Phyllodes tumors with and without fibroadenoma-like areas display distinct genomic features and may evolve through distinct pathways

Breast fibroepithelial lesions (fibroadenomas and phyllodes tumors) are underpinned by recurrent; MED12; exon 2 mutations, which are more common in fibroadenomas and benign phyllodes tumors.; TERT; promoter hotspot mutations have been documented in phyllodes tumors, and found to be more frequent in borderline and malignant lesions. Several lines of evidence suggest that a subset of phyllodes tumors might arise from fibroadenomas. Here we sought to investigate the genetic differences between phyllodes tumors with fibroadenoma-like areas vs. those without. We retrieved data for 16 borderline/ malignant phyllodes tumors, including seven phyllodes tumors with fibroadenoma-like areas and nine phyllodes tumors without fibroadenoma-like areas, which had been previously subjected to targeted capture massively parallel sequencing. Whilst; MED12; exon 2 mutations were significantly more frequent in tumors with fibroadenoma-like areas (71 vs. 11%), an enrichment in genetic alterations targeting; bona fide; cancer genes was found in those without fibroadenoma-like areas, in particular in; EGFR; mutations and amplifications (78 vs. 14%). No significant difference in the frequency of; TERT; genetic alterations was observed (71% in cases with fibroadenoma-like areas vs 56% in those without fibroadenoma-like areas). Our data suggest that the development of phyllodes tumors might follow two different evolutionary pathways: a; MED12; -mutant pathway that involves the progression from a fibroadenoma to a malignant phyllodes tumor; and a; MED12; -wild-type pathway, where malignant phyllodes tumors arise de novo through the acquisition of genetic alterations targeting cancer genes. Additional studies are warranted to confirm our observations and define whether the outcome differs between both pathways

Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma

Purpose:; Lobular carcinoma; in situ; (LCIS) is a preinvasive lesion of the breast. We sought to define its genomic landscape, whether intralesion genetic heterogeneity is present in LCIS, and the clonal relatedness between LCIS and invasive breast cancers.; Experimental Design:; We reanalyzed whole-exome sequencing (WES) data and performed a targeted amplicon sequencing validation of mutations identified in 43 LCIS and 27 synchronous more clinically advanced lesions from 24 patients [9 ductal carcinomas; in situ; (DCIS), 13 invasive lobular carcinomas (ILC), and 5 invasive ductal carcinomas (IDC)]. Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic trees were defined using validated computational methods.; Results:; WES of 43 LCIS lesions revealed a genomic profile similar to that previously reported for ILCs, with; CDH1; mutations present in 81% of the lesions. Forty-two percent (18/43) of LCIS were found to be clonally related to synchronous DCIS and/or ILCs, with clonal evolutionary patterns indicative of clonal selection and/or parallel/branched progression. Intralesion genetic heterogeneity was higher among LCIS clonally related to DCIS/ILC than in those nonclonally related to DCIS/ILC. A shift from aging to APOBEC-related mutational processes was observed in the progression from LCIS to DCIS and/or ILC in a subset of cases.; Conclusions:; Our findings support the contention that LCIS has a repertoire of somatic genetic alterations similar to that of ILCs, and likely constitutes a nonobligate precursor of breast cancer. Intralesion genetic heterogeneity is observed in LCIS and should be considered in studies aiming to develop biomarkers of progression from LCIS to more advanced lesions

Genomic profiling of primary and recurrent Adult Granulosa Cell Tumors of the Ovary

Adult-type granulosa cell tumor (aGCT) is a rare malignant ovarian sex cord-stromal tumor, harboring recurrent FOXL2 c.C402G/p.C134W hotspot mutations in 97% of cases. These tumors are considered to have a favorable prognosis, however aGCTs have a tendency for local spread and late recurrences, which are associated with poor survival rates. We sought to determine the genetic alterations associated with aGCT disease progression. We subjected primary non-recurrent aGCTs (n = 7), primary aGCTs that subsequently recurred (n = 9) and their matched recurrences (n = 9), and aGCT recurrences without matched primary tumors (n = 10) to targeted massively parallel sequencing of ≥410 cancer-related genes. In addition, three primary non-recurrent aGCTs and nine aGCT recurrences were subjected to FOXL2 and TERT promoter Sanger sequencing analysis. All aGCTs harbored the FOXL2 C134W hotspot mutation. TERT promoter mutations were found to be significantly more frequent in recurrent (18/28, 64%) than primary aGCTs (5/19, 26%, p = 0.017). In addition, mutations affecting TP53, MED12, and TET2 were restricted to aGCT recurrences. Pathway annotation of altered genes demonstrated that aGCT recurrences displayed an enrichment for genetic alterations affecting cell cycle pathway-related genes. Analysis of paired primary and recurrent aGCTs revealed that TERT promoter mutations were either present in both primary tumors and matched recurrences or were restricted to the recurrence and absent in the respective primary aGCT. Clonal composition analysis of these paired samples further revealed that aGCTs display intra-tumor genetic heterogeneity and harbor multiple clones at diagnosis and relapse. We observed that in a subset of cases, recurrences acquired additional genetic alterations not present in primary aGCTs, including TERT, MED12, and TP53 mutations and CDKN2A/B homozygous deletions. Albeit harboring relatively simple genomes, our data provide evidence to suggest that aGCTs are genetically heterogeneous tumors and that TERT promoter mutations and/or genetic alterations affecting other cell cycle-related genes may be associated with disease progression and recurrences

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.</p

Immunohistochemical Assessment of HRAS Q61R Mutations in Breast Adenomyoepitheliomas

AIMS Breast adenomyoepitheliomas (AMEs) are uncommon tumors. Most estrogen receptor (ER)-positive AMEs have mutations in PI3K pathway genes, whereas ER-negative AMEs usually harbor concurrent mutations affecting the HRAS Q61 hotspot and PI3K pathway genes. Here, we sought to determine the sensitivity and specificity of RAS Q61R immunohistochemical (IHC) analysis for detection of HRAS Q61R mutations in AMEs. METHODS AND RESULTS 26 AME (14 ER-positive, 12 ER-negative) previously subjected to massively parallel sequencing (n=21) or Sanger sequencing (n=5) of the HRAS Q61 hotspot locus were included in this study. All AMEs were subjected to IHC using a monoclonal (SP174) RAS Q61R-specific antibody, in addition to detailed histopathologic analysis. Nine ER-negative AMEs harbored HRAS mutations, including Q61R (n=7) and Q61K (n=2) mutations. 5/7 (71%) AMEs with HRAS Q61R mutations were positive by IHC, whereas none of the AMEs lacking HRAS Q61R mutations (n=17) were immunoreactive. RAS Q61R immunoreactivity was restricted to the myoepithelium in 80% (4/5) of cases, whereas one case displayed immunoreactivity in both the epithelial and myoepithelial components. RAS Q61R IHC-positive AMEs were associated with infiltrative borders (P<0.001), necrosis (P<0.01) and mitotic index in the epithelial (P<0.05) and myoepithelial (P<0.01) components. RAS Q61R IHC assessment did not detect Q61K mutations (0/2). CONCLUSIONS IHC analysis of RAS Q61R displays a high specificity (100%) and moderate sensitivity (71%) for detection of HRAS Q61R mutations in breast AMEs, and appears not to detect HRAS Q61K mutations. IHC analysis of RAS Q61R may constitute a useful marker in the diagnostic workup of ER-negative AMEs

Assessment of HMGA2 and PLAG1 rearrangements in breast adenomyoepitheliomas

Genetics: uncommon breast tumors linked genetically to salivary gland cancer A subset of benign breast tumors known as adenomyoepitheliomas may be driven by gene fusions found in related cancers elsewhere in the body. Adenomyoepitheliomas are rare benign tumors characterized by the proliferation of both luminal epithelial cells and adjacent myoepithelial cells. Since these tumors resemble a common type of salivary gland cancer called pleomorphic adenoma that often harbors genomic rearrangements involving two particular genes, Jorge Reis-Filho from Memorial Sloan Kettering Cancer Center in New York City, USA, and colleagues looked for similar oncogenic fusions in 13 breast adenomyoepitheliomas with no known causative genetic alterations. They identified a gene fusion in one of their 13 tumor samples, suggesting that a subset of adenomyoepitheliomas may be genetically related to pleomorphic adenomas. The findings could aid in future treatment of both diseases

Immunohistochemical assessment of HRAS

AIMS Breast adenomyoepitheliomas (AMEs) are uncommon tumors. Most estrogen receptor (ER)-positive AMEs have mutations in PI3K pathway genes, whereas ER-negative AMEs usually harbor concurrent mutations affecting the HRAS Q61 hotspot and PI3K pathway genes. Here, we sought to determine the sensitivity and specificity of RAS Q61R immunohistochemical (IHC) analysis for detection of HRAS Q61R mutations in AMEs. METHODS AND RESULTS 26 AME (14 ER-positive, 12 ER-negative) previously subjected to massively parallel sequencing (n=21) or Sanger sequencing (n=5) of the HRAS Q61 hotspot locus were included in this study. All AMEs were subjected to IHC using a monoclonal (SP174) RAS Q61R-specific antibody, in addition to detailed histopathologic analysis. Nine ER-negative AMEs harbored HRAS mutations, including Q61R (n=7) and Q61K (n=2) mutations. 5/7 (71%) AMEs with HRAS Q61R mutations were positive by IHC, whereas none of the AMEs lacking HRAS Q61R mutations (n=17) were immunoreactive. RAS Q61R immunoreactivity was restricted to the myoepithelium in 80% (4/5) of cases, whereas one case displayed immunoreactivity in both the epithelial and myoepithelial components. RAS Q61R IHC-positive AMEs were associated with infiltrative borders (P<0.001), necrosis (P<0.01) and mitotic index in the epithelial (P<0.05) and myoepithelial (P<0.01) components. RAS Q61R IHC assessment did not detect Q61K mutations (0/2). CONCLUSIONS IHC analysis of RAS Q61R displays a high specificity (100%) and moderate sensitivity (71%) for detection of HRAS Q61R mutations in breast AMEs, and appears not to detect HRAS Q61K mutations. IHC analysis of RAS Q61R may constitute a useful marker in the diagnostic workup of ER-negative AMEs