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1.
Cell ; 166(1): 126-39, 2016 Jun 30.
Article in English | MEDLINE | ID: mdl-27368101

ABSTRACT

The HIF transcription factor promotes adaptation to hypoxia and stimulates the growth of certain cancers, including triple-negative breast cancer (TNBC). The HIFα subunit is usually prolyl-hydroxylated by EglN family members under normoxic conditions, causing its rapid degradation. We confirmed that TNBC cells secrete glutamate, which we found is both necessary and sufficient for the paracrine induction of HIF1α in such cells under normoxic conditions. Glutamate inhibits the xCT glutamate-cystine antiporter, leading to intracellular cysteine depletion. EglN1, the main HIFα prolyl-hydroxylase, undergoes oxidative self-inactivation in the absence of cysteine both in biochemical assays and in cells, resulting in HIF1α accumulation. Therefore, EglN1 senses both oxygen and cysteine.


Subject(s)
Breast Neoplasms/metabolism , Cysteine/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Hypoxia-Inducible Factor-Proline Dioxygenases/metabolism , Paracrine Communication , Triple Negative Breast Neoplasms/metabolism , Amino Acid Transport System y+/metabolism , Animals , Glutamic Acid/metabolism , Humans , MCF-7 Cells , Mice
2.
Cell ; 154(2): 311-324, 2013 Jul 18.
Article in English | MEDLINE | ID: mdl-23830207

ABSTRACT

Tumor cells metastasize to distant organs through genetic and epigenetic alterations, including changes in microRNA (miR) expression. Here we find miR-22 triggers epithelial-mesenchymal transition (EMT), enhances invasiveness and promotes metastasis in mouse xenografts. In a conditional mammary gland-specific transgenic (TG) mouse model, we show that miR-22 enhances mammary gland side-branching, expands the stem cell compartment, and promotes tumor development. Critically, miR-22 promotes aggressive metastatic disease in MMTV-miR-22 TG mice, as well as compound MMTV-neu or -PyVT-miR-22 TG mice. We demonstrate that miR-22 exerts its metastatic potential by silencing antimetastatic miR-200 through direct targeting of the TET (Ten eleven translocation) family of methylcytosine dioxygenases, thereby inhibiting demethylation of the mir-200 promoter. Finally, we show that miR-22 overexpression correlates with poor clinical outcomes and silencing of the TET-miR-200 axis in patients. Taken together, our findings implicate miR-22 as a crucial epigenetic modifier and promoter of EMT and breast cancer stemness toward metastasis.


Subject(s)
Breast Neoplasms/pathology , Chromatin Assembly and Disassembly , Epithelial-Mesenchymal Transition , Gene Expression Regulation, Neoplastic , MicroRNAs/metabolism , Neoplasm Metastasis , Neoplastic Stem Cells/metabolism , 5-Methylcytosine/analogs & derivatives , Animals , Breast Neoplasms/metabolism , Cytosine/analogs & derivatives , Cytosine/metabolism , Humans , Mice , Mice, Transgenic , Neoplasm Transplantation , Proto-Oncogene Proteins/metabolism , RNA Interference , Transplantation, Heterologous
3.
Nature ; 611(7936): 594-602, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36352222

ABSTRACT

Genome sequencing of cancers often reveals mosaics of different subclones present in the same tumour1-3. Although these are believed to arise according to the principles of somatic evolution, the exact spatial growth patterns and underlying mechanisms remain elusive4,5. Here, to address this need, we developed a workflow that generates detailed quantitative maps of genetic subclone composition across whole-tumour sections. These provide the basis for studying clonal growth patterns, and the histological characteristics, microanatomy and microenvironmental composition of each clone. The approach rests on whole-genome sequencing, followed by highly multiplexed base-specific in situ sequencing, single-cell resolved transcriptomics and dedicated algorithms to link these layers. Applying the base-specific in situ sequencing workflow to eight tissue sections from two multifocal primary breast cancers revealed intricate subclonal growth patterns that were validated by microdissection. In a case of ductal carcinoma in situ, polyclonal neoplastic expansions occurred at the macroscopic scale but segregated within microanatomical structures. Across the stages of ductal carcinoma in situ, invasive cancer and lymph node metastasis, subclone territories are shown to exhibit distinct transcriptional and histological features and cellular microenvironments. These results provide examples of the benefits afforded by spatial genomics for deciphering the mechanisms underlying cancer evolution and microenvironmental ecology.


Subject(s)
Breast Neoplasms , Carcinoma, Intraductal, Noninfiltrating , Clonal Evolution , Clone Cells , Genomics , Female , Humans , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Carcinoma, Intraductal, Noninfiltrating/genetics , Carcinoma, Intraductal, Noninfiltrating/pathology , Clonal Evolution/genetics , Clone Cells/metabolism , Clone Cells/pathology , Mutation , Tumor Microenvironment/genetics , Whole Genome Sequencing , Transcriptome , Reproducibility of Results , Microdissection , Algorithms
4.
Cell ; 149(5): 994-1007, 2012 May 25.
Article in English | MEDLINE | ID: mdl-22608083

ABSTRACT

Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.


Subject(s)
Breast Neoplasms/genetics , Cell Transformation, Neoplastic , Clonal Evolution , Mutation , Algorithms , Chromosome Aberrations , Female , Humans , Point Mutation
5.
Cell ; 149(5): 979-93, 2012 May 25.
Article in English | MEDLINE | ID: mdl-22608084

ABSTRACT

All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed.


Subject(s)
Breast Neoplasms/genetics , DNA Mutational Analysis , Genome-Wide Association Study , Mutation , APOBEC-1 Deaminase , BRCA2 Protein/genetics , Cytidine Deaminase/metabolism , Female , Genes, BRCA1 , High-Throughput Nucleotide Sequencing , Humans
6.
Cell ; 145(6): 926-40, 2011 Jun 10.
Article in English | MEDLINE | ID: mdl-21663795

ABSTRACT

The epithelial-mesenchymal transition (EMT) has been associated with the acquisition of motility, invasiveness, and self-renewal traits. During both normal development and tumor pathogenesis, this change in cell phenotype is induced by contextual signals that epithelial cells receive from their microenvironment. The signals that are responsible for inducing an EMT and maintaining the resulting cellular state have been unclear. We describe three signaling pathways, involving transforming growth factor (TGF)-ß and canonical and noncanonical Wnt signaling, that collaborate to induce activation of the EMT program and thereafter function in an autocrine fashion to maintain the resulting mesenchymal state. Downregulation of endogenously synthesized inhibitors of autocrine signals in epithelial cells enables the induction of the EMT program. Conversely, disruption of autocrine signaling by added inhibitors of these pathways inhibits migration and self-renewal in primary mammary epithelial cells and reduces tumorigenicity and metastasis by their transformed derivatives.


Subject(s)
Autocrine Communication , Breast Neoplasms/metabolism , Breast/cytology , Neoplastic Stem Cells/metabolism , Paracrine Communication , Stem Cells/metabolism , Animals , Bone Morphogenetic Proteins/metabolism , Breast/metabolism , Breast/pathology , Breast Neoplasms/pathology , Cell Movement , Epithelial Cells/metabolism , Epithelial-Mesenchymal Transition , Female , Humans , Mammary Glands, Animal/cytology , Mammary Glands, Animal/drug effects , Mesoderm/metabolism , Mice , Signal Transduction , Transforming Growth Factor beta/metabolism , Wnt Proteins/metabolism
7.
Cell ; 137(6): 1032-46, 2009 Jun 12.
Article in English | MEDLINE | ID: mdl-19524507

ABSTRACT

MicroRNAs are well suited to regulate tumor metastasis because of their capacity to coordinately repress numerous target genes, thereby potentially enabling their intervention at multiple steps of the invasion-metastasis cascade. We identify a microRNA exemplifying these attributes, miR-31, whose expression correlates inversely with metastasis in human breast cancer patients. Overexpression of miR-31 in otherwise-aggressive breast tumor cells suppresses metastasis. We deploy a stable microRNA sponge strategy to inhibit miR-31 in vivo; this allows otherwise-nonaggressive breast cancer cells to metastasize. These phenotypes do not involve confounding influences on primary tumor development and are specifically attributable to miR-31-mediated inhibition of several steps of metastasis, including local invasion, extravasation or initial survival at a distant site, and metastatic colonization. Such pleiotropy is achieved via coordinate repression of a cohort of metastasis-promoting genes, including RhoA. Indeed, RhoA re-expression partially reverses miR-31-imposed metastasis suppression. These findings indicate that miR-31 uses multiple mechanisms to oppose metastasis.


Subject(s)
Breast Neoplasms/metabolism , Gene Expression Regulation, Neoplastic , MicroRNAs/metabolism , Neoplasm Metastasis , Animals , Cell Line, Tumor , Cytoskeletal Proteins/genetics , Frizzled Receptors/genetics , Humans , Integrin alpha5/genetics , Membrane Proteins/genetics , Receptors, G-Protein-Coupled/genetics , rhoA GTP-Binding Protein/genetics
8.
Breast Cancer Res Treat ; 202(1): 191-201, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37589839

ABSTRACT

PURPOSE: A 3-biomarker homologous recombination deficiency (HRD) score is a key component of a currently FDA-approved companion diagnostic assay to identify HRD in patients with ovarian cancer using a threshold score of ≥ 42, though recent studies have explored the utility of a lower threshold (GIS ≥ 33). The present study evaluated whether the ovarian cancer thresholds may also be appropriate for major breast cancer subtypes by comparing the genomic instability score (GIS) distributions of BRCA1/2-deficient estrogen receptor-positive breast cancer (ER + BC) and triple-negative breast cancer (TNBC) to the GIS distribution of BRCA1/2-deficient ovarian cancer. METHODS: Ovarian cancer and breast cancer (ER + BC and TNBC) tumors from ten study cohorts were sequenced to identify pathogenic BRCA1/2 mutations, and GIS was calculated using a previously described algorithm. Pathologic complete response (pCR) to platinum therapy was evaluated in a subset of TNBC samples. For TNBC, a threshold was set and threshold validity was assessed relative to clinical outcomes. RESULTS: A total of 560 ovarian cancer, 805 ER + BC, and 443 TNBC tumors were included. Compared to ovarian cancer, the GIS distribution of BRCA1/2-deficient samples was shifted lower for ER + BC (p = 0.015), but not TNBC (p = 0.35). In the subset of TNBC samples, univariable logistic regression models revealed that GIS status using thresholds of ≥ 42 and ≥ 33 were significant predictors of response to platinum therapy. CONCLUSIONS: This study demonstrated that the GIS thresholds used for ovarian cancer may also be appropriate for TNBC, but not ER + BC. GIS thresholds in TNBC were validated using clinical response data to platinum therapy.


Subject(s)
Ovarian Neoplasms , Triple Negative Breast Neoplasms , Humans , Female , BRCA1 Protein/genetics , Platinum , BRCA2 Protein/genetics , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/epidemiology , Triple Negative Breast Neoplasms/genetics , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/epidemiology , Ovarian Neoplasms/genetics , Genomic Instability , Homologous Recombination
9.
Genome Res ; 29(3): 356-366, 2019 03.
Article in English | MEDLINE | ID: mdl-30692147

ABSTRACT

Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.


Subject(s)
Biomarkers, Tumor/genetics , Breast Neoplasms/genetics , RNA/genetics , Biomarkers, Tumor/metabolism , Breast Neoplasms/pathology , CREB-Binding Protein/genetics , CREB-Binding Protein/metabolism , Carrier Proteins/genetics , Carrier Proteins/metabolism , Female , Humans , Lymphatic Metastasis , MCF-7 Cells , RNA/metabolism , RNA, Circular , Repressor Proteins/genetics , Repressor Proteins/metabolism , Transcriptome
10.
Mod Pathol ; 34(6): 1185-1193, 2021 06.
Article in English | MEDLINE | ID: mdl-33462368

ABSTRACT

The homologous recombination deficiency (HRD) score integrates three DNA-based measures of genomic instability, and has been understudied in prostate cancer. Given the recent FDA approval of two PARP inhibitors for prostate cancer, HRD score analysis could help to refine treatment selection. We assessed HRD score (defined as the sum of loss-of-heterozygosity, telomeric allelic imbalance, and large-scale state transitions) in three cohorts of primary prostate cancer, including a Johns Hopkins University (JHU) cohort with germline mutations in BRCA2, ATM, or CHEK2 (n = 64), the TCGA cohort (n = 391), and the PROGENE cohort (n = 102). In the JHU cohort, tumors with germline BRCA2 mutations had higher HRD scores (median = 27) than those with germline ATM or CHEK2 mutations (median = 16.5 [p = 0.029] and 9 [p < 0.001], respectively). For TCGA tumors without underlying HR pathway mutations, the median HRD score was 11, significantly lower than ovarian carcinoma lacking BRCA1/2 mutations (median = 28). In the absence of HR gene mutations, the median HRD score was unexpectedly higher among prostate cancers with TP53 mutations versus those without (17 vs. 11; p = 0.015); this finding was confirmed in the PROGENE cohort (24 vs. 16; p = 0.001). Finally, among eight BRCA2-altered patients who received olaparib, progression-free survival trended longer in those with HRD scores above versus below the median (14.9 vs. 9.9 months). We conclude that HRD scores are low in primary prostate cancer and higher in cases with germline BRCA2 or somatic TP53 mutations. Germline BRCA2-altered cases have significantly higher HRD scores than germline ATM-altered or CHEK2-altered cases, consistent with the lower efficacy of PARP inhibitors among the latter.


Subject(s)
Ataxia Telangiectasia Mutated Proteins/genetics , BRCA2 Protein/genetics , Genomic Instability/genetics , Prostatic Neoplasms/genetics , Adult , Aged , Allelic Imbalance/genetics , Biomarkers, Tumor/genetics , Germ-Line Mutation/genetics , Humans , Loss of Heterozygosity/genetics , Male , Middle Aged
11.
Oncologist ; 24(3): 305-312, 2019 03.
Article in English | MEDLINE | ID: mdl-30651399

ABSTRACT

Resistance to endocrine therapy (ET) is common in patients with hormone receptor positive (HR+) advanced breast cancer (ABC). Consequently, new targeted treatment options are needed in the post-ET setting, with validated biomarkers to inform treatment decisions. Hyperactivation of the phosphoinositide 3-kinase (PI3K) signaling pathway is common in ABC and is implicated in resistance to ET. The most frequent mechanism of PI3K pathway activation is activating mutations or amplification of PIK3CA, which encodes the α-isoform of the catalytic subunit of PI3K. Combining buparlisib, a pan-PI3K-targeted agent, with ET demonstrated modest clinical benefits in patients with aromatase inhibitor-resistant, HR+, human epidermal growth receptor 2 negative (HER2-) ABC in two phase III trials. Importantly, greater efficacy gains were observed in individuals with PIK3CA-mutated disease versus PIK3CA-wild-type tumors. Although the challenging safety profile did not support widespread use of this treatment combination, isoform-selective PI3K inhibitors may improve tolerability. In early clinical trials, promising disease control benefits were demonstrated with the PI3K isoform-selective inhibitors alpelisib and taselisib in patients with PIK3CA-mutated HR+, HER2- ABC. Ongoing biomarker-guided phase II/III studies may provide further opportunities to identify patients most likely to benefit from treatment with PI3K inhibitors and provide insight into optimizing the therapeutic index of PI3K inhibitors. Challenges facing the implementation of routine PIK3CA mutation testing must be addressed promptly so robust and reproducible genotyping can be obtained with liquid and tumor biopsies in a timely and cost-effective manner. IMPLICATIONS FOR PRACTICE: The development of phosphoinositide 3-kinase (PI3K) inhibitors, especially those that selectively target isoforms, may be an effective strategy for overcoming endocrine therapy resistance in hormone receptor positive, human epidermal growth receptor 2 negative advanced breast cancer. Early-phase studies have confirmed that patients with PIK3CA mutations respond best to PI3Kα-isoform inhibition. Ongoing phase III trials will provide further data regarding the efficacy and safety of PI3K inhibitors in patients with different biomarker profiles.


Subject(s)
Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Phosphatidylinositol 3-Kinases/genetics , Receptor, ErbB-2/genetics , Biomarkers, Tumor/genetics , Breast Neoplasms/pathology , Female , Humans
12.
Nature ; 500(7463): 415-21, 2013 Aug 22.
Article in English | MEDLINE | ID: mdl-23945592

ABSTRACT

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.


Subject(s)
Cell Transformation, Neoplastic/genetics , Mutagenesis/genetics , Mutation/genetics , Neoplasms/genetics , Aging/genetics , Algorithms , Cell Transformation, Neoplastic/pathology , Cytidine Deaminase/genetics , DNA/genetics , DNA/metabolism , DNA Mutational Analysis , Humans , Models, Genetic , Mutagenesis, Insertional/genetics , Mutagens/pharmacology , Neoplasms/enzymology , Neoplasms/pathology , Organ Specificity , Reproducibility of Results , Sequence Deletion/genetics , Transcription, Genetic/genetics
13.
Surg Innov ; 26(1): 50-56, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30295149

ABSTRACT

PURPOSE: Initial studies have shown that optical coherence tomography (OCT) is an effective margin-evaluation tool for breast-conserving surgery, but methods for the interpretation of breast OCT images have not been directly studied. In this work, breast pathologies were assessed with a handheld OCT probe. OCT images and corresponding histology were used to develop guidelines for the identification of breast tissue features in OCT images. METHODS: Mastectomy and breast-conserving surgery specimens from 26 women were imaged with a handheld OCT probe. During standard pathology specimen dissection, representative 1-cm × 1-cm tissue regions were grossly identified, assessed with OCT, inked for orientation and image-matching purposes, and processed. Histology slides corresponding to the OCT image region were digitally photographed. OCT and histology images from the same region were paired by selecting the best structural matches. RESULTS: In total, 2880 OCT images were acquired from 26 breast specimens (from 26 patients) and 48 matching OCT-histology image pairs were identified. These matched image pairs illustrate tissue types including adipose tissue, dense fibrosis, fibroadipose tissue, blood vessels, regular and hyperplastic ducts and lobules, cysts, cyst, fibroadenoma, invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, calcifications, and biopsy cavities. Differentiation between pathologies was achieved by considering feature boundaries, interior appearance, posterior shadowing or enhancement, and overall morphologic patterns. CONCLUSIONS: This is the first work to systematically catalog the critical features of breast OCT images. The results indicate that OCT can be used to identify and distinguish between benign and malignant features in human breast tissue.


Subject(s)
Breast Neoplasms/diagnostic imaging , Breast Neoplasms/surgery , Mastectomy, Segmental/methods , Tomography, Optical Coherence/methods , Adult , Aged , Biopsy, Needle , Breast Neoplasms/pathology , Case-Control Studies , Female , Humans , Image Processing, Computer-Assisted , Immunohistochemistry , Margins of Excision , Middle Aged , Reference Values , Tissue Embedding
14.
Genome Res ; 25(6): 814-24, 2015 06.
Article in English | MEDLINE | ID: mdl-25963125

ABSTRACT

Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.


Subject(s)
DNA, Mitochondrial/genetics , Genome, Human , Genome, Mitochondrial/genetics , Neoplasms/genetics , Amino Acid Sequence , Cell Line, Tumor , Cell Nucleus/genetics , Chromosomes/genetics , DNA Copy Number Variations , DNA End-Joining Repair , DNA Replication , HeLa Cells , Humans , In Situ Hybridization, Fluorescence , Mitochondria/genetics , Molecular Sequence Data , Reproducibility of Results , Sequence Analysis, DNA
15.
Nature ; 486(7403): 405-9, 2012 Jun 20.
Article in English | MEDLINE | ID: mdl-22722202

ABSTRACT

Breast carcinoma is the leading cause of cancer-related mortality in women worldwide, with an estimated 1.38 million new cases and 458,000 deaths in 2008 alone. This malignancy represents a heterogeneous group of tumours with characteristic molecular features, prognosis and responses to available therapy. Recurrent somatic alterations in breast cancer have been described, including mutations and copy number alterations, notably ERBB2 amplifications, the first successful therapy target defined by a genomic aberration. Previous DNA sequencing studies of breast cancer genomes have revealed additional candidate mutations and gene rearrangements. Here we report the whole-exome sequences of DNA from 103 human breast cancers of diverse subtypes from patients in Mexico and Vietnam compared to matched-normal DNA, together with whole-genome sequences of 22 breast cancer/normal pairs. Beyond confirming recurrent somatic mutations in PIK3CA, TP53, AKT1, GATA3 and MAP3K1, we discovered recurrent mutations in the CBFB transcription factor gene and deletions of its partner RUNX1. Furthermore, we have identified a recurrent MAGI3-AKT3 fusion enriched in triple-negative breast cancer lacking oestrogen and progesterone receptors and ERBB2 expression. The MAGI3-AKT3 fusion leads to constitutive activation of AKT kinase, which is abolished by treatment with an ATP-competitive AKT small-molecule inhibitor.


Subject(s)
Breast Neoplasms/classification , Breast Neoplasms/genetics , Mutation/genetics , Translocation, Genetic/genetics , Algorithms , Breast Neoplasms/pathology , Core Binding Factor Alpha 2 Subunit/genetics , Core Binding Factor beta Subunit/genetics , DNA Mutational Analysis , Exome/genetics , Female , Gene Fusion/genetics , Humans , Membrane Proteins/genetics , Mexico , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Proto-Oncogene Proteins c-akt/genetics , Proto-Oncogene Proteins c-akt/metabolism , Vietnam
16.
Proc Natl Acad Sci U S A ; 111(42): 15184-9, 2014 Oct 21.
Article in English | MEDLINE | ID: mdl-25246570

ABSTRACT

Distinguishing tumor from normal glandular breast tissue is an important step in breast-conserving surgery. Because this distinction can be challenging in the operative setting, up to 40% of patients require an additional operation when traditional approaches are used. Here, we present a proof-of-concept study to determine the feasibility of using desorption electrospray ionization mass spectrometry imaging (DESI-MSI) for identifying and differentiating tumor from normal breast tissue. We show that tumor margins can be identified using the spatial distributions and varying intensities of different lipids. Several fatty acids, including oleic acid, were more abundant in the cancerous tissue than in normal tissues. The cancer margins delineated by the molecular images from DESI-MSI were consistent with those margins obtained from histological staining. Our findings prove the feasibility of classifying cancerous and normal breast tissues using ambient ionization MSI. The results suggest that an MS-based method could be developed for the rapid intraoperative detection of residual cancer tissue during breast-conserving surgery.


Subject(s)
Breast Neoplasms, Male/pathology , Breast Neoplasms/pathology , Neoplasms/pathology , Spectrometry, Mass, Electrospray Ionization , Adult , Aged , Biomarkers, Tumor , Breast Neoplasms/metabolism , Breast Neoplasms, Male/metabolism , Fatty Acids/chemistry , Female , Humans , Lipids/chemistry , Male , Mastectomy , Middle Aged , Neoplasms/metabolism , Oleic Acid/chemistry , Recurrence
17.
Mol Cancer ; 15: 2, 2016 Jan 05.
Article in English | MEDLINE | ID: mdl-26728511

ABSTRACT

BACKGROUND: Zinc (Zn) hyper-accumulates in breast tumors and malignant cell lines compared to normal mammary epithelium. The mechanisms responsible for Zn accumulation and the consequence of Zn dysregulation are poorly understood. METHODS: Microarrays were performed to assess differences in the expression of Zn transporters and metallothioneins (MTs) in human breast tumors and breast cancer cell lines. Real-time PCR and immunoblotting were employed to profile Zn transporter expression in representative luminal (T47D), basal (MDA-MB-231), and non-malignant (MCF10A) cell lines. Zn distribution in human tumors was assessed by X-ray fluorescence imaging. Zn distribution and content in cell lines was measured using FluoZin-3 imaging, and quantification and atomic absorption spectroscopy. Functional consequences of ZnT2 over-expression in MDA-MB-231 cells including invasion, proliferation, and cell cycle were measured using Boyden chambers, MTT assays, and flow cytometry, respectively. RESULTS: Gene expression profiling of human breast tumors and breast cancer cell lines identified subtype-specific dysregulation in the Zn transporting network. X-ray fluorescence imaging of breast tumor tissues revealed Zn hyper-accumulation at the margins of Luminal breast tumors while Zn was more evenly distributed within Basal tumors. While both T47D and MDA-MB-231 cells hyper-accumulated Zn relative to MCF10A cells, T47D cells accumulated 2.5-fold more Zn compared to MDA-MB-231 cells. FluoZin-3 imaging indicated that Zn was sequestered into numerous large vesicles in T47D cells, but was retained in the cytoplasm and found in fewer and larger, amorphous sub-cellular compartments in MDA-MB-231 cells. The differences in Zn localization mirrored the relative abundance of the Zn transporter ZnT2; T47D cells over-expressed ZnT2, whereas MDA-MB-231 cells did not express ZnT2 protein due to proteasomal degradation. To determine the functional relevance of the lack of ZnT2 in MDA-MB-231cells, cells were transfected to express ZnT2. ZnT2 over-expression led to Zn vesicularization, shifts in cell cycle, enhanced apoptosis, and reduced proliferation and invasion. CONCLUSIONS: This comprehensive analysis of the Zn transporting network in malignant breast tumors and cell lines illustrates that distinct subtype-specific dysregulation of Zn management may underlie phenotypic characteristics of breast cancers such as grade, invasiveness, metastatic potential, and response to therapy.


Subject(s)
Breast Neoplasms/classification , Breast Neoplasms/pathology , Intracellular Space/metabolism , Zinc/metabolism , Apoptosis , Breast Neoplasms/genetics , Cation Transport Proteins/metabolism , Cell Cycle , Cell Line, Tumor , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Neoplasm Invasiveness , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Oligonucleotide Array Sequence Analysis , Phenotype , Proteasome Endopeptidase Complex/metabolism , Proteolysis , RNA, Messenger/genetics , RNA, Messenger/metabolism , Subcellular Fractions/metabolism
18.
Histopathology ; 68(1): 45-56, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26348644

ABSTRACT

Breast lesions comprise a family of heterogeneous entities with variable patterns of presentation, morphology and clinical behaviour. The majority of breast lesions are classified traditionally into benign and malignant conditions and their behaviour can, in the vast majority of cases, be predicted with a reasonable degree of accuracy. However, there remain lesions which show borderline features and lie in a grey zone between benign and malignant, as their behaviour cannot be predicted reliably. Defined pathological categorization of such lesions is challenging, and for some entities is recognized to be subjective and include a range of diagnoses, and forms of terminology, which may trigger over- or undertreatment. The rarity of these lesions makes the acquisition of clinical evidence problematic and limits the development of a sufficient evidence base to support informed decision-making by clinicians and patients. Emerging molecular evidence is providing a greater understanding of the biology of these lesions, but this may or may not be reflected in their clinical behaviour. Herein we discuss some breast lesions that are associated with uncertainty regarding classification and behaviour, and hence management. These include biologically invasive malignant lesions associated with uncertain metastatic potential, such as low-grade adenosquamous carcinoma, low-grade fibromatosis-like spindle cell carcinoma and encapsulated papillary carcinoma. Other lesions of uncertain malignant nature remain, such as mammary cylindroma, atypical microglandular adenosis, mammary pleomorphic adenoma and infiltrating epitheliosis. The concept of categories of (1) breast lesions of uncertain malignant nature and (2) breast lesions of limited metastatic potential are proposed with details of which histological entities could be included in each category, and their management implications are discussed.


Subject(s)
Breast Neoplasms/pathology , Breast/pathology , Carcinoma, Adenosquamous/pathology , Carcinoma/pathology , Fibroma/pathology , Diagnosis, Differential , Female , Humans
19.
Histopathology ; 68(1): 5-21, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26768026

ABSTRACT

Phyllodes tumours constitute an uncommon but complex group of mammary fibroepithelial lesions. Accurate and reproducible grading of these tumours has long been challenging, owing to the need to assess multiple stratified histological parameters, which may be weighted differently by individual pathologists. Distinction of benign phyllodes tumours from cellular fibroadenomas is fraught with difficulty, due to overlapping microscopic features. Similarly, separation of the malignant phyllodes tumour from spindle cell metaplastic carcinoma and primary breast sarcoma can be problematic. Phyllodes tumours are treated by surgical excision. However, there is no consensus on the definition of an appropriate surgical margin to ensure completeness of excision and reduction of recurrence risk. Interpretive subjectivity, overlapping histological diagnostic criteria, suboptimal correlation between histological classification and clinical behaviour and the lack of robust molecular predictors of outcome make further investigation of the pathogenesis of these fascinating tumours a matter of active research. This review consolidates the current understanding of their pathobiology and clinical behaviour, and includes proposals for a rational approach to the classification and management of phyllodes tumours.


Subject(s)
Breast Neoplasms/pathology , Breast/pathology , Carcinoma/pathology , Fibroadenoma/pathology , Phyllodes Tumor/pathology , Sarcoma/pathology , Consensus , Diagnosis, Differential , Female , Humans
20.
Cancer Cell ; 12(2): 160-70, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17692807

ABSTRACT

We investigated the influence of normal cell phenotype on the neoplastic phenotype by comparing tumors derived from two different normal human mammary epithelial cell populations, one of which was isolated using a new culture medium. Transformation of these two cell populations with the same set of genetic elements yielded cells that formed tumor xenografts exhibiting major differences in histopathology, tumorigenicity, and metastatic behavior. While one cell type (HMECs) yielded squamous cell carcinomas, the other cell type (BPECs) yielded tumors closely resembling human breast adenocarcinomas. Transformed BPECs gave rise to lung metastases and were up to 10(4)-fold more tumorigenic than transformed HMECs, which are nonmetastatic. Hence, the pre-existing differences between BPECs and HMECs strongly influence the phenotypes of their transformed derivatives.


Subject(s)
Breast Neoplasms/genetics , Breast Neoplasms/pathology , Breast/cytology , Cell Transformation, Neoplastic , Epithelial Cells/cytology , Adenocarcinoma/etiology , Adenocarcinoma/pathology , Adult , Animals , Antigens, Polyomavirus Transforming/metabolism , Biomarkers, Tumor/metabolism , Carcinoma, Squamous Cell/etiology , Carcinoma, Squamous Cell/pathology , Cell Division , Cells, Cultured , Female , Gene Expression Profiling , Genes, ras/physiology , Humans , Mice , Mice, Inbred BALB C , Mice, Inbred NOD , Mice, Nude , Mice, SCID , Middle Aged , Transplantation, Heterologous
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