Radisky, Derek C.

Abstract Transcriptome profiling using RNA sequencing (RNA-seq) of bulk formalin-fixed paraffin-embedded (FFPE) tissue blocks is a standard method in biomedical research. However, when used on tissues with diverse cell type compositions, it yields averaged gene expression profiles, complicating biomarker identification due to variations in cell proportions. To address the need for optimized strategies for defining individual cell type compositions from bulk FFPE samples, we constructed single-cell RNA-seq reference data for breast tissue and tested cell type deconvolution methods. Initial simulation experiments showed similar performances across multiple commonly used deconvolution methods. However, the introduction of FFPE artifacts significantly impacted their performances, with a root mean squared error (RMSE) ranging between 0.04 and 0.17. Scaden, a deep learning-based method, consistently outperformed the others, demonstrating robustness against FFPE artifacts. Testing these methods on our 62-sample RNA-seq benign breast disease cohort in which cell type composition was estimated using digital pathology approaches, we found that pre-filtering of the reference data enhanced the accuracy of most methods, realizing up to a 32% reduction in RMSE. To support further research efforts in this domain, we introduce SCdeconR, an R package designed for streamlined cell type deconvolution assessments and downstream analyses.

Abstract Background: In breast cancer, the spatial relationship between immune and tumor cells is increasingly recognized as critical in determining the efficacy of neoadjuvant therapy (NAT). This study investigated how the distribution of immune cells, particularly CD8+ T cells, relative to tumor cells affects treatment outcomes. Methods: Biopsies from 104 breast cancer patients were examined, both pre- and post-NAT, using multiplex immunohistochemistry (mIHC). This study focused on the density and distribution of CD8+ T cells, CD68+ macrophages, FoxP3+ regulatory T cells, and other immune markers. Results: The spatial proximity of CD8+ T cells within 20 µm of cancer cells (N20-CD8+T) was strongly correlated with improved clinical outcomes across diverse tumor subtypes and NAT regimens. A significant post-NAT decrease in CD4+, CD68+, and FoxP3+ cells highlights notable shifts in the tumor immune landscape. A noteworthy finding was the positive correlation between CXCL9 expression and N20-CD8+T cells, suggesting a mechanism for immune cell recruitment and interaction within the tumor microenvironment. These results highlight the complex interplay among NAT, immune cell modifications, and patient outcomes. Conclusions: This study revealed that the proximity of N20-CD8+ T cells to tumor cells is consistently associated with favorable NAT outcomes, transcending tumor subtypes, and treatment differences. This highlights the potential of immune cell dynamics, especially CD8+ T cells, as predictive biomarkers for therapeutic responses in breast cancer, underscoring their vital role in tumor immunity.

Abstract Objectives: Mammographic microcalcifications (calcs) are a sentinel marker of in-situ and invasive breast cancer (BC) but most calcs reflect benign breast disease (BBD). BBD comprises a diverse set of lesions, variably associated with increased BC risk. While calc frequency data for the modern era are limited, historically, calcs were reported in 11% of BBD biopsies. Some studies suggest that calcs in BBD impact BC risks; however, the frequency and BC risks associated with calcs during the percutaneous biopsy era have not been clearly established. Accordingly, we assessed the association of calcs with specific BBD lesions and BC risk in a large contemporaneous BBD cohort including detailed pathology review. Methods: A cohort of 4,819 patients with percutaneously diagnosed BBD from 2002-2013 at Mayo Clinic, were identified. The cohort was followed from 6 months after biopsy until censoring, BC diagnosis, or December 2021. Mean follow-up was 11.3 (SD=5.1) years for BBD patients who remained cancer-free in follow-up compared with 7.4 (SD=4.3) years for cases. Histology of all biopsies were reviewed microscopically to record pathologic findings. A natural language processing algorithm (NLPA) was developed and utilized to identify the presence of calcs based on pathology reports. NLPA results were compared to 300 matched biopsy reports, taken as ground truth. We performed age-adjusted Cox proportional hazards regression to assess hazard ratios (HRs) with 95% confidence intervals (CIs) for specific BBD lesions, stratified by the presence (calc+) or absence of calcs (calcs-), with estimation of an interaction term to test for differences in risks by calc strata. Standardized incidence ratios (SIRs) estimated risks for calc+ and calc- BBD lesions versus matched strata for Iowa SEER population-based BC incidence rates. Results: The NLPA achieved sensitivity=0.993 and specificity=0.986. Overall, 42.8% of BBD biopsies were calc+, including 49.1% of biopsies preceding BC and 42.4% of biopsies not preceding BC (Chi-square p=0.02). Overall, risks of BC among women with BBD calc+ biopsies did not differ significantly from those of women with calc- BBD: HR=1.13 (95% CI: 0.90,1.41), p=0.290. SIRs were also similar for the two groups; women with BBD calc+ biopsies had an SIR =2.00 (95% CI: 1.72, 2.33) and BBD calc- biopsies yielded an SIR= 1.91 (95% CI: 1.64,2.22) (Table 1). HRs were similar for specific calc+ and calc- BBD lesions, with progressively higher risks for non-proliferative disease (NP), proliferative disease without atypia (PDWA) and atypical hyperplasia (AH) (pinteraction=0.55). Interaction terms were not significant for any specific lesion, apart from a marginally significant result for dilated ducts, wherein risks were marginally higher for calc- lesions (pInteraction =0.048), perhaps representing a chance finding. SIRs for calc+ versus calc- BBD lesions were also similar. Overall, 77.3% of AH was calc+; for AH calc+, SIR=3.76 (95%CI: 2.74-5.17) and for AH calc-, SIR=4.41 (95%CI: 2.56-7.59). Conclusion: In this recent, larger percutaneous BBD cohort, calcs were present in 42.8% of all specimens, representing a marked increase compared with historical BBD data, particularly those dominated by surgical biopsy for diagnosis and preceding implementation of full-field digital mammography. In this study, calcs in percutaneously diagnosed BBD were not associated with increased BC risk. Table 1: Comparison of standard incidence ratio of subsequent breast cancer with and without microcalcifications in benign breast disease by histologic impression (NP = non-proliferative disease, PDWA = proliferative disease without atypia, and AH = atypical hyperplasia). (1) compared to Iowa SEER population Citation Format: Sarah Schrup, Robert Vierkant, Stacey Winham, Celine Vachon, Derek Radisky, Jodi Carter, Laura Pacheco-Spann, Matthew Jensen, Amy Degnim, Mark Sherman. Benign breast disease and microcalcifications in percutaneous biopsies and breast cancer risk [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS07-02.

While RNA sequencing and multi-omic approaches have significantly advanced cancer diagnosis and treatment, their limitation in preserving critical spatial information has been a notable drawback. This spatial context is essential for understanding cellular interactions and tissue dynamics. Multiplex digital spatial profiling (MDSP) technologies overcome this limitation by enabling the simultaneous analysis of transcriptome and proteome data within the intact spatial architecture of tissues. In breast cancer research, MDSP has emerged as a promising tool, revealing complex biological questions related to disease evolution, identifying biomarkers, and discovering drug targets. This review highlights the potential of MDSP to revolutionize clinical applications, ranging from risk assessment and diagnostics to prognostics, patient monitoring, and the customization of treatment strategies, including clinical trial guidance. We discuss the major MDSP techniques, their applications in breast cancer research, and their integration in clinical practice, addressing both their potential and current limitations. Emphasizing the strategic use of MDSP in risk stratification for women with benign breast disease, we also highlight its transformative potential in reshaping the landscape of breast cancer research and treatment.

Abstract Over 1 million women in the U.S. undergo radiologically guided percutaneous biopsies annually. Of these, 75% reveal benign breast disease (BBD), typically surrounded by normal breast lobules, which are proposed to reflect the biology of the breast parenchyma diffusely. With aging, normal lobules undergo involution, and delays in this process are linked to increased breast cancer (BC) risk. Because BBD patients are at increased risk of developing BC, and pathologic classification only stratifies risks among groups of patients, novel methods for individual BC risk prediction are needed to guide precision management. Prior literature has shown that most proliferating epithelial cells in normal lobules do not express estrogen receptor (i.e., ER-/Ki67+), whereas co-expression is frequent in BC precursors and in BCs (i.e., ER+/Ki67+). Thus we developed and applied a novel quantitative dual ER/Ki67 stain to BBD biopsies from the well-characterized contemporary Mayo Clinic BBD cohort (2002-2013) to assess differences by levels of lobular involution and tissue type (BBD vs. normal), as well as associations with BC risk. We identified 100 BBD biopsies preceding BC (cases) and 100 biopsies from cancer-free women (controls), frequency-matched on age and length of follow-up. A multiplex immunofluorescence assay was developed to detect ER/Ki67 coexpression in cytokeratin positive epithelial cells in normal lobules or BBD lesions in FFPE tissue sections. An inverse normal transformation was applied to cell counts and proportions and associations were assessed for levels of lobular involution, tissue type (normal lobule vs. BBD), and case status using t-tests and linear regression models. The final data set included 1152 normal lobules or BBD lesions in biopsies of 177 subjects (88 cases and 89 controls). In univariate analyses, normal lobules showing delayed age related involution included higher counts of ER-/Ki67+, ER+/Ki67- and ER+/Ki67+ cells, and the lowest proportion of ER+/Ki67- cells (p<0.03; all). In separate analyses comparing presence vs. absence, detection of any ER+/Ki67+ cells was suggestively more common in non-involuted vs. involuted lobules. Compared with normal lobules, BBD showed higher counts and proportions of ER+/Ki67- and ER+/Ki67+ cells and lower values for ER-/Ki67+ (all p<0.001). In these preliminary results, marker expression in normal lobules and in BBD did not differ by case-control status. Preliminarily, we find that ER+/Ki67+ cells are increased in normal lobules with delayed age-related involution and in BBD lesions, consistent with their associations with increased BC risk. These findings are consistent with the risk reducing effects of endocrine chemoprevention and may serve as useful biomarkers in prevention therapy. In this analysis, limited to only a few lobules and BBD lesions per biopsy, ER+/Ki67+ cell counts and proportions did not vary significantly by case-control status. Citation Format: Melody L. Stallings-Mann, Robert A. Vierkant, Stacey J. Winham, Bryan McCauley, Matt R. Jensen, Sophie Noel, Laura Pacheco-Spann, Celine M. Vachon, Amy C. Degnim, Derek C. Radisky, Mark E. Sherman. Measurement of ER and Ki67 coexpression in cytokeratin positive epithelial cells in benign breast disease (BBD) percutaneous biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB328.

Abstract Background: Age-related lobular involution (ARLI), characterized by regression of breast epithelial tissue during the peri-and post-menopausal period, plays a crucial role in breast cancer risk. Delayed or incomplete ARLI is linked with increased postmenopausal breast cancer susceptibility.This study focuses on unraveling the molecular mechanisms of ARLI, drawing parallels with the well-characterized postpartum involution (PPI). Our aim was to discover biomarkers differentiating women who progressed through ARLI from those with stagnant ARLI. Methods: We utilized the Mayo Clinic Benign Breast Disease (BBD) cohort, analyzing 108 perimenopausal women aged 45-55 who had a subsequent benign biopsy between 2-15 years later. We assessed Lobular Involution (Ll) status by comparing the number and size of lobules in initial and subsequent biopsies. RNA profiling of initial biopsies was performed using NanoString 10360 and BC360, identifying differentially expressed genes between ARLI progression and stagnation. Immunohistochemistry (IHC) mapped the expression of these biomarkers in epithelial lobules. Results: We identified 37 genes with significant differential expression, highlighting Leukemia Inhibitory Factor Receptor (LIFR) as upregulated in ARLI stagnant samples. LIFR, part of the IL-6 cytokine signaling pathway, is known for its role in the induction of apoptosis during PPI via pSTAT3 activation. Our IHC analyses of initial biopsies of women who differentially progress through ARLI confirmed differential expression of LIFR that is coordinately regulated with pSTAT3. Conclusion: Our findings reveal significant parallels between ARLI and PPI. Future research will assess how LIFR/pSTAT3 signaling is linked to induction of apoptotic markers in perimenopausal women and will investigate how anomalies in the LIFR/pSTAT3 pathway might contribute to heightened breast cancer risk in women with delayed or incomplete ARLI. This study not only sheds light on the complex biological processes of aging in breast tissue but also opens new avenues for breast cancer risk assessment and prevention strategies. Citation Format: Jaida C. Lue, Derek Radisky, Melody Stallings-Mann, Mark Sherman, Amy Degnim, Bryan McCauley, Tanya Hoskin. Deciphering the link between aging, lobular involution, and breast cancer risk: The role of LIFR/pSTAT3 signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 849.

Abstract Triple negative breast cancer (TNBC) represents an aggressive and therapeutically challenging breast cancer subtype with higher incidence and mortality rates in non-Hispanic Black (NHB) women. This disparity persists even after adjusting for socioeconomic factors, tumor biology, and quality of care. The study aims to unravel specific molecular mechanisms underlying this disparity, with a focus on Hedgehog signaling pathways in premenopausal NHB women. Understanding these mechanisms is vital for developing targeted therapies and personalized medicine approaches to address these health disparities. Our research utilized a unique cohort of NHB and non-Hispanic White (NHW) women who underwent breast reduction surgery at the Mayo Clinic and donated breast tissue samples for our study. We isolated RNA from whole tissue sections from a cohort of 12 NHB and 40 NHW women who were parous and premenopausal at time of surgery. We performed gene expression profiling using NanoString BC360 and IO360 assays. This allowed us to identify a distinct gene expression signature characteristic of basal-like/TNBC and indicative of heightened activity in the Hedgehog signaling pathway. We also employed advanced cell culture techniques to generate tissue organoids and subculture human mammary epithelial cells (HMECs) that preserve the intrinsic characteristics of the original tissue samples. We found that significantly differential expression of IL20RA and SOX10, principal factors in the gene expression signature, were preserved in both the derived organoids and the HMECs. These results suggest a potential intrinsic difference in the activation of the Hedgehog pathway in the breast epithelial cells of NHB women. This activation may contribute to increased proliferation and transformation of basal stem cells within the breast, possibly fueling the development and progression of TNBC. The implication of activated Hedgehog signaling in NHB women opens new avenues for understanding TNBC disparities. IL20RA and SOX10 represent potential biomarkers for TNBC risk that may serve as a stratification tool for NHB women. The results of this study have the potential to improve assessment and management of TNBC risk among NHB women, thereby contributing significantly to reducing health disparities in breast cancer outcomes. Citation Format: Jennifer Vanessa Cabezas, Savanna Touré, Matthew Wilson, Melody L. Stallings Mann, Laura M. Pacheco-Spann, Joshua W. Ogony, Mark E. Sherman, Derek C. Radisky. Identifying molecular mechanisms in triple negative breast cancer disparities: Unveiling the role of Hedgehog signaling in non-Hispanic Black women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2139.

Abstract Breast cancer (BC) remains a leading health concern worldwide and is often undetected until the cancer metastasizes. Early detection can limit the need for aggressive treatments and improve prognosis. We analyzed early immune and molecular markers in benign breast disease (BBD) biopsies prior to BC development to identify women at elevated risk of developing node-positive invasive BC, which might direct surveillance and prevention efforts aimed at reducing incidence of this disease. Utilizing the Mayo Clinic BBD cohort, we compared women who developed node-positive BC following their BBD biopsy (cases; n=42) with those who remained cancer-free (controls; n=37), matched on patient age and biopsy date. We used NanoString nCounter system to identify differentially expressed genes (DEGs) between cases and controls. We also developed a multiplex immunofluorescence (mIF) approach using Opal system by Akoya Biosciences for comprehensive marker detection in FFPE tissue, enabling correlation of cells expressing DEGs with innate and adaptive immune cells. Digitized images were segmented, and cell phenotyping, and spatial relationships were compared between cases and controls. Our findings revealed significantly increased expression levels of IRF8 (interferon regulatory factor 8, a factor involved in immune cell differentiation) in controls as compared to cases and found that increased IRF8 expression in cases is correlated with delayed cancer onset. Additionally, controls exhibited higher frequencies of CD4+, CD8+, CD68+, CD20+ and CD11c+ immune cells, and lower frequency of Ki67+ staining, with a notable increase of CD11c+/CD68+ cells, a marker for M1 type macrophages, indicating a pro-inflammatory, antitumorigenic immune microenvironment polarization. Furthermore, our mIF analyses offer new insights into spatial biomarker localization, enhancing prognostic accuracy. Our findings suggest that decreased numbers of immune cells in BBD biopsies may be associated with increased risk of developing axillary node-positive BC. This research underscores the importance of dissecting molecular and immune interactions in BBD for assessing the risk of this disease. Our results have the potential to improve individualized risk assessment, leading to more targeted surveillance and informed screening, potentially reducing BC incidence and mortality through early intervention. This study not only contributes to our understanding of BC pathogenesis but also opens avenues for developing novel preventive strategies. Citation Format: Matilde Rossi, Nicole Cruz-Reyes, Melody L. Stallings Mann, Bryan M. McCauley, Tanya L. Hoskin, Robert A. Vierkant, Stacey J. Winham, Amy C. Degnim, Mark E. Sherman, Derek C. Radisky. Interferon regulatory factor 8 (IRF8) as a biomarker for early detection and prevention of axillary lymph node-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4773.

Abstract Benign breast disease (BBD) affects over one million women annually in the United States and is diagnosed in nearly half of all women during their lifetime. Pseudoangiomatous stromal hyperplasia (PASH), a common BBD subtype, is characterized by an overaccumulation of tissue fibroblasts. Current research suggests a pivotal role of the immune microenvironment in progression of BBD to breast cancer, suggesting its composition as a determinant of breast cancer risk. Our study evaluates whether fibroblast variations and immune microenvironment differences in BBD biopsies containing PASH lesions are associated with subsequent breast cancer development. We evaluated BBD biopsies from women who subsequently developed breast cancer (cases, N=5) or remained cancer-free (controls, N=5). Using Opal-based multiplex immunofluorescence (mIF) assays, we mapped expression of fibroblast markers linked to breast cancer associated fibroblasts (CAFs), including vimentin (VIM), smooth muscle actin (ACTA2), fibroblast specific protein-1 (S100A4/FSP1), fibroblast associated protein (FAP), integrin beta-1 (CD29/ITGB1), and platelet derived growth factor receptor beta (PDGFRβ) and markers of key immune cells (T cells: CD4, CD8; dendritic cells: CD11c; B cells: CD20; and macrophages: CD68) along with MKI67 as a proliferation marker. Our results revealed marked differences in fibroblast marker expression and immune cell populations between these groups in the normal lobules in the BBD biopsies. PASH cases showed elevated PDGFRβ and CD29/ITGB1 expression in VIM-positive fibroblasts, markers characteristic of CAF subtypes known to accumulate in more aggressive tumor microenvironments. Conversely, a higher percentage of FSP1+/VIM+ cells, similar to that of a different CAF subtype, was noted in the lobules of PASH controls. This difference in biomarker expression, along with corresponding variations in immune cell counts, suggests a complex interplay between fibroblast composition and immune response that ultimately modulate cancer risk in PASH-containing BBD tissues. Additionally, increased MKI67 expression in PASH cases potentially signals the higher likelihood of cancer development. This work advances our understanding of fibroblast heterogeneity in BBD and its implications for breast cancer risk and progression, and paves the way for innovative strategies to improve clinical outcomes for BBD patients to reduce their incidence of breast cancer. Citation Format: Nicole Cruz-Reyes, Matilde Rossi, Melody Stallings Mann, Bryan McCauley, Tanya Hoskin, Robert Vierkant, Stacey Winham, Amy Degnim, Mark E. Sherman, Derek C. Radisky. Fibroblast diversity and immune microenvironment in pseudoangiomatous stromal hyperplasia (PASH): Associations with breast cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 283.

AbstractThe fibrotic tumor microenvironment is a pivotal therapeutic target. Nintedanib, a clinically approved multikinase antifibrotic inhibitor, is effective against lung adenocarcinoma (ADC) but not squamous cell carcinoma (SCC). Previous studies have implicated the secretome of tumor‐associated fibroblasts (TAFs) in the selective effects of nintedanib in ADC, but the driving factor(s) remained unidentified. Here we examined the role of tissue inhibitor of metalloproteinase‐1 (TIMP‐1), a tumor‐promoting cytokine overproduced in ADC‐TAFs. To this aim, we combined genetic approaches with in vitro and in vivo preclinical models based on patient‐derived TAFs. Nintedanib reduced TIMP‐1 production more efficiently in ADC‐TAFs than SCC‐TAFs through a SMAD3‐dependent mechanism. Cell culture experiments indicated that silencing TIMP1 in ADC‐TAFs abolished the therapeutic effects of nintedanib on cancer cell growth and invasion, which were otherwise enhanced by the TAF secretome. Consistently, co‐injecting ADC cells with TIMP1‐knockdown ADC‐TAFs into immunocompromised mice elicited a less effective reduction of tumor growth and invasion under nintedanib treatment compared to tumors bearing unmodified fibroblasts. Our results unveil a key mechanism underlying the selective mode of action of nintedanib in ADC based on the excessive production of TIMP‐1 in ADC‐TAFs. We further pinpoint reduced SMAD3 expression and consequent limited TIMP‐1 production in SCC‐TAFs as key for the resistance of SCC to nintedanib. These observations strongly support the emerging role of TIMP‐1 as a critical regulator of therapy response in solid tumors.