Dissecting the mammary gland one cell at a time

PPML-Omics: A privacy-preserving federated machine learning method protects patients' privacy in omic data

Modern machine learning models toward various tasks with omic data analysis give rise to threats of privacy leakage of patients involved in those datasets. Here, we proposed a secure and privacy-preserving machine learning method (PPML-Omics) by designing a decentralized differential private federated learning algorithm. We applied PPML-Omics to analyze data from three sequencing technologies and addressed the privacy concern in three major tasks of omic data under three representative deep learning models. We examined privacy breaches in depth through privacy attack experiments and demonstrated that PPML-Omics could protect patients' privacy. In each of these applications, PPML-Omics was able to outperform methods of comparison under the same level of privacy guarantee, demonstrating the versatility of the method in simultaneously balancing the privacy-preserving capability and utility in omic data analysis. Furthermore, we gave the theoretical proof of the privacy-preserving capability of PPML-Omics, suggesting the first mathematically guaranteed method with robust and generalizable empirical performance in protecting patients' privacy in omic data.

Demystifying Breast Disease Markers

Breast imaging radiologists regularly perform image-guided biopsies of suspicious breast lesions based on features that are associated with a likelihood of malignancy ranging from 2% to greater than 95% (Breast Imaging Reporting and Data System categories 4 and 5). As diagnostic partners, pathologists perform histopathologic assessment of these tissue samples to confirm a diagnosis. Correlating the imaging findings with the histopathologic results is an integral aspect of multidisciplinary breast care. Assessment of radiologic-pathologic concordance is vital in guiding appropriate management, as it enables identification of discordant results, minimizing the chance of misdiagnosis. Undersampling can lead to false-negative results, with the frequencies of false-negative diagnoses varying on the basis of multiple factors, including biopsy type (eg, core needle, vacuum-assisted needle), needle gauge, and type of lesion sampled at biopsy (ie, mass, calcifications, asymmetry, architectural distortion). Improving a radiologist's knowledge of macroscopic and microscopic breast anatomy and more common breast diseases and their expected imaging findings ensures more accurate radiologic-pathologic correlation and management recommendations. The histopathologic and molecular characteristics of biopsy-sampled breast lesions aid in making an accurate diagnosis. Hematoxylin-eosin staining provides critical morphologic details, whereas immunohistochemical staining enables molecular characterization of many benign and malignant lesions, which is critical for tailored treatment. The authors review commonly encountered benign and malignant breast diseases, their corresponding histopathologic phenotypes, and the histopathologic markers that are essential to clinching the diagnosis of these entities. As part of a multidisciplinary team that provides optimal patient care, radiologists should be knowledgeable of the foundations of histopathologic diagnosis and the implications for patient management to ensure appropriate radiologic-pathologic concordance. ©RSNA, 2023 Quiz questions for this article are available in the supplemental material.

Mature white adipocyte plasticity during mammary gland remodelling and cancer

Mammary gland growth and differentiation predominantly rely on stromal-epithelial cellular communication. Specifically, mammary adipocytes play a crucial role in ductal morphogenesis, as well as in the proliferation and differentiation of mammary epithelial cells. The process of lactation entails a reduction in the levels of white adipose tissue associated with the MG, allowing for the expansion of milk-producing epithelial cells. Subsequently, during involution and the regression of the milk-producing unit, adipocyte layers resurface, occupying the vacated space. This dynamic phenomenon underscores the remarkable plasticity and expansion of adipose tissue. Traditionally considered terminally differentiated, adipocytes have recently been found to exhibit plasticity in certain contexts. Unraveling the significance of this cell type within the MG could pave the way for novel approaches to reduce the risk of breast cancer and enhance lactation performance. Moreover, a comprehensive understanding of adipocyte trans- and de-differentiation processes holds promise for the development of innovative therapeutic interventions targeting cancer, fibrosis, obesity, type 2 diabetes, and other related diseases. Additionally, adipocytes may find utility in the realm of regenerative medicine. This review article provides a comprehensive examination of recent advancements in our understanding of MG remodelling, with a specific focus on the tissue-specific functions of adipocytes and their role in the development of cancer. By synthesizing current knowledge in this field, it aims to consolidate our understanding of adipocyte biology within the context of mammary gland biology, thereby fostering further research and discovery in this vital area.

Automated Classification of Breast Cancer Across the Spectrum of ERBB2 Expression Focusing on Heterogeneous Tumors With Low Human Epidermal Growth Factor Receptor 2 Expression

PURPOSE

Although pharmaceutical companies conduct clinical trials of novel human epidermal growth factor receptor 2 (HER2)-low-directed drugs, diagnosing HER2-low cancer by immunohistochemistry (IHC) and in situ hybridization (ISH) remains challenging. This study investigates the performance of first-in-kind computerized intelligence to classify samples across gene expression levels and differentiate HER2-low tumors.

MATERIALS AND METHODS

We classified 251 samples: 142 primary invasive breast cancers (IBCs), 75 ductal carcinomas in situ (DCIS), and 34 mammaplasties (reference) using mRNA expression data from the QuantiGene Plex 2.0 assay. We used g3mclass probabilistic software to assess the number of classes in the assay data, the mean and the variance in each class, diagnostic cutoffs, and the prevalence of each class in the study population.

RESULTS

HER2-low (IHC score of 1+ or 2+/ISH-) accounted for 31% of IBC. First, we discovered that HER2-low tumors were represented by cases with normal ERBB2 transcript levels that were expected to produce physiologic levels of HER2 (70%) and cases with abnormally upregulated unamplified ERBB2 (30%). We termed the latter cancers ERBB2-up as they do not meet the standard definitions for ERBB2 overexpression and amplification. Second, HER2-low IBC classified as ERBB2-up had not only abnormally increased luminal growth and adhesion markers (ERBB2, ESR1, PGR, IGF1R, VAV2, VAV3, KRT8, CDH1) but also downregulated myoepithelial marker (KRT5). The vascularization (RAP1 and C3G), immune cell infiltration (VAV1), and mesenchymal transition (CDH2) markers were dysregulated. Finally, in the independent cohort of DCIS, 40% of HER2-low DCIS shared similar traits with HER2-low IBC except for rare downregulation of KRT5 and no change in C3G, VAV1, and CDH2.

CONCLUSION

We demonstrated how innovative bioinformatic tools could help diagnose cancer across the spectrum of ERBB2 expression to aid decision making for HER2-low.

Fur removal promotes an earlier expression of involution-related genes in mammary gland of lactating mice

Peak lactation occurs when milk production is at its highest. The factors limiting peak lactation performance have been subject of intense debate. Milk production at peak lactation appears limited by the capacity of lactating females to dissipate body heat generated as a by-product of processing food and producing milk. As a result, manipulations that enhance capacity to dissipate body heat (such as fur removal) increase peak milk production. We investigated the potential correlates of shaving-induced increases in peak milk production in laboratory mice. By transcriptomic profiling of the mammary gland, we searched for the mechanisms underlying experimentally increased milk production and its consequences for mother-young conflict over weaning, manifested by advanced or delayed involution of mammary gland. We demonstrated that shaving-induced increases in milk production were paradoxically linked to reduced expression of some milk synthesis-related genes. Moreover, the mammary glands of shaved mice had a gene expression profile indicative of earlier involution relative to unshaved mice. Once provided with enhanced capacity to dissipate body heat, shaved mice were likely to rear their young to independence faster than unshaved mothers.

Conflict, violence, and warfare among early farmers in Northwestern Europe

Bioarchaeological evidence of interpersonal violence and early warfare presents important insights into conflict in past societies. This evidence is critical for understanding the motivations for violence and its effects on opposing and competing individuals and groups across time and space. Selecting the Neolithic of northwestern Europe as an area for study, the present paper examines the variation and societal context for the violence recorded in the human skeletal remains from this region as one of the most important elements of human welfare. Compiling data from various sources, it becomes apparent that violence was endemic in Neolithic Europe, sometimes reaching levels of intergroup hostilities that ended in the utter destruction of entire communities. While the precise comparative quantification of healed and unhealed trauma remains a fundamental problem, patterns emerge that see conflict likely fostered by increasing competition between settled and growing communities, e.g., for access to arable land for food production. The further development of contextual information is paramount in order to address hypotheses on the motivations, origins, and evolution of violence as based on the study of human remains, the most direct indicator for actual small- and large-scale violence.

Intramammary rapamycin administration to calves induces epithelial stem cell self-renewal and latent cell proliferation and milk protein expression

Mammary epithelial stem cells differentiate to create the basal and luminal layers of the gland. Inducing the number of differentiating bovine mammary stem cells may provide compensating populations for the milk-producing cells that die during lactation. Inhibition of mTOR activity by rapamycin signals self-renewal of intestinal stem cells, with similar consequences in the mouse mammary gland and in bovine mammary implants maintained in mice. The implementation of these results in farm animals for better mammary development and production was studied in 3-month-old calves. mTOR activity decreased by ~50% in mammary epithelial cells subjected to 3-week rapamycin administration, with no negative consequences on mammary morphology or β-casein expression. Subsequently, stem cell self-renewal was induced, reflected by a higher propagation rate of cultures from rapamycin-treated glands compared to respective controls and higher expression of selected markers. Followed by 4-day estrogen and progesterone administration, rapamycin significantly induced proliferation rate. Higher numbers of basal and luminal PCNA⁺ cells were detected in small ducts near the elongating sites as compared to large ducts, in which only luminal cells were affected. Rapamycin administration resulted in induction of individual milk protein genes’ expression, which was negatively correlated to their endogenous levels. The inductive effect of rapamycin on luminal cell number was confirmed in organoid cultures, but milk protein expression decreased, probably due to lack of oscillation in rapamycin levels. In conclusion, intramammary rapamycin administration is an effective methodology to reduce mTOR activity in bovine mammary epithelial cells and consequently, induce stem cell self-renewal. The latent positive effect of rapamycin on epithelial cell proliferation and its potential to improve milk protein expression in calves may have beneficial implications for mature cows.

Integration of Single-Cell Transcriptomics With a High Throughput Functional Screening Assay to Resolve Cell Type, Growth Kinetics, and Stemness Heterogeneity Within the Comma-1D Cell Line

Cell lines are one of the most frequently implemented model systems in life sciences research as they provide reproducible high throughput testing. Differentiation of cell cultures varies by line and, in some cases, can result in functional modifications within a population. Although research is increasingly dependent on these in vitro model systems, the heterogeneity within cell lines has not been thoroughly investigated. Here, we have leveraged high throughput single-cell assays to investigate the Comma-1D mouse cell line that is known to differentiate in culture. Using scRNASeq and custom single-cell phenotype assays, we resolve the clonal heterogeneity within the referenced cell line on the genomic and functional level. We performed a cohesive analysis of the transcriptome of 5,195 sequenced cells, of which 85.3% of the total reads successfully mapped to the mm10-3.0.0 reference genome. Across multiple gene expression analysis pipelines, both luminal and myoepithelial lineages were observed. Deep differential gene expression analysis revealed eight subclusters identified as luminal progenitor, luminal differentiated, myoepithelial differentiated, and fibroblast subpopulations-suggesting functional clustering within each lineage. Gene expression of published mammary stem cell (MaSC) markers Epcam, Cd49f, and Sca-1 was detected across the population, with 116 (2.23%) sequenced cells expressing all three markers. To gain insight into functional heterogeneity, cells with patterned MaSC marker expression were isolated and phenotypically investigated through a custom single-cell high throughput assay. The comparison of growth kinetics demonstrates functional heterogeneity within each cell cluster while also illustrating significant limitations in current cell isolation methods. We outlined the upstream use of our novel automated cell identification platform-to be used prior to single-cell culture-for reduced cell stress and improved rare cell identification and capture. Through compounding single-cell pipelines, we better reveal the heterogeneity within Comma-1D to identify subpopulations with specific functional characteristics.

Induced mammary cancer in rat models: pathogenesis, genetics, and relevance to female breast cancer

Mammary cancer, or breast cancer in women, is a polygenic disease with a complex etiopathogenesis. While much remains elusive regarding its origin, it is well established that chemical carcinogens and endogenous estrogens contribute significantly to the initiation and progression of this disease. Rats have been useful models to study induced mammary cancer. They develop mammary tumors with comparable histopathology to humans and exhibit differences in resistance or susceptibility to mammary cancer depending on strain. While some rat strains (e.g., Sprague-Dawley) readily form mammary tumors following treatment with the chemical carcinogen, 7,12-dimethylbenz[a]-anthracene (DMBA), other strains (e.g., Copenhagen) are resistant to DMBA-induced mammary carcinogenesis. Genetic linkage in inbred strains has identified strain-specific quantitative trait loci (QTLs) affecting mammary tumors, via mechanisms that act together to promote or attenuate, and include 24 QTLs controlling the outcome of chemical induction, 10 QTLs controlling the outcome of estrogen induction, and 4 QTLs controlling the outcome of irradiation induction. Moreover, and based on shared factors affecting mammary cancer etiopathogenesis between rats and humans, including orthologous risk regions between both species, rats have served as useful models for identifying methods for breast cancer prediction and treatment. These studies in rats, combined with alternative animal models that more closely mimic advanced stages of breast cancer and/or human lifestyles, will further improve our understanding of this complex disease.

NRG1/ERBB3/ERBB2 Axis Triggers Anchorage-Independent Growth of Basal-like/Triple-Negative Breast Cancer Cells

Simple Summary

Breast cancer is a heterogeneous disease, categorized into distinct subgroups with different clinical prognoses and treatment strategies. This study aimed to evaluate the role of ERBB3 in different molecular subtypes of breast cancers. Despite ERBB3/HER3 and its partner ERBB2/HER2 showing low expression levels in basal-like/triple-negative breast cancers, stratification of basal-like patients according to ERBB3 mRNA expression levels highlighted a correlation between higher ERBB3 levels and shorter relapse-free patients’ survival. In vitro analyses unveiled that the activation of the NRG1/ERBB3/ERBB2 axis robustly induces anchorage-independent growth of basal-like/triple-negative breast cancer cellular models, without significant effects on cell proliferation, differentiation, and migration in adhesion. Overall, our data suggest that ERBB2/ERBB3 plays an oncogenic role in basal-like/triple-negative breast cancer patients, suggesting its neutralization as a therapeutic strategy for these breast cancer subtypes, which today have very limited treatment opportunities.

Abstract

ERBB3, also known as HER3, is a tyrosine kinase transmembrane receptor of the ERBB family. Upon binding to neuregulin 1 (NRG1), ERBB3 preferentially dimerizes with HER2 (ERBB2), in turn inducing aggressive features in several cancer types. The analysis of a dataset of breast cancer patients unveiled that higher ERBB3 mRNA expression correlates with shorter relapse-free survival in basal-like breast cancers, despite low ERBB3 expression in this breast cancer subtype. Administration of neuregulin 1 beta (NRG1β) significantly affected neither cellular proliferation nor the basal migratory ability of basal-like/triple-negative quasi-normal MCF10A breast cells, cultured in mono-layer conditions. Furthermore, no significant regulation in cell morphology or in the expression of basal/myoepithelial and luminal markers was observed upon stimulation with NRG1β. In non-adherent conditions, NRG1β administration to MCF10A cells did not significantly influence cell survival; however, it robustly induced cell growth as spheroids (3D growth). Intriguingly, a remarkable upregulation of ERBB3 and ERBB2 protein abundance was observed in 3D compared to 2D cell cultures, and NRG1β-induced 3D cell growth was efficiently prevented by the anti-HER2 monoclonal antibody pertuzumab. Similar results were obtained by the analysis of basal-like/triple-negative breast cancer cellular models, MDA-MB-468 and MDA-MB-231 cells, in which NRG1β induced anchorage-independent cell growth that in turn was prevented or reduced by the simultaneous administration of anti-HER2 neutralizing antibodies. Finally, the ability of pertuzumab in suppressing NRG1β-induced 3D growth was also evaluated and confirmed in MCF10A engineered with HER2-overexpression. We suggest that the NRG1/ERBB3/ERBB2 pathway promotes the anchorage-independent growth of basal-like breast cancer cells. Importantly, we provide evidence that ERBB2 neutralization, in particular by pertuzumab, robustly inhibits this process. Our results pave the way towards the development of novel anticancer strategies for basal-like breast cancer patients based on the interception of the NRG1/ERBB3/ERBB2 signaling axis.

Single-cell RNA profiling identifies diverse cellular responses to EWSR1/FLI1 downregulation in Ewing sarcoma cells

BACKGROUND

The EWSR1/FLI1 gene fusion is the most common rearrangement leading to cell transformation in Ewing sarcoma (ES). Previous studies have indicated that expression at the cellular level is heterogeneous, and that levels of expression may oscillate, conferring different cellular characteristics. In ES the role of EWSR1/FLI1 in regulating subpopulation dynamics is currently unknown.

METHODS

We used siRNA to transiently suppress EWSR1/FLI1 expression and followed population dynamics using both single cell expression profiling, CyTOF and functional assays to define characteristics of exponentially growing ES cells and of ES cells in which EWSR1/FLI1 had been downregulated. Novel transcriptional states with distinct features were assigned using random forest feature selection in combination with machine learning. Cells isolated from ES xenografts in immune-deficient mice were interrogated to determine whether characteristics of specific subpopulations of cells in vitro could be identified. Stem-like characteristics were assessed by primary and secondary spheroid formation in vitro, and invasion/motility was determined for each identified subpopulation. Autophagy was determined by expression profiling, cell sorting and immunohistochemical staining.

RESULTS

We defined a workflow to study EWSR1/FLI1 driven transcriptional states and phenotypes. We tracked EWSR1/FLI1 dependent proliferative activity over time to discover sources of intra-tumoral diversity. Single-cell RNA profiling was used to compare expression profiles in exponentially growing populations (si-Control) or in two dormant populations (D1, D2) in which EWSR1/FLI1 had been suppressed. Three distinct transcriptional states were uncovered contributing to ES intra-heterogeneity. Our predictive model identified ~1% cells in a dormant-like state and ~ 2-4% cells with stem-like and neural stem-like features in an exponentially proliferating ES cell line and in ES xenografts. Following EWSR1/FLI1 knockdown, cells re-entering the proliferative cycle exhibited greater stem-like properties, whereas for those cells remaining quiescent, FAM134B-dependent dormancy may provide a survival mechanism.

CONCLUSIONS

We show that time-dependent changes induced by suppression of oncogenic EWSR1/FLI1 expression induces dormancy, with different subpopulation dynamics. Cells re-entering the proliferative cycle show enhanced stem-like characteristics, whereas those remaining dormant for prolonged periods appear to survive through autophagy. Cells with these characteristics identified in exponentially growing cell populations and in tumor xenografts may confer drug resistance and could potentially contribute to metastasis.

Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis

The female mammary epithelium undergoes reorganization during development, pregnancy, and menopause, linking higher risk with breast cancer development. To characterize these periods of complex remodeling, here we report integrated 50 K mouse and 24 K human mammary epithelial cell atlases obtained by single-cell RNA sequencing, which covers most lifetime stages. Our results indicate a putative trajectory that originates from embryonic mammary stem cells which differentiates into three epithelial lineages (basal, luminal hormone-sensing, and luminal alveolar), presumably arising from unipotent progenitors in postnatal glands. The lineage-specific genes infer cells of origin of breast cancer using The Cancer Genome Atlas data and single-cell RNA sequencing of human breast cancer, as well as the association of gland reorganization to different breast cancer subtypes. This comprehensive mammary cell gene expression atlas ( https://mouse-mammary-epithelium-integrated.cells.ucsc.edu ) presents insights into the impact of the internal and external stimuli on the mammary epithelium at an advanced resolution.

The molecular basis of mammary gland development and epithelial differentiation

Our understanding of the molecular events underpinning the development of mammalian organ systems has been increasing rapidly in recent years. With the advent of new and improved next-generation sequencing methods, we are now able to dig deeper than ever before into the genomic and epigenomic events that play critical roles in determining the fates of stem and progenitor cells during the development of an embryo into an adult. In this review, we detail and discuss the genes and pathways that are involved in mammary gland development, from embryogenesis, through maturation into an adult gland, to the role of pregnancy signals in directing the terminal maturation of the mammary gland into a milk producing organ that can nurture the offspring. We also provide an overview of the latest research in the single-cell genomics of mammary gland development, which may help us to understand the lineage commitment of mammary stem cells (MaSCs) into luminal or basal epithelial cells that constitute the mammary gland. Finally, we summarize the use of 3D organoid cultures as a model system to study the molecular events during mammary gland development. Our increased investigation of the molecular requirements for normal mammary gland development will advance the discovery of targets to predict breast cancer risk and the development of new breast cancer therapies.

Mammary gland adipocytes in lactation cycle, obesity and breast cancer

The mammary gland (MG) is an exocrine gland present in female mammals responsible for the production and secretion of milk during the process of lactation. It is mainly composed by epithelial cells and adipocytes. Among the features that make the MG unique there are 1) its highly plastic properties displayed during pregnancy, lactation and involution (all steps belonging to the lactation cycle) and 2) its requirement to grow in close association with adipocytes which are absolutely necessary to ensure MG's proper development at puberty and remodeling during the lactation cycle. Although MG adipocytes play such a critical role for the gland development, most of the studies have focused on its epithelial component only, leaving the role of the neighboring adipocytes largely unexplored. In this review we aim to describe evidences regarding MG's adipocytes role and properties in physiologic conditions (gland development and lactation cycle), obesity and breast cancer, emphasizing the existing gaps in the literature which deserve further investigation.

Mammary gland development from a single cell 'omics view

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.

Antioxidative Molecules in Human Milk and Environmental Contaminants

Breastfeeding provides overall beneficial health to the mother-child dyad and is universally recognized as the preferred feeding mode for infants up to 6-months and beyond. Human milk provides immuno-protection and supplies nutrients and bioactive compounds whose concentrations vary with lactation stage. Environmental and dietary factors potentially lead to excessive chemical exposure in critical windows of development such as neonatal life, including lactation. This review discusses current knowledge on these environmental and dietary contaminants and summarizes the known effects of these chemicals in human milk, taking into account the protective presence of antioxidative molecules. Particular attention is given to short- and long-term effects of these contaminants, considering their role as endocrine disruptors and potential epigenetic modulators. Finally, we identify knowledge gaps and indicate potential future research directions.

Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland

The developing mammary gland depends on several transcription-dependent networks to define cellular identities and differentiation trajectories. Recent technological advancements that allow for single-cell profiling of gene expression have provided an initial picture into the epithelial cellular heterogeneity across the diverse stages of gland maturation. Still, a deeper dive into expanded molecular signatures would improve our understanding of the diversity of mammary epithelial and non-epithelial cellular populations across different tissue developmental stages, mouse strains and mammalian species. Here, we combined differential mammary gland fractionation approaches and transcriptional profiles obtained from FACS-isolated mammary cells to improve our definitions of mammary-resident, cellular identities at the single-cell level. Our approach yielded a series of expression signatures that illustrate the heterogeneity of mammary epithelial cells, specifically those of the luminal fate, and uncovered transcriptional changes to their lineage-defined, cellular states that are induced during gland development. Our analysis also provided molecular signatures that identified non-epithelial mammary cells, including adipocytes, fibroblasts and rare immune cells. Lastly, we extended our study to elucidate expression signatures of human, breast-resident cells, a strategy that allowed for the cross-species comparison of mammary epithelial identities. Collectively, our approach improved the existing signatures of normal mammary epithelial cells, as well as elucidated the diversity of non-epithelial cells in murine and human breast tissue. Our study provides a useful resource for future studies that use single-cell molecular profiling strategies to understand normal and malignant breast development.

Remodeling of Zn2+ homeostasis upon differentiation of mammary epithelial cells

Zinc is the second most abundant transition metal in humans and an essential nutrient required for growth and development of newborns. During lactation, mammary epithelial cells differentiate into a secretory phenotype, uptake zinc from blood circulation, and export it into mother's milk. At the cellular level, many zinc-dependent cellular processes, such as transcription, metabolism of nutrients, and proliferation are involved in the differentiation of mammary epithelial cells. Using mouse mammary epithelial cells as a model system, we investigated the remodeling of zinc homeostasis during differentiation induced by treatment with the lactogenic hormones cortisol and prolactin. RNA-Seq at different stages of differentiation revealed changes in global gene expression, including genes encoding zinc-dependent proteins and regulators of zinc homeostasis. Increases in mRNA levels of three zinc homeostasis genes, Slc39a14 (ZIP14) and metallothioneins (MTs) I and II were induced by cortisol but not by prolactin. The cortisol-induced increase was partially mediated by the nuclear glucocorticoid receptor signaling pathway. An increase in the cytosolic labile Zn2+ pool was also detected in lactating mammary cells, consistent with upregulation of MTs. We found that the zinc transporter ZIP14 was important for the expression of a major milk protein, whey acid protein (WAP), as knockdown of ZIP14 dramatically decreased WAP mRNA levels. In summary, our study demonstrated remodeling of zinc homeostasis upon differentiation of mammary epithelial cells resulting in changes in cytosolic Zn2+ and differential expression of zinc homeostasis genes, and these changes are important for establishing the lactation phenotype.

Effects of Sphingosine-1-Phosphate on Cell Viability, Differentiation, and Gene Expression of Adipocytes

Sphingosine-1-phosphate (S1P) is a highly potent sphingolipid metabolite, which controls numerous physiological and pathological process via its extracellular and intracellular functions. The breast is mainly composed of epithelial cells (mammary gland) and adipocytes (stroma). Adipocytes play an important role in regulating the normal functions of the breast. Compared to the vast amount studies on breast epithelial cells, the functions of S1P in breast adipocytes are much less known. Thus, in the current study, we used human preadipocyte cell lines SGBS and mouse preadipocyte cell line 3T3-L1 as in vitro models to evaluate the effects of S1P on cell viability, differentiation, and gene expression in adipocytes. Our results showed that S1P increased cell viability in SGBS and 3T3-L1 preadipocytes but moderately reduced cell viability in differentiated SGBS and 3T3-L1 adipocytes. S1P was also shown to inhibit adipogenic differentiation of SGBS and 3T3-L1 at concentration higher than 1000 nM. Transcriptome analyses showed that S1P was more influential on gene expression in differentiated adipocytes. Furthermore, our network analysis in mature adipocytes showed that the upregulated DEGs (differentially expressed genes) were related to regulation of lipolysis, PPAR (peroxisome proliferator-activated receptor) signaling, alcoholism, and toll-like receptor signaling, whereas the downregulated DEGs were overrepresented in cytokine-cytokine receptor interaction, focal adhesion, starch and sucrose metabolism, and nuclear receptors pathways. Together previous studies on the functions of S1P in breast epithelial cells, the current study implicated that S1P may play a critical role in modulating the bidirectional regulation of adipocyte-extracellular matrix-epithelial cell axis and maintaining the normal physiological functions of the breast.

Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer

Simple Summary

The human body is composed of multiple cell types that form structures and carry out the functions of specific tissues. The human breast is mainly known for the milk ducts organized by epithelial cells, but also contains many other cell types of little-known identity. In this study, we employed the single-cell sequencing technology to ascertain the various cell types present in the normal breast. The results showed 10 distinct cell types that included three epithelial and other novel cell types. The gene signatures of five cell types (three epithelial, one fibroblast subset, and immune cells) matched to the gene expression profiles of >85% breast tumors cataloged in The Cancer Gene Atlas dataset, suggesting their significant contribution to breast cancer. These findings provide a framework for the better mapping of the cellular composition in the breast and its relationship to breast disease.

Abstract

The human breast is composed of diverse cell types. Studies have delineated mammary epithelial cells, but the other cell types in the breast have scarcely been characterized. In order to gain insight into the cellular composition of the tissue, we performed droplet-mediated RNA sequencing of 3193 single cells isolated from a postmenopausal breast tissue without enriching for epithelial cells. Unbiased clustering analysis identified 10 distinct cell clusters, seven of which were nonepithelial devoid of cytokeratin expression. The remaining three cell clusters expressed cytokeratins (CKs), representing breast epithelial cells; Cluster 2 and Cluster 7 cells expressed luminal and basal CKs, respectively, whereas Cluster 9 cells expressed both luminal and basal CKs, as well as other CKs of unknown specificity. To assess which cell type(s) potentially contributes to breast cancer, we used the differential gene expression signature of each cell cluster to derive gene set variation analysis (GSVA) scores and classified breast tumors in The Cancer Gene Atlas (TGGA) dataset (n = 1100) by assigning the highest GSVA scoring cell cluster number for each tumor. The results showed that five clusters (Clusters 2, 3, 7, 8, and 9) could categorize >85% of breast tumors collectively. Notably, Cluster 2 (luminal epithelial) and Cluster 3 (fibroblast) tumors were equally prevalent in the luminal breast cancer subtypes, whereas Cluster 7 (basal epithelial) and Cluster 9 (other epithelial) tumors were present primarily in the triple-negative breast cancer (TNBC) subtype. Cluster 8 (immune) tumors were present in all subtypes, indicating that immune cells may contribute to breast cancer regardless of the subtypes. Cluster 9 tumors were significantly associated with poor patient survival in TNBC, suggesting that this epithelial cell type may give rise to an aggressive TNBC subset.

Expression pattern analysis and drug differential sensitivity of cancer-associated fibroblasts in triple-negative breast cancer

Triple-negative breast cancer (TNBC) has the characteristics of a complex molecular landscape, aggressive or high proliferation leading to poor prognosis, and behavioral heterogeneity. The purpose of the present study was to determine the spatiotemporal expression of α-smooth muscle actin (α-SMA)-positive cancer-associated fibroblasts (CAFs) at histological level in 4T1 tumors and to predict the sensitivity to 138 drugs in patients with TNBC according to α-SMA expression. The quantitative results of fibrosis showed that the volume of 4T1 tumors correlated positively with the area of tumor fibrosis. Furthermore, we divided 4T1 tumors according to the degree of fibrosis and characterized the molecular characteristics of the four regions. Finally, the difference in the signaling pathways and sensitivity to 138 drugs was analyzed in patients with TNBC according to α-SMA expression combined with The Cancer Genome Atlas (TCGA) database. The myogenesis, TGF-β, and Notch signaling pathways were upregulated and the patients with TNBC were significantly differentially sensitive to 25 drugs. The results of in vivo experiments showed that the inhibitory effect of embelin on 4T1 tumors with high α-SMA expression was greater than that on 4TO7 tumors with low α-SMA expression. At the same time, embelin significantly decreased α-SMA and PDGFRA expression in 4T1 tumors compared with the control group. Our findings add to understanding of CAF distribution in the 4T1 tumor microenvironment and its possible role in treating cancer.

Distinct Expression Patterns of Fibrillar Collagen Types I, III, and V in Association with Mammary Gland Remodeling during Pregnancy, Lactation and Weaning

The mammary gland structurally and functionally remodels during pregnancy, during lactation and after weaning. There are three types of fibrillar collagens, types I, III, and V, in mammary stromal tissue. While the importance of the fibrillar structure of collagens for mammary morphogenesis has been suggested, the expression patterns of each type of fibrillar collagen in conjunction with mammary remodeling remain unclear. In this study, we investigated their expression patterns during pregnancy, parturition, lactation and involution. Type I collagen showed a well-developed fibril structure during pregnancy, but the fibrillar structure of type I collagen then became sparse at parturition and during lactation, which was concurrent with the downregulation of its mRNA and protein levels. The well-developed fibrillar structure of type I collagen reappeared after weaning. On the other hand, type V collagen showed a well-developed fibrillar structure and upregulation in the lactation period but not in the periods of pregnancy and involution. Type III collagen transiently developed a dense fibrillar network at the time of parturition and exhibited drastic increases in mRNA expression. These results indicate that each type of fibrillar collagen is distinctly involved in structural and functional remodeling in mammary glands during pregnancy, parturition, lactation, and involution after weaning. Furthermore, in vitro studies of mammary epithelial cells showed regulatory effects of type I collagen on cell adhesion, cell proliferation, ductal branching, and β-casein secretion. Each type of fibrillar collagen may have different roles in defining the cellular microenvironment in conjunction with structural and functional mammary gland remodeling.

Integrating single-cell RNA-sequencing and functional assays to decipher mammary cell states and lineage hierarchies

The identification and molecular characterization of cellular hierarchies in complex tissues is key to understanding both normal cellular homeostasis and tumorigenesis. The mammary epithelium is a heterogeneous tissue consisting of two main cellular compartments, an outer basal layer containing myoepithelial cells and an inner luminal layer consisting of estrogen receptor-negative (ER⁻) ductal cells and secretory alveolar cells (in the fully functional differentiated tissue) and hormone-responsive estrogen receptor-positive (ER⁺) cells. Recent publications have used single-cell RNA-sequencing (scRNA-seq) analysis to decipher epithelial cell differentiation hierarchies in human and murine mammary glands, and reported the identification of new cell types and states based on the expression of the luminal progenitor cell marker KIT (c-Kit). These studies allow for comprehensive and unbiased analysis of the different cell types that constitute a heterogeneous tissue. Here we discuss scRNA-seq studies in the context of previous research in which mammary epithelial cell populations were molecularly and functionally characterized, and identified c-Kit⁺ progenitors and cell states analogous to those reported in the recent scRNA-seq studies.

Organoid cultures from normal and cancer-prone human breast tissues preserve complex epithelial lineages

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.

Single-cell RNA-sequencing analysis of estrogen- and endocrine-disrupting chemical-induced reorganization of mouse mammary gland

Menopause is a critical window of susceptibility for its sensitivity to endocrine disrupting chemicals due to the decline of endogenous estrogen. Using a surgical menopausal (ovariectomized) mouse model, we assessed how mammary tissue was affected by both 17β-estradiol (E2) and polybrominated diphenyl ethers (PBDEs). As flame retardants in household products, PBDEs are widely detected in human serum. During physiologically-relevant exposure to E2, PBDEs enhanced E2-mediated regrowth of mammary glands with terminal end bud-like structures. Analysis of mammary gland RNA revealed that PBDEs both augmented E2-facilitated gene expression and modulated immune regulation. Through single-cell RNA sequencing (scRNAseq) analysis, E2 was found to induce Pgr expression in both Esr1+ and Esr1- luminal epithelial cells and Ccl2 expression in Esr1+ fibroblasts. PBDEs promote the E2-AREG-EGFR-M2 macrophage pathway. Our findings support that E2 + PBDE increases the risk of developing breast cancer through the expansion of estrogen-responsive luminal epithelial cells and immune modulation.