Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections

The COVID-19 pandemic, driven by the SARS-CoV-2 virus and its variants, highlights the important role of understanding host-viral molecular interactions influencing infection outcomes. Alternative splicing post-infection can impact both host responses and viral replication. We analyzed RNA splicing patterns in immune cells across various SARS-CoV-2 variants, considering immunization status. Using a dataset of 190 RNA-seq samples from our prior studies, we observed a substantial deactivation of alternative splicing and RNA splicing-related genes in COVID-19 patients. The alterations varied significantly depending on the infecting variant and immunization history. Notably, Alpha or Beta-infected patients differed from controls, while Omicron-infected patients displayed a splicing profile closer to controls. Particularly, vaccinated Omicron-infected individuals showed a distinct dynamic in alternative splicing patterns not widely shared among other groups. Our findings underscore the intricate interplay between SARS-CoV-2 variants, vaccination-induced immunity, and alternative splicing, emphasizing the need for further investigations to deepen understanding and guide therapeutic development.

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we propose that RNA-seq should be considered a diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers insights into a patient's immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 196 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that-combined with sequence alignments and BLASTp-they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.

Variant- and Vaccination-Specific Alternative Splicing Profiles in SARS-CoV-2 Infections

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, and its subsequent variants has underscored the importance of understanding the host-viral molecular interactions to devise effective therapeutic strategies. A significant aspect of these interactions is the role of alternative splicing in modulating host responses and viral replication mechanisms. Our study sought to delineate the patterns of alternative splicing of RNAs from immune cells across different SARS-CoV-2 variants and vaccination statuses, utilizing a robust dataset of 190 RNA-seq samples from our previous studies, encompassing an average of 212 million reads per sample. We identified a dynamic alteration in alternative splicing and genes related to RNA splicing were highly deactivated in COVID-19 patients and showed variant- and vaccination-specific expression profiles. Overall, Omicron-infected patients exhibited a gene expression profile akin to healthy controls, unlike the Alpha or Beta variants. However, significantly, we found identified a subset of infected individuals, most pronounced in vaccinated patients infected with Omicron variant, that exhibited a specific dynamic in their alternative splicing patterns that was not widely shared amongst the other groups. Our findings underscore the complex interplay between SARS-CoV-2 variants, vaccination-induced immune responses, and alternative splicing, emphasizing the necessity for further investigations into these molecular cross-talks to foster deeper understanding and guide strategic therapeutic development.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1-3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we argue that RNA-seq should be considered a routine diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers vital insights into a patient's immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 240 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that - combined with sequence alignments and pBLAST - they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.

Unlocking Translational Potential: Conditionally Reprogrammed Cells in Advancing Breast Cancer Research

Preclinical in vitro models play an important role in studying cancer cell biology and facilitating translational research, especially in the identification of drug targets and drug discovery studies. This is particularly relevant in breast cancer, where the global burden of disease is quite high based on prevalence and a relatively high rate of lethality. Predictive tools to select patients who will be responsive to invasive or morbid therapies (radiotherapy, chemotherapy, immunotherapy, and/or surgery) are relatively lacking. To be clinically relevant, a model must accurately replicate the biology and cellular heterogeneity of the primary tumor. Addressing these requirements and overcoming the limitations of most existing cancer cell lines, which are typically derived from a single clone, we have recently developed conditional reprogramming (CR) technology. The CR technology refers to a co-culture system of primary human normal or tumor cells with irradiated murine fibroblasts in the presence of a Rho-associated kinase inhibitor to allow the primary cells to acquire stem cell properties and the ability to proliferate indefinitely in vitro without any exogenous gene or viral transfection. This innovative approach fulfills many of these needs and offers an alternative that surpasses the deficiencies associated with traditional cancer cell lines. These CR cells (CRCs) can be reprogrammed to maintain a highly proliferative state and reproduce the genomic and histological characteristics of the parental tissue. Therefore, CR technology may be a clinically relevant model to test and predict drug sensitivity, conduct gene profile analysis and xenograft research, and undertake personalized medicine. This review discusses studies that have applied CR technology to conduct breast cancer research.

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

Motivation

Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs.

Results

We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (v) predicts miRNA binding sites on circRNAs, (vi) systematically investigates potential circRNA-miRNA sponging events, (vii) creates a network of competing endogenous RNAs and (viii) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research.

Availability and implementation

https://github.com/biomedbigdata/circRNA-sponging.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Esr1 but Not CYP19A1 Overexpression in Mammary Epithelial Cells during Reproductive Senescence Induces Pregnancy-Like Proliferative Mammary Disease Responsive to Anti-Hormonals

Molecular-level analyses of breast carcinogenesis benefit from vivo disease models. Estrogen receptor 1 (Esr1) and cytochrome P450 family 19 subfamily A member 1 (CYP19A1) overexpression targeted to mammary epithelial cells in genetically engineered mouse models induces largely similar rates of proliferative mammary disease in prereproductive senescent mice. Herein, with natural reproductive senescence, Esr1 overexpression compared with CYP19A1 overexpression resulted in significantly higher rates of preneoplasia and cancer. Before reproductive senescence, Esr1, but not CYP19A1, overexpressing mice are tamoxifen resistant. However, during reproductive senescence, Esr1 mice exhibited responsiveness. Both Esr1 and CYP19A1 are responsive to letrozole before and after reproductive senescence. Gene Set Enrichment Analyses of RNA-sequencing data sets showed that higher disease rates in Esr1 mice were accompanied by significantly higher expression of cell proliferation genes, including members of prognostic platforms for women with early-stage hormone receptor-positive disease. Tamoxifen and letrozole exposure induced down-regulation of these genes and resolved differences between the two models. Both Esr1 and CYP19A1 overexpression induced abnormal developmental patterns of pregnancy-like gene expression. This resolved with progression through reproductive senescence in CYP19A1 mice, but was more persistent in Esr1 mice, resolving only with tamoxifen and letrozole exposure. In summary, genetically engineered mouse models of Esr1 and CYP19A1 overexpression revealed a diversion of disease processes resulting from the two distinct molecular pathophysiological mammary gland-targeted intrusions into estrogen signaling during reproductive senescence.

Overexpression of Estrogen Receptor α in Mammary Glands of Aging Mice Is Associated with a Proliferative Risk Signature and Generation of Estrogen Receptor α-Positive Mammary Adenocarcinomas

Age is a risk factor for human estrogen receptor-positive breast cancer, with highest prevalence following menopause. While transcriptome risk profiling is available for human breast cancers, it is not yet developed for prognostication for primary or secondary breast cancer development utilizing at-risk breast tissue. Both estrogen receptor α (ER) and aromatase overexpression have been linked to human breast cancer. Herein, conditional genetically engineered mouse models of estrogen receptor 1 (Esr1) and cytochrome P450 family 19 subfamily A member 1 (CYP19A1) were used to show that induction of Esr1 overexpression just before or with reproductive senescence and maintained through age 30 months resulted in significantly higher prevalence of estrogen receptor-positive adenocarcinomas than CYP19A1 overexpression. All adenocarcinomas tested showed high percentages of ER+ cells. Mammary cancer development was preceded by a persistent proliferative transcriptome risk signature initiated within 1 week of transgene induction that showed parallels to the Prosigna/Prediction Analysis of Microarray 50 human prognostic signature for early-stage human ER+ breast cancer. CYP19A1 mice also developed ER+ mammary cancers, but histology was more divided between adenocarcinoma and adenosquamous, with one ER- adenocarcinoma. Results demonstrate that, like humans, generation of ER+ adenocarcinoma in mice was facilitated by aging mice past the age of reproductive senescence. Esr1 overexpression was associated with a proliferative estrogen pathway-linked signature that preceded appearance of ER+ mammary adenocarcinomas.

Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients

Omicron is currently the dominant SARS-CoV-2 variant and several sublineages have emerged. Questions remain about the impact of previous SARS-CoV-2 exposure on cross-variant immune responses elicited by the SARS-CoV-2 Omicron sublineage BA.2 compared to BA.1. Here we show that without previous history of COVID-19, BA.2 infection induces a reduced immune response against all variants of concern (VOC) compared to BA.1 infection. The absence of ACE2 binding in sera of previously naïve BA.1 and BA.2 patients indicates a lack of meaningful neutralization. In contrast, anti-spike antibody levels and neutralizing activity greatly increased in the BA.1 and BA.2 patients with a previous history of COVID-19. Transcriptome analyses of peripheral immune cells showed significant differences in immune response and specific antibody generation between BA.1 and BA.2 patients as well as significant differences in expression of specific immune genes. In summary, prior infection status significantly impacts the innate and adaptive immune response against VOC following BA.2 infection.

Mouse Mammary Gland Whole Mount Density Assessment across Different Morphologies Using a Bifurcated Program for Image Processing

Mammographic density is associated with increased breast cancer risk. Conventional visual assessment of murine mouse models does not include quantified total density analysis. A bifurcated method was sufficient to obtain relative density scores on a broad range of two-dimensional whole mount images that contained both normal and abnormal findings. Image processing techniques, including a ridge operator and a gaussian denoising method, were used to isolate background away from mammary epithelium and use mean pixel intensity to represent mammary density on genetically engineered mouse models for breast cancer in mice 4 to 29 months of age. The bifurcated method allowed for application of an optimal image processing approach for the structural elements present in the whole mount images. Gaussian denoising was the optimal approach when more dense lobular growth and tertiary branching dominate and a ridge operator when epithelial growth was more sparse and secondary branching was the more dominant structural feature. The two processing approaches were combined in a single experimental flow program using an initial image density measurement as the decision point between the two approaches. Higher density was associated with lobular growth, tertiary branching, fibrotic stroma, and presence of cancer. The significance of the study is development of a readily accessible program for digital assessment of mammary gland whole mount density across a range of mammary gland morphologies.

Comprehensive analysis of immune responses in CLL patients after heterologous COVID-19 vaccination

Patients with chronic lymphocytic leukemia (CLL) treated with B-cell pathway inhibitors and anti-CD20 antibodies exhibit low humoral response rate (RR) following SARS-CoV-2 vaccination. To investigate the relationship between the initial transcriptional response to vaccination with ensuing B and T cell immune responses, we performed a comprehensive immune transcriptome analysis flanked by antibody and T cell assays in peripheral blood prospectively collected from 15 CLL/SLL patients vaccinated with heterologous BNT162b2/ChAdOx1 with follow up at a single institution. The two-dose antibody RR was 40% increasing to 53% after booster. Patients on BTKi, venetoclax ± anti-CD20 antibody within 12 months of vaccination responded less well than those under BTKi alone. The two-dose T cell RR was 80% increasing to 93% after booster. Transcriptome studies revealed that seven patients showed interferon-mediated signaling activation within 2 days and one at 7 days after vaccination. Increasing counts of COVID-19 specific IGHV genes correlated with B-cell reconstitution and improved humoral RR. T cell responses in CLL patients appeared after vaccination regardless of treatment status. A higher humoral RR was associated with BTKi treatment and B-cell reconstitution. Boosting was particularly effective when intrinsic immune status was improved by CLL-treatment.

Heterologous ChAdOx1-BNT162b2 vaccination in Korean cohort induces robust immune and antibody responses that includes Omicron

Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than BNT162b2-BNT162b2. Here, we investigated the molecular transcriptome, germline allelic variants of immunoglobulin loci, and anti-Omicron antibody levels in 46 office and lab workers from the Republic of Korea following ChAdOx1-BNT162b2 vaccination. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml to 14,000 AU/ml to 142,000 AU/ml one, three and seven days following the second vaccination. Titers against VOC, including Omicron, were two-fold to three-fold lower, yet higher than those measured following BNT162b2-BNT162b2 vaccination. RNA-seq of peripheral immune cells demonstrated activation of interferon pathways with increased IGHV clonal transcripts encoding neutralizing antibodies. scRNA-seq revealed enriched B cell and CD4⁺ T cell responses in both ChAdOx1-BNT162b2 and BNT162b2-BNT162b2 recipients, but a stronger clonal expansion of memory B cells with ChAdOx1-BNT162b2. In summary, heterologous ChAdOx1-BNT162b2 provides an innate and adaptive immune response that exceeds homologous BNT162b2 vaccination.

Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients

Antibody response following Omicron infection is reported to be less robust than that to other variants. Here we investigated how prior vaccination and/or prior infection modulates that response. Disease severity, antibody responses and immune transcriptomes were characterized in four groups of Omicron-infected outpatients (n=83): unvaccinated/no prior infection, vaccinated/no prior infection, unvaccinated/prior infection and vaccinated/prior infection. The percentage of patients with asymptomatic or mild disease was highest in the vaccinated/no prior infection group (87%) and lowest in the unvaccinated/no prior infection group (47%). Significant anti-Omicron spike antibody levels and neutralizing activity were detected in the vaccinated group immediately after infection but were not present in the unvaccinated/no prior infection group. Within two weeks, antibody levels against Omicron, increased. Omicron neutralizing activity in the vaccinated group exceeded that of the prior infection group. No increase in neutralizing activity in the unvaccinated/no prior infection group was seen. The unvaccinated/prior infection group showed an intermediate response. We then investigated the early transcriptomic response following Omicron infection in these outpatient populations and compared it to that found in unvaccinated hospitalized patients with Alpha infection. Omicron infected patients showed a gradient of transcriptional response dependent upon whether or not they were previously vaccinated or infected. Vaccinated patients showed a significantly blunted interferon response as compared to both unvaccinated Omicron infected outpatients and unvaccinated Alpha infected hospitalized patients typified by the response of specific gene classes such as OAS and IFIT that control anti-viral responses and IFI27, a predictor of disease outcome.

mRNA vaccination in octogenarians 15 and 20 months after recovery from COVID-19 elicits robust immune and antibody responses that include Omicron

Knowledge about the impact of prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the elderly on mRNA vaccination response is needed to appropriately address the demand for additional vaccinations in this vulnerable population. Here, we show that octogenarians, a high-risk population, mount a sustained SARS-CoV-2 spike-specific immunoglobulin G (IgG) antibody response for 15 months following infection. This response boosts antibody levels 35-fold upon receiving a single dose of BNT162b2 mRNA vaccine 15 months after recovery from coronavirus disease 2019 (COVID-19). In contrast, antibody responses in naive individuals boost only 6-fold after a second vaccine. Spike-specific angiotensin-converting enzyme 2 (ACE2) antibody binding responses in the previously infected octogenarians following two vaccine doses exceed those found in a naive cohort after two doses. RNA sequencing (RNA-seq) demonstrates activation of interferon-induced genetic programs, which persist only in the previously infected. A preferential increase of specific immunoglobulin G heavy chain variable (IGHV) clonal transcripts that are the basis of neutralizing antibodies is observed only in the previously infected nuns.

Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients.. [PMID: 35441161 PMCID: PMC9016656 DOI: 10.1101/2022.04.07.22273565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Omicron is currently the dominant SARS-CoV-2 variant and several sublineages have emerged. Questions remain about the impact of previous SARS-CoV-2 exposure on cross-variant immune responses elicited by BA.2 infection compared to BA.1. Here we show that without previous history of COVID-19, BA.2 infection induces a reduced immune response against all variants of concern (VOC) compared to BA.1 infection. The absence of ACE2 binding in sera of previously naïve BA.1 and BA.2 patients indicates a lack of meaningful neutralization. In contrast, anti-spike antibody levels and neutralizing activity greatly increased in the BA.1 and BA.2 patients with a previous history of COVID-19. Transcriptome analyses of peripheral immune cells showed significant differences in immune response and specific antibody generation between BA.1 and BA.2 patients as well as significant differences in expression of specific immune genes. In summary, prior infection status significantly impacts the innate and adaptive immune response against VOC following BA.2 infection.

Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module

Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. While viral infections elicit a conserved immune response, it is not known whether SARS-CoV-2 variants, which display enhanced binding to the ACE2 receptor and reduced neutralizing activity by vaccine-elicited antibodies, prompt specific genomic immune responses. To test this, we generated and investigated the transcriptomes in BCs from hospitalized patients infected with either the Alpha variant (n = 36) or with the Alpha variant that had acquired the E484K escape mutation (Alpha+E484K) (n = 13). We identified a gene module preferentially activated in patients infected with the Alpha+E484K variant and in patients infected with the Beta (n = 9) and Gamma (n = 3) variants that also carry by the E484K escape mutation. The E484K signature was enriched for genes preferentially expressed in monocytes and linked to severe viral infection. However, both cohorts had undergone similar treatments and no differences in disease severity were reported suggesting that this signature reflects a variant response and does not necessarily associate with disease outcome. Additionally, longitudinal transcriptome analyses revealed a more persistent retention of immune signatures in Alpha+E484K patients throughout the entire course of COVID-19 disease and convalescence. While the OAS1 Neanderthal mutation has been linked to a milder COVID-19 pathology, we did not identify significant immune transcriptomes differences in the 25 patients homozygous for this mutation. Our study offers insights into distinct molecular immune responses elicited by SARS-CoV-2 variants carrying the E484K escape mutation throughout the COVID-19 disease.

Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19

Knowledge about the impact of prior SARS-CoV-2 infection of the elderly on mRNA vaccination response is needed to appropriately address the need for booster vaccination in this vulnerable population. To address this, we investigated antibody and genomic immune responses in 16 elderly (avg. 81 yrs.) individuals that had received a single booster dose of BNT162b vaccine 15 months after recovering from COVID-19. Spike-specific IgG antibody levels increased in each of the study participants from an average of 710 U/ml prior to the vaccination to more than 40,000 U/ml within ten weeks after the vaccination. In contrast, anti-spike-specific IgG antibody levels averaged 2,190 U/ml in 14 healthy SARS-CoV-2-naïve individuals (avg. 58 yrs.) ten weeks after the second dose of BNT162b. RNA-seq conducted on PBMCs demonstrated the activation of interferon-activated genetic programs in both cohorts within one day. Unlike their transient induction in the younger naïve population, persistent activity and the initiation of additional cell cycle regulated programs were obtained in the older COVID-19 recovered population. Here we show that the elderly, a high-risk population, can mount a strong antibody and a persistent molecular immune response upon receiving a single dose of mRNA vaccine 15 months after recovery from COVID-19.

Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation

Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 2021 1 . This variant is of concern due to reduced neutralizing activity by vaccine-elicited antibodies 2,3 . However, it is not known whether this single amino acid change leads to an altered immune response. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. Lastly, the immune transcriptome of patients infected with additional variants (B.1.258, B.1.1.163 and B.1.7.7) displayed a reduced activation compared to patients infected with B.1.1.7. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression.

Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant

Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. The B.1.351 variant carrying the escape mutation E484K in the receptor binding domain is of particular concern due to reduced immunological protection following vaccination. Protection can manifest as early as 10 days following immunization with full protection two weeks following the second dose, but the course is not well-characterized for variants. Here, we investigated the immune transcriptome of six elderly individuals (average age 82 yr.) from an old people's home, who contracted B.1.351, with four having received the first dose of BNT162b eight to 11 days prior to the onset of COVID-19 symptoms. The patients were hospitalized and received dexamethasone treatment. Immune transcriptomes were established from PBMCs approximately 10 and 35 days after the onset of COVID-19 symptomology. RNA-seq revealed a more intensive immune response in vaccinated patients as compared to unvaccinated ones. Specifically, transcription factors linked to the JAK/STAT pathway, interferon stimulated genes, and genes associated with innate antiviral immunity and COVID-19-SARS-CoV-2 infection were highly enriched in vaccinated patients. This rendered the transcriptomes of the older vaccinated group significantly different than older unvaccinated individuals infected at the same institution and more similar to the immune response of younger unvaccinated individuals (age range 48-62) following B.1.351 infection. All individuals in this study whether vaccinated or not were hospitalized due to B.1.351 infection and one vaccinated patient died illustrating that although an enhanced immune response was documented infection it was insufficient to protect from disease. This highlights the need for maintaining physical distancing and prevention measures throughout the time course of vaccination in older adults.

Enabling exercise prescription for survivors of cancer

Although exercise is widely recommended for survivors of cancer, readily implementable approaches for evaluating exercise tolerance enabling exercise prescriptions at appropriate levels of cardiovascular exertion are not always available. We evaluated the utility of modified Harvard Step tests within the context of a standard physical examination for fitness evaluation and exercise prescription for survivors of cancer across a range of age, BMI and exercise history. While 52% of presenting individuals with a past cancer diagnosis were able to complete a 3-min test at pace with a reduced 9-in. step, adoption of self-determined pacing, test duration and completion on a flat surface enabled relative fitness rating and appropriate exercise prescription for the remaining survivors. Younger age and more vigorous exercise histories correlated with completion of the standard 3-min test at pace, but all 9-in. formats led to exercise prescriptions more vigorous than current activity. The physical examination setting expedited inclusion of core and specific muscle group strength testing. The approach is adaptable to a range of health care settings, providers, and patients, providing a shared opportunity for providers and patients to evaluate exercise tolerance. It can be used to further expand incorporation of exercise testing and prescription into routine care.

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community

To investigate prevalence of ongoing activation of inflammation following asymptomatic SARS-CoV-2 infection we characterized immune cell transcriptomes from 43 asymptomatic seropositive and 52 highly exposed seronegative individuals with few underlying health issues following a community superspreading event. Four mildly symptomatic seropositive individuals examined three weeks after infection as positive controls demonstrated immunological activation. Approximately four to six weeks following the event, the two asymptomatic groups showed no significant differences. Two seropositive patients with underlying genetic disease impacting immunological activation were included (Cystic Fibrosis (CF), Nuclear factor-kappa B Essential Modulator (NEMO) deficiency). CF, but not NEMO, associated with significant immune transcriptome differences including some associated with severe SARS-CoV-2 infection (IL1B, IL17A, respective receptors). All subjects remained in their usual state of health from event through five-month follow-up. Here, asymptomatic infection resolved without evidence of prolonged immunological activation. Inclusion of subjects with underlying genetic disease illustrated the pathophysiological importance of context on impact of immunological response.

Conditional Reprogramming for Patient-Derived Cancer Models and Next-Generation Living Biobanks

Traditional cancer models including cell lines and animal models have limited applications in both basic and clinical cancer research. Genomics-based precision oncology only help 2-20% patients with solid cancer. Functional diagnostics and patient-derived cancer models are needed for precision cancer biology. In this review, we will summarize applications of conditional cell reprogramming (CR) in cancer research and next generation living biobanks (NGLB). Together with organoids, CR has been cited in two NCI (National Cancer Institute, USA) programs (PDMR: patient-derived cancer model repository; HCMI: human cancer model initiatives. HCMI will be distributed through ATCC). Briefly, the CR method is a simple co-culture technology with a Rho kinase inhibitor, Y-27632, in combination with fibroblast feeder cells, which allows us to rapidly expand both normal and malignant epithelial cells from diverse anatomic sites and mammalian species and does not require transfection with exogenous viral or cellular genes. Establishment of CR cells from both normal and tumor tissue is highly efficient. The robust nature of the technique is exemplified by the ability to produce 2 × 106 cells in five days from a core biopsy of tumor tissue. Normal CR cell cultures retain a normal karyotype and differentiation potential and CR cells derived from tumors retain their tumorigenic phenotype. CR also allows us to enrich cancer cells from urine (for bladder cancer), blood (for prostate cancer), and pleural effusion (for non-small cell lung carcinoma). The ability to produce inexhaustible cell populations using CR technology from small biopsies and cryopreserved specimens has the potential to transform biobanking repositories (NGLB: next-generation living biobank) and current pathology practice by enabling genetic, biochemical, metabolomic, proteomic, and biological assays, including chemosensitivity testing as a functional diagnostics tool for precision cancer medicine. We discussed analyses of patient-derived matched normal and tumor models using a case with tongue squamous cell carcinoma as an example. Last, we summarized applications in cancer research, disease modeling, drug discovery, and regenerative medicine of CR-based NGLB.

Peroxisome proliferator-activated receptor gamma and BRCA1

Peroxisome proliferator-activated receptor gamma agonists have been proposed as breast cancer preventives. Individuals who carry a mutated copy of BRCA1, DNA repair-associated gene, are at increased risk for development of breast cancer. Published data in the field suggest there could be interactions between peroxisome proliferator-activated receptor gamma and BRCA1 that could influence the activity of peroxisome proliferator-activated receptor gamma agonists for prevention. This review explores these possible interactions between peroxisome proliferator-activated receptor gamma, peroxisome proliferator-activated receptor gamma agonists and BRCA1 and discusses feasible experimental directions to provide more definitive information on the potential connections.

Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing

Restricted availability of cell and animal models is a rate-limiting step for investigation of salivary gland neoplasm pathophysiology and therapeutic response. Conditionally reprogrammed cell (CRC) technology enables establishment of primary epithelial cell cultures from patient material. This study tested a translational workflow for acquisition, expansion and testing of CRC-derived primary cultures of salivary gland neoplasms from patients presenting to an academic surgical practice. Results showed that cultured cells were sufficient for epithelial cell-specific transcriptome characterization to detect candidate therapeutic pathways and fusion genes, and for screening for cancer risk-associated single nucleotide polymorphisms (SNPs) and driver gene mutations through exome sequencing. Focused study of primary cultures of a low-grade mucoepidermoid carcinoma demonstrated amphiregulin-mechanistic target of rapamycin-protein kinase B (AKT; AKT1) pathway activation, identified through bioinformatics and subsequently confirmed as present in primary tissue and preserved through different secondary 2D and 3D culture media and xenografts. Candidate therapeutic testing showed that the allosteric AKT inhibitor MK2206 reproducibly inhibited cell survival across different culture formats. By contrast, the cells appeared resistant to the adenosine triphosphate competitive AKT inhibitor GSK690693. Procedures employed here illustrate an approach for reproducibly obtaining material for pathophysiological studies of salivary gland neoplasms, and other less common epithelial cancer types, that can be executed without compromising pathological examination of patient specimens. The approach permits combined genetic and cell-based physiological and therapeutic investigations in addition to more traditional pathologic studies, and can be used to build sustainable bio-banks for future inquiries.This article has an associated First Person interview with the first author of the paper.

The PPARγ agonist efatutazone delays invasive progression and induces differentiation of ductal carcinoma in situ

PURPOSE

Ductal carcinoma in situ (DCIS) is a pre-invasive lesion of the breast considered a precursor of invasive ductal carcinoma. This study aimed to determine whether activated PPARγ acts as a tumor suppressor in human DCIS progression.

METHODS

We utilized the high-affinity PPARγ agonist, efatutazone, to activate endogenous PPARγ in a well-defined model for the progression of basal (triple negative) DCIS, MCFDCIS cells, cultured under 2D and 3D conditions. We studied the effects of activated PPARγ on DCIS progression in MCFDCIS xenograft and C3(1)/Tag transgenic mice treated with 30 mg/kg of efatutazone.

RESULTS

In vitro, efatutazone did not alter the MCFDCIS cell proliferation but induced phenotypic and gene expression changes, indicating that activated PPARγ is able to differentiate MCFDCIS cells into more luminal and lactational-like cells. In addition, MCFDCIS tumorsphere formation in 3D was reduced by PPARγ activation. In vivo, efatutazone-treated MCFDCIS tumors exhibited fat deposition along with upregulation of PPARγ responsive genes in both epithelial and stromal compartments, suggesting features of milk-producing mammary epithelial cell differentiation. The efatutazone-treated lesions were less invasive with fewer CD44+/p63+ basal progenitor cells. PPARγ activation downregulated Akt phosphorylation in these tumors, although the ERK pathway remained unchanged. Similar trends in gene expression changes consistent with lactational and luminal cell differentiation were observed in the C3(1)/Tag mouse model after efatutazone treatment.

CONCLUSIONS

Our data suggest that activation of the PPARγ pathway differentiates DCIS lesions and may be a useful approach to delay DCIS progression.

Abstract 2234: Efatutazone reduces mammosphere formation in Brca1WT/fl11/Cre/p53+/- and Brca1fl11/fl11/Cre/p53+/- mice

Introduction: Efatutazone, a PPAR gamma agonist, may affect tumor growth through the induction of terminal cell differentiation. Thus, we hypothesize that efatutazone could affect progenitor cell number. Here, we evaluate progenitor cell number by measuring mammospheres, which is considered one way to measure potential progenitor cells.

Methods: Two month old Brca1WT/fl11/Cre/p53+/- (n= 14) and Brca1fl11/fl11/Cre/p53+/- (n= 10) C57Bl/6 mice were randomly placed on either control or treated with efatutazone through the diet (30-mg/kg concentration, F3028, rodent diet, grain-based, 1/2-in pellets; Bio-Serv, Frenchtown, NJ) with necropsy at four months and isolation of primary mammary epithelial cells from thoracic glands for studies of mammosphere formation using SCIVAX 96-well low adhesion nanoculture plates (Organogenix, Inc., Japan) using EpiCult-B Mouse Media (Stem Cell Technology, Inc., Vancouver, Canada) with 0,1,5, and 10% fetal bovine serum (FBS) added. Thoracic mammary gland tissue was frozen at -20°C followed by isolation of RNA and evaluation of PPAR gamma pathway gene expression by real-time RT-PCR using TaqMan® Array Mouse Lipid Regulated Genes (Thermo Fisher Scientific, Inc., Waltham MA). One inguinal gland was fixed for mammary gland whole mount and the other inguinal gland was formalin-fixed and paraffin-embedded for histology.

Results: SCIVAX nanoculture plates showed reproducible increases in mammosphere numbers with increasing FBS concentrations (p <0.05 one-way, Kruskal-Wallis). A significant increase in sphere number was seen in Brca1fl11/fl11/Cre/p53+/- compared to Brca1WT/fl11/Cre/p53+/- mice (p<0.05 one-way, Kruskall Wallis). Efatutazone treatment significantly decreased sphere numbers in Brca1WT/fl11/Cre/p53+/- and in Brca1fl11/fl11/Cre/p53+/- mice (p<0.05 one-way, Kruskall Wallis). Expression of PPAR gamma pathway genes were increased at the RNA level with statistically significant increases in Acadvl, Tnf, Alox5 (p<0.05) and Il1B, Srebf2, Hmgcs1, Hmgcr (p<0.01) genes (BootsRatio, http://rht.iconcologia.net/stats/br/several.html) in mice on efatutazone as compared to control diet.

Discussion: SCIVAX nanoculture plates can be used to quantitatively evaluate and compare mammosphere numbers between different genotypes and treatment groups. The higher numbers of mammospheres found with loss of both Brca1 copies as compared to one copy is consistent with previously published literature. The decrease in mammosphere numbers with efatutazone treatment could be secondary to its differentiating impact on mammary epithelial cells.

Conclusion: While efatutazone statistically significantly reduced mammosphere numbers, the absolute reduction was less the 25%.

Citation Format: Sahar J. Alothman, Shan Chao, Weisheng Wang, Priscilla A. Furth. Efatutazone reduces mammosphere formation in Brca1WT/fl11/Cre/p53+/- and Brca1fl11/fl11/Cre/p53+/- mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2234. doi:10.1158/1538-7445.AM2017-2234

Abstract 2729: A significant differential sensitivity to AKT inhibitors GSK690693 and MK-2206 2HI was identified in primary cells established from a low-grade mucoepidermoid carcinoma

The AKT pathway is frequently activated in cancer cells and is a defined target for therapeutic intervention.

Methods: RNA expression levels of candidate AKT pathway genes (AREG, EGFR, AKT, mTOR, GSK3α/β) were defined following RNAseq of replicate primary cell cultures (GUMC220 and GUMC221), which were established independently from two areas of the same low-grade salivary mucoepidermoid carcinoma (MEC). Protein expression and phosphorylation levels of the corresponding gene products were characterized using immunohistochemistry on FFPE sections from the original patient tumor, cell pellets, and cell line generated patient-derived xenografts and through western blotting of proteins extracted from cells grown under different culture conditions before and after treatment with AKT inhibitors GSK690693 (ATP-competitive) and MK-2206 2HCl (allosteric inhibitor). The effects of GSK690693 and MK-2206 2HCl on cell viability were tested at different concentrations ranging from 1.2-40μM in 2D and 3D conditions with three different culture media (Conditional media+ ROCK kinase inhibitor Y27632, conditional media without Y27632, and EpiCult-C BasalTM) using CellTiter-GloTM. Doxorubicin was used as a comparative control for evaluating the impact of a chemotherapeutic on cell viability and DMSO as a negative vehicle control. MDA-MB-453 cells were tested as a positive control for MK-2206 2HCl and GSK690693 sensitivity.

Results: Replicate primary cell cultures showed the same chemosensitivity results. MK-2206 2HCl induced a significantly greater reduction in cell viability as compared to GSK690693 in the MEC primary cells. This differential response was replicated in all three 2D culture medias tested (GUMC220_CMY p= 0.0017, GUMC220_CM p=0.0004, GUMC220_EpiC p<0.0001, GUMC221_CMY p=0.0010, GUMC221_CM p<0.0001, and GUMC221_EpiC p=0.0041, One-way ANOVA) with the same pattern reproduced in 3D cultures. Expected changes in levels of p-AKT(Ser473), GSK3α/β, p-GSK3α/β, and p-mTOR were found following treatment with both drugs as compared to vehicle controls. In MK-2206 2HCl treated cells, expression levels were all reduced whereas in GSK690693 treated cells, p-AKT(Ser473), p-AKT(Thr308) were increased and GSK3α/β, p-GSK3α/β, p-mTOR reduced.

Conclusion: Characterization of primary cell cultures using RNAseq led to the identification of a potentially druggable pathway. Direct testing revealed a differential response to the two AKT inhibitors evaluated. Although the two primary cell cultures were established from two geographically distinct areas of the same tumor, response to drug testing was the same and reproducible across different culture modalities. Studies establish the feasibility of deriving primary cells for drug testing and personalized therapy, even from small tumors.

Citation Format: Ahmad M. Alamri, Priscilla A. Furth. A significant differential sensitivity to AKT inhibitors GSK690693 and MK-2206 2HI was identified in primary cells established from a low-grade mucoepidermoid carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2729. doi:10.1158/1538-7445.AM2017-2729

Responsiveness of Brca1 and Trp53 Deficiency-Induced Mammary Preneoplasia to Selective Estrogen Modulators versus an Aromatase Inhibitor in Mus musculus

An intervention study initiated at age 4 months compared the impact of tamoxifen (25 mg), raloxifene (22.5 mg), and letrozole (2.5 mg) administered by 60-day release subcutaneous pellet on mammary preneoplasia prevalence at age 6 months in conditional genetically engineered mouse models with different Breast cancer 1 (Brca1) gene dosages targeted to mammary epithelial cells and germline Tumor protein P53 (Trp53) haploinsufficiency (10-16/cohort). The proportion of unexposed control mice demonstrating mammary preneoplasia at age 6 months was highest in Brca1^{fl11/fl11/Cre/p53-/+} (54%) mice followed by Brca1^{WT/fl11/Cre/p53-/+} mice (30%). By age 12 months, invasive mammary cancers appeared in 80% of Brca1^{fl11/fl11/Cre/p53-/+} and 42% of Brca1^{WT/fl11/Cre/p53-/+} control unexposed mice. The spectrum of cancer histology was similar in both models without somatic mutation of the nongenetically engineered Brca1, Trp53, Brca2, or Death-associated protein kinase 3 (Dapk3) alleles. Two-month exposure to tamoxifen, raloxifene, and letrozole significantly reduced estrogen-mediated tertiary branching by 65%, 71%, and 78%, respectively, in Brca1^{fl11/fl11/Cre/p53-/+} mice at age 6 months. However, only letrozole significantly reduced hyperplastic alveolar nodules (HAN) prevalence (by 52%) and number (by 30%) and invasive cancer appeared despite tamoxifen exposure. In contrast, tamoxifen significantly reduced HAN number by 95% in Brca1^{WT/fl11/Cre/p53-/+} mice. Control mice with varying combinations of the different genetically modified alleles and MMTV-Cre transgene demonstrated that the combination of Brca1 insufficiency and Trp53 haploinsufficiency was required for appearance of preneoplasia and no individual genetic alteration confounded the response to tamoxifen. In summary, although specific antihormonal approaches showed effectiveness, with Brca1 gene dosage implicated as a possible modifying variable, more effective chemopreventive approaches for Brca1 mutation-induced cancer may require alternative and/or additional agents. Cancer Prev Res; 10(4); 244-54. ©2017 AACR.

Abstract 4280: Paralleled workflow for expansion of limited patient material using CRC for in vitro/PDX/biological/genetic studies of a low-grade mucoepidermoid carcinoma

Acquiring live cancer cells preserving original characteristics is a critical step for precision medicine. Here we illustrate a paralleled workflow using a low-grade sublingual salivary mucoepidermoid carcinoma (MEC) as an example. Methods: Working under IRB approval, tissue from two distinct regions of a MEC were obtained and primary epithelial cell cultures established using CRC (F medium with Rho Kinase (ROCK) inhibitor Y-27632 with irradiated Swiss 3T3-J2 mouse fibroblast feeder cells). Epithelial cells were separated from feeders to test under non-CRC conditions including 2D (MammoCult™), colony formation in Matrigel (F medium, Y-27632), patient derived xenograft (PDX) formation (10*6 cells/50:50 matrigel/PBS/mammary fatpad), and RNA and DNA extracted for RNAseq, exome sequencing and PCR/RT-PCR for a CRTC1-MAML2 fusion gene (reported in MEC). Sequences were analyzed for relative transcript abundance, differentially expressed genes (DEGs), and single nucleotide polymorphisms (SNPs) (TopHat/CuffLinks, SAMTOOLS, variant database: dbSNP & 1000G, UCSC hg19) between the two MEC regions and fusion genes (FusionCatcher). Potentially pathophysiological SNPs were identified (OMIM and SNPedia). Gene ontology was performed on transcriptome data (PARTEK Genomic Suite, Pathway Studio). Immunohistochemistry (IHC) was used to compare protein expression of selected DEG and downstream effectors in original cancer and surrounding normal tissue, cell pellets, Matrigel colonies and PDX (confirmed as human using MAB1273). Results: CRC cultures established from both sites grew similarly under all in vitro and in vivo conditions. PDX showed well-differentiated histology comparable to original cancer. One of the 11 DEG was amphiregulin but protein expression was equivalent in the two cell cultures. Amphiregulin, EGFR, p-EGFR, p-AKT, and mTOR were expressed in vitro (CRC and non-CRC), in vivo (PDX) and in original cancer, where they were up-regulated as compared to surrounding normal tissue. Five potentially pathophysiologically significant SNPs were detected (BRCA2 (rs144848), TP53 (rs1042522), AURKA (rs2273535), DBYD (rs1801265), and (SOD2 rs4880)) but no CRCTC1-MAML2 fusion gene. FusionCatcher detected a possible novel fusion product currently under investigation. Conclusion: The paralleled approach provided sufficient material to identify amphiregulin as an upregulated growth factor pathway in a CRTC1-MAML2 fusion gene negative MEC. Previously, amphiregulin upregulation was pathophysiologically linked to the CRTC1-MAML2 fusion gene. Results from the two MEC sites were biologically concordant and genetically similar. In summary, CRC can be used to expand limited patient derived material for more extensive studies under non-CRC conditions. Support: R56DE023259 (PAF)

Citation Format: Ahmad M. Alamri, Xuefeng Liu, Weisheng Wang, Xiaogang Zhong, Bhaskar Kallakury, Bruce Davidson, Priscilla A. Furth. Paralleled workflow for expansion of limited patient material using CRC for in vitro/PDX/biological/genetic studies of a low-grade mucoepidermoid carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4280.

Primary cancer cell culture: mammary-optimized vs conditional reprogramming

The impact of different culture conditions on biology of primary cancer cells is not always addressed. Here, conditional reprogramming (CRC) was compared with mammary-optimized EpiCult-B (EpiC) for primary mammary epithelial cell isolation and propagation, allograft generation, and genome-wide transcriptional consequences using cancer and non-cancer mammary tissue from mice with different dosages of Brca1 and p53 Selective comparison to DMEM was included. Primary cultures were established with all three media, but CRC was most efficient for initial isolation (P<0.05). Allograft development was faster using cells grown in EpiC compared with CRC (P<0.05). Transcriptome comparison of paired CRC and EpiC cultures revealed 1700 differentially expressed genes by passage 20. CRC promoted Trp53 gene family upregulation and increased expression of epithelial differentiation genes, whereas EpiC elevated expression of epithelial-mesenchymal transition genes. Differences did not persist in allografts where both methods yielded allografts with relatively similar transcriptomes. Restricting passage (<7) reduced numbers of differentially expressed genes below 50. In conclusion, CRC was most efficient for initial cell isolation but EpiC was quicker for allograft generation. The extensive culture-specific gene expression patterns that emerged with longer passage could be limited by reducing passage number when both culture transcriptomes were equally similar to that of the primary tissue. Defining impact of culture condition and passage on the transcriptome of primary cells could assist experimental design and interpretation. For example, differences that appear with passage and culture condition are potentially exploitable for comparative studies targeting specific biological networks in different transcriptional environments.

Abstract 2286: Spontaneous mammary cancer development in genetically engineered mice with only one copy of Brca1 disrupted in combination with Trp53 haploinsufficiency

Background: Women carrying one mutated copy of BRCA1 are disposed to developing breast cancer. BRCA1-mutation-related cancers often harbor TRP53 mutations. Previously established genetically engineered mouse (GEM) models with spontaneous mammary cancer development have both copies of Brca1 disrupted in combination with Trp53 haploinsufficiency. Here we characterized cancer development in GEM with only one copy of Brca1 disrupted in mammary epithelial cells using Cre-Lox technology in combination with germ-line Trp53 haploinsufficiency. Methods: From our Brca1f11fT11/MMTV-Cre/Trp53+/− breeding program we noted mammary cancer development in female Brca1f11/WT11/MMTV-Cre/Trp53+/− mice. The time-course of mammary hyperplasia and cancer development was characterized in these mice. Mice were euthanized at age 6 months (n = 9) or when the largest tumor reached 1 cm3 or at 12 months if no tumor developed (n = 12). Cancers were resected, inguinal mammary glands processed for histology and thoracic mammary glands flash frozen or processed for primary cell culture. Hyperplastic alveolar nodules (HANs) and branching patterns were detected using inguinal mammary gland whole mounts. Histology was read on H&E stained slides and immunohistochemistry (IHC) performed for ERα, PGR and HER2 on cancer specimens. Results: Thirty-three percent of the mice developed palpable mammary tumors by age 12 months. Forty-four percent of the mice exhibited HANs at age 6 months and 56% at age 12 months. One mouse developed a female reproductive tract cancer. Three mice developed single palpable mammary adenocarcinomas. One mouse developed two cancers, one palpable spindloid and one non-palpable anaplastic carcinoma. Two adenocarcinomas have completed IHC studies and are ER/PGR/HER2 negative. Multilayered ductal hyperplasia was present only in 12-month-old mice (89%). Two-layered lobular-type hyperplasia was found in 33% of 6-month-old and 100% of 12-month-old mice. Primary cell cultures were established from both cancers attempted. Conclusions: Here we report development of a Brca1 insufficiency mouse model more representative of disease development in women who carry only one allele with a BRCA1-mutation. Similar to models with both Brca1 copies disrupted, Trp53 haploinsufficiency was required for cancer progression. The spectrum of mammary cancer histology was similar to that previously reported when both Brca1 alleles were disrupted. This model represents a tool for investigation of preventive strategies in the face of Brca1 and Trp53 haploinsufficiency and study of possible interactions between this genetic background and genetic and environmental factors that may promote cancer development.

Citation Format: Sahar Alothman, Svenja Groeneveld, Ahmad Alamri, Bhaskar Kallakury, Priscilla A. Furth. Spontaneous mammary cancer development in genetically engineered mice with only one copy of Brca1 disrupted in combination with Trp53 haploinsufficiency. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2286. doi:10.1158/1538-7445.AM2015-2286

Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase overexpressing mice defines an immune-associated gene signature linked to tamoxifen resistance

Response to breast cancer chemoprevention can depend upon host genetic makeup and initiating events leading up to preneoplasia. Increased expression of aromatase and estrogen receptor (ER) is found in conjunction with breast cancer. To investigate response or resistance to endocrine therapy, mice with targeted overexpression of Esr1 or CYP19A1 to mammary epithelial cells were employed, representing two direct pathophysiological interventions in estrogen pathway signaling. Both Esr1 and CYP19A1 overexpressing mice responded to letrozole with reduced hyperplastic alveolar nodule prevalence and decreased mammary epithelial cell proliferation. CYP19A1 overexpressing mice were tamoxifen sensitive but Esr1 overexpressing mice were tamoxifen resistant. Increased ER expression occurred with tamoxifen resistance but no consistent changes in progesterone receptor, pSTAT3, pSTAT5, cyclin D1 or cyclin E levels in association with response or resistance were found. RNA-sequencing (RNA-seq) was employed to seek a transcriptome predictive of tamoxifen resistance using these models and a second tamoxifen-resistant model, BRCA1 deficient/Trp53 haploinsufficient mice. Sixty-eight genes associated with immune system processing were upregulated in tamoxifen-resistant Esr1- and Brca1-deficient mice, whereas genes related to aromatic compound metabolic process were upregulated in tamoxifen-sensitive CYP19A1 mice. Interferon regulatory factor 7 was identified as a key transcription factor regulating these 68 immune processing genes. Two loci encoding novel transcripts with high homology to human immunoglobulin lambda-like polypeptide 1 were uniquely upregulated in the tamoxifen-resistant models. Letrozole proved to be a successful alternative to tamoxifen. Further study of transcriptional changes associated with tamoxifen resistance including immune-related genes could expand our mechanistic understanding and lead to biomarkers predictive of escape or response to endocrine therapies.

Abstract 3918: Characterizing growth features, allograft generation and transcriptomes of cultured conditionally reprogrammed cells (CRC) prepared from primary triple negative cancer from Brca1-mutant mice

Background: Efficient acquisition of primary cancer cells for genetic and pharmacological testing is a means towards individualized cancer treatment. Genetically engineered mouse models of triple negative mammary cancer were used to compare culture conditions conditionally reprogrammed cell culture CRC with a rho kinase inhibitor (Y-27632) and irradiated J2 feeder cells, EpiCult™, DMEM for establishment efficiency, differentiation, fibroblast contamination, and allograft generation. Goals: 1) Evaluate mammary cancer progenitor cells by allograft and secondary culture 2) Compare RNA-seq transcriptomes in cells and allografts with different Brca1 gene dosages (100%, 50%, 0%) Methods: Triple negative invasive adenocarcinomas from 4 mouse genotypes, all carrying a p53-null allele, were analyzed: A) 1 mutant Brca1 allele; B) 2 mutant Brca1 alleles; C) 1 mutant Brca1 allele and 1 human aromatase transgene; D) human aromatase transgene. Cancers were divided and growth assessed in CRC, EpiCult™ and DMEM cultures. Illumina (V2scriptseq) RNA-seq libraries were prepared from cell pellets and allografts. One million cells injected into mammary gland fat pads of nude mice generated allografts divided for histology/DNA analyses, secondary culture and RNAseq. Transcript abundance and differentially expressed genes were determined after assembling transcriptomes with Cufflinks. Results: CRC was the most efficient methodology based on rapidity and percentage cancer specimens successfully cultured and paucity of fibroblasts. Brca1 gene dosage made no difference in culture efficiency. Differentiation markers were expressed at significantly higher levels in CRC whereas markers of epithelial mesenchymal transition were expressed higher in EpiCult™. Allografts were derived from CRC and EpiCult™ but not DMEM. Genetic testing confirmed allografts were derived from original endogenous cancer cells. Some individual allografts derived from the same culture exhibited different growth curves and histology, suggesting tumor cell heterogeneity within cultures. Overall, palpable EpiCult™ allografts appeared significantly earlier than CRC allografts (p&lt;0.05 Chi Square). RNAseq analyses distinguished gene expression patterns dependent upon culture condition as distinct from those determined by underlying genetics. Summary: CRC technology was an efficient means of generating primary cancer cell cultures, maintained epithelial cell differentiation better than other methods, had no fibroblast contamination, and preserved cancer progenitor cells.

Citation Format: Ahmad M. Alamri, Svenja Groeneveld, Keunsoo Kang, Sarah Dabydeen, Weisheng Wang, Lothar Hennighausen, Bhaskar Kallakury, Xuefeng Liu, Priscilla A. Furth. Characterizing growth features, allograft generation and transcriptomes of cultured conditionally reprogrammed cells (CRC) prepared from primary triple negative cancer from Brca1-mutant mice. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3918. doi:10.1158/1538-7445.AM2014-3918

Abstract 5576: Tamoxifen fails to induce regression of mammary preneoplasia in mice lacking either one or two intact BRCA1 genes in combination with p53 haploinsufficiency but without evidence of in vivo agonist activity

Background: Reduced BRCA1 and/or p53 function in mammary tissue is associated with tamoxifen resistance in vivo and in vitro. A shift towards tamoxifen agonist activity with reduced BRCA1 function is found in vitro. The goal of this study was to identify which combinations of disrupted Brca1 and p53 gene(s) result in preneoplasia and test for tamoxifen resistance and activity in vivo. Methods: Brca1 homozygous and heterozygous conditional exon 11 knockout and wildtype mice all carrying MMTV-Cre on a p53 wildtype or haploinsufficient background received a 25 mg 60-day constant release tamoxifen pellet (Innovative Research of America, Sarasota, FL) or sham surgery at age 4m, euthanasia/necropsy at age 6m and mammary glands taken for whole mount, histological and western blot (pERK / ERK and pHistone/Histone ratios, cleaved PARP). Cohorts of untreated Brca1f11/WT11/MMTV-Cre/p53+/- and Brca1f11/f11/MMTV-Cre/p53+/- mice were observed to age 12m for mammary cancer. Fisher's exact and Kruskal-Wallis tests were used for statistical analyses. Results: Hyperplastic alveolar nodules at age 6m and cancer development at age 12m were limited to Brca1f11/WT11/MMTV-Cre/p53+/- and Brca1f11/f11/MMTV-Cre/p53+/- mice. Ductal hyperplasia was detected in Brca1f11/WT11/MMTV-Cre/p53+/+, Brca1f11/f11/MMTV-Cre/p53+/+, Brca1f11/WT11/MMTV-Cre/p53+/-, Brca1f11/f11/MMTV-Cre/p53+/- and Brca1WT11/WT11/MMTV-Cre/p53+/- but not wildtype mice. Only Brca1f11/WT11/MMTV-Cre/p53+/+ and Brca1f11/f11/MMTV-Cre/p53+/+ mice showed significant reductions in ductal hyperplasia on tamoxifen. In contrast prevalence of ductal hyperplasia and/or hyperplastic alveolar nodules was not altered by tamoxifen in Brca1WT11/WT11/MMTV-Cre/p53+/-, Brca1f11/WT11/MMTV-Cre/p53+/- or Brca1f11/f11/MMTV-Cre/p53+/- mice. No evidence of tamoxifen activity was found as proliferation measures were either reduced (percentage mammary epithelial cells with nuclear-localized PCNA) or unchanged (pERK / ERK and pHistone/Histone ratios) with tamoxifen treatment in all genotypes. Cleaved PARP was detected in tamoxifen-treated but not control mice. Conclusions: p53 haploinsufficiency in combination with loss of either one or two copies of intact Brca1 was sufficient to induce hyperplastic alveolar nodules and cancer. Tamoxifen resistance was found in all p53 haploinsufficient mice. There was no indication of a shift towards tamoxifen agonist activity, that is, no increase in expression of any proliferative marker with Brca1 deficiency, and apoptosis was activated. Alternative pathways for tamoxifen resistance involving p53 may be responsible for the tamoxifen resistance observed in Brca1 deficient preneoplastic mammary epithelial cells.

Citation Format: Sahar J. Alothman, Weisheng Wang, Priscilla A. Furth. Tamoxifen fails to induce regression of mammary preneoplasia in mice lacking either one or two intact BRCA1 genes in combination with p53 haploinsufficiency but without evidence of in vivo agonist activity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5576. doi:10.1158/1538-7445.AM2014-5576

The methyltransferase EZH2 is not required for mammary cancer development, although high EZH2 and low H3K27me3 correlate with poor prognosis of ER-positive breast cancers

Enhancer of zeste homolog 2 (EZH2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) and its demethylation is catalyzed by UTX. EZH2 levels are frequently elevated in breast cancer and have been proposed to control gene expression through regulating repressive H3K27me3 marks. However, it is not fully established whether breast cancers with different levels of H3K27me3, EZH2 and UTX exhibit different biological behaviors. Levels of H3K27me3, EZH2 and UTX and their prognostic significance were evaluated in 146 cases of breast cancer. H3K27me3 levels were higher in HER2-negative samples. EZH2 expression was higher in cancers that were LN+, size > 20mm, and with higher tumor grade and stage. Using a Cox regression model, H3K27me3 levels and EZH2 expression were identified as independent prognostic factors for overall survival for all the breast cancers studied as well as the ER-positive subgroup. The combination of low H3K27me3 and high EZH2 expression levels were significantly associated with shorter survival. UTX expression was not significantly associated with prognosis and there were no correlations between H3K27me3 levels and EZH2/UTX expression. To determine if EZH2 is required to establish H3K27me3 marks in mammary cancer, Brca1 and Ezh2 were deleted in mammary stem cells in mice. Brca1-deficient mammary cancers with unaltered H3K27me3 levels developed in the absence of EZH2, demonstrating that EZH2 is not a mandatory H3K27 methyltransferase in mammary neoplasia and providing genetic evidence for biological independence between H3K27me3 and EZH2 in this tissue.

Genetically engineered ERα-positive breast cancer mouse models

The majority of human breast cancers are estrogen receptor-positive (ER+), but this has proven challenging to model in genetically engineered mice. This review summarizes information on 21 mouse models that develop ER+ mammary cancer. Where available, information on cancer pathology and gene expression profiles is referenced to assist in understanding which histological subtype of ER+ human cancer each model might represent. ESR1, CCDN1, prolactin, TGFα, AIB1, ESPL1, and WNT1 overexpression, PIK3CA gain of function, as well as loss of P53 (Trp53) or STAT1 are associated with ER+ mammary cancer. Treatment with the PPARγ agonist efatutazone in a mouse with Brca1 and p53 deficiency and 7,12-dimethylbenz(a)anthracene exposure in combination with an activated myristoylated form of AKT1 also induce ER+ mammary cancer. A spontaneous mutant in nude mice that develops metastatic ER+ mammary cancer is included. Age of cancer development ranges from 3 to 26 months and the percentage of cancers that are ER+ vary from 21 to 100%. Not all models are characterized as to their estrogen dependency and/or response to anti-hormonal therapy. Strain backgrounds include C57Bl/6, FVB, BALB/c, 129S6/SvEv, CB6F1, and NIH nude. Most models have only been studied on one strain background. In summary, while a range of models are available for studies of pathogenesis and therapy of ER+ breast cancers, many could benefit from further characterization, and opportunity for development of new models remains.

Trp63 is regulated by STAT5 in mammary tissue and subject to differentiation in cancer

Transformation-related protein 63 (Trp63), the predominant member of the Trp53 family, contributes to epithelial differentiation and is expressed in breast neoplasia. Trp63 features two distinct promoters yielding specific mRNAs encoding two major TRP63 isoforms, a transactivating transcription factor and a dominant negative isoform. Specific TRP63 isoforms are linked to cell cycle arrest, apoptosis, survival, and epithelial mesenchymal transition (EMT). Although TRP63 overexpression in cultured cells is used to elucidate functions, little is known about Trp63 regulation in normal and cancerous mammary tissues. This study used ChIP-seq to interrogate transcription factor binding and histone modifications of the Trp63 locus in mammary tissue and RNA-seq and immunohistochemistry to gauge gene expression. H3K4me2 and H3K4me3 marks coincided only with the proximal promoter, supporting RNA-seq data showing the predominance of the dominant negative isoform. STAT5 bound specifically to the Trp63 proximal promoter and Trp63 mRNA levels were elevated upon deleting Stat5 from mammary tissue, suggesting its role as a negative regulator. The dominant negative TRP63 isoform was localized to nuclei of basal mammary epithelial cells throughout reproductive cycles and retained in a majority of the triple-negative cancers generated from loss of full-length Brca1. Increased expression of dominant negative isoforms was correlated with developmental windows of increased progesterone receptor binding to the proximal Trp63 promoter and decreased expression during lactation was correlated with STAT5 binding to the same region. TRP63 is present in the majority of triple-negative cancers resulting from loss of Brca1 but diminished in less differentiated cancer subtypes and in cancer cells undergoing EMT.

Human Pancreatic Cancer-Associated Stellate Cells Remain Activated after in vivo Chemoradiation

Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extensive fibrotic reaction or desmoplasia and complex involvement of the surrounding tumor microenvironment. Pancreatic stellate cells are a key mediator of the pancreatic matrix and they promote progression and invasion of pancreatic cancer by increasing cell proliferation and offering protection against therapeutic interventions. Our study utilizes human tumor-derived pancreatic stellate cells (HTPSCs) isolated from fine needle aspirates of pancreatic cancer tissue from patients with locally advanced, unresectable pancreatic adenocarcinoma before and after treatment with full-dose gemcitabine plus concurrent hypo-fractionated stereotactic radiosurgery. We show that HTPSCs survive in vivo chemotherapy and radiotherapy treatment and display a more activated phenotype post-therapy. These data support the idea that stellate cells play an essential role in supporting and promoting pancreatic cancer and further research is needed to develop novel treatments targeting the pancreatic tumor microenvironment.

Oestrogen receptor-alpha regulates non-canonical Hedgehog-signalling in the mammary gland

Mesenchymal dysplasia (mes) mice harbour a truncation in the C-terminal region of the Hh-ligand receptor, Patched-1 (mPtch1). While the mes variant of mPtch1 binds to Hh-ligands with an affinity similar to that of wild type mPtch1 and appears to normally regulate canonical Hh-signalling via smoothened, the mes mutation causes, among other non-lethal defects, a block to mammary ductal elongation at puberty. We demonstrated previously Hh-signalling induces the activation of Erk1/2 and c-src independently of its control of smo activity. Furthermore, mammary epithelial cell-directed expression of an activated allele of c-src rescued the block to ductal elongation in mes mice, albeit with delayed kinetics. Given that this rescue was accompanied by an induction in estrogen receptor-alpha (ERα) expression and that complex regulatory interactions between ERα and c-src are required for normal mammary gland development, it was hypothesized that expression of ERα would also overcome the block to mammary ductal elongation at puberty in the mes mouse. We demonstrate here that conditional expression of ERα in luminal mammary epithelial cells on the mes background facilitates ductal morphogenesis with kinetics similar to that of the MMTV-c-src(Act) mice. We demonstrate further that Erk1/2 is activated in primary mammary epithelial cells by Shh-ligand and that this activation is blocked by the inhibitor of c-src, PP2, is partially blocked by the ERα inhibitor, ICI 182780 but is not blocked by the smo-inhibitor, SANT-1. These data reveal an apparent Hh-signalling cascade operating through c-src and ERα that is required for mammary gland morphogenesis at puberty.

STAT signaling in different breast cancer sub-types

This review summarizes information on expression of Signal Transducer and Activator of Transcription (STAT)s 1, 2, 3, 4, 5a/b and 6 in cancer cells from different human breast cancer sub-types. STAT proteins, especially STATs 1, 3 and 5a/b are expressed in some but not all cancers from all of the different major breast cancer sub-types. However, well-designed studies comparing expression patterns at the protein level in cancer and surrounding stromal cells are still needed to fully examine links with prognosis and therapeutic response. Moreover, it is not yet known if distinct expression patterns of STAT proteins could have dissimilar impacts in different sub-types, especially between the luminal A and B ER+ sub-types and the different TNBC sub-types. Recent data indicating that STAT 5 can be activated secondary to a therapeutic intervention and mediate resistance suggests that expression patterns should not only be examined in pre-treatment but also post-treatment samples from different sub-types.

Cardiomyocyte-specific Estrogen Receptor Alpha Increases Angiogenesis, Lymphangiogenesis and Reduces Fibrosis in the Female Mouse Heart Post-Myocardial Infarction

Experimental studies showed that 17β-estradiol (E2) and activated Estrogen Receptors (ER) protect the heart from ischemic injury. However, the underlying molecular mechanisms are not well understood. To investigate the role of ER-alpha (ERα) in cardiomyocytes in the setting of myocardial ischemia, we generated transgenic mice with cardiomyocyte-specific overexpression of ERα (ERα-OE) and subjected them to Myocardial Infarction (MI). At the basal level, female and male ERα-OE mice showed increased Left Ventricular (LV) mass, LV volume and cardiomyocyte length. Two weeks after MI, LV volume was significantly increased and LV wall thickness decreased in female and male WT-mice and male ERα-OE, but not in female ERα-OE mice. ERα-OE enhanced expression of angiogenesis and lymphangiogenesis markers (Vegf, Lyve-1), and neovascularization in the peri-infarct area in both sexes. However, attenuated level of fibrosis and higher phosphorylation of JNK signaling pathway could be detected only in female ERα-OE after MI. In conclusion, our study indicates that ERα protects female mouse cardiomyocytes from the sequelae of ischemia through induction of neovascularization in a paracrine fashion and impaired fibrosis, which together may contribute to the attenuation of cardiac remodelling.

Abstract P5-07-03: The nuclear coactivator amplified in breast cancer 1 maintains tumor initiating cells during development of ductal carcinoma in situ

Introduction: Ductal Carcinoma In Situ (DCIS) has become the most diagnosed breast tumor type in North America. Amplified In Breast Cancer 1 (AIB1) is amplified in 5 to 10% of primary breast tumors. We have recently demonstrated that AIB1 causes development of DCIS lesions in the mammary gland of 30% of the AIB1 transgenic mice. Our laboratory has also shown that deletion of one allele of AIB1 prevents HER2-induced mammary tumor development in mice, suggesting a pivotal role of AIB1 during earlier stage of breast cancer. We hypothesize that AIB1-mediated pathways promote the transformation of the mammary epithelial cells and the alterations of the functional integrity of the mammary gland. By contrast, decrease in AIB1 functionality may result in prevented DCIS initiation and development.

Results: We show by immunohistochemistry that AIB1 is expressed at low levels in normal breast but is highly expressed in DCIS lesions. We investigated the impact of decreasing AIB1 expression on the early transformed MCFDCIS cell line. MCFDCIS cells generate multiacinar disorganized structures with filling of the lumen, loss of polarization and escape from the proliferative suppression. Reduction of AIB1 in human MCFDCIS cells restored a more normal mammary acinar structure with basement membrane in 3D growth in Matrigel. Then, we studied the effect of regulating AIB1 on the histopathology development of the DCIS lesions both prior to DCIS development or in existing MCFDCIS lesions in a xenograft mouse model by subcutaneously injecting MCFDCIS cells deficient or not in AIB1 into nude mice. The MCFDCIS xenografted tumors obtained reproduced the human breast cancer progression and displayed multiple comedo DCIS-like lesions. Decreased levels of AIB1 in MCFDCIS cells, inhibited tumor growth and led to smaller, necrotic lesions. To investigate how AIB1 affects initiation and progression of DCIS, we compared global gene expression changes in MCFDCIS cells +/-AIB1 shRNA in vitro using cDNA array analysis. Among the most significant expression changes observed were genes that are differentially expressed in Breast Cancer Initiating Cells (BCIC) including CD24 and members of the NOTCH signaling pathway (DLL1 and DLL3). We demonstrated by flow cytometric and immunohistochemical analysis that AIB1 reduction in MCFDCIS cells was correlated with significant reduction in the CD24-/CD44+ BCIC population, and a decrease in myoepithelial progenitor cells in the DCIS lesions in vitro and in vivo. Loss of AIB1 in MCFDCIS cells was also accompanied by a loss of expression of NOTCH 2, 3 and 4, JAG2, HES1, GATA3, HER2 and HER3 in vivo.

Conclusions: These data indicate that AIB1 plays a central role in the initiation and maintenance of DCIS and that reduction of AIB1 causes loss of BCIC, loss of components of the NOTCH, HER2 and HER3 signaling pathways and fewer DCIS myoepithelial progenitor cells in vivo. We propose that increased expression of AIB1, through maintenance of BCIC, facilitates formation of DCIS, a necessary step prior to development of invasive disease. Thus, targeting AIB1 may represent a new therapeutic paradigm especially for women with AIB1-positive primary tumor.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-07-03.

The nuclear coactivator amplified in breast cancer 1 maintains tumor-initiating cells during development of ductal carcinoma in situ

The key molecular events required for the formation of Ductal Carcinoma in Situ (DCIS) and its progression to invasive breast carcinoma have not been defined. Here we show that the nuclear receptor coactivator Amplified In Breast cancer 1 (AIB1) is expressed at low levels in normal breast but is highly expressed in DCIS lesions. This is of significance since reduction of AIB1 in human MCFDCIS cells restored a more normal 3D mammary acinar structure. Reduction of AIB1 in MCFDCIS cells, both prior to DCIS development or in existing MCFDCIS lesions in vivo, inhibited tumor growth and led to smaller, necrotic lesions. AIB1 reduction in MCFDCIS cells was correlated with significant reduction in the CD24−/CD44+ Breast Cancer Initiating Cells (BCIC) population, and a decrease in myoepithelial progenitor cells in the DCIS lesions in vitro and in vivo. Loss of AIB1 in MCFDCIS cells was also accompanied by a loss of expression of NOTCH 2, 3 and 4, JAG2, HES1, GATA3, HER2 and HER3 in vivo. These signaling molecules have been associated with differentiation of breast epithelial progenitor cells. These data indicate that AIB1 plays a central role in the initiation and maintenance of DCIS and that reduction of AIB1 causes loss of BCIC, loss of components of the NOTCH, HER2 and HER3 signaling pathways and fewer DCIS myoepithelial progenitor cells in vivo. We propose that increased expression of AIB1, through maintenance of BCIC, facilitates formation of DCIS, a necessary step prior to development of invasive disease.

The PPARγ agonist efatutazone increases the spectrum of well-differentiated mammary cancer subtypes initiated by loss of full-length BRCA1 in association with TP53 haploinsufficiency

Peroxisome proliferator-activated receptor gamma (PPARγ) agonists have anticancer activity and influence cell differentiation. We examined the impact of the selective PPARγ agonist efatutazone on mammary cancer pathogenesis in a mouse model of BRCA1 mutation. Mice with conditional loss of full-length BRCA1 targeted to mammary epithelial cells in association with germline TP53 insufficiency were treated with efatutazone through the diet starting at age 4 months and were euthanized at age 12 months or when palpable tumor reached 1 cm(3). Although treatment did not reduce percentage of mice developing invasive cancer, it significantly reduced prevalence of noninvasive cancer and total number of cancers per mouse and increased prevalence of well-differentiated cancer subtypes not usually seen in this mouse model. Invasive cancers from controls were uniformly estrogen receptor α negative and undifferentiated, whereas well-differentiated estrogen receptor α-positive papillary invasive cancers appeared in efatutazone-treated mice. Expression levels of phosphorylated AKT and CDK6 were significantly reduced in the cancers developing in efatutazone-treated mice. Efatutazone treatment reduced rates of mammary epithelial cell proliferation and development of hyperplastic alveolar nodules and increased expression levels of the PPARγ target genes Adfp, Fabp4, and Pdhk4 in preneoplastic mammary tissue. Intervention efatutazone treatment in mice with BRCA1 deficiency altered mammary cancer development by promoting development of differentiated invasive cancer and reducing prevalence of noninvasive cancer and preneoplastic disease.

Abstract 197: Reduction in lobular but not ductal hyperplasia by the PGR inhibitor ORG33628 in a CYP19A1 overexpressing mouse model of breast cancer risk

Background: The Women's Health Initiative demonstrated increased breast cancer risk in women exposed to estrogen with progesterone. Genetically engineered mice with conditional mammary epithelial cell targeted Cytochrome P45019A1 (CYP19A1/aromatase) over-expression (tet-op-CYP19A1/MMTV-rtTA mice) tested the impact of a selective progesterone receptor (PGR) inhibitor, ORG33628, on mammary hyperplasia and cancer development. This model demonstrates increased percentages of PGR+ mammary epithelial cells (MECs) cells at the hyperplastic stage and triple negative (Estrogen Receptor (ER)-, PGR-, Receptor tyrosine-protein kinase erbB-2 (HER2/neu)-) adenocarcinomas.

Purpose: Test if ORG33628 reduces mammary hyperplasia and blocks cancer formation in tet-op-CYP19A1/MMTV-rtTA mice.

Methods: Female tet-op-CYP19A1/MMTV-rtTA mice were implanted subcutaneously with a pellet containing either ORG33628 7.5mg (60-day release) or placebo at age 10m. A smaller study tested ORG33628 in CYP19A1/MMTV-rtTA/trp53+/- mice. Mice were necropsied at age 12m and mammary tissue examined to determine if ORG33628 altered lobular/ductal hyperplasia prevalence or blocked progression to hyperplastic alveolar nodules (HANs) or cancer. Immunohistochemistry (IHC) was employed to compare MEC proliferative index (PI) (Ki-67) and percentage of MECs expressing nuclear-localized ER/PGR. An uterotropic assay tested if ORG33628 blocked estrogen-induced changes in the uterus/cervix. Ovariectomized 6w old mice were implanted subcutaneously with pellets of 0.72g 17β-estradiol and either ORG33628 or placebo, necropsied 3 days later, and uterine weight, PI and ER/PGR expression compared in uterine and cervical epithelium and stroma.

Results: ORG33628 treatment reduced lobular hyperplasia prevalence (Fisher's exact, p&lt;0.05) and percentages of PGR+ MEC (9.3% to 5.2%, t-test, p&lt;0.05), but did not alter ductal hyperplasia or HAN prevalence or block cancer formation. ORG33628 reduced estrogen-induced uterine weight gain (t-test, p&lt;0.05) and PI in cervical epithelium (38.6% to 15%, t-test, p&lt;0.05) in the uterotropic assay.

Conclusions: ORG33628 reduced lobular but not ductal hyperplasia and did not prevent progression to HANs or cancer. In normal development, estrogen plays the more important role in ductal development and progesterone in lobular development paralleling the isolated impact of ORG33628 on lobular disease here. These results suggest that reducing ductal hyperplasia may be a prerequisite for cancer prevention or that reducing lobular hyperplasia at 10m in this model is too late due to the presence of triple negative cancer progenitor cells.

Support: P30CA051008, RO1CA112176, T32CA009686-15, KG080359. Content solely responsibility of authors and does not necessarily represent official NCI/NIH views.

Citation Format: Sarah A. Dabydeen, Weisheng Wang, Edgar S. Diaz-Cruz, Levy Kopelovich, Robert I. Glazer, Priscilla A. Furth. Reduction in lobular but not ductal hyperplasia by the PGR inhibitor ORG33628 in a CYP19A1 overexpressing mouse model of breast cancer risk. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 197. doi:10.1158/1538-7445.AM2013-197