1
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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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2
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Müller L, Di Benedetto S. Immunosenescence and Cytomegalovirus: Exploring Their Connection in the Context of Aging, Health, and Disease. Int J Mol Sci 2024; 25:753. [PMID: 38255826 PMCID: PMC10815036 DOI: 10.3390/ijms25020753] [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: 11/18/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Aging induces numerous physiological alterations, with immunosenescence emerging as a pivotal factor. This phenomenon has attracted both researchers and clinicians, prompting profound questions about its implications for health and disease. Among the contributing factors, one intriguing actor in this complex interplay is human cytomegalovirus (CMV), a member of the herpesvirus family. Latent CMV infection exerts a profound influence on the aging immune system, potentially contributing to age-related diseases. This review delves into the intricate relationship between immunosenescence and CMV, revealing how chronic viral infection impacts the aging immune landscape. We explore the mechanisms through which CMV can impact both the composition and functionality of immune cell populations and induce shifts in inflammatory profiles with aging. Moreover, we examine the potential role of CMV in pathologies such as cardiovascular diseases, cancer, neurodegenerative disorders, COVID-19, and Long COVID. This review underlines the importance of understanding the complex interplay between immunosenescence and CMV. It offers insights into the pathophysiology of aging and age-associated diseases, as well as COVID-19 outcomes among the elderly. By unraveling the connections between immunosenescence and CMV, we gain a deeper understanding of aging's remarkable journey and the profound role that viral infections play in transforming the human immune system.
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Affiliation(s)
- Ludmila Müller
- Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany
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3
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Jokela TA, Dane MA, Smith RL, Devlin KL, Shalabi S, Lopez JC, Miyano M, Stampfer MR, Korkola JE, Gray JW, Heiser LM, LaBarge MA. Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments. Cell Signal 2024; 113:110958. [PMID: 37935340 PMCID: PMC10696611 DOI: 10.1016/j.cellsig.2023.110958] [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: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023]
Abstract
Microenvironment signals are potent determinants of cell fate and arbiters of tissue homeostasis, however understanding how different microenvironment factors coordinately regulate cellular phenotype has been experimentally challenging. Here we used a high-throughput microenvironment microarray comprised of 2640 unique pairwise signals to identify factors that support proliferation and maintenance of primary human mammary luminal epithelial cells. Multiple microenvironment factors that modulated luminal cell number were identified, including: HGF, NRG1, BMP2, CXCL1, TGFB1, FGF2, PDGFB, RANKL, WNT3A, SPP1, HA, VTN, and OMD. All of these factors were previously shown to modulate luminal cell numbers in painstaking mouse genetics experiments, or were shown to have a role in breast cancer, demonstrating the relevance and power of our high-dimensional approach to dissect key microenvironmental signals. RNA-sequencing of primary epithelial and stromal cell lineages identified the cell types that express these signals and the cognate receptors in vivo. Cell-based functional studies confirmed which effects from microenvironment factors were reproducible and robust to individual variation. Hepatocyte growth factor (HGF) was the factor most robust to individual variation and drove expansion of luminal cells via cKit+ progenitor cells, which expressed abundant MET receptor. Luminal cells from women who are genetically high risk for breast cancer had significantly more MET receptor and may explain the characteristic expansion of the luminal lineage in those women. In ensemble, our approach provides proof of principle that microenvironment signals that control specific cellular states can be dissected with high-dimensional cell-based approaches.
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Affiliation(s)
- Tiina A Jokela
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Mark A Dane
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Rebecca L Smith
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Kaylyn L Devlin
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Sundus Shalabi
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; Faculty of Medicine, Arab American University of Palestine, Jenin, Palestine
| | - Jennifer C Lopez
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James E Korkola
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA.
| | - Mark A LaBarge
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; Center for Cancer Biomarkers Research (CCBIO), University of Bergen, Bergen, Norway; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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4
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Gray GK, Girnius N, Kuiken HJ, Henstridge AZ, Brugge JS. Single-cell and spatial analyses reveal a tradeoff between murine mammary proliferation and lineage programs associated with endocrine cues. Cell Rep 2023; 42:113293. [PMID: 37858468 PMCID: PMC10840493 DOI: 10.1016/j.celrep.2023.113293] [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: 05/25/2023] [Revised: 08/25/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Although distinct epithelial cell types have been distinguished in glandular tissues such as the mammary gland, the extent of heterogeneity within each cell type and the degree of endocrine control of this diversity across development are incompletely understood. By combining mass cytometry and cyclic immunofluorescence, we define a rich array of murine mammary epithelial cell subtypes associated with puberty, the estrous cycle, and sex. These subtypes are differentially proliferative and spatially segregate distinctly in adult versus pubescent glands. Further, we identify systematic suppression of lineage programs at the protein and RNA levels as a common feature of mammary epithelial expansion during puberty, the estrous cycle, and gestation and uncover a pervasive enrichment of ribosomal protein genes in luminal cells elicited specifically during progesterone-dominant expansionary periods. Collectively, these data expand our knowledge of murine mammary epithelial heterogeneity and connect endocrine-driven epithelial expansion with lineage suppression.
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Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; The Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hendrik J Kuiken
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Aylin Z Henstridge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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5
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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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6
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Senapati P, Miyano M, Sayaman RW, Basam M, Leung A, LaBarge MA, Schones DE. Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells. Genome Res 2023; 33:1229-1241. [PMID: 37463750 PMCID: PMC10547379 DOI: 10.1101/gr.277511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
A primary function of DNA methylation in mammalian genomes is to repress transposable elements (TEs). The widespread methylation loss that is commonly observed in cancer cells results in the loss of epigenetic repression of TEs. The aging process is similarly characterized by changes to the methylome. However, the impact of these epigenomic alterations on TE silencing and the functional consequences of this have remained unclear. To assess the epigenetic regulation of TEs in aging, we profiled DNA methylation in human mammary luminal epithelial cells (LEps)-a key cell lineage implicated in age-related breast cancers-from younger and older women. We report here that several TE subfamilies function as regulatory elements in normal LEps, and a subset of these display consistent methylation changes with age. Methylation changes at these TEs occurred at lineage-specific transcription factor binding sites, consistent with loss of lineage specificity. Whereas TEs mainly showed methylation loss, CpG islands (CGIs) that are targets of the Polycomb repressive complex 2 (PRC2) show a gain of methylation in aging cells. Many TEs with methylation loss in aging LEps have evidence of regulatory activity in breast cancer samples. We furthermore show that methylation changes at TEs impact the regulation of genes associated with luminal breast cancers. These results indicate that aging leads to DNA methylation changes at TEs that undermine the maintenance of lineage specificity, potentially increasing susceptibility to breast cancer.
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Affiliation(s)
- Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143-0981, USA
| | - Mudaser Basam
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
- Center for Cancer Biomarker Research, University of Bergen, 5021 Bergen, Norway
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA;
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
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7
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Kumar T, Nee K, Wei R, He S, Nguyen QH, Bai S, Blake K, Pein M, Gong Y, Sei E, Hu M, Casasent AK, Thennavan A, Li J, Tran T, Chen K, Nilges B, Kashikar N, Braubach O, Ben Cheikh B, Nikulina N, Chen H, Teshome M, Menegaz B, Javaid H, Nagi C, Montalvan J, Lev T, Mallya S, Tifrea DF, Edwards R, Lin E, Parajuli R, Hanson S, Winocour S, Thompson A, Lim B, Lawson DA, Kessenbrock K, Navin N. A spatially resolved single-cell genomic atlas of the adult human breast. Nature 2023; 620:181-191. [PMID: 37380767 DOI: 10.1038/s41586-023-06252-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
The adult human breast is comprised of an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue1-3. Although most previous studies have focused on the breast epithelial system4-6, many of the non-epithelial cell types remain understudied. Here we constructed the comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics study profiled 714,331 cells from 126 women, and 117,346 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data reveal abundant perivascular, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide a reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.
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Affiliation(s)
- Tapsi Kumar
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Nee
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Runmin Wei
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Siyuan He
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Quy H Nguyen
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Shanshan Bai
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kerrigan Blake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Math, Computational & Systems Biology, University of California, Irvine, Irvine, CA, USA
| | - Maren Pein
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Yanwen Gong
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Math, Computational & Systems Biology, University of California, Irvine, Irvine, CA, USA
| | - Emi Sei
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Min Hu
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Anna K Casasent
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jianzhuo Li
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Tuan Tran
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | | | - Hui Chen
- Department of Pathology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Mediget Teshome
- Department of Breast Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Brian Menegaz
- Department of Pathology and Immunology, Baylor Medical College, Houston, TX, USA
| | - Huma Javaid
- Department of Pathology and Immunology, Baylor Medical College, Houston, TX, USA
| | - Chandandeep Nagi
- Department of Pathology and Immunology, Baylor Medical College, Houston, TX, USA
| | - Jessica Montalvan
- Department of Pathology and Immunology, Baylor Medical College, Houston, TX, USA
| | - Tatyana Lev
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Math, Computational & Systems Biology, University of California, Irvine, Irvine, CA, USA
| | - Sharmila Mallya
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Delia F Tifrea
- Chao Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Robert Edwards
- Chao Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Erin Lin
- Chao Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Ritesh Parajuli
- Chao Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Summer Hanson
- Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | | | | | - Bora Lim
- Department of Medicine, Section of Hematology and Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Devon A Lawson
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
| | - Nicholas Navin
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
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8
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Liu Z, Liang Q, Ren Y, Guo C, Ge X, Wang L, Cheng Q, Luo P, Zhang Y, Han X. Immunosenescence: molecular mechanisms and diseases. Signal Transduct Target Ther 2023; 8:200. [PMID: 37179335 PMCID: PMC10182360 DOI: 10.1038/s41392-023-01451-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate and adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend to develop a characteristic inflammatory state that expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is a typical phenomenon linked to immunosenescence and it is considered the major risk factor for age-related diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, and epigenetic alterations are striking features of immunosenescence. Disturbed T-cell pools and chronic antigen stimulation mediate premature senescence of immune cells, and senescent immune cells develop a proinflammatory senescence-associated secretory phenotype that exacerbates inflammaging. Although the underlying molecular mechanisms remain to be addressed, it is well documented that senescent T cells and inflammaging might be major driving forces in immunosenescence. Potential counteractive measures will be discussed, including intervention of cellular senescence and metabolic-epigenetic axes to mitigate immunosenescence. In recent years, immunosenescence has attracted increasing attention for its role in tumor development. As a result of the limited participation of elderly patients, the impact of immunosenescence on cancer immunotherapy is unclear. Despite some surprising results from clinical trials and drugs, it is necessary to investigate the role of immunosenescence in cancer and other age-related diseases.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Qimeng Liang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 4500052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
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9
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Kumar T, Nee K, Wei R, He S, Nguyen QH, Bai S, Blake K, Gong Y, Pein M, Sei E, Hu M, Casasent A, Thennavan A, Li J, Tran T, Chen K, Nilges B, Kashikar N, Braubach O, Cheikh BB, Nikulina N, Chen H, Teshome M, Menegaz B, Javaid H, Nagi C, Montalvan J, Tifrea DF, Edwards R, Lin E, Parajuli R, Winocour S, Thompson A, Lim B, Lawson DA, Kessenbrock K, Navin N. A spatially resolved single cell genomic atlas of the adult human breast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.22.537946. [PMID: 37163043 PMCID: PMC10168262 DOI: 10.1101/2023.04.22.537946] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While previous studies have mainly focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics data profiled 535,941 cells from 62 women, and 120,024 nuclei from 20 women, identifying 11 major cell types and 53 cell states. These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Our spatial mapping using three technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells in the ducts and lobules, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide an unprecedented reference of adult normal breast tissue for studying mammary biology and disease states such as breast cancer.
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10
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Romaniello D, Gelfo V, Pagano F, Sgarzi M, Morselli A, Girone C, Filippini DM, D’Uva G, Lauriola M. IL-1 and senescence: Friends and foe of EGFR neutralization and immunotherapy. Front Cell Dev Biol 2023; 10:1083743. [PMID: 36712972 PMCID: PMC9877625 DOI: 10.3389/fcell.2022.1083743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Historically, senescence has been considered a safe program in response to multiple stresses in which cells undergo irreversible growth arrest. This process is characterized by morphological and metabolic changes, heterochromatin formation, and secretion of inflammatory components, known as senescence-associated secretory phenotype (SASP). However, recent reports demonstrated that anti-cancer therapy itself can stimulate a senescence response in tumor cells, the so-called therapy-induced senescence (TIS), which may represent a temporary bypass pathway that promotes drug resistance. In this context, several studies have shown that EGFR blockage, by TKIs or moAbs, promotes TIS by increasing IL-1 cytokine production, thus pushing cells into a "pseudo-senescent" state. Today, senotherapeutic agents are emerging as a potential strategy in cancer treatment thanks to their dual role in annihilating senescent cells and simultaneously preventing their awakening into a resistant and aggressive form. Here, we summarize classic and recent findings about the cellular processes driving senescence and SASP, and we provide a state-of-the-art of the anti-cancer strategies available so far that exploits the activation and/or blockade of senescence-based mechanisms.
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Affiliation(s)
- Donatella Romaniello
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola -Malpighi Polyclinic, Bologna, Italy
| | - Valerio Gelfo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola -Malpighi Polyclinic, Bologna, Italy
| | - Federica Pagano
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Michela Sgarzi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Alessandra Morselli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Cinzia Girone
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Daria Maria Filippini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy,Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Gabriele D’Uva
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola -Malpighi Polyclinic, Bologna, Italy,National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems (INBB), Bologna, Italy
| | - Mattia Lauriola
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy,Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola -Malpighi Polyclinic, Bologna, Italy,*Correspondence: Mattia Lauriola,
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11
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Cellular and molecular mechanisms of breast cancer susceptibility. Clin Sci (Lond) 2022; 136:1025-1043. [PMID: 35786748 DOI: 10.1042/cs20211158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022]
Abstract
There is a plethora of recognized risk factors for breast cancer (BC) with poorly understood or speculative biological mechanisms. The lack of prevention options highlights the importance of understanding the mechanistic basis of cancer susceptibility and finding new targets for breast cancer prevention. Until now, we have understood risk and cancer susceptibility primarily through the application of epidemiology and assessing outcomes in large human cohorts. Relative risks are assigned to various human behaviors and conditions, but in general the associations are weak and there is little understanding of mechanism. Aging is by far the greatest risk factor for BC, and there are specific forms of inherited genetic risk that are well-understood to cause BC. We propose that bringing focus to the biology underlying these forms of risk will illuminate biological mechanisms of BC susceptibility.
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12
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Ductal keratin 15 + luminal progenitors in normal breast exhibit a basal-like breast cancer transcriptomic signature. NPJ Breast Cancer 2022; 8:81. [PMID: 35821504 PMCID: PMC9276673 DOI: 10.1038/s41523-022-00444-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Normal breast luminal epithelial progenitors have been implicated as cell of origin in basal-like breast cancer, but their anatomical localization remains understudied. Here, we combine collection under the microscope of organoids from reduction mammoplasties and single-cell mRNA sequencing (scRNA-seq) of FACS-sorted luminal epithelial cells with multicolor imaging to profile ducts and terminal duct lobular units (TDLUs) and compare them with breast cancer subtypes. Unsupervised clustering reveals eleven distinct clusters and a differentiation trajectory starting with keratin 15+ (K15+) progenitors enriched in ducts. Spatial mapping of luminal progenitors is confirmed at the protein level by staining with critical duct markers. Comparison of the gene expression profiles of normal luminal cells with those of breast cancer subtypes suggests a strong correlation between normal breast ductal progenitors and basal-like breast cancer. We propose that K15+ basal-like breast cancers originate in ductal progenitors, which emphasizes the importance of not only lineages but also cellular position within the ductal-lobular tree.
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13
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Gray GK, Li CMC, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D'Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev Cell 2022; 57:1400-1420.e7. [PMID: 35617956 DOI: 10.1016/j.devcel.2022.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/23/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]
Abstract
The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.
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Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Carman Man-Chung Li
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jennifer M Rosenbluth
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Jia-Ren Lin
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Ron C J Schackmann
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Walter L Goh
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Kaitlin Moore
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Hana K Shapiro
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Shaolin Mei
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Kurt D'Andrea
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine L Nathanson
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter K Sorger
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Sandro Santagata
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA.
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14
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Delfarah A, Hartel NG, Zheng D, Yang J, Graham NA. Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells. J Proteome Res 2021; 20:5169-5179. [PMID: 34637314 DOI: 10.1021/acs.jproteome.1c00659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Senescence is a permanent cell cycle arrest that occurs in response to cellular stress and promotes age-related disease. Because senescence differs greatly depending on cell type and senescence inducer, continued progress in the characterization of senescent cells is needed. Here, we analyzed primary human mammary epithelial cells (HMECs), a model system for aging and cancer, using mass spectrometry-based proteomics. By integrating data from replicative senescence, immortalization by telomerase reactivation, and quiescence, we identified a robust proteomic signature of HMEC senescence consisting of 34 upregulated and 10 downregulated proteins. This approach identified known senescence biomarkers including β-galactosidase (GLB1) as well as novel senescence biomarkers including catechol O-methyltransferase (COMT), synaptic vesicle membrane protein VAT-1 homolog (VAT1), and plastin-1/3 (PLS1/PLS3). Gene ontology enrichment analysis demonstrated that senescent HMECs upregulated lysosomal proteins and downregulated RNA metabolic processes. In addition, a classification model based on our proteomic signature successfully discriminated proliferating and senescent HMECs at the transcriptional level. Finally, we found that the HMEC senescence signature was positively and negatively correlated with proteomic alterations in HMEC aging and breast cancer, respectively. Taken together, our results demonstrate the power of proteomics to identify cell type-specific signatures of senescence and advance the understanding of senescence in HMECs.
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Affiliation(s)
- Alireza Delfarah
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Nicolas G Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - DongQing Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Jesse Yang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States.,Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, United States
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15
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Hinz S, Manousopoulou A, Miyano M, Sayaman RW, Aguilera KY, Todhunter ME, Lopez JC, Sohn LL, Wang LD, LaBarge MA. Deep proteome profiling of human mammary epithelia at lineage and age resolution. iScience 2021; 24:103026. [PMID: 34522866 PMCID: PMC8426267 DOI: 10.1016/j.isci.2021.103026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/16/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
Age is the major risk factor in most carcinomas, yet little is known about how proteomes change with age in any human epithelium. We present comprehensive proteomes comprised of >9,000 total proteins and >15,000 phosphopeptides from normal primary human mammary epithelia at lineage resolution from ten women ranging in age from 19 to 68 years. Data were quality controlled and results were biologically validated with cell-based assays. Age-dependent protein signatures were identified using differential expression analyses and weighted protein co-expression network analyses. Upregulation of basal markers in luminal cells, including KRT14 and AXL, were a prominent consequence of aging. PEAK1 was identified as an age-dependent signaling kinase in luminal cells, which revealed a potential age-dependent vulnerability for targeted ablation. Correlation analyses between transcriptome and proteome revealed age-associated loss of proteostasis regulation. Age-dependent proteome changes in the breast epithelium identified heretofore unknown potential therapeutic targets for reducing breast cancer susceptibility.
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Affiliation(s)
- Stefan Hinz
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
| | - Antigoni Manousopoulou
- Departments of Pediatrics and ImmunoOncology, City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
| | - Rosalyn W. Sayaman
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kristina Y. Aguilera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | | | - Jennifer C. Lopez
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
| | - Lydia L. Sohn
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley 94720-1740, USA
| | - Leo D. Wang
- Departments of Pediatrics and ImmunoOncology, City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
- Center for Cancer and Aging Research, Duarte, USA
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16
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Zirbes A, Joseph J, Lopez JC, Sayaman RW, Basam M, Seewaldt VL, LaBarge MA. Changes in Immune Cell Types with Age in Breast are Consistent with a Decline in Immune Surveillance and Increased Immunosuppression. J Mammary Gland Biol Neoplasia 2021; 26:247-261. [PMID: 34341887 PMCID: PMC8566425 DOI: 10.1007/s10911-021-09495-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
A majority of breast cancers (BC) are age-related and we seek to determine what cellular and molecular changes occur in breast tissue with age that make women more susceptible to cancer initiation. Immune-epithelial cell interactions are important during mammary gland development and the immune system plays an important role in BC progression. The composition of human immune cell populations is known to change in peripheral blood with age and in breast tissue during BC progression. Less is known about changes in immune populations in normal breast tissue and how their interactions with mammary epithelia change with age. We quantified densities of T cells, B cells, and macrophage subsets in pathologically normal breast tissue from 122 different women who ranged in age from 24 to 74 years old. Donor-matched peripheral blood from a subset of 20 donors was analyzed by flow cytometry. Tissue immune cell densities and localizations relative to the epithelium were quantified in situ with machine learning-based image analyses of multiplex immunohistochemistry-stained tissue sections. In situ results were corroborated with flow cytometry analyses of peri-epithelial immune cells from primary breast tissue preparations and transcriptome analyses of public data from bulk tissue reduction mammoplasties. Proportions of immune cell subsets in breast tissue and donor-matched peripheral blood were not correlated. Density (cells/mm2) of T and B lymphocytes in situ decreased with age. T cells and macrophages preferentially localized near or within epithelial bilayers, rather than the intralobular stroma. M2 macrophage density was higher than M1 macrophage density and this difference was due to higher density of M2 in the intralobular stroma. Transcriptional signature analyses suggested age-dependent decline in adaptive immune cell populations and functions and increased innate immune cell activity. T cells and macrophages are so intimately associated with the epithelia that they are embedded within the bilayer, suggesting an important role for immune-epithelial cell interactions. Age-associated decreased T cell density in peri-epithelial regions, and increased M2 macrophage density in intralobular stroma suggests the emergence of a tissue microenvironment that is simultaneously immune-senescent and immunosuppressive with age.
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Affiliation(s)
- Arrianna Zirbes
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA
| | - Jesuchristopher Joseph
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Jennifer C Lopez
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Cancer Metabolism Training Program, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Mudaser Basam
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Victoria L Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA.
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.
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17
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Shalabi SF, Miyano M, Sayaman RW, Lopez JC, Jokela TA, Todhunter ME, Hinz S, Garbe JC, Stampfer MR, Kessenbrock K, Seewaldt VE, LaBarge MA. Evidence for accelerated aging in mammary epithelia of women carrying germline BRCA1 or BRCA2 mutations. NATURE AGING 2021; 1:838-849. [PMID: 35187501 PMCID: PMC8849557 DOI: 10.1038/s43587-021-00104-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During aging in the human mammary gland, luminal epithelial cells lose lineage fidelity by expressing markers normally expressed in myoepithelial cells. We hypothesize that loss of lineage fidelity is a general manifestation of epithelia that are susceptible to cancer initiation. In the present study, we show that histologically normal breast tissue from younger women who are susceptible to breast cancer, as a result of harboring a germline mutation in BRCA1, BRCA2 or PALB2 genes, exhibits hallmarks of accelerated aging. These include proportionately increased luminal epithelial cells that acquired myoepithelial markers, decreased proportions of myoepithelial cells and a basal differentiation bias or failure of differentiation of cKit+ progenitors. High-risk luminal and myoepithelial cells are transcriptionally enriched for genes of the opposite lineage, inflammatory- and cancer-related pathways. We have identified breast-aging hallmarks that reflect a convergent biology of cancer susceptibility, regardless of the specific underlying genetic or age-dependent risk or the associated breast cancer subtype.
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Affiliation(s)
- Sundus F Shalabi
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA.,Medical Research Center, Al-Quds University, Jerusalem, Palestine
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Cancer Metabolism Training Program, City of Hope, Duarte, CA, USA.,Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer C Lopez
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Tiina A Jokela
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Michael E Todhunter
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Stefan Hinz
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - James C Garbe
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kai Kessenbrock
- Biological Chemistry Department, University of California, Irvine, CA, USA
| | - Victoria E Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Cancer Metabolism Training Program, City of Hope, Duarte, CA, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Center for Cancer and Aging, City of Hope, Duarte, CA, USA.,Center for Cancer Biomarkers Research, University of Bergen, Bergen, Norway
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18
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Virtanen S, Schulte R, Stingl J, Caldas C, Shehata M. High-throughput surface marker screen on primary human breast tissues reveals further cellular heterogeneity. Breast Cancer Res 2021; 23:66. [PMID: 34120626 PMCID: PMC8201685 DOI: 10.1186/s13058-021-01444-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 05/31/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Normal human breast tissues are a heterogeneous mix of epithelial and stromal subtypes in different cell states. Delineating the spectrum of cellular heterogeneity will provide new insights into normal cellular properties within the breast tissue that might become dysregulated in the initial stages of cancer. Investigation of surface marker expression provides a valuable approach to resolve complex cell populations. However, the majority of cell surface maker expression of primary breast cells have not been investigated. METHODS To determine the differences in expression of a range of uninvestigated cell surface markers between the normal breast cell subpopulations, primary human breast cells were analysed using high-throughput flow cytometry for the expression of 242 cell surface proteins in conjunction with EpCAM/CD49f staining. RESULTS We identified 35 surface marker proteins expressed on normal breast epithelial and/or stromal subpopulations that were previously unreported. We also show multiple markers were equally expressed in all cell populations (e.g. CD9, CD59, CD164) while other surface markers were confirmed to be enriched in different cell lineages: CD24, CD227 and CD340 in the luminal compartment, CD10 and CD90 in the basal population, and CD34 and CD140b on stromal cells. CONCLUSIONS Our dataset of CD marker expression in the normal breast provides better definition for breast cellular heterogeneity.
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Affiliation(s)
- Siru Virtanen
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Reiner Schulte
- Cambridge Institute for Medical Research, Cambridge University, Cambridge, CB2 0XY, UK
| | - John Stingl
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Carlos Caldas
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Mona Shehata
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK.
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19
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Twigger AJ, Khaled WT. Mammary gland development from a single cell 'omics view. Semin Cell Dev Biol 2021; 114:171-185. [PMID: 33810979 PMCID: PMC8158430 DOI: 10.1016/j.semcdb.2021.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/09/2021] [Accepted: 03/21/2021] [Indexed: 02/06/2023]
Abstract
Understanding the complexity and heterogeneity of mammary cell subpopulations is vital to delineate the mechanisms behind breast cancer development, progression and prevention. Increasingly sophisticated tools for investigating these cell subtypes has led to the development of a greater understanding of these cell subtypes, complex interplay of certain subtypes and their developmental potential. Of note, increasing accessibility and affordability of single cell technologies has led to a plethora of studies being published containing data from mammary cell subtypes and their differentiation potential in both mice and human data sets. Here, we review the different types of single cell technologies and how they have been used to improve our understanding of mammary gland development.
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Affiliation(s)
- Alecia-Jane Twigger
- Department of Pharmacology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
| | - Walid T Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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20
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Fresques T, LaBarge MA. <PE-AT>Contributions of Yap and Taz dysfunction to breast cancer initiation, progression, and aging-related susceptibility. ACTA ACUST UNITED AC 2021; 1:5-18. [PMID: 33693435 DOI: 10.1002/aac2.12011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Yap and Taz are co-transcription factors that have been implicated in the development of many cancers. Here, we review the literature that analyzes the function of Yap/Taz in normal breast and breast cancer contexts. Our review of the literature suggests that that Yap and Taz are involved in breast cancer and Taz, in particular, is involved in the triple negative subtype. Nevertheless, the precise contexts in which Yap/Taz contribute to specific breast cancer phenotypes remains unclear. Indeed, Yap/Taz dysregulation acts differentially and in multiple epithelial cell types during early breast cancer progression. We propose Yap/Taz activation promotes breast cancer phenotypes in breast cancer precursor cells. Further, Yap dysregulation as a result of aging in breast tissue may result in microenvironments that increase the fitness of breast cancer precursor cells relative to the normal epithelia. <PE-FRONTEND>.
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Affiliation(s)
- Tara Fresques
- Beckman Research Institute at City of Hope, City of Hope National Medical Center, Duarte, CA USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, City of Hope National Medical Center, Duarte, CA USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Center for Cancer Biomarkers Research, University of Bergen, Norway
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21
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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22
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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23
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Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing. Cell Rep 2020; 33:108566. [PMID: 33378681 PMCID: PMC7898263 DOI: 10.1016/j.celrep.2020.108566] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Aging is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations in the mammary gland. Here, we leverage high-throughput single-cell RNA sequencing to generate a detailed transcriptomic atlas of young and aged murine mammary tissues. By analyzing epithelial, stromal, and immune cells, we identify age-dependent alterations in cell proportions and gene expression, providing evidence that suggests alveolar maturation and physiological decline. The analysis also uncovers potential pro-tumorigenic mechanisms coupled to the age-associated loss of tumor suppressor function and change in microenvironment. In addition, we identify a rare, age-dependent luminal population co-expressing hormone-sensing and secretory-alveolar lineage markers, as well as two macrophage populations expressing distinct gene signatures, underscoring the complex heterogeneity of the mammary epithelia and stroma. Collectively, this rich single-cell atlas reveals the effects of aging on mammary physiology and can serve as a useful resource for understanding aging-associated cancer risk. Using single-cell RNA-sequencing, Li et al. compare mammary epithelia and stroma in young and aged mice. Age-dependent changes at cell and gene levels provide evidence suggesting alveolar maturation, functional deterioration, and potential pro-tumorigenic and inflammatory alterations. Additionally, identification of heterogeneous luminal and macrophage subpopulations underscores the complexity of mammary lineages.
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24
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Pelissier Vatter FA, Lucotti S, Zhang H. Recent Advances in Experimental Models of Breast Cancer Exosome Secretion, Characterization and Function. J Mammary Gland Biol Neoplasia 2020; 25:305-317. [PMID: 33351162 DOI: 10.1007/s10911-020-09473-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer (BC) is responsible for 15% of all the cancer deaths among women in the USA. The tumor microenvironment (TME) has the potential to act as a driver of breast cancer progression and metastasis. The TME is composed of stromal cells within an extracellular matrix and soluble cytokines, chemokines and extracellular vesicles and nanoparticles that actively influence cell behavior. Extracellular vesicles include exosomes, microvesicles and large oncosomes that orchestrate fundamental processes during tumor progression through direct interaction with target cells. Long before tumor cell spread to future metastatic sites, tumor-secreted exosomes enter the circulation and establish distant pre-metastatic niches, hospitable and permissive milieus for metastatic colonization. Emerging evidence suggests that breast cancer exosomes promote tumor progression and metastasis by inducing vascular leakiness, angiogenesis, invasion, immunomodulation and chemoresistance. Exosomes are found in almost all physiological fluids including plasma, urine, saliva, and breast milk, providing a valuable resource for the development of non-invasive cancer biomarkers. Here, we review work on the role of exosomes in breast cancer progression and metastasis, and describe the most recent advances in models of exosome secretion, isolation, characterization and functional analysis. We highlight the potential applications of plasma-derived exosomes as predictive biomarkers for breast cancer diagnosis, prognosis and therapy monitoring. We finally describe the therapeutic approaches of exosomes in breast cancer.
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Affiliation(s)
- Fanny A Pelissier Vatter
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA.
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Haiying Zhang
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
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25
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Lian J, Yue Y, Yu W, Zhang Y. Immunosenescence: a key player in cancer development. J Hematol Oncol 2020; 13:151. [PMID: 33168037 PMCID: PMC7653700 DOI: 10.1186/s13045-020-00986-z] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Immunosenescence is a process of immune dysfunction that occurs with age and includes remodeling of lymphoid organs, leading to changes in the immune function of the elderly, which is closely related to the development of infections, autoimmune diseases, and malignant tumors. T cell-output decline is an important feature of immunosenescence as well as the production of senescence-associated secretory phenotype, increased glycolysis, and reactive oxygen species. Senescent T cells exhibit abnormal phenotypes, including downregulation of CD27, CD28, and upregulation of CD57, killer cell lectin-like receptor subfamily G, Tim-3, Tight, and cytotoxic T-lymphocyte-associated protein 4, which are tightly related to malignant tumors. The role of immunosenescence in tumors is sophisticated: the many factors involved include cAMP, glucose competition, and oncogenic stress in the tumor microenvironment, which can induce the senescence of T cells, macrophages, natural killer cells, and dendritic cells. Accordingly, these senescent immune cells could also affect tumor progression. In addition, the effect of immunosenescence on the response to immune checkpoint blocking antibody therapy so far is ambiguous due to the low participation of elderly cancer patients in clinical trials. Furthermore, many other senescence-related interventions could be possible with genetic and pharmacological methods, including mTOR inhibition, interleukin-7 recombination, and NAD+ activation. Overall, this review aims to highlight the characteristics of immunosenescence and its impact on malignant tumors and immunotherapy, especially the future directions of tumor treatment through senescence-focused strategies.
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Affiliation(s)
- Jingyao Lian
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450052, Henan, China
| | - Ying Yue
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450052, Henan, China.,Clinical Laboratory, Henan Medical College Hospital Workers, Zhengzhou, 450000, Henan, China
| | - Weina Yu
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450052, Henan, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China. .,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450052, Henan, China.
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26
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Engelsen AST, Wnuk-Lipinska K, Bougnaud S, Pelissier Vatter FA, Tiron C, Villadsen R, Miyano M, Lotsberg ML, Madeleine N, Panahandeh P, Dhakal S, Tan TZ, Peters SD, Grøndal S, Aziz SM, Nord S, Herfindal L, Stampfer MR, Sørlie T, Brekken RA, Straume O, Halberg N, Gausdal G, Thiery JP, Akslen LA, Petersen OW, LaBarge MA, Lorens JB. AXL Is a Driver of Stemness in Normal Mammary Gland and Breast Cancer. iScience 2020; 23:101649. [PMID: 33103086 PMCID: PMC7578759 DOI: 10.1016/j.isci.2020.101649] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
The receptor tyrosine kinase AXL is associated with epithelial plasticity in several solid tumors including breast cancer and AXL-targeting agents are currently in clinical trials. We hypothesized that AXL is a driver of stemness traits in cancer by co-option of a regulatory function normally reserved for stem cells. AXL-expressing cells in human mammary epithelial ducts co-expressed markers associated with multipotency, and AXL inhibition abolished colony formation and self-maintenance activities while promoting terminal differentiation in vitro. Axl-null mice did not exhibit a strong developmental phenotype, but enrichment of Axl + cells was required for mouse mammary gland reconstitution upon transplantation, and Axl-null mice had reduced incidence of Wnt1-driven mammary tumors. An AXL-dependent gene signature is a feature of transcriptomes in basal breast cancers and reduced patient survival irrespective of subtype. Our interpretation is that AXL regulates access to epithelial plasticity programs in MaSCs and, when co-opted, maintains acquired stemness in breast cancer cells.
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Affiliation(s)
- Agnete S T Engelsen
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy Cancer Campus Grand Paris, 94800 Villejuif, France
| | | | - Sebastien Bougnaud
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
| | - Fanny A Pelissier Vatter
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
| | - Crina Tiron
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - René Villadsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Copenhagen N 2200, Denmark
| | - Masaru Miyano
- Biolgical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91910, USA
| | - Maria L Lotsberg
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
| | - Noëlly Madeleine
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Pouda Panahandeh
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Sushil Dhakal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Tuan Zea Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | | | - Sturla Grøndal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Sura M Aziz
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Silje Nord
- Department of Cancer Research, Oslo University Hospital, 0310 Oslo, Norway
| | - Lars Herfindal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Martha R Stampfer
- Biolgical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Therese Sørlie
- Department of Cancer Research, Oslo University Hospital, 0310 Oslo, Norway
| | - Rolf A Brekken
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Oddbjørn Straume
- Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Department of Oncology and Medical Physics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Gro Gausdal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Jean Paul Thiery
- Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy Cancer Campus Grand Paris, 94800 Villejuif, France.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, A-STAR, Singapore 138673, Singapore.,Bioland Laboratory, Guangzhou Regenerative Medicine and Health, Bio-island, Guangzhou, 510320, China
| | - Lars A Akslen
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Ole W Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Copenhagen N 2200, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, Copenhagen, Copenhagen N 2200, Denmark
| | - Mark A LaBarge
- Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Biolgical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91910, USA
| | - James B Lorens
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
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27
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Wei X, Lu Y, Zhang X, Chen ML, Wang JH. Recent advances in single-cell ultra-trace analysis. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Rosenbluth JM, Schackmann RCJ, Gray GK, Selfors LM, Li CMC, Boedicker M, Kuiken HJ, Richardson A, Brock J, Garber J, Dillon D, Sachs N, Clevers H, Brugge JS. Organoid cultures from normal and cancer-prone human breast tissues preserve complex epithelial lineages. Nat Commun 2020; 11:1711. [PMID: 32249764 PMCID: PMC7136203 DOI: 10.1038/s41467-020-15548-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, organoid technology has been used to generate a large repository of breast cancer organoids. Here we present an extensive evaluation of the ability of organoid culture technology to preserve complex stem/progenitor and differentiated cell types via long-term propagation of normal human mammary tissues. Basal/stem and luminal progenitor cells can differentiate in culture to generate mature basal and luminal cell types, including ER+ cells that have been challenging to maintain in culture. Cells associated with increased cancer risk can also be propagated. Single-cell analyses of matched organoid cultures and native tissues by mass cytometry for 38 markers provide a higher resolution representation of the multiple mammary epithelial cell types in the organoids, and demonstrate that protein expression patterns of the tissue of origin can be preserved in culture. These studies indicate that organoid cultures provide a valuable platform for studies of mammary differentiation, transformation, and breast cancer risk. Organoid technology has enabled the generation of several breast cancer organoids. Here, the authors combine propagation of normal human mammary tissues with mass cytometry to evaluate the ability of organoid culture technologies to preserve stem cells and differentiated cell types.
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Affiliation(s)
- Jennifer M Rosenbluth
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Ron C J Schackmann
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - G Kenneth Gray
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Carman Man-Chung Li
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Mackenzie Boedicker
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Hendrik J Kuiken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Andrea Richardson
- Department of Pathology, Brigham & Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Jane Brock
- Department of Pathology, Brigham & Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Judy Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham & Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Norman Sachs
- Hubrecht Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
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29
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Lotsberg ML, Wnuk-Lipinska K, Terry S, Tan TZ, Lu N, Trachsel-Moncho L, Røsland GV, Siraji MI, Hellesøy M, Rayford A, Jacobsen K, Ditzel HJ, Vintermyr OK, Bivona TG, Minna J, Brekken RA, Baguley B, Micklem D, Akslen LA, Gausdal G, Simonsen A, Thiery JP, Chouaib S, Lorens JB, Engelsen AST. AXL Targeting Abrogates Autophagic Flux and Induces Immunogenic Cell Death in Drug-Resistant Cancer Cells. J Thorac Oncol 2020; 15:973-999. [PMID: 32018052 PMCID: PMC7397559 DOI: 10.1016/j.jtho.2020.01.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/29/2019] [Accepted: 01/19/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Acquired cancer therapy resistance evolves under selection pressure of immune surveillance and favors mechanisms that promote drug resistance through cell survival and immune evasion. AXL receptor tyrosine kinase is a mediator of cancer cell phenotypic plasticity and suppression of tumor immunity, and AXL expression is associated with drug resistance and diminished long-term survival in a wide range of malignancies, including NSCLC. METHODS We aimed to investigate the mechanisms underlying AXL-mediated acquired resistance to first- and third-generation small molecule EGFR tyrosine kinase inhibitors (EGFRi) in NSCLC. RESULTS We found that EGFRi resistance was mediated by up-regulation of AXL, and targeting AXL reduced reactivation of the MAPK pathway and blocked onset of acquired resistance to long-term EGFRi treatment in vivo. AXL-expressing EGFRi-resistant cells revealed phenotypic and cell signaling heterogeneity incompatible with a simple bypass signaling mechanism, and were characterized by an increased autophagic flux. AXL kinase inhibition by the small molecule inhibitor bemcentinib or siRNA mediated AXL gene silencing was reported to inhibit the autophagic flux in vitro, bemcentinib treatment blocked clonogenicity and induced immunogenic cell death in drug-resistant NSCLC in vitro, and abrogated the transcription of autophagy-associated genes in vivo. Furthermore, we found a positive correlation between AXL expression and autophagy-associated gene signatures in a large cohort of human NSCLC (n = 1018). CONCLUSION Our results indicate that AXL signaling supports a drug-resistant persister cell phenotype through a novel autophagy-dependent mechanism and reveals a unique immunogenic effect of AXL inhibition on drug-resistant NSCLC cells.
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Affiliation(s)
- Maria L Lotsberg
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Katarzyna Wnuk-Lipinska
- Department of Biomedicine, University of Bergen, Bergen, Norway; BerGenBio ASA, Bergen, Norway
| | - Stéphane Terry
- INSERM UMR 1186, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ning Lu
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Laura Trachsel-Moncho
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Gro V Røsland
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | | | | | - Austin Rayford
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Kirstine Jacobsen
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Henrik J Ditzel
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark; Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Olav K Vintermyr
- Department of Pathology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Trever G Bivona
- Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - John Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Surgery, Pharmacology and Internal Medicine, UT Southwestern Medical Center, Dallas, Texas
| | - Rolf A Brekken
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Surgery, Pharmacology and Internal Medicine, UT Southwestern Medical Center, Dallas, Texas
| | - Bruce Baguley
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jean Paul Thiery
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; INSERM UMR 1186, Gustave Roussy, Université Paris-Saclay, Villejuif, France; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Biomedical Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, A-STAR, Singapore; Guangzhou Institutes of Biomedicine and Health, Guangzhou, People's Republic of China; Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, Hong Kong University, Hong Kong
| | - Salem Chouaib
- Department of Pathology, Haukeland University Hospital, Bergen, Norway; Thumbay Research Institute for Precision Medicine, GMU Ajman, United Arab Emirates
| | - James B Lorens
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Agnete Svendsen Tenfjord Engelsen
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway; INSERM UMR 1186, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
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30
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Turner OC, Aeffner F, Bangari DS, High W, Knight B, Forest T, Cossic B, Himmel LE, Rudmann DG, Bawa B, Muthuswamy A, Aina OH, Edmondson EF, Saravanan C, Brown DL, Sing T, Sebastian MM. Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology. Toxicol Pathol 2019; 48:277-294. [DOI: 10.1177/0192623319881401] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Toxicologic pathology is transitioning from analog to digital methods. This transition seems inevitable due to a host of ongoing social and medical technological forces. Of these, artificial intelligence (AI) and in particular machine learning (ML) are globally disruptive, rapidly growing sectors of technology whose impact on the long-established field of histopathology is quickly being realized. The development of increasing numbers of algorithms, peering ever deeper into the histopathological space, has demonstrated to the scientific community that AI pathology platforms are now poised to truly impact the future of precision and personalized medicine. However, as with all great technological advances, there are implementation and adoption challenges. This review aims to define common and relevant AI and ML terminology, describe data generation and interpretation, outline current and potential future business cases, discuss validation and regulatory hurdles, and most importantly, propose how overcoming the challenges of this burgeoning technology may shape toxicologic pathology for years to come, enabling pathologists to contribute even more effectively to answering scientific questions and solving global health issues. [Box: see text]
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Affiliation(s)
- Oliver C. Turner
- Novartis, Novartis Institutes for Biomedical Research, Preclinical Safety, East Hanover, NJ, USA
| | - Famke Aeffner
- Amgen Inc, Research, Comparative Biology and Safety Sciences, San Francisco, CA, USA
| | | | - Wanda High
- High Preclinical Pathology Consulting, Rochester, NY, USA
| | - Brian Knight
- Boehringer Ingelheim Pharmaceuticals Incorporated, Nonclinical Drug Safety, Ridgefield, CT, USA
| | | | - Brieuc Cossic
- Roche, Pharmaceutical Research and Early Development (pRED), Roche Innovation Center, Basel, Switzerland
| | - Lauren E. Himmel
- Division of Animal Care, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | | | - Elijah F. Edmondson
- Pathology/Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, NIH, Frederick, MD, USA
| | - Chandrassegar Saravanan
- Novartis, Novartis Institutes for Biomedical Research, Preclinical Safety, Cambridge, MA, USA
| | | | - Tobias Sing
- Novartis, Novartis Institutes for Biomedical Research, NIBR Informatics, Basel, Switzerland
| | - Manu M. Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
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31
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Fresques T, Zirbes A, Shalabi S, Samson S, Preto S, Stampfer MR, LaBarge MA. Breast Tissue Biology Expands the Possibilities for Prevention of Age-Related Breast Cancers. Front Cell Dev Biol 2019; 7:174. [PMID: 31555644 PMCID: PMC6722426 DOI: 10.3389/fcell.2019.00174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022] Open
Abstract
Preventing breast cancer before it is able to form is an ideal way to stop breast cancer. However, there are limited existing options for prevention of breast cancer. Changes in the breast tissue resulting from the aging process contribute to breast cancer susceptibility and progression and may therefore provide promising targets for prevention. Here, we describe new potential targets, immortalization and inflammaging, that may be useful for prevention of age-related breast cancers. We also summarize existing studies of warfarin and metformin, current drugs used for non-cancerous diseases, that also may be repurposed for breast cancer prevention.
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Affiliation(s)
- Tara Fresques
- Department of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Arrianna Zirbes
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Center for Cancer and Aging Research, Beckman Research Institute at City of Hope, Duarte, CA, United States
| | - Sundus Shalabi
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Center for Cancer and Aging Research, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Medical Research Center, Al-Quds University, Jerusalem, Palestine
| | - Susan Samson
- Breast Science Advocacy Core, Breast Oncology Program, University of California, San Francisco, San Francisco, CA, United States
| | | | - Martha R Stampfer
- Department of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mark A LaBarge
- Department of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Center for Cancer and Aging Research, Beckman Research Institute at City of Hope, Duarte, CA, United States
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32
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Lam VK, Nguyen T, Phan T, Chung BM, Nehmetallah G, Raub CB. Machine Learning with Optical Phase Signatures for Phenotypic Profiling of Cell Lines. Cytometry A 2019; 95:757-768. [PMID: 31008570 DOI: 10.1002/cyto.a.23774] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/22/2019] [Accepted: 04/03/2019] [Indexed: 12/29/2022]
Abstract
Robust and reproducible profiling of cell lines is essential for phenotypic screening assays. The goals of this study were to determine robust and reproducible optical phase signatures of cell lines for classification with machine learning and to correlate optical phase parameters to motile behavior. Digital holographic microscopy (DHM) reconstructed phase maps of cells from two pairs of cancer and non-cancer cell lines. Seventeen image parameters were extracted from each cell's phase map, used for linear support vector machine learning, and correlated to scratch wound closure and Boyden chamber chemotaxis. The classification accuracy was between 90% and 100% for the six pairwise cell line comparisons. Several phase parameters correlated with wound closure rate and chemotaxis across the four cell lines. The level of cell confluence in culture affected phase parameters in all cell lines tested. Results indicate that optical phase features of cell lines are a robust set of quantitative data of potential utility for phenotypic screening and prediction of motile behavior. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Van K Lam
- Department of Biomedical Engineering, The Catholic University of America, Washington, DC
| | - Thanh Nguyen
- Department of Electrical Engineering and Computer Science, The Catholic University of America, Washington, DC
| | - Thuc Phan
- Department of Electrical Engineering and Computer Science, The Catholic University of America, Washington, DC
| | - Byung-Min Chung
- Department of Biology, The Catholic University of America, Washington, DC
| | - George Nehmetallah
- Department of Electrical Engineering and Computer Science, The Catholic University of America, Washington, DC
| | - Christopher B Raub
- Department of Biomedical Engineering, The Catholic University of America, Washington, DC
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33
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Abstract
CITRUS is a supervised machine learning algorithm designed to analyze single cell data, identify cell populations, and identify changes in the frequencies or functional marker expression patterns of those populations that are significantly associated with an outcome. The algorithm is a black box that includes steps to cluster cell populations, characterize these populations, and identify the significant characteristics. This chapter describes how to optimize the use of CITRUS by combining it with upstream and downstream data analysis and visualization tools.
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34
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Lee JK, Bloom J, Zubeldia-Plazaola A, Garbe JC, Stampfer MR, LaBarge MA. Different culture media modulate growth, heterogeneity, and senescence in human mammary epithelial cell cultures. PLoS One 2018; 13:e0204645. [PMID: 30273377 PMCID: PMC6166958 DOI: 10.1371/journal.pone.0204645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 08/16/2018] [Indexed: 02/07/2023] Open
Abstract
The ability to culture normal human mammary epithelial cells (HMEC) greatly facilitates experiments that seek to understand both normal mammary cell biology and the many differences between normal and abnormal human mammary epithelia. To maximize in vivo relevance, the primary cell culture conditions should maintain cells in states that resemble in vivo as much as possible. Towards this goal, we compared the properties of HMEC strains from two different reduction mammoplasty tissues that were grown in parallel using different media and culture conditions. Epithelial organoids were initiated into three different media: two commonly used serum-free-media, MCDB 170-type (e.g. MEGM) and WIT-P, and a low stress media, M87A. Growth, lineage heterogeneity, p16 protein expression, and population doublings to senescence were measured for each culture condition. MCDB 170 caused rapid senescence and loss of heterogeneity within 2 to 3 passages, but some cultures went through the 1 to 2 month process of selection to generate clonal finite post-selection post-stasis cells. WIT-P caused impressive expansion of luminal cells in 2nd passage followed by their near complete disappearance by passage 4 and senescence shortly thereafter. M87A supported as much as twice the number of population doublings compared to either serum-free medium, and luminal and myoepithelial cells were present for as many as 8 passages. Thus, of the three media compared, WIT-P and MCDB 170 imposed rapid senescence and loss of lineage heterogeneity, phenotypes consistent with cells maintained in high-stress conditions, while M87A supported cultures that maintained multiple lineages and robust growth for up to 60 population doublings. In conjunction with previous studies examining the molecular properties of cultures grown in these media, we conclude that M87A medium is most able to support long-term culture of multiple lineages similar to in vivo conditions, thereby facilitating investigations of normal HMEC biology relevant to the mammary gland in situ.
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Affiliation(s)
- Jonathan K. Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Jessica Bloom
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
| | | | - James C. Garbe
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Martha R. Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail: (MAL); (MRS)
| | - Mark A. LaBarge
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
- * E-mail: (MAL); (MRS)
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