Angela Burleigh

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time—to our knowledge—in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.

Recent advances in next generation sequencing have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1–13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.

ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium

The telomeric amplicon at 8p12 is common in oestrogen receptor‐positive (ER+) breast cancers. Array‐CGH and expression analyses of 1172 primary breast tumours revealed that ZNF703 was the single gene within the minimal amplicon and was amplified predominantly in the Luminal B subtype. Amplification was shown to correlate with increased gene and protein expression and was associated with a distinct expression signature and poor clinical outcome. ZNF703 transformed NIH 3T3 fibroblasts, behaving as a classical oncogene, and regulated proliferation in human luminal breast cancer cell lines and immortalized human mammary epithelial cells. Manipulation of ZNF703 expression in the luminal MCF7 cell line modified the effects of TGFβ on proliferation. Overexpression of ZNF703 in normal human breast epithelial cells enhanced the frequency of in vitro colony‐forming cells from luminal progenitors. Taken together, these data strongly point to ZNF703 as a novel oncogene in Luminal B breast cancer.

A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation

IntroductionThe extracellular signals regulating mammary epithelial cell growth are of relevance to understanding the pathophysiology of mammary epithelia, yet they remain poorly characterized. In this study, we applied an unbiased approach to understanding the functional role of signalling molecules in several models of normal physiological growth and translated these results to the biological understanding of breast cancer subtypes.MethodsWe developed and utilized a cytogenetically normal clonal line of hTERT immortalized human mammary epithelial cells in a fibroblast-enhanced co-culture assay to conduct a genome-wide small interfering RNA (siRNA) screen for evaluation of the functional effect of silencing each gene. Our selected endpoint was inhibition of growth. In rigorous postscreen validation processes, including quantitative RT-PCR, to ensure on-target silencing, deconvolution of pooled siRNAs and independent confirmation of effects with lentiviral short-hairpin RNA constructs, we identified a subset of genes required for mammary epithelial cell growth. Using three-dimensional Matrigel growth and differentiation assays and primary human mammary epithelial cell colony assays, we confirmed that these growth effects were not limited to the 184-hTERT cell line. We utilized the METABRIC dataset of 1,998 breast cancer patients to evaluate both the differential expression of these genes across breast cancer subtypes and their prognostic significance.ResultsWe identified 47 genes that are critically important for fibroblast-enhanced mammary epithelial cell growth. This group was enriched for several axonal guidance molecules and G protein–coupled receptors, as well as for the endothelin receptor PROCR. The majority of genes (43 of 47) identified in two dimensions were also required for three-dimensional growth, with HSD17B2, SNN and PROCR showing greater than tenfold reductions in acinar formation. Several genes, including PROCR and the neuronal pathfinding molecules EFNA4 and NTN1, were also required for proper differentiation and polarization in three-dimensional cultures. The 47 genes identified showed a significant nonrandom enrichment for differential expression among 10 molecular subtypes of breast cancer sampled from 1,998 patients. CD79A, SERPINH1, KCNJ5 and TMEM14C exhibited breast cancer subtype–independent overall survival differences.ConclusionDiverse transmembrane signals are required for mammary epithelial cell growth in two-dimensional and three-dimensional conditions. Strikingly, we define novel roles for axonal pathfinding receptors and ligands and the endothelin receptor in both growth and differentiation.

The testosterone-dependent and independent transcriptional networks in the hypothalamus of Gpr54 and Kiss1 knockout male mice are not fully equivalent

BackgroundHumans and mice with loss of function mutations in GPR54 (KISS1R) or kisspeptin do not progress through puberty, caused by a failure to release GnRH. The transcriptional networks regulated by these proteins in the hypothalamus have yet to be explored by genome-wide methods.ResultsWe show here, using 1 million exon mouse arrays (Exon 1.0 Affymetrix) and quantitative polymerase chain reaction (QPCR) validation to analyse microdissected hypothalamic tissue from Gpr54 and Kiss1 knockout mice, the extent of transcriptional regulation in the hypothalamus. The sensitivity to detect important transcript differences in microdissected RNA was confirmed by the observation of counter-regulation of Kiss1 expression in Gpr54 knockouts and confirmed by immunohistochemistry (IHC). Since Gpr54 and Kiss1 knockout animals are effectively pre-pubertal with low testosterone (T) levels, we also determined which of the validated transcripts were T-responsive and which varied according to genotype alone. We observed four types of transcriptional regulation (i) genotype only dependent regulation, (ii) T only dependent regulation, (iii) genotype and T-dependent regulation with interaction between these variables, (iv) genotype and T-dependent regulation with no interaction between these variables. The results implicate for the first time several transcription factors (e.g. Npas4, Esr2), proteases (Klk1b22), and the orphan 10-transmembrane transporter TMEM144 in the biology of GPR54/kisspeptin function in the hypothalamus. We show for the neuronal activity regulated transcription factor NPAS4, that distinct protein over-expression is seen in the hypothalamus and hippocampus in Gpr54 knockout mice. This links for the first time the hypothalamic-gonadal axis with this important regulator of inhibitory synapse formation. Similarly we confirm TMEM144 up-regulation in the hypothalamus by RNA in situ hybridization and western blot.ConclusionsTaken together, global transcriptional profiling shows that loss of GPR54 and kisspeptin are not fully equivalent in the mouse hypothalamus.

Of Germ Cells, Trophoblasts, and Cancer Stem Cells

The trophoblastic theory of cancer, proposed in the early 1900s by Dr John Beard, may not initially seem relevant to current cancer models and treatments. However, the underpinnings of this theory are remarkably similar to those of the cancer stem cell (CSC) theory. Beard noticed that a significant fraction of germ cells never reach their final destination as they migrate during embryonic development from the hindgut to the germinal ridge. In certain situations, upon aberrant stimulation, these vagrant germ cells are able to generate tumors. Simplistically, the CSC theory surmises that a small population of tumorigenic cells exists, which initiate and maintain tumors, and these cells have a likely origin in normal stem cells. Both these theories are based on the potential of a single primitive cell to form a tumor. This has a major implication for cancer therapy, in that only a small percentage of cells need to be targeted to ablate a tumor.

Topical rapamycin (sirolimus) for the treatment of uncomplicated tufted angiomas in two children and review of the literature

The mTOR inhibitor rapamycin is used systemically for the treatment of vascular lesions. We report the first use of topical rapamycin for the successful treatment of two cases of tufted angioma. The evidence for the use of topical rapamycin in other dermatologic conditions is summarized to aid in clinical decision making on preparations and anticipated side effects.

Skin Confident: A skin health and acne educational intervention to improve Acne Quality of Life measures in adolescents

remover was not provided. The survey was offered to all participants voluntarily. A total of 123 subjects participated in the skin cancer screening, with 118 of them responding to the survey (a 95.9% response rate). The survey questions and responses are shown in Table I. There were 87 females and 31 males; 102 of the 118 respondents (86.4%) had at least a college education. More than half of the female respondents (47 of 87 [54%]) reported wearing nail polish at the time of screening—on their fingernails only (9 of 87 [10.3%]), on their toenails only (17 of 87 [19.5%]), or both (21 of 87 [24.1%]). Many respondents (70 of 118 [59.3%]) reported nail problems, with 5.1% of them (6 of 118) reporting a brown or black line on 1 or more nails. Most participants (82 of 118 [69.5%]) were not aware that examination of the nails was a part of a complete skin examination. In contrast, most participants (73 of 118 [61.9%]) were aware that scalp and hair examinations were integral to a complete skin examination. Almost all respondents (112 of 118 [94.9%]) stated that the advertisements did not mention that their nails would be examined during the skin cancer screening, and the same number of respondents (112 of 118 [94.9%]) reported that the advertisements did not advise removing nail polish for the screening. Advertisements for this skin cancer screening event ( poster and the AAD website) did not mention nail examinations or specify that nail polish should be removed before the screening. Furthermore, the AAD skin cancer screening form does not have schematics of the nails to record potential malignancies during the screening (Fig 1). However, the AAD website defines a dermatologist as a physician who specializes in treating the skin, hair, nails, and mucous membranes. The AAD screened 66,639 people in 2017 (Yvonne Urbikas, AAD, personal communication, May 22, 2018). Free skin cancer screenings are opportunities to simply and effectively screen patients for skin and nail malignancies so that they can be referred for further follow-up and/or biopsy. Our results suggest the need for increased efforts in educating patients that nails are an integral part of complete skin examinations. To that end, the AAD and skin screening sites should advertise, document, and include the nails in these screenings.

Pediatric longitudinal melanonychia

A 9-year-old boy of Asian descent was referred to the outpatient pediatric dermatology clinic with an asymptomatic linear brown discolouration affecting his left middle fingernail ([Figure 1A][1]). This discolouration had been present for about one year and had not changed in thickness or pigment

Abstract 1611: Epithelial-mesenchymal-epithelial transition induced by long term exposure to TGFB1 creates cellular heterogeneity

Reversible and dynamic transitions between epithelial and mesenchymal cellular states (EMT/MET) contribute to cancer progression and dissemination. Whereas EMT facilitates initial steps of tumour cell detachment, MET is likely required for colonization at distant sites. Although MET is generally perceived as mirroring EMT, we hypothesize that MET entails its own set of novel and/or differentially active molecular circuitries, generating cells with features distinct from the original epithelial state. Using an in vitro TGFβ1-induced EMT/MET model, we demonstrated that MET generates co-existing heterogeneous cell populations (Reverted-Epithelial or RE-cells) with novel phenotypic and functional properties, such as increased self-renewal, in vivo increased tumourigenicity and distinct chemoresistance properties. Overall, our results indicate that MET is a permissive process, driving cellular plasticity towards heterogeneity and with it, creating novel biological signatures of relevance for cancer growth. Citation Format: Patricia Oliveira, Joana Carvalho, Sara Rocha, Mafalda Azevedo, Andre F. Vieira, Daniel Ferreira, Nuno Mendes, Ines Reis, Joao Vinagre, Alireza Heravi-Moussavi, Joana B. Nunes, Jorge Lima, Valdemar Maximo, Angela Burleigh, Calvin Roskelley, Joana Paredes, Fatima Carneiro, David Huntsman, Carla Oliveira. Epithelial-mesenchymal-epithelial transition induced by long term exposure to TGFB1 creates cellular heterogeneity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1611.