breast cancer (BC) to investigate the tumour evolution before and after neoadjuvant chemotherapy and surgery. The results were achieved due to the development of PDOs from tissues collected before (O-PRE) and after (O-POST) treatment. METHODS PDO cultures were characterized by histology, immunohistochemistry (IHC), transmission electron microscopy (TEM), scanning electron microscopy (SEM), confocal microscopy, flow cytometry, real-time PCR, bulk RNA-seq, single-cell RNA sequencing (scRNA-seq) and drug screening. RESULTS Both PDO cultures recapitulated the histological and molecular profiles of the original tissues, and they showed typical mammary gland organization, confirming their reliability as a personalized in vitro model. Compared with O-PRE, O-POST had a greater proliferation rate with a significant increase in the Ki67 proliferation index. Moreover O-POST exhibited a more stem-like and aggressive phenotype, with increases in the CD24low/CD44low and EPCAMlow/CD49fhigh cell populations characterized by increased tumour initiation potential and multipotency and metastatic potential in invasive lobular carcinoma. Analysis of ErbB receptor expression indicated a decrease in HER-2 expression coupled with an increase in EGFR expression in O-POST. In this context, deregulation of the PI3K/Akt signalling pathway was assessed by transcriptomic analysis, confirming the altered transcriptional profile. Finally, transcriptomic single-cell analysis identified 11 cell type clusters, highlighting the selection of the luminal component and the decrease in the number of Epithelial-mesenchymal transition cell types in O-POST. CONCLUSION Neoadjuvant treatment contributed to the enrichment of cell populations with luminal phenotypes that were more resistant to chemotherapy in O-POST. PDOs represent an excellent 3D cell model for assessing disease evolution.
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Affiliation(s)
- Serena Mazzucchelli
- Dipartimento di Scienze Biomediche e Cliniche, Università di Milano, Via G. B. Grassi 74, 20157, Milan, Italy.
| | - Lorena Signati
- Dipartimento di Scienze Biomediche e Cliniche, Università di Milano, Via G. B. Grassi 74, 20157, Milan, Italy
| | - Letizia Messa
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133, Milan, Italy
- Pediatric Research Center "Romeo and Enrica Invernizzi", Università di Milano, 20157, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Buzzi Children's Hospital, 20154, Milan, Italy
| | - Alma Franceschini
- Microenvironment and Biomarkers of Solid Tumors, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Arianna Bonizzi
- Istituti Clinici Scientifici Maugeri IRCCS, 27100, Pavia, Italy
| | - Lorenzo Castagnoli
- Microenvironment and Biomarkers of Solid Tumors, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Patrizia Gasparini
- Epigenomics and Biomarkers of Solid Tumors, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Clarissa Consolandi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Via F. lli Cervi 93, 20054, Segrate, Italy
| | - Eleonora Mangano
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Via F. lli Cervi 93, 20054, Segrate, Italy
| | - Paride Pelucchi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Via F. lli Cervi 93, 20054, Segrate, Italy
| | - Ingrid Cifola
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Via F. lli Cervi 93, 20054, Segrate, Italy
| | - Tania Camboni
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Via F. lli Cervi 93, 20054, Segrate, Italy
| | - Marco Severgnini
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Via F. lli Cervi 93, 20054, Segrate, Italy
| | - Laura Villani
- Istituti Clinici Scientifici Maugeri IRCCS, 27100, Pavia, Italy
| | | | - Stephana Carelli
- Pediatric Research Center "Romeo and Enrica Invernizzi", Università di Milano, 20157, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Buzzi Children's Hospital, 20154, Milan, Italy
| | - Serenella M Pupa
- Microenvironment and Biomarkers of Solid Tumors, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Buzzi Children's Hospital, 20154, Milan, Italy
| | - Fabio Corsi
- Dipartimento di Scienze Biomediche e Cliniche, Università di Milano, Via G. B. Grassi 74, 20157, Milan, Italy.
- Istituti Clinici Scientifici Maugeri IRCCS, 27100, Pavia, Italy.
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19
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Teschendorff AE. Computational single-cell methods for predicting cancer risk. Biochem Soc Trans 2024; 52:1503-1514. [PMID: 38856037 DOI: 10.1042/bst20231488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Despite recent biotechnological breakthroughs, cancer risk prediction remains a formidable computational and experimental challenge. Addressing it is critical in order to improve prevention, early detection and survival rates. Here, I briefly summarize some key emerging theoretical and computational challenges as well as recent computational advances that promise to help realize the goals of cancer-risk prediction. The focus is on computational strategies based on single-cell data, in particular on bottom-up network modeling approaches that aim to estimate cancer stemness and dedifferentiation at single-cell resolution from a systems-biological perspective. I will describe two promising methods, a tissue and cell-lineage independent one based on the concept of diffusion network entropy, and a tissue and cell-lineage specific one that uses transcription factor regulons. Application of these tools to single-cell and single-nucleus RNA-seq data from stages prior to invasive cancer reveal that they can successfully delineate the heterogeneous inter-cellular cancer-risk landscape, identifying those cells that are more likely to turn cancerous. Bottom-up systems biological modeling of single-cell omic data is a novel computational analysis paradigm that promises to facilitate the development of preventive, early detection and cancer-risk prediction strategies.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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20
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Nicotra R, Lutz C, Messal HA, Jonkers J. Rat Models of Hormone Receptor-Positive Breast Cancer. J Mammary Gland Biol Neoplasia 2024; 29:12. [PMID: 38913216 PMCID: PMC11196369 DOI: 10.1007/s10911-024-09566-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024] Open
Abstract
Hormone receptor-positive (HR+) breast cancer (BC) is the most common type of breast cancer among women worldwide, accounting for 70-80% of all invasive cases. Patients with HR+ BC are commonly treated with endocrine therapy, but intrinsic or acquired resistance is a frequent problem, making HR+ BC a focal point of intense research. Despite this, the malignancy still lacks adequate in vitro and in vivo models for the study of its initiation and progression as well as response and resistance to endocrine therapy. No mouse models that fully mimic the human disease are available, however rat mammary tumor models pose a promising alternative to overcome this limitation. Compared to mice, rats are more similar to humans in terms of mammary gland architecture, ductal origin of neoplastic lesions and hormone dependency status. Moreover, rats can develop spontaneous or induced mammary tumors that resemble human HR+ BC. To date, six different types of rat models of HR+ BC have been established. These include the spontaneous, carcinogen-induced, transplantation, hormone-induced, radiation-induced and genetically engineered rat mammary tumor models. Each model has distinct advantages, disadvantages and utility for studying HR+ BC. This review provides a comprehensive overview of all published models to date.
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Affiliation(s)
- Raquel Nicotra
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Oncode Institute, Amsterdam, Netherlands.
| | - Hendrik A Messal
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Oncode Institute, Amsterdam, Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Oncode Institute, Amsterdam, Netherlands.
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21
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Regner MJ, Garcia-Recio S, Thennavan A, Wisniewska K, Mendez-Giraldez R, Felsheim B, Spanheimer PM, Parker JS, Perou CM, Franco HL. Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598858. [PMID: 38948758 PMCID: PMC11212881 DOI: 10.1101/2024.06.13.598858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Annotation of the cis-regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding of tumor biology. Herein, we present a compendium of matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors and healthy mammary tissues processed immediately following surgical resection. We identify the most likely cell-of-origin for luminal breast tumors and basal breast tumors and then introduce a novel methodology that implements linear mixed-effects models to systematically quantify associations between regions of chromatin accessibility (i.e. regulatory elements) and gene expression in malignant cells versus normal mammary epithelial cells. These data unveil regulatory elements with that switch from silencers of gene expression in normal cells to enhancers of gene expression in cancer cells, leading to the upregulation of clinically relevant oncogenes. To translate the utility of this dataset into tractable models, we generated matched scATAC-seq and scRNA-seq profiles for breast cancer cell lines, revealing, for each subtype, a conserved oncogenic gene expression program between in vitro and in vivo cells. Together, this work highlights the importance of non-coding regulatory mechanisms that underlie oncogenic processes and the ability of single-cell multi-omics to define the regulatory logic of BC cells at single-cell resolution.
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Affiliation(s)
- Matthew J. Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Raul Mendez-Giraldez
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brooke Felsheim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Clinical and Translational Cancer Research, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00935
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22
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Brugge J, Chang KC, Silvestri F, Olipant M, Martinez-Gakidis MA, Orgill D, Garber J, Dillon D. Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness. RESEARCH SQUARE 2024:rs.3.rs-4463390. [PMID: 38947074 PMCID: PMC11213202 DOI: 10.21203/rs.3.rs-4463390/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Organoid cultures offer a powerful technology to investigate many different aspects of development, physiology, and pathology of diverse tissues. Unlike standard tissue culture of primary breast epithelial cells, breast organoids preserve the epithelial lineages and architecture of the normal tissue. However, existing organoid culture methods are tedious, difficult to scale, and do not robustly retain estrogen receptor (ER) expression and responsiveness in long-term culture. Here, we describe a modified culture method to generate and maintain organoids as suspension cultures in reconstituted basement membrane (™Matrigel). This method improves organoid growth and uniformity compared to the conventional Matrigel dome embedding method, while maintaining the fidelity of the three major epithelial lineages. Using this adopted method, we are able to culture and passage purified hormone sensing (HS) cells that retain ER responsiveness upon estrogen stimulation in long-term culture. This culture system presents a valuable platform to study the events involved in initiation and evolution of ER-positive breast cancer.
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23
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Shah OS, Nasrazadani A, Foldi J, Atkinson JM, Kleer CG, McAuliffe PF, Johnston TJ, Stallaert W, da Silva EM, Selenica P, Dopeso H, Pareja F, Mandelker D, Weigelt B, Reis-Filho JS, Bhargava R, Lucas PC, Lee AV, Oesterreich S. Spatial molecular profiling of mixed invasive ductal-lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.09.557013. [PMID: 38915645 PMCID: PMC11195088 DOI: 10.1101/2023.09.09.557013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Mixed invasive ductal and lobular carcinoma (MDLC) is a rare histologic subtype of breast cancer displaying both E-cadherin positive ductal and E-cadherin negative lobular morphologies within the same tumor, posing challenges with regard to anticipated clinical management. It remains unclear whether these distinct morphologies also have distinct biology and risk of recurrence. Our spatially-resolved transcriptomic, genomic, and single-cell profiling revealed clinically significant differences between ductal and lobular tumor regions including distinct intrinsic subtype heterogeneity (e.g., MDLC with TNBC/basal ductal and ER+/luminal lobular regions), distinct enrichment of senescence/dormancy and oncogenic (ER and MYC) signatures, genetic and epigenetic CDH1 inactivation in lobular, but not ductal regions, and single-cell ductal and lobular sub-populations with unique oncogenic signatures further highlighting intra-regional heterogeneity. Altogether, we demonstrated that the intra-tumoral morphological/histological heterogeneity within MDLC is underpinned by intrinsic subtype and oncogenic heterogeneity which may result in prognostic uncertainty and therapeutic dilemma. Significance MDLC displays both ductal and lobular tumor regions. Our multi-omic profiling approach revealed that these morphologically distinct tumor regions harbor distinct intrinsic subtypes and oncogenic features that may cause prognostic uncertainty and therapeutic dilemma. Thus histopathological/molecular profiling of individual tumor regions may guide clinical decision making and benefit patients with MDLC, particularly in the advanced setting where there is increased reliance on next generation sequencing.
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24
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Zhang M, Zhou K, Wang Z, Liu T, Stevens LE, Lynce F, Chen WY, Peng S, Xie Y, Zhai D, Chen Q, Shi Y, Shi H, Yuan Z, Li X, Xu J, Cai Z, Guo J, Shao N, Lin Y. A Subpopulation of Luminal Progenitors Secretes Pleiotrophin to Promote Angiogenesis and Metastasis in Inflammatory Breast Cancer. Cancer Res 2024; 84:1781-1798. [PMID: 38507720 PMCID: PMC11148543 DOI: 10.1158/0008-5472.can-23-2640] [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: 08/31/2023] [Revised: 01/19/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Inflammatory breast cancer (IBC) is a highly aggressive subtype of breast cancer characterized by rapidly arising diffuse erythema and edema. Genomic studies have not identified consistent alterations and mechanisms that differentiate IBC from non-IBC tumors, suggesting that the microenvironment could be a potential driver of IBC phenotypes. Here, using single-cell RNA sequencing, multiplex staining, and serum analysis in patients with IBC, we identified enrichment of a subgroup of luminal progenitor (LP) cells containing high expression of the neurotropic cytokine pleiotrophin (PTN) in IBC tumors. PTN secreted by the LP cells promoted angiogenesis by directly interacting with the NRP1 receptor on endothelial tip cells located in both IBC tumors and the affected skin. NRP1 activation in tip cells led to recruitment of immature perivascular cells in the affected skin of IBC, which are correlated with increased angiogenesis and IBC metastasis. Together, these findings reveal a role for cross-talk between LPs, endothelial tip cells, and immature perivascular cells via PTN-NRP1 axis in the pathogenesis of IBC, which could lead to improved strategies for treating IBC. SIGNIFICANCE Nonmalignant luminal progenitor cells expressing pleiotrophin promote angiogenesis by activating NRP1 and induce a prometastatic tumor microenvironment in inflammatory breast cancer, providing potential therapeutic targets for this aggressive breast cancer subtype.
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Affiliation(s)
- Mengmeng Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaiwen Zhou
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zilin Wang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Liu
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Filipa Lynce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wendy Y Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sui Peng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Duanyang Zhai
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qianjun Chen
- Department of Breast Oncology, Traditional Chinese Medicine Hospital of Guangdong Province, Guangzhou, Guangdong, China
| | - Yawei Shi
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhongyu Yuan
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoping Li
- Department of Breast Oncology, Jiangmen Central Hospital, Jiangmen, China
| | - Juan Xu
- Department of Breast Oncology, Maternal and Child Health Care Hospital of Guangdong Province, Guangzhou, China
| | - Zhenhai Cai
- Department of Breast Oncology, Jieyang People's Hospital, Jieyang, China
| | - Jianping Guo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Nan Shao
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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25
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Joo EH, Kim S, Park D, Lee T, Park WY, Han KY, Lee JE. Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer. Int J Mol Sci 2024; 25:5876. [PMID: 38892065 PMCID: PMC11172245 DOI: 10.3390/ijms25115876] [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: 03/20/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Hormone receptor-positive and HER2-negative breast cancer (HR+/HER2-BC) is the most common type with a favorable prognosis under endocrine therapy. However, it still demonstrates unpredictable progression and recurrences influenced by high tumoral diversity and microenvironmental status. To address these heterogeneous molecular characteristics of HR+/HER2-BC, we aimed to simultaneously characterize its transcriptomic landscape and genetic architecture at the same resolution. Using advanced single-cell RNA and DNA sequencing techniques together, we defined four distinct tumor subtypes. Notably, the migratory tumor subtype was closely linked to genomic alterations of EGFR, related to the tumor-promoting behavior of IL6-positive inflammatory tumor-associated fibroblast, and contributing to poor prognosis. Our study comprehensively utilizes integrated analysis to uncover the complex dynamics of this breast cancer subtype, highlighting the pivotal role of the migratory tumor subtype in influencing surrounding cells. This sheds light on potential therapeutic targets by offering enhanced insights for HR+/HER2-BC treatment.
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Affiliation(s)
- Eun Hye Joo
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; (E.H.J.); (W.-Y.P.)
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea
| | - Sangmin Kim
- Department of Breast Cancer Center, Samsung Medical Center, Seoul 06351, Republic of Korea;
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Donghyun Park
- Planit Healthcare Inc., Seoul 06235, Republic of Korea;
| | - Taeseob Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea;
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; (E.H.J.); (W.-Y.P.)
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; (E.H.J.); (W.-Y.P.)
| | - Jeong Eon Lee
- Department of Breast Cancer Center, Samsung Medical Center, Seoul 06351, Republic of Korea;
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
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26
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Li B, Kwon C. Mesendodermal cells fail to contribute to heart formation following blastocyst injection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595392. [PMID: 38826381 PMCID: PMC11142170 DOI: 10.1101/2024.05.22.595392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Blastocyst complementation offers an opportunity for generating transplantable whole organs from donor sources. Pluripotent stem cells (PSCs) have traditionally served as the primary donor cells due to their ability to differentiate into any type of body cell. However, the use of PSCs raises ethical concerns, particularly regarding their uncontrollable differentiation potential to undesired cell lineages such as brain and germline cells. To address this issue, various strategies have been explored, including the use of genetically modified PSCs with restricted lineage potential or lineage-specified progenitor cells as donors. In this study, we tested whether nascent mesendodermal cells (MECs), which appear during early gastrulation, can be used as donor cells. To do this, we induced Bry-GFP+ MECs from mouse embryonic stem cells (ESCs) and introduced them into the blastocyst. While donor ESCs gave rise to various regions of embryos, including the heart, Bry-GFP+ MECs failed to contribute to the host embryos. This finding suggests that MECs, despite being specified from PSCs within a few days, lack the capacity to assimilate into the developing embryo.
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Affiliation(s)
- Biyi Li
- Division of Cardiology, Department of Medicine, Department of Biomedical Engineering, Department of Cell Biology, Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Department of Biomedical Engineering, Department of Cell Biology, Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
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27
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Worley J, Noh H, You D, Turunen MM, Ding H, Paull E, Griffin AT, Grunn A, Zhang M, Guillan K, Bush EC, Brosius SJ, Hibshoosh H, Mundi PS, Sims P, Dalerba P, Dela Cruz FS, Kung AL, Califano A. Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.562798. [PMID: 38798673 PMCID: PMC11118419 DOI: 10.1101/2023.11.08.562798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Tumors frequently harbor isogenic yet epigenetically distinct subpopulations of multi-potent cells with high tumor-initiating potential-often called Cancer Stem-Like Cells (CSLCs). These can display preferential resistance to standard-of-care chemotherapy. Single-cell analyses can help elucidate Master Regulator (MR) proteins responsible for governing the transcriptional state of these cells, thus revealing complementary dependencies that may be leveraged via combination therapy. Interrogation of single-cell RNA sequencing profiles from seven metastatic breast cancer patients, using perturbational profiles of clinically relevant drugs, identified drugs predicted to invert the activity of MR proteins governing the transcriptional state of chemoresistant CSLCs, which were then validated by CROP-seq assays. The top drug, the anthelmintic albendazole, depleted this subpopulation in vivo without noticeable cytotoxicity. Moreover, sequential cycles of albendazole and paclitaxel-a commonly used chemotherapeutic -displayed significant synergy in a patient-derived xenograft (PDX) from a TNBC patient, suggesting that network-based approaches can help develop mechanism-based combinatorial therapies targeting complementary subpopulations.
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Affiliation(s)
- Jeremy Worley
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Heeju Noh
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mikko M Turunen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Hongxu Ding
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pharmacy Practice & Science, College of Pharmacy, University of Arizona, Tucson, Arizona, USA 85721
| | - Evan Paull
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Aaron T Griffin
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Adina Grunn
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Mingxuan Zhang
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Kristina Guillan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erin C Bush
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Samantha J Brosius
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hanina Hibshoosh
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, USA 10032
| | - Prabhjot S Mundi
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
| | - Peter Sims
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Piero Dalerba
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, USA 10032
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Califano
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
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28
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Hosohama L, Tifrea DF, Nee K, Park SY, Wu J, Habowski AN, Van C, Seldin MM, Edwards RA, Waterman ML. Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591144. [PMID: 38712298 PMCID: PMC11071458 DOI: 10.1101/2024.04.25.591144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Several classification systems have been developed to define tumor subtypes in colorectal cancer (CRC). One system proposes that tumor heterogeneity derives in part from distinct cancer stem cell populations that co-exist as admixtures of varying proportions. However, the lack of single cell resolution has prohibited a definitive identification of these types of stem cells and therefore any understanding of how each influence tumor phenotypes. Here were report the isolation and characterization of two cancer stem cell subtypes from the SW480 CRC cell line. We find these cancer stem cells are oncogenic versions of the normal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations from intestinal crypts and that their gene signatures are consistent with the "Admixture" and other CRC classification systems. Using publicly available single cell RNA sequencing (scRNAseq) data from CRC patients, we determine that RSC and CBC cancer stem cells are commonly co-present in human CRC. To characterize influences on the tumor microenvironment, we develop subtype-specific xenograft models and we define their tumor microenvironments at high resolution via scRNAseq. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, undifferentiated, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization.
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Affiliation(s)
- Linzi Hosohama
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
| | - Delia F. Tifrea
- Department of Pathology & Laboratory Medicine, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
| | - Kevin Nee
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
| | - Sung Yun Park
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
| | - Jie Wu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
| | - Amber N. Habowski
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
| | - Cassandra Van
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
| | - Marcus M. Seldin
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
- Cancer Research Institute, University of California, Irvine, California
| | - Robert A. Edwards
- Department of Pathology & Laboratory Medicine, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
- Cancer Research Institute, University of California, Irvine, California
| | - Marian L. Waterman
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, California
- Chao Family Comprehensive Cancer Center, University of California, Irvine, California
- Cancer Research Institute, University of California, Irvine, California
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29
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Ning L, Quan C, Wang Y, Wu Z, Yuan P, Xie N. scRNA-seq characterizing the heterogeneity of fibroblasts in breast cancer reveals a novel subtype SFRP4 + CAF that inhibits migration and predicts prognosis. Front Oncol 2024; 14:1348299. [PMID: 38686196 PMCID: PMC11056562 DOI: 10.3389/fonc.2024.1348299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Cancer-associated fibroblasts (CAFs) are a diverse group of cells that significantly impact the tumor microenvironment and therapeutic responses in breast cancer (BC). Despite their importance, the comprehensive profile of CAFs in BC remains to be fully elucidated. Methods To address this gap, we utilized single-cell RNA sequencing (scRNA-seq) to delineate the CAF landscape within 14 BC normal-tumor paired samples. We further corroborated our findings by analyzing several public datasets, thereby validating the newly identified CAF subtype. Additionally, we conducted coculture experiments with BC cells to assess the functional implications of this CAF subtype. Results Our scRNA-seq analysis unveiled eight distinct CAF subtypes across five tumor and six adjacent normal tissue samples. Notably, we discovered a novel subtype, designated as SFRP4+ CAFs, which was predominantly observed in normal tissues. The presence of SFRP4+ CAFs was substantiated by two independent scRNA-seq datasets and a spatial transcriptomics dataset. Functionally, SFRP4+ CAFs were found to impede BC cell migration and the epithelial-mesenchymal transition (EMT) process by secreting SFRP4, thereby modulating the WNT signaling pathway. Furthermore, we established that elevated expression levels of SFRP4+ CAF markers correlate with improved survival outcomes in BC patients, yet paradoxically, they predict a diminished response to neoadjuvant chemotherapy in cases of triple-negative breast cancer. Conclusion This investigation sheds light on the heterogeneity of CAFs in BC and introduces a novel SFRP4+ CAF subtype that hinders BC cell migration. This discovery holds promise as a potential biomarker for refined prognostic assessment and therapeutic intervention in BC.
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Affiliation(s)
- Lvwen Ning
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chuntao Quan
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| | - Yue Wang
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhijie Wu
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| | - Peixiu Yuan
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
| | - Ni Xie
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
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30
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Mohammadi E, Dashti S, Shafizade N, Jin H, Zhang C, Lam S, Tahmoorespur M, Mardinoglu A, Sekhavati MH. Drug repositioning for immunotherapy in breast cancer using single-cell analysis. NPJ Syst Biol Appl 2024; 10:37. [PMID: 38589404 PMCID: PMC11001976 DOI: 10.1038/s41540-024-00359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Immunomodulatory peptides, while exhibiting potential antimicrobial, antifungal, and/or antiviral properties, can play a role in stimulating or suppressing the immune system, especially in pathological conditions like breast cancer (BC). Thus, deregulation of these peptides may serve as an immunotherapeutic strategy to enhance the immune response. In this meta-analysis, we utilized single-cell RNA sequencing data and known therapeutic peptides to investigate the deregulation of these peptides in malignant versus normal human breast epithelial cells. We corroborated our findings at the chromatin level using ATAC-seq. Additionally, we assessed the protein levels in various BC cell lines. Moreover, our in-house drug repositioning approach was employed to identify potential drugs that could positively impact the relapse-free survival of BC patients. Considering significantly deregulated therapeutic peptides and their role in BC pathology, our approach aims to downregulate B2M and SLPI, while upregulating PIGR, DEFB1, LTF, CLU, S100A7, and SCGB2A1 in BC epithelial cells through our drug repositioning pipeline. Leveraging the LINCS L1000 database, we propose BRD-A06641369 for B2M downregulation and ST-4070043 and BRD-K97926541 for SLPI downregulation without negatively affecting the MHC complex as a significantly correlated pathway with these two genes. Furthermore, we have compiled a comprehensive list of drugs for the upregulation of other selected immunomodulatory peptides. Employing an immunotherapeutic approach by integrating our drug repositioning pipeline with single-cell analysis, we proposed potential drugs and drug targets to fortify the immune system against BC.
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Affiliation(s)
- Elyas Mohammadi
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Samira Dashti
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Neda Shafizade
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Han Jin
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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31
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Reed AD, Pensa S, Steif A, Stenning J, Kunz DJ, Porter LJ, Hua K, He P, Twigger AJ, Siu AJQ, Kania K, Barrow-McGee R, Goulding I, Gomm JJ, Speirs V, Jones JL, Marioni JC, Khaled WT. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nat Genet 2024; 56:652-662. [PMID: 38548988 PMCID: PMC11018528 DOI: 10.1038/s41588-024-01688-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 02/09/2024] [Indexed: 04/17/2024]
Abstract
Here we use single-cell RNA sequencing to compile a human breast cell atlas assembled from 55 donors that had undergone reduction mammoplasties or risk reduction mastectomies. From more than 800,000 cells we identified 41 cell subclusters across the epithelial, immune and stromal compartments. The contribution of these different clusters varied according to the natural history of the tissue. Age, parity and germline mutations, known to modulate the risk of developing breast cancer, affected the homeostatic cellular state of the breast in different ways. We found that immune cells from BRCA1 or BRCA2 carriers had a distinct gene expression signature indicative of potential immune exhaustion, which was validated by immunohistochemistry. This suggests that immune-escape mechanisms could manifest in non-cancerous tissues very early during tumor initiation. This atlas is a rich resource that can be used to inform novel approaches for early detection and prevention of breast cancer.
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Affiliation(s)
- Austin D Reed
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sara Pensa
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Adi Steif
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jack Stenning
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Linsey J Porter
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Kui Hua
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Peng He
- EMBL European Bioinformatics Institute, Hinxton, UK
- Sanger Institute, Hinxton, UK
| | - Alecia-Jane Twigger
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Abigail J Q Siu
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Katarzyna Kania
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rachel Barrow-McGee
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Iain Goulding
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Jennifer J Gomm
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Valerie Speirs
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
- Aberdeen Cancer Centre, Aberdeen, UK
| | - J Louise Jones
- Breast Cancer Now Tissue Bank, Centre for Tumour Biology, Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, UK
| | - John C Marioni
- CRUK, Cambridge Institute, University of Cambridge, Cambridge, UK.
- EMBL European Bioinformatics Institute, Hinxton, UK.
- Sanger Institute, Hinxton, UK.
- Genentech, San Francisco, CA, USA.
| | - Walid T Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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32
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Pang L, Xiang F, Yang H, Shen X, Fang M, Li R, Long Y, Li J, Yu Y, Pang B. Single-cell integrative analysis reveals consensus cancer cell states and clinical relevance in breast cancer. Sci Data 2024; 11:289. [PMID: 38472225 DOI: 10.1038/s41597-024-03127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024] Open
Abstract
High heterogeneity and complex interactions of malignant cells in breast cancer has been recognized as a driver of cancer progression and therapeutic failure. However, complete understanding of common cancer cell states and their underlying driver factors remain scarce and challenging. Here, we revealed seven consensus cancer cell states recurring cross patients by integrative analysis of single-cell RNA sequencing data of breast cancer. The distinct biological functions, the subtype-specific distribution, the potential cells of origin and the interrelation of consensus cancer cell states were systematically elucidated and validated in multiple independent datasets. We further uncovered the internal regulons and external cell components in tumor microenvironments, which contribute to the consensus cancer cell states. Using the state-specific signature, we also inferred the abundance of cells with each consensus cancer cell state by deconvolution of large breast cancer RNA-seq cohorts, revealing the association of immune-related state with better survival. Our study provides new insights for the cancer cell state composition and potential therapeutic strategies of breast cancer.
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Affiliation(s)
- Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Fengyu Xiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Huan Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xinyue Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Ming Fang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Ran Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongjin Long
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jiali Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yonghuan Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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33
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Zorc M, Dolinar M, Dovč P. A Single-Cell Transcriptome of Bovine Milk Somatic Cells. Genes (Basel) 2024; 15:349. [PMID: 38540408 PMCID: PMC10970057 DOI: 10.3390/genes15030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 06/14/2024] Open
Abstract
The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The process of lactation in cows serves as an excellent model for studying the biological aspects of lactation with the aim of exploring the mechanistic base of this complex trait at the cellular level. In this study, we analyzed the milk transcriptome at the single-cell level by conducting scRNA-seq analysis on milk samples from two Holstein Friesian cows at mid-lactation (75 and 93 days) using the 10× Chromium platform. Cells were pelleted and fat was removed from milk by centrifugation. The cell suspension from each cow was loaded on separate channels, resulting in the recovery of 9313 and 14,544 cells. Library samples were loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument. After filtering at the cell and gene levels, a total of 7988 and 13,973 cells remained, respectively. We were able to reconstruct different cell types (milk-producing cells, progenitor cells, macrophages, monocytes, dendritic cells, T cells, B cells, mast cells, and neutrophils) in bovine milk. Our findings provide a valuable resource for identifying regulatory elements associated with various functions of the mammary gland such as lactation, tissue renewal, native immunity, protein and fat synthesis, and hormonal response.
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Affiliation(s)
| | | | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (M.Z.); (M.D.)
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34
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Tang L, Ye J. Commentary: Mammokine directs beige adipocytes to reserve energy for milk production in breast. Acta Pharm Sin B 2024; 14:1472-1476. [PMID: 38486985 PMCID: PMC10935006 DOI: 10.1016/j.apsb.2023.11.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 03/17/2024] Open
Affiliation(s)
- Lina Tang
- Metabolic Disease Research Center, Zhengzhou University Affiliated Zhengzhou Central Hospital, Zhengzhou 450007, China
| | - Jianping Ye
- Metabolic Disease Research Center, Zhengzhou University Affiliated Zhengzhou Central Hospital, Zhengzhou 450007, China
- Research Center for Basic Medicine, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
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35
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Monnier L, Cournède PH. A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. PLoS Comput Biol 2024; 20:e1011880. [PMID: 38386700 PMCID: PMC10914288 DOI: 10.1371/journal.pcbi.1011880] [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: 07/21/2023] [Revised: 03/05/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology produces an unprecedented resolution at the level of a unique cell, raising great hopes in medicine. Nevertheless, scRNA-seq data suffer from high variations due to the experimental conditions, called batch effects, preventing any aggregated downstream analysis. Adversarial Information Factorization provides a robust batch-effect correction method that does not rely on prior knowledge of the cell types nor a specific normalization strategy while being adapted to any downstream analysis task. It compares to and even outperforms state-of-the-art methods in several scenarios: low signal-to-noise ratio, batch-specific cell types with few cells, and a multi-batches dataset with imbalanced batches and batch-specific cell types. Moreover, it best preserves the relative gene expression between cell types, yielding superior differential expression analysis results. Finally, in a more complex setting of a Leukemia cohort, our method preserved most of the underlying biological information for each patient while aligning the batches, improving the clustering metrics in the aggregated dataset.
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Affiliation(s)
- Lily Monnier
- Paris-Saclay University, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), Gif-sur-Yvette, France
| | - Paul-Henry Cournède
- Paris-Saclay University, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), Gif-sur-Yvette, France
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36
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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37
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Doerfler R, Yerneni S, Newby A, Chaudhary N, Shu A, Fein K, Hofstatter Azambuja J, Whitehead KA. Characterization and comparison of human and mouse milk cells. PLoS One 2024; 19:e0297821. [PMID: 38295101 PMCID: PMC10830055 DOI: 10.1371/journal.pone.0297821] [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: 08/07/2023] [Accepted: 01/12/2024] [Indexed: 02/02/2024] Open
Abstract
Recent data has characterized human milk cells with unprecedented detail and provided insight into cell populations. While such analysis of freshly expressed human milk has been possible, studies of cell functionality within the infant have been limited to animal models. One commonly used animal model for milk research is the mouse; however, limited data are available describing the composition of mouse milk. In particular, the maternal cells of mouse milk have not been previously characterized in detail, in part due to the difficulty in collecting sufficient volumes of mouse milk. In this study, we have established a method to collect high volumes of mouse milk, isolate cells, and compare the cell counts and types to human milk. Surprisingly, we found that mouse milk cell density is three orders of magnitude higher than human milk. The cell types present in the milk of mice and humans are similar, broadly consisting of mammary epithelial cells and immune cells. These results provide a basis of comparison for mouse and human milk cells and will inform the most appropriate uses of mouse models for the study of human phenomena.
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Affiliation(s)
- Rose Doerfler
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Saigopalakrishna Yerneni
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Alexandra Newby
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Namit Chaudhary
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Ashley Shu
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Katherine Fein
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Juliana Hofstatter Azambuja
- Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Kathryn A. Whitehead
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
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38
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Xu K, Yu D, Zhang S, Chen L, Liu Z, Xie L. Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data. Genes (Basel) 2024; 15:100. [PMID: 38254989 PMCID: PMC10815467 DOI: 10.3390/genes15010100] [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: 12/23/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
The heterogeneity and intricate cellular architecture of complex cellular ecosystems play a crucial role in the progression and therapeutic response of cancer. Understanding the regulatory relationships of malignant cells at the invasive front of the tumor microenvironment (TME) is important to explore the heterogeneity of the TME and its role in disease progression. In this study, we inferred malignant cells at the invasion front by analyzing single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data of ER-positive (ER+) breast cancer patients. In addition, we developed a software pipeline for constructing intercellular gene regulatory networks (IGRNs), which help to reduce errors generated by single-cell communication analysis and increase the confidence of selected cell communication signals. Based on the constructed IGRN between malignant cells at the invasive front of the TME and the immune cells of ER+ breast cancer patients, we found that a high expression of the transcription factors FOXA1 and EZH2 played a key role in driving tumor progression. Meanwhile, elevated levels of their downstream target genes (ESR1 and CDKN1A) were associated with poor prognosis of breast cancer patients. This study demonstrates a bioinformatics workflow of combining scRNA-seq and ST data; in addition, the study provides the software pipelines for constructing IGRNs automatically (cIGRN). This strategy will help decipher cancer progression by revealing bidirectional signaling between invasive frontline malignant tumor cells and immune cells, and the selected signaling molecules in the regulatory network may serve as biomarkers for mechanism studies or therapeutic targets.
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Affiliation(s)
- Kun Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Dongshuo Yu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Siwen Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
| | - Zhenhao Liu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
| | - Lu Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, The Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (D.Y.); (S.Z.)
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Northey JJ, Hayward MK, Yui Y, Stashko C, Kai F, Mouw JK, Thakar D, Lakins JN, Ironside AJ, Samson S, Mukhtar RA, Hwang ES, Weaver VM. Mechanosensitive hormone signaling promotes mammary progenitor expansion and breast cancer risk. Cell Stem Cell 2024; 31:106-126.e13. [PMID: 38181747 PMCID: PMC11050720 DOI: 10.1016/j.stem.2023.12.002] [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: 06/01/2023] [Revised: 09/19/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Tissue stem-progenitor cell frequency has been implicated in tumor risk and progression, but tissue-specific factors linking these associations remain ill-defined. We observed that stiff breast tissue from women with high mammographic density, who exhibit increased lifetime risk for breast cancer, associates with abundant stem-progenitor epithelial cells. Using genetically engineered mouse models of elevated integrin mechanosignaling and collagen density, syngeneic manipulations, and spheroid models, we determined that a stiff matrix and high mechanosignaling increase mammary epithelial stem-progenitor cell frequency and enhance tumor initiation in vivo. Augmented tissue mechanics expand stemness by potentiating extracellular signal-related kinase (ERK) activity to foster progesterone receptor-dependent RANK signaling. Consistently, we detected elevated phosphorylated ERK and progesterone receptors and increased levels of RANK signaling in stiff breast tissue from women with high mammographic density. The findings link fibrosis and mechanosignaling to stem-progenitor cell frequency and breast cancer risk and causally implicate epidermal growth factor receptor-ERK-dependent hormone signaling in this phenotype.
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Affiliation(s)
- Jason J Northey
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mary-Kate Hayward
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yoshihiro Yui
- Research Institute, Nozaki Tokushukai Hospital, Tanigawa 2-10-50, Daito, Osaka 574-0074, Japan
| | - Connor Stashko
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA
| | - FuiBoon Kai
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N1N4, Canada; Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Janna K Mouw
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dhruv Thakar
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathon N Lakins
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alastair J Ironside
- Department of Pathology, Western General Hospital, NHS Lothian, Edinburgh EH42XU, UK
| | - Susan Samson
- UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rita A Mukhtar
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Valerie M Weaver
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
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40
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Minello A, Carreira A. BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele. J Mol Biol 2024; 436:168277. [PMID: 37714298 DOI: 10.1016/j.jmb.2023.168277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Since their discovery in the late 20th century, significant progress has been made in elucidating the functions of the tumor suppressor proteins BRCA1 and BRCA2. These proteins play vital roles in maintaining genome integrity, including DNA repair, replication fork protection, and chromosome maintenance. It is well-established that germline mutations in BRCA1 and BRCA2 increase the risk of breast and ovarian cancer; however, the precise mechanism underlying tumor formation in this context is not fully understood. Contrary to the long-standing belief that the loss of the second wild-type allele is necessary for tumor development, a growing body of evidence suggests that tumorigenesis can occur despite the presence of a single functional allele. This entails that heterozygosity in BRCA1/2 confers haploinsufficiency, where a single copy of the gene is not sufficient to fully suppress tumor formation. Here we provide an overview of the findings and the ongoing debate regarding BRCA haploinsufficiency. We further put out the challenges in studying this topic and discuss its potential relevance in the prevention and treatment of BRCA-related cancers.
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Affiliation(s)
- Anna Minello
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Aura Carreira
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France; Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid 28049, Spain.
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41
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Xi P, Liu S, Tang J, Wang X, Liu Y, Wang X, Hu S, Wang K, Li W, Cai Z, Shi H, Dai P. Single-cell transcriptomics reveals ferrimagnetic vortex iron oxide nanoring-mediated mild magnetic hyperthermia exerts antitumor effects by alleviating macrophage suppression in breast cancer. Biomed Pharmacother 2024; 170:115954. [PMID: 38039753 DOI: 10.1016/j.biopha.2023.115954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/13/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
The potential of Ferrimagnetic vortex iron oxide nanoring-mediated mild magnetic hyperthermia (FVIO-MHT) in solid tumor therapy has been demonstrated. However, the impact of FVIO-MHT on the tumor microenvironment (TME) remains unclear. This study utilized single-cell transcriptome sequencing to examine the alterations in the TME in response to FVIO-MHT in breast cancer. The results revealed the cellular composition within the tumor microenvironment (TME) was primarily modified due to a decrease in tumor cells and an increased infiltration of myeloid cells. Subsequently, an enhancement in active oxygen (ROS) metabolism was observed, indicating oxidative damage to tumor cells. Interestingly, FVIO-MHT reprogrammed the macrophages' phenotypes, as evidenced by alterations in the transcriptome characteristics associated with both classic and alternative activated phenotypes. And an elevated level of ROS generation and oxidative phosphorylation suggested that activated phagocytosis and inflammation occurred in macrophages. Additionally, cell-cell communication analysis revealed that FVIO-MHT attenuated the suppression between tumor cells and macrophages by inhibiting phagocytic checkpoint and macrophage migration inhibitory factor signaling pathways. Inhibition of B2m, an anti-phagocytosis checkpoint, could promote macrophage-mediated phagocytosis and significantly inhibit tumor growth. These data emphasize FVIO-MHT may promote the antitumor capabilities of macrophages by alleviating the suppression between tumor cells and macrophages.
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Affiliation(s)
- Pei Xi
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China; Shaanxi Lifegen Co., Ltd., Xi' an, China
| | - Shihui Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Jiaxuan Tang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Xun Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Yongkang Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Xinxin Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Shuwei Hu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Kaixuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Wang Li
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Zhiye Cai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China
| | - Hailong Shi
- School of Basic Medicine, Shaanxi University of Chinese Medicine, Xi'an-Xianyang New Economic Zone, 712046 Shaanxi, China.
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, 710069 Shaanxi, China; Shaanxi Lifegen Co., Ltd., Xi' an, China.
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42
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Pagnotta SM. Unsupervised Single-Cell Clustering with Asymmetric Within-Sample Transformation and Per-Cluster Supervised Features Selection. Methods Mol Biol 2024; 2812:155-168. [PMID: 39068361 DOI: 10.1007/978-1-0716-3886-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
This chapter shows applying the Asymmetric Within-Sample Transformation to single-cell RNA-Seq data matched with a previous dropout imputation. The asymmetric transformation is a special winsorization that flattens low-expressed intensities and preserves highly expressed gene levels. Before a standard hierarchical clustering algorithm, an intermediate step removes noninformative genes according to a threshold applied to a per-gene entropy estimate. Following the clustering, a time-intensive algorithm is shown to uncover the molecular features associated with each cluster. This step implements a resampling algorithm to generate a random baseline to measure up/downregulated significant genes. To this aim, we adopt a GLM model as implemented in DESeq2 package. We render the results in graphical mode. While the tools are standard heat maps, we introduce some data scaling to clarify the results' reliability.
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Affiliation(s)
- Stefano Maria Pagnotta
- Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy.
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Nale V, Chiodi A, Di Nanni N, Cifola I, Moscatelli M, Cocola C, Gnocchi M, Piscitelli E, Sula A, Zucchi I, Reinbold R, Milanesi L, Mezzelani A, Pelucchi P, Mosca E. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC Bioinformatics 2023; 24:445. [PMID: 38012590 PMCID: PMC10680269 DOI: 10.1186/s12859-023-05563-y] [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: 06/01/2022] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
INTRODUCTION Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data. RESULTS scMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics. CONCLUSIONS The analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.
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Affiliation(s)
- Valentina Nale
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alice Chiodi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ingrid Cifola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Marco Moscatelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Cinzia Cocola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Matteo Gnocchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Eleonora Piscitelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ada Sula
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ileana Zucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Rolland Reinbold
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alessandra Mezzelani
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Paride Pelucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
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Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
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45
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Kim H, Aliar K, Tharmapalan P, McCloskey CW, Kuttanamkuzhi A, Grünwald BT, Palomero L, Mahendralingam MJ, Waas M, Mer AS, Elliott MJ, Zhang B, Al-Zahrani KN, Langille ER, Parsons M, Narala S, Hofer S, Waterhouse PD, Hakem R, Haibe-Kains B, Kislinger T, Schramek D, Cescon DW, Pujana MA, Berman HK, Khokha R. Differential DNA damage repair and PARP inhibitor vulnerability of the mammary epithelial lineages. Cell Rep 2023; 42:113256. [PMID: 37847590 DOI: 10.1016/j.celrep.2023.113256] [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: 02/03/2023] [Revised: 09/02/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
It is widely assumed that all normal somatic cells can equally perform homologous recombination (HR) and non-homologous end joining in the DNA damage response (DDR). Here, we show that the DDR in normal mammary gland inherently depends on the epithelial cell lineage identity. Bioinformatics, post-irradiation DNA damage repair kinetics, and clonogenic assays demonstrated luminal lineage exhibiting a more pronounced DDR and HR repair compared to the basal lineage. Consequently, basal progenitors were far more sensitive to poly(ADP-ribose) polymerase inhibitors (PARPis) in both mouse and human mammary epithelium. Furthermore, PARPi sensitivity of murine and human breast cancer cell lines as well as patient-derived xenografts correlated with their molecular resemblance to the mammary progenitor lineages. Thus, mammary epithelial cells are intrinsically divergent in their DNA damage repair capacity and PARPi vulnerability, potentially influencing the clinical utility of this targeted therapy.
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Affiliation(s)
- Hyeyeon Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Kazeera Aliar
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Pirashaanthy Tharmapalan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Curtis W McCloskey
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Barbara T Grünwald
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Luis Palomero
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908 Barcelona, Catalonia, Spain
| | - Mathepan J Mahendralingam
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Matthew Waas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mitchell J Elliott
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Bowen Zhang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Khalid N Al-Zahrani
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Ellen R Langille
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael Parsons
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Swami Narala
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stefan Hofer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul D Waterhouse
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 2N2, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Daniel Schramek
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Miquel A Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908 Barcelona, Catalonia, Spain
| | - Hal K Berman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Rama Khokha
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 2N2, Canada.
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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47
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Walker BL, Nie Q. NeST: nested hierarchical structure identification in spatial transcriptomic data. Nat Commun 2023; 14:6554. [PMID: 37848426 PMCID: PMC10582109 DOI: 10.1038/s41467-023-42343-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023] Open
Abstract
Spatial gene expression in tissue is characterized by regions in which particular genes are enriched or depleted. Frequently, these regions contain nested inside them subregions with distinct expression patterns. Segmentation methods in spatial transcriptomic (ST) data extract disjoint regions maximizing similarity over the greatest number of genes, typically on a particular spatial scale, thus lacking the ability to find region-within-region structure. We present NeST, which extracts spatial structure through coexpression hotspots-regions exhibiting localized spatial coexpression of some set of genes. Coexpression hotspots identify structure on any spatial scale, over any possible subset of genes, and are highly explainable. NeST also performs spatial analysis of cell-cell interactions via ligand-receptor, identifying active areas de novo without restriction of cell type or other groupings, in both two and three dimensions. Through application on ST datasets of varying type and resolution, we demonstrate the ability of NeST to reveal a new level of biological structure.
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Affiliation(s)
- Benjamin L Walker
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, 92627, USA
- Department of Mathematics, University of California Irvine, Irvine, CA, 92627, USA
| | - Qing Nie
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, 92627, USA.
- Department of Mathematics, University of California Irvine, Irvine, CA, 92627, USA.
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92627, USA.
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48
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Wang H, Canasto-Chibuque C, Kim JH, Hohl M, Leslie C, Reis-Filho JS, Petrini JH. Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562529. [PMID: 37905095 PMCID: PMC10614814 DOI: 10.1101/2023.10.16.562529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The Mre11 complex (comprising Mre11, Rad50, Nbs1) is integral to the maintenance of genome stability. We previously showed that a hypomorphic Mre11 mutant mouse strain ( Mre11 ATLD1/ATLD1 ) was highly susceptible to oncogene induced breast cancer. Here we used a mammary organoid system to examine which Mre11 dependent responses are tumor suppressive. We found that Mre11 ATLD1/ATLD1 organoids exhibited an elevated interferon stimulated gene (ISG) signature and sustained changes in chromatin accessibility. This Mre11 ATLD1/ATLD1 phenotype depended on DNA binding of a nuclear innate immune sensor, IFI205. Ablation of Ifi205 in Mre11 ATLD1/ATLD1 organoids restored baseline and oncogene-induced chromatin accessibility patterns to those observed in WT . Implantation of Mre11 ATLD1/ATLD1 organoids and activation of oncogene led to aggressive metastatic breast cancer. This outcome was reversed in implanted Ifi205 -/- Mre11 ATLD1/ATLD1 organoids. These data reveal a connection between innate immune signaling and tumor suppression in mammary epithelium. Given the abundance of aberrant DNA structures that arise in the context of genome instability syndromes, the data further suggest that cancer predisposition in those contexts may be partially attributable to tonic innate immune transcriptional programs.
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49
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Niu M, Zhang Y, Luo J, Sinson JC, Thompson AM, Zong C. Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561356. [PMID: 37873375 PMCID: PMC10592685 DOI: 10.1101/2023.10.09.561356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Accurate detection of somatic mutations in single tumor cells is greatly desired as it allows us to quantify the single-cell mutation burden and construct the mutation-based phylogenetic tree. Here we developed scNanoSeq chemistry and profiled 842 single cells from 21 human breast cancer samples. The majority of the mutation-based phylogenetic trees comprise a characteristic stem evolution followed by the clonal sweep. We observed the subtype-dependent lengths in the stem evolution. To explain this phenomenon, we propose that the differences are related to different reprogramming required for different subtypes of breast cancer. Furthermore, we reason that the time that the tumor-initiating cell took to acquire the critical clonal-sweep-initiating mutation by random chance set the time limit for the reprogramming process. We refer to this model as a reprogramming and critical mutation co-timing (RCMC) subtype model. Next, in the sweeping clone, we observed that tumor cells undergo a branched evolution with rapidly decreasing selection. In the most recent clades, effectively neutral evolution has been reached, resulting in a substantially large number of mutational heterogeneities. Integrative analysis with 522-713X ultra-deep bulk whole genome sequencing (WGS) further validated this evolution mode. Mutation-based phylogenetic trees also allow us to identify the early branched cells in a few samples, whose phylogenetic trees support the gradual evolution of copy number variations (CNVs). Overall, the development of scNanoSeq allows us to unveil novel insights into breast cancer evolution.
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50
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Sahoo S, Ramu S, Nair MG, Pillai M, San Juan BP, Milioli HZ, Mandal S, Naidu CM, Mavatkar AD, Subramaniam H, Neogi AG, Chaffer CL, Prabhu JS, Somarelli JA, Jolly MK. Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.558960. [PMID: 37873432 PMCID: PMC10592858 DOI: 10.1101/2023.09.30.558960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. It manifests along multiple phenotypic axes and decoding the interconnections among these different axes is crucial to understand its molecular origins and to develop novel therapeutic strategies to control it. Here, we use multi-modal transcriptomic data analysis - bulk, single-cell and spatial transcriptomics - from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity - two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. These patterns were inherent in methylation profiles, suggesting an epigenetic crosstalk between EMT and lineage plasticity in breast cancer. Mathematical modelling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes recapitulate and thus elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and to identify possible interventions to restrict it.
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Affiliation(s)
- Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Madhumathy G Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
- Current affiliation: Feinberg School of Medicine, Northwestern University, Chicago, 60611, USA
| | - Beatriz P San Juan
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Chandrakala M Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Apoorva D Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Harini Subramaniam
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Arpita G Neogi
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Christine L Chaffer
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- University of New South Wales, UNSW Medicine, UNSW Sydney, NSW, 2052, Australia
| | - Jyothi S Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
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