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Breast white adipose tissue inflammation (BWATi) is associated with obesity and higher breast cancer risk among non-Hispanic white women. Obesity is prevalent in Hispanic/Latina patients with breast cancer, and the occurrence of BWATi in this population is not well-characterized. The association between BWATi and body mass index (BMI) was evaluated in Hispanic/Latina patients with breast cancer who underwent mastectomy. BWATi was defined as the presence of crown-like structures of the breast (CLS-B), detected by CD68 IHC in nontumor breast tissue. BWATi severity was quantified as number of CLS-B/cm2. Adipocyte diameter was measured using hematoxylin and eosin-stained breast tissue sections. Preoperative BMI (within 1 week prior to mastectomy) was categorized as normal (18.5–2), overweight (25.0–2), class I obesity (30.0–2), and class II–III obesity (35.0 kg/m2 or above). Patient charts were abstracted to record clinicopathologic features and liver function tests Ptrend 0.27 CLS-B/cm2) was associated with higher BMI (Ptrend = 0.046) and greater adipocyte diameter (P = 0.04). Adjusting for BMI, neoadjuvant chemotherapy, and elevated alanine aminotransferase were associated with severe BWATi, and current smoking was associated with mild BWATi (all P < 0.05). BWATi was associated with higher BMI in Hispanic/Latina patients with breast cancer, consistent with previously described associations in other populations.

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Supplementary Data from Obesity Is Associated with Inflammation and Elevated Aromatase Expression in the Mouse Mammary Gland

Clinicopathologic features stratified by treatment arm (RNA-seq analysis population).

Supplementary Data from Dietary Polyphenols Suppress Elevated Levels of Proinflammatory Mediators and Aromatase in the Mammary Gland of Obese Mice

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Supplementary Data from Increased Levels of Urinary PGE-M, a Biomarker of Inflammation, Occur in Association with Obesity, Aging, and Lung Metastases in Patients with Breast Cancer

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Supplementary Figure 1 - PDF file 44K, Supplementary Figure 1A-D. Median hormone levels at baseline, C2 and EOS

PDF file - 409K, SNP call plots from the CALGB 40101 patient genotyping on the Illumina 610-Quad platform for the patient/LCL overlap SNPs in genes. R is the combined SNP intensity and theta is the allelic intensity ratio.

Supplementary Methods detailing the methods employed for Copy number alteration (CNA) analysis, Sanger sequencing and supplementary references.

Supplemental Figure 1. Study Design and Patient Disposition Supplemental Figure 2. Change in serum creatinine by visit Supplemental Figure 3. Change in blood urea nitrogen (BUN) by visit Supplemental Figure 4. Maximum observed value in cystatin C by visit Supplemental Figure 5. Minimum Observed Value in Neutrophils by Visit

PDF file - 1866K, The 11 overlap SNPs within genes associated with both patient paclitaxel-induced sensory peripheral neuropathy (P < 0.05) and LCL paclitaxel-induced cytotoxicity (P < 0.001). The Kaplan Meier plots show the probability of the first instance of Grade 2 or greater neuropathy (event) as a function of cumulative paclitaxel dose. The boxplots show the survival of LCLs treated with 12.5 nM paclitaxel (adjusted for percent CEU ancestry) versus each genotype.

Purpose: Response to a complex trastuzumab-based regimen is affected by multiple features of the tumor and its microenvironment. Developing a predictive algorithm is key to optimizing HER2-targeting therapy.Experimental Design: We analyzed 137 pretreatment tumors with mRNA-seq and DNA exome sequencing from CALGB 40601, a neoadjuvant phase III trial of paclitaxel plus trastuzumab with or without lapatinib in stage II to III HER2-positive breast cancer. We adopted an Elastic Net regularized regression approach that controls for covarying features within high-dimensional data. First, we applied 517 known gene expression signatures to develop an Elastic Net model to predict pCR, which we validated on 143 samples from four independent trials. Next, we performed integrative analyses incorporating clinicopathologic information with somatic mutation status, DNA copy number alterations (CNA), and gene signatures.Results: The Elastic Net model using only gene signatures predicted pCR in the validation sets (AUC = 0.76). Integrative analyses showed that models containing gene signatures, clinical features, and DNA information were better pCR predictors than models containing a single data type. Frequently selected variables from the multiplatform models included amplifications of chromosome 6p, TP53 mutation, HER2-enriched subtype, and immune signatures. Variables predicting resistance included Luminal/ER+ features.Conclusions: Models using RNA only, as well as integrated RNA and DNA models, can predict pCR with improved accuracy over clinical variables. Somatic DNA alterations (mutation, CNAs), tumor molecular subtype (HER2E, Luminal), and the microenvironment (immune cells) were independent predictors of response to trastuzumab and paclitaxel-based regimens. This highlights the complexity of predicting response in HER2-positive breast cancer. Clin Cancer Res; 24(21); 5292–304. ©2018 AACR.

Supplementary Table Legend from The 6q22.33 Locus and Breast Cancer Susceptibility

Purpose: We sought to show the relevance of a lymphoblastoid cell line (LCL) model in the discovery of clinically relevant genetic variants affecting chemotherapeutic response by comparing LCL genome-wide association study (GWAS) results to clinical GWAS results.Experimental Design: A GWAS of paclitaxel-induced cytotoxicity was conducted in 247 LCLs from the HapMap Project and compared with a GWAS of sensory peripheral neuropathy in patients with breast cancer (n = 855) treated with paclitaxel in the Cancer and Leukemia Group B (CALGB) 40101 trial. Significant enrichment was assessed by permutation resampling analysis.Results: We observed an enrichment of LCL cytotoxicity-associated single-nucleotide polymorphisms (SNP) in the sensory peripheral neuropathy-associated SNPs from the clinical trial with concordant allelic directions of effect (empirical P = 0.007). Of the 24 SNPs that overlap between the clinical trial (P < 0.05) and the preclinical cytotoxicity study (P < 0.001), 19 of them are expression quantitative trait loci (eQTL), which is a significant enrichment of this functional class (empirical P = 0.0447). One of these eQTLs is located in RFX2, which encodes a member of the DNA-binding regulatory factor X family. Decreased expression of this gene by siRNA resulted in increased sensitivity of Neuroscreen-1(NS-1; rat pheochromocytoma) cells to paclitaxel as measured by reduced neurite outgrowth and increased cytotoxicity, functionally validating the involvement of RFX2 in nerve cell response to paclitaxel.Conclusions: The enrichment results and functional example imply that cellular models of chemotherapeutic toxicity may capture components of the underlying polygenic architecture of related traits in patients. Clin Cancer Res; 19(2); 491–9. ©2012 AACR.

Supplemental Table 1. Post-discontinuation therapies

Purpose: The phase II MONARCH 1 study was designed to evaluate the single-agent activity and adverse event (AE) profile of abemaciclib, a selective inhibitor of CDK4 and CDK6, in women with refractory hormone receptor–positive (HR+), HER2− metastatic breast cancer (MBC).Experimental Design: MONARCH 1 was a phase II single-arm open-label study. Women with HR+/HER2− MBC who had progressed on or after prior endocrine therapy and had 1 or 2 chemotherapy regimens in the metastatic setting were eligible. Abemaciclib 200 mg was administered orally on a continuous schedule every 12 hours until disease progression or unacceptable toxicity. The primary objective of MONARCH 1 was investigator-assessed objective response rate (ORR). Other endpoints included clinical benefit rate, progression-free survival (PFS), and overall survival (OS).Results: Patients (n = 132) had a median of 3 (range, 1–8) lines of prior systemic therapy in the metastatic setting, 90.2% had visceral disease, and 50.8% had ≥3 metastatic sites. At the 12-month final analysis, the primary objective of confirmed objective response rate was 19.7% (95% CI, 13.3–27.5; 15% not excluded); clinical benefit rate (CR+PR+SD≥6 months) was 42.4%, median progression-free survival was 6.0 months, and median overall survival was 17.7 months. The most common treatment-emergent AEs of any grade were diarrhea, fatigue, and nausea; discontinuations due to AEs were infrequent (7.6%).Conclusions: In this poor-prognosis, heavily pretreated population with refractory HR+/HER2− metastatic breast cancer, continuous dosing of single-agent abemaciciclib was well tolerated and exhibited promising clinical activity. Clin Cancer Res; 23(17); 5218–24. ©2017 AACR.

Supplemental Figure 2. Tumor PU-H71 retention at 24 hours post-injection (quantified by standard uptake value) is not explained by plasma radiotracer exposure (quantified by plasma AUC from 10 min to 4 h post-injection, see Methods), as indicated by Spearman Test R-value.

Supplemental Figure 1. Tumor retention of PU-H71 tracer varied considerably between patients. Tumor retention expressed as tumor:bloodpool SUV ratio (y-axis) measured on PET at 4 and 24 hours post tracer-injection.

Supplementary Figure S4: Morphologic and immunophenotypic features of case MB-T88. Supplementary Figure S5: GATA3 mutational spectrum in male breast cancer and female breast cancer and the impact of selected mutations on the survival of male breast cancer patients.

Tumor PU-H71 retention at 24 hours post-injection (quantified by standard uptake value) is not explained by plasma radiotracer exposure (quantified by plasma AUC from 10 min to 4 h post-injection, see Methods), as indicated by Spearman Test R-value.

Supplementary Table S7: Comparative analysis of the frequencies of mutations in luminal A-like and luminal B-like male breast cancer. Supplementary Table S8: Comparative analysis of genes affecting selected functional pathways. Supplementary Table S9: Mutational frequency of male breast cancer vs subsets of female breast cancer from the TCGA study. Supplementary Table S10: Potentially targetable genes mutated exclusively in ER-positive/HER2-negative male breast cancer.

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Supplementary Legend - PDF file 22K, Supplementary Legend

Supplementary Table S11: Comparative analysis of the frequencies of mutations in luminal A-like male breast cancers and subsets of luminal A female breast cancers from the TCGA study. Supplementary Table S12: Comparative analysis of the frequencies of mutations in luminal B-like male breast cancers and subsets of luminal B female breast cancers from the TCGA study.

Supplementary Figure 2 - PDF file 275K, Supplementary Figure 2A-D. Changes in hormone levels over time per patient; responders (stable disease >6 months) highlighted in red

Supplementary figures and methods

PDF file - 68K, Expression and eQTL status of the patient/LCL overlap genes and SNPs.

Purpose: Male breast cancer is rare, and its genomic landscape has yet to be fully characterized. Lacking studies in men, treatment of males with breast cancer is extrapolated from results in females with breast cancer. We sought to define whether male breast cancers harbor somatic genetic alterations in genes frequently altered in female breast cancers.Experimental Design: All male breast cancers were estrogen receptor–positive, and all but two were HER2-negative. Fifty-nine male breast cancers were subtyped by immunohistochemistry, and tumor–normal pairs were microdissected and subjected to massively parallel sequencing targeting all exons of 241 genes frequently mutated in female breast cancers or DNA-repair related. The repertoires of somatic mutations and copy number alterations of male breast cancers were compared with that of subtype-matched female breast cancers.Results: Twenty-nine percent and 71% of male breast cancers were immunohistochemically classified as luminal A–like or luminal B–like, respectively. Male breast cancers displayed a heterogeneous repertoire of somatic genetic alterations that to some extent recapitulated that of estrogen receptor (ER)-positive/HER2-negative female breast cancers, including recurrent mutations affecting PIK3CA (20%) and GATA3 (15%). ER-positive/HER2-negative male breast cancers, however, less frequently harbored 16q losses, and PIK3CA and TP53 mutations than ER-positive/HER2-negative female breast cancers. In addition, male breast cancers were found to be significantly enriched for mutations affecting DNA repair–related genes.Conclusions: Male breast cancers less frequently harbor somatic genetic alterations typical of ER-positive/HER2-negative female breast cancers, such as PIK3CA and TP53 mutations and losses of 16q, suggesting that at least a subset of male breast cancers are driven by a distinct repertoire of somatic changes. Given the genomic differences, caution may be needed in the application of biologic and therapeutic findings from studies of female breast cancers to male breast cancers. Clin Cancer Res; 22(16); 4045–56. ©2016 AACR.

PET detects subcentimeter PU-H71 retention by breast cancer metastases. 65-year-old female with stage IV breast cancer, off-treatment. 124I-PU-H71 PET (right), CT (left), and fusion PET/CT (middle) images show corresponding axial planes of chest, obtained 24 hours post-injection. Tracer has cleared from blood (asterisk, aorta) with sustained PU-H71 retention by biopsy-proven subcentimeter pulmonary metastasis (arrow) and left internal mammary and mediastinal nodal metastases (arrowheads).

Supplementary Figure 1: Validation of somatic mutations in orthogonal methods. Supplementary Figure S2: Mutations and copy number alterations in ER-positive/HER2-negative male and female breast cancers. Supplementary Figure S3: Cancer cell fraction and clonality of non-synonymous mutations in male breast cancer.

Recently, we identified a novel breast cancer susceptibility locus at 6q22.33 following a genome-wide association study in the Ashkenazi Jewish genetic isolate. To replicate these findings, we did a case-control association analysis on 6q22.33 (rs2180341) in an additional 487 Ashkenazi Jewish breast cancer cases and in an independent non-Jewish, predominantly European American, population of 1,466 breast cancer cases and 1,467 controls. We confirmed the 6q22.33 association with breast cancer risk in the replication cohorts [per-allele odds ratio (OR), 1.18; 95% confidence interval (95% CI), 1.04-1.33; P = 0.0083], with the strongest effect in the aggregate meta-analysis of 3,039 breast cancer cases and 2,616 Ashkenazi Jewish and non-Jewish controls (per-allele OR, 1.24; 95% CI, 1.13-1.36; P = 3.85 × 10-7). We also showed that the association was slightly stronger with estrogen receptor–positive tumors (per-allele OR, 1.35; 95% CI, 1.20-1.51; P = 2.2 × 10-5) compared with estrogen receptor–negative tumors (per-allele OR, 1.19; 95% CI, 0.97-1.47; P = 0.1). Furthermore, this study provides a novel insight into the functional significance of 6q22.33 in breast cancer susceptibility. Due to the stronger association of 6q22.33 with estrogen receptor–positive breast cancer, we examined the effect of candidate genes on estrogen receptor response elements. Upon transfection of overexpressed RNF146 in the MCF-7 breast cancer cell line, we observed diminished expression of an estrogen receptor response element reporter construct. This study confirms the association of 6q22.33 with breast cancer, with slightly stronger effect in estrogen receptor–positive tumors. Further functional studies of candidate genes are in progress, and a large replication analysis is being completed as part of an international consortium. (Cancer Epidemiol Biomarkers Prev 2009;18(9):2468–75)

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Methods that support the supplemental data provided

Supplementary Figure S1. White adipose tissue inflammation. A. CLS-B positive breast WAT. H&E (upper panel) and anti-CD68 immunostaining (lower panel); 40x (left panel) and 400x (right panel). Arrow indicates CLS-B. B. CLS-B negative breast WAT. H&E (upper panel) and anti-CD68 immunostaining (lower panel); 40x (left panel) and 400x (right panel). WAT, white adipose tissue; CLS-B, crown-like structures of the breast.

Supplementary eTables 1-12

Supplementary Table 1 from The 6q22.33 Locus and Breast Cancer Susceptibility

PDF file - 65K, Empirical P-values generated from patient/LCL enrichment analyses using a range of P-value inclusion thresholds for SNP overlap.

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Purpose: Obesity, insulin resistance, and elevated levels of circulating proinflammatory mediators are associated with poorer prognosis in early-stage breast cancer. To investigate whether white adipose tissue (WAT) inflammation represents a potential unifying mechanism, we examined the relationship between breast WAT inflammation and the metabolic syndrome and its prognostic importance.Experimental Design: WAT inflammation was defined by the presence of dead/dying adipocytes surrounded by macrophages forming crown-like structures (CLS) of the breast. Two independent groups were examined in cross-sectional (cohort 1) and retrospective (cohort 2) studies. Cohort 1 included 100 women undergoing mastectomy for breast cancer risk reduction (n = 10) or treatment (n = 90). Metabolic syndrome–associated circulating factors were compared by CLS-B status. The association between CLS of the breast and the metabolic syndrome was validated in cohort 2, which included 127 women who developed metastatic breast cancer. Distant recurrence-free survival (dRFS) was compared by CLS-B status.Results: In cohorts 1 and 2, breast WAT inflammation was detected in 52 of 100 (52%) and 52 of 127 (41%) patients, respectively. Patients with breast WAT inflammation had elevated insulin, glucose, leptin, triglycerides, C-reactive protein, and IL6 and lower high-density lipoprotein cholesterol and adiponectin (P < 0.05) in cohort 1. In cohort 2, breast WAT inflammation was associated with hyperlipidemia, hypertension, and diabetes (P < 0.05). Compared with patients without breast WAT inflammation, the adjusted HR for dRFS was 1.83 (95% CI, 1.07–3.13) for patients with inflammation.Conclusions: WAT inflammation, a clinically occult process, helps to explain the relationship between metabolic syndrome and worse breast cancer prognosis. Clin Cancer Res; 22(9); 2283–9. ©2015 AACR.

Purpose:124I-PU-H71 is an investigational first-in-class radiologic agent specific for imaging tumor epichaperome formations. The intracellular epichaperome forms under cellular stress and is a clinically validated oncotherapeutic target. We conducted a first-in-human study of microdose 124I-PU-H71 for PET to study in vivo biodistribution, pharmacokinetics, metabolism, and safety; and the feasibility of epichaperome-targeted tumor imaging.Experimental Design:Adult patients with cancer (n = 30) received 124I-PU-H71 tracer (201±12 MBq, Results:124I-PU-H71 PET detected tumors of different cancer types (breast, lymphoma, neuroblastoma, genitourinary, gynecologic, sarcoma, and pancreas). 124I-PU-H71 was retained by tumors for several days while it cleared rapidly from bones, healthy soft tissues, and blood. Radiation dosimetry is favorable and patients suffered no adverse effects.Conclusions:Our first-in-human results demonstrate the safety and feasibility of noninvasive in vivo detection of tumor epichaperomes using 124I-PU-H71 PET, supporting clinical development of PU-H71 and other epichaperome-targeted therapeutics.

Preclinical and clinical models of HER2-positive breast cancer show that human epidermal growth factor receptor 2 (HER2)-targeted therapy with trastuzumab adds significant benefits and modest risks to conventional cytotoxic therapies. Building on this advance will likely depend on elucidation of relevant signaling pathways and mechanisms of action for effective HER2-targeted therapies. (Clin Cancer Res 2009;15(20):6311–3)

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Supplementary Figures 1-5