Immune profiling of pre- and post-treatment breast cancer tissues from the SWOG S0800 neoadjuvant trial

BACKGROUND

How the immune microenvironment changes during neoadjuvant chemotherapy of primary breast cancer is not well understood.

METHODS

We analyzed pre- and post-treatment samples from 60 patients using the NanoString PanCancer IO360™ assay to measure the expression of 750 immune-related genes corresponding to 14 immune cell types and various immune functions, and assessed TIL counts and PD-L1 protein expression by immunohistochemistry. Treatment associated changes in gene expression levels were compared using t-test with Bonferroni correction. TIL count, PD-L1 protein and immune metagenes were compared using Wilcoxon test. Baseline immune markers were correlated with pathologic complete response (pCR) using estrogen receptor and treatment arm adjusted logistic regression.

RESULTS

At baseline, high TIL counts and high expression of chemoattractant cytokines (CCL21, CCL19) and cytotoxic T cell markers were associated with higher pCR rate. High expression of stromal genes (VEGFB, TGFB3, PDGFB, FGFR1, IGFR1), mast and myeloid inflammatory cell metagenes, stem cell related genes (CD90, WNT11, CTNNB1) and CX3CR1, and IL11RA were associated with residual disease (RD). After treatment, in cases with pCR, TIL counts and most immune genes decreased significantly. Among RD cases, TIL counts and PD-L1 expression did not change but cellular stress and hypoxia associated genes (DUSP1, EGR1), and IL6, CD36, CXCL2, CD69 and the IL8/VEGF metagene increased.

CONCLUSIONS

Activated T cells in the tumor microenvironment are associated with pCR whereas stromal functions are associated with residual disease. Most immune functions decrease during neoadjuvant chemotherapy but several immunotherapy targets (PD-L1, IL6, IL8) remain expressed in RD suggesting potential therapeutic strategies.

Antiproliferative Sesquiterpenes from the Red Sea Soft Coral Sarcophyton Glaucum

The Red Sea soft coral Sarcophyton glaucum was investigated for its sesquiterpene content. A novel 1,2-dioxolane sesquiterpene alcohol, dioxosarcoguaiacol (1) along with the known (+)-alloaromadendrene are reported. The structure of the new sesquiterpene was determined on the basis of extensive spectral analyses. (+)-Alloaromadendrene showed potent inhibition of the proliferation of the highly malignant + SA mammary epithelial cells at a dose of 20μM.

Abstract P4-03-01: Pathway level complementarity of germline and somatic events in breast cancer

Background: Progression from a normal cell state to cancer requires multiple genomic hits in key regulatory pathways. In the case of hereditary cancer syndromes, some of these hits occur in the germline, but additional somatic mutations are required for malignant transformation. We hypothesize that this paradigm could be extended to sporadic cancers as well. What somatic mutation function as a cancer driver event may be determined by the constellation of germline variants a person is born with. We propose that even rare, non-recurrent, high functional impact germline variants in genes involved in cancer-related pathways could influence the biological impact of somatic mutations in other cancer-related genes. The goal of the current analysis was to examine associations between pathway alterations caused by high functional impact germline variants or somatic mutations in the “hallmarks of cancer” pathways in breast cancer.

Methods: We obtained germline DNA sequencing and copy number variation (CNV) data from the breast cancer TCGA cohort. After population clustering with the HapMap cohort, we selected a homogeneous group of 796 patients of Western European ancestry and downloaded the matching somatic mutations (SNVs and INDELs) that were available for 750 cases, that comprise the current study population. Germline CNVs were classified as recurrent or rare losses or gains. Potentially pathogenic germline variants (SNPs) were obtained from the PanCancer Altas project. All germline or somatic mutations were mapped at the gene level to the 50 Cancer Hallmarks pathway collection. We designated a pathway mutated if at least 1 gene had a germline or a somatic mutation. Complementarity between pathway alterations by germline and somatic events were evaluated using the Fisher exact test adjusted for multiple comparisons.

Results: At the germline level, 2,057 genes were affected by CNVs (mean 30, range 3-151 genes/patient), and a total of 43 genes carried germline pathogenic SNPs that affected 13.8% of the patients. At the somatic level, we detected 40,881 high functional impact mutations (mean 54.3, range 1-3889 mutations/patient) in 13,080 genes (mean 50.8, range 1-3166 genes/patient). The 50 Cancer Hallmark pathways contained 4386 genes (mean 146.5, range 32-200 genes/pathway), and were mutated in the majority of the patients (85% germline, 93% somatic). Several pathways, such as HEME_METABOLISM, INTERFERON_ALPHA_RESPONSE, and KRAS_SIGNALING, were frequently affected by germline alterations, while the somatic mutations were most frequently involved in the COMPLEMENT, E2F_TARGET, and UV_RESPONSE_UP. Interaction analysis revealed co-occurrence between MYC_TARGETS_V1 (germline) and UV_RESPONSE_DN (somatic) or MTORC1_SINGALING (somatic) (p<0.01), and TNFA_SIGNALING_VIA_NFKB (germline) and IL6_JAK_STAT3_SIGNALING (germline) with E2F_TARGETS (somatic) (p<0.01). We also observed an exclusive relationship between germline alterations in BILE_ACID_METABOLISM and somatic mutations in COMPLEMENT pathway (p<0.01).

Conclusions: Our results highlight the importance of pathway-level analysis of germline alterations in breast cancer, which might help to understand the interrelationship between germline and somatic alterations in breast cancer.

Citation Format: Qing T, Marczyk M, Wali V, Gunasekharan V, Patwardhan G, Pusztai L, Hatzis C. Pathway level complementarity of germline and somatic events in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-03-01.

Comparison of epigenetic aging in normal breast tissue from women with and without breast cancer

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Background: Age is one of the most important risk factors for developing breast cancer. However, why increasing age is associated with increasing incidence of breast cancer remains poorly understood. We hypothesize that accumulated epigenetic alterations in the breast contribute to the development of breast cancer, and that such changes accumulate more rapidly in the breast during the lifetime of women who develop breast cancer as compared to their healthy peers. We therefore sought to identify an epigenetic pattern of accelerated breast tissue “aging” in women with breast cancer. Methods: Samples of normal breast tissue were collected from four cohorts of women: age < 50 years with and without breast cancer, and age ≥50 years with and without breast cancer (BC). Samples were obtained from the Susan G. Komen Tissue Bank at IU Simon Cancer Center, reduction mammoplasties and adjuvant mastectomy specimens at Yale. The Illumina Human 450K BeadChip microarray was used to generate DNA methylation profiles. Data was analyzed using the “Epigenetic Clock”, a published biomarker of aging based on 353 specific CpGs in the human genome. Clinical data collected for each subject included: age, height, weight, ethnicity, medical and reproductive history, tobacco and alcohol use, family history of breast cancer, current medications, and tumor characteristics. Results: Normal breast tissue samples from 90 subjects were analyzed (age < 50 with BC = 22, age < 50 without BC = 30, age ≥50 with BC = 15, age ≥50 without BC = 23). Age range was 24-82 years and 18-82 years for cohorts with and without BC respectively. In the cohort with BC, 95% of tumors were estrogen receptor-positive. Overall, DNA methylation tissue age (DNAmAge) was strongly correlated with chronologic age (r = 0.88, p < 0.001). However, normal breast tissue from women with breast cancer demonstrated significantly accelerated DNAmAge as compared to healthy peers (p < 0.001). Conclusions: Normal breast tissue from women with breast cancer demonstrates evidence of an accelerated epigenetic "aging" process. DNAmAge of normal breast tissue may prove to be a useful tool in identifying those women at highest risk, and lend insight into novel mechanisms of breast cancer prevention.

Abstract P4-06-05: Transcriptional heterogeneity correlates with chemotherapy sensitivity in triple negative breast cancer and varies by molecular subtype

Purpose: Different molecular subtypes of breast cancer are believed to have different degrees of molecular heterogeneity. However, the heterogeneity of breast cancer subtypes has not been formally compared. The goal of this analysis was to develop metrics of global transcriptional heterogeneity, compare heterogeneity across breast cancer subtypes and assess whether heterogeneity metrics correlate with sensitivity to chemotherapy in basal-like cancers.

Methods: Affymetrix U133A gene expression data from 836 breast cancers (basal n = 219, HER2-like n = 147, luminal A n = 343, luminal B n = 127) were analyzed. Among the basal-like cancers, 128 received neoadjuvant chemotherapy (pathologic complete response, pCR, n = 44; residual disease, RD, n = 94). Molecular class was assigned by the PAM50 classifier. We used the average pairwise Pearson distance, the sum of eigenvalues of the correlation matrix and multi-dimensional scaling dispersions of the probe set expression values to quantify heterogeneity. Distribution of each metric within the different subtypes was estimated from 500 bootstrapped cohorts of 80 cases in each subtype. We used analysis of variance (ANOVA) to evaluate the significance of the differences in heterogeneity between subtypes.

Results: All three heterogeneity metrics yielded concordant results. Within subtypes, heterogeneity was greatest in basal-like cancers followed by HER2-like, luminal B and luminal A (see figure). Luminal A cancers were distinctly less heterogeneous than the rest. Basal-like cancers with RD were more heterogeneous than those with pCR. The best metric to separate basal tumors with pCR versus RD was the sum of eigenvalues shown below.

Conclusion: Breast cancer molecular subtypes differ in transcriptional heterogeneity. Luminal A cancers have the lowest within group heterogeneity while basal like cancers have the highest. Among the basal-like cancers, those with high chemotherapy sensitivity (pCR) are more homogeneous than those with RD suggesting that transcriptional heterogeneity might be contributing to increased resistance to therapy in this subgroup.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-06-05.

Anticancer and anti-inflammatory sulfur-containing semisynthetic derivatives of sarcophine

Sarcophine (1), a cembranoid diterpene is known to inhibit the process of tumorigenesis. Sarcophine can be isolated in large amounts from the Red Sea soft coral Sarcophyton glaucum and hence is an ideal target for semisynthetic or biocatalytic modifications. Hydroxylated derivatives of 1 were reported to improve its anticancer activity. Despite the promising results and ready availability, there are limited attempts towards further diversifying the library of sarcophine derivatives. Hence, the current study targets the epoxide ring to generate sulfur-containing derivatives of sarcophine by reacting it with ammonium thiocyanate and Lawesson's reagent. Structure elucidation of the products was based on extensive 1D and 2D NMR and high resolution mass spectrometry, in addition to mechanistic considerations. The effect of these derivatives on highly malignant +SA mammary epithialial cell proliferation is reported. Anti-inflammatory potential of sarcophine and its derivatives is also demonstrated.

Evaluation of the efficacy, safety and tolerability of Tacrolimus ointment in Indian patients of moderate to severe atopic dermatitis: a multicentric, open label, phase III study

AIM OF STUDY

Tacrolimus, a topical immunomodulator, has been introduced as a new treatment for moderate to severe atopic dermatitis. The present study was conducted to evaluate the efficacy, safety and tolerability of Tacrolimus ointment in patients of atopic dermatitis in an Indian setting.

METHODS

The present study was a prospective, open, multicentric, Phase III trial. The duration of study was 5 weeks, including a 3-week active treatment period, preceded by a 1-week washout phase and followed by a 1-week follow-up phase. Patients diagnosed to be suffering from moderate to severe atopic dermatitis as per the Rajka and Langeland criteria were treated with Tacrolimus ointment 0.03% twice daily. Efficacy was assessed by modified Eczema Area Sensitivity Index (mEASI) score, patient's and physician's global assessment. Tolerability and safety was assessed by physical examination, laboratory parameters and evaluation of adverse events.

RESULTS

There was a statistically significant decrease in the modified Eczema Area Sensitivity Index (mEASI) score (P< 0.05). Patient's and Physician's global evaluation of treatment was complete resolution to very good improvement in most of the patients. The laboratory values were within normal limits. The drug was well tolerated.

CONCLUSIONS

This study confirms the efficacy and safety of Tacrolimus ointment 0.03% in Indian patients of moderate to severe atopic dermatitis.

Iatrogenic pulmonary overpressure accident

An unconscious victim of an overdose was intubated with an endotracheal tube to prevent aspiration. The respiratory therapist deflated the cuff of the endotracheal tube to allow for a retrograde oral air leak and then tightly attached the oxygen tube directly to the endotracheal tube. Seconds later there was a loud pop as the oxygen tube blew off the end of the endotracheal tube. The patient sustained both a hemodynamic and a neurologic decompensation as the result of marked pulmonary overinflation, with bilateral pneumothoraces and probable cerebral and coronary artery air emboli. We present the case in the hope that it will help avoid any such future occurrences.