Genomic Landscape of Normal and Breast Cancer Tissues in a Hungarian Pilot Cohort

A limited number of studies have focused on the mutational landscape of breast cancer in different ethnic populations within Europe and compared the data with other ethnic groups and databases. We performed whole-genome sequencing of 63 samples from 29 Hungarian breast cancer patients. We validated a subset of the identified variants at the DNA level using the Illumina TruSight Oncology (TSO) 500 assay. Canonical breast-cancer-associated genes with pathogenic germline mutations were CHEK2 and ATM. Nearly all the observed germline mutations were as frequent in the Hungarian breast cancer cohort as in independent European populations. The majority of the detected somatic short variants were single-nucleotide polymorphisms (SNPs), and only 8% and 6% of them were deletions or insertions, respectively. The genes most frequently affected by somatic mutations were KMT2C (31%), MUC4 (34%), PIK3CA (18%), and TP53 (34%). Copy number alterations were most common in the NBN, RAD51C, BRIP1, and CDH1 genes. For many samples, the somatic mutational landscape was dominated by mutational processes associated with homologous recombination deficiency (HRD). Our study, as the first breast tumor/normal sequencing study in Hungary, revealed several aspects of the significantly mutated genes and mutational signatures, and some of the copy number variations and somatic fusion events. Multiple signs of HRD were detected, highlighting the value of the comprehensive genomic characterization of breast cancer patient populations

Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents

Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint also give rise to somatic mutation patterns that can be used for treatment prediction.Using whole genome sequencing of an isogenic knockout cell line panel, we find a universal HR deficiency-specific base substitution signature that is similar to COSMIC signature 3. In contrast, we detect different deletion phenotypes corresponding to specific HR mutants. The inactivation of BRCA2 or PALB2 leads to larger deletions, typically with microhomology, when compared to the disruption of BRCA1, RAD51 paralogs, or RAD54. Comparison with the deletion spectrum of Cas9 cut sites suggests that most spontaneously arising genomic deletions are not the consequence of double-strand breaks. Surprisingly, the inactivation of checkpoint kinases ATM and CHK2 has no mutagenic consequences. Analysis of tumor exomes with biallelic inactivating mutations in the investigated genes confirms the validity of the cell line models. We present a comprehensive analysis of sensitivity of the investigated mutants to 13 therapeutic agents for the purpose of correlating genomic mutagenic phenotypes with drug sensitivity.Our results suggest that no single genomic mutational class shows perfect correlation with sensitivity to common treatments, but the contribution of COSMIC signature 3 to base substitutions, or a combined measure of different features, may be reasonably good at predicting platinum and PARP inhibitor sensitivity

Bone homeostasis and breast cancer: implications for complex therapy and the maintenance of bone integrity

The standard of care in bone metastases is antiresorptive therapy. If present in the bone, tumor cells induce a vicious cycle by stimulating the osteoclasts, which further accelerates tumor progression. The widely-used bisphosphonates or the new therapeutic option, denosumab an inhibitor of the receptor activator of NF-kappaB ligand (RANKL), interrupt this vicious cycle, inhibit tumor growth, and in clinical practice prevent skeleton-related events. Adjuvant oncological therapy, including chemotherapy and endocrine manipulations (ovarian ablation and tamoxifen in premenopausal, and aromatase inhibitors in postmenopausal women), increases the bone turnover and the risk of fracture. Awareness is essential for the diagnosis and treatment of cancer therapy-induced bone loss, or its prevention with appropriate calcium and vitamin D supplementation. A new possibility has been suggested for the prevention of relapse: the use of bisphosphonates in the adjuvant setting. Three large studies and their meta-analyses indicate that the inhibition of bone remodeling prevents the growth of dormant tumor cells and cancer relapse in the population of postmenopausal patients with a low-estrogen environment in the skeleton. The similar potential of a RANKL inhibitor is currently under evaluation. Since the maintenance of bone integrity is necessary for the prevention of both therapy-related side-effects and progression of the disease, the management of breast cancer at any stage requires a careful consideration of the bone homeostasis

Differential immunostaining of various types of breast carcinomas for growth hormone-releasing hormone receptor - Apocrine epithelium and carcinomas emerging as uniformly positive

Different classes of breast cancers were explored for their positivity for growth hormone-releasing hormone receptors (GHRH-R) in this pilot study, as no systematic evaluation of such tumors has been performed to date. Seventy-two small primary breast carcinomas were evaluated for GHRH-R expression by immunohistochemistry using a polyclonal antibody and a cutoff value of 10% staining. GHRH-R positivity was detected in 58% of all cases, 20/23 (87%) of invasive lobular carcinomas (ILC) and 22/46 (48%) of invasive ductal carcinomas (IDC). GHRH-R positivity was more frequent in grade 2 tumors (86%), as compared to grade 1 (18%) or grade 3 (47%) cancers. GHRH-R expression was not associated with mitotic scores, the Ki-67 labeling indices or nodal status. IDCs with casting-type calcifications on the mammogram showed positivity for GHRH-R in 9/12 (75%) cases. Most importantly, apocrine epithelium, and all 10 apocrine carcinomas added later to the study were GHRH-R-positive. These preliminary results suggest a greater than average GHRH-R expression in ILCs and IDCs associated with casting-type calcifications on the mammogram. Apocrine carcinomas seem uniformly positive for GHRH-R. Whether these findings could indicate a potential role of GHRH-antagonists in targeted treatment of these types of breast cancer requires further studies

Different Methods of Pretreatment Ki-67 Labeling Index Evaluation in Core Biopsies of Breast Cancer Patients Treated with Neoadjuvant Chemotherapy and Their Relation to Response to Therapy

Increased proliferation activity of breast cancer cells evaluated by Ki-67 immunohistochemistry, i.e. a high Ki-67 labeling index (Ki-67 LI), may predict better tumor regression in case of neoadjuvant chemotherapy. Despite recommendations for the evaluation of Ki-67 LI, there are variations in methodology. We assessed the effect of different evaluation methods on the Ki-67 LI in patients with different response to neoadjuvant chemotherapy. Thirty pretreatment core-biopsy samples of patients receiving neoadjuvant docetaxel-epirubicin chemotherapy with or without capecitabine were evaluated for their Ki-67 LI. Pathologic regression was categorized as no regression, partial regression and complete regression, with 10 cases in each category. Three antibodies (MIB1, B56, SP6), 4 observers and 4 methods (counting or estimating on glass slides and counting or estimating on representative digital images) were compared. The Kruskal-Wallis test and analyses of variance were performed to investigate the differences in Ki-67 LIs between different clinical outcomes (tumor regression categories). Breast carcinomas with pathological complete regression had a higher mean Ki-67 LI than tumors not achieving complete regression with any methods, observers and antibodies investigated, although there was a variation between different evaluations in what may represent high proliferation. Estimating the Ki-67 LI on digital images representing the highest proliferation in the core biopsy seemed the best in separating complete responders from non-responders. High Ki-67 LI values were more likely associated with pathological complete regression independently of the method of evaluation used, although the definition of high proliferation is problematic. Estimating the Ki-67 LI may be an adequate method of evaluation