Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 4_Supplement ( 2018-02-15), p. P2-05-08-P2-05-08
    Abstract: Introduction: Mucinous carcinoma of the breast (MCB) is a rare histologic form of estrogen receptor (ER)-positive invasive carcinoma, accounting for up to 2% of breast cancers. MCBs are characterized by clusters of tumor cells floating in lakes of extracellular mucin, and are classified into mucinous A (paucicellular) and mucinous B (hypercellular) subtypes. Some MCBs are found admixed with invasive ductal carcinoma components, and then classified as mixed MCBs. The aims of this study were to determine the repertoire of somatic mutations of MCBs and to ascertain whether these genetic alterations are distinct from those identified in common forms of ER+/HER2- invasive breast cancers (IBCs). We also sought to determine whether the mucinous and ductal components of mixed MCBs would be clonally related. Materials and methods: Thirty MCBs including 25 pure MCBs (n=13 mucinous A, n=12 mucinous B) and five mixed MCBs were microdissected and subjected to whole exome sequencing. Each tumor component of mixed cases was microdissected and analyzed separately. Somatic mutations, copy number alterations and mutational signatures were defined using state-of-the-art bioinformatics methods. The mutational repertoire of MCBs was compared with that of ER+/HER2- IBCs (n = 240) from The Cancer Genome Atlas (TCGA) breast cancer study. Results: The genes most frequently mutated in MCBs were GATA3 (27%, 8/30, all frameshift mutations), KMT2C (13%, 4/30) and MAP3K1 (10%, 3/30). No significant differences were identified in single gene comparisons between mucinous A and mucinous B MCBs or between pure MCBs and the mucinous component of mixed MCBs (Fisher's exact tests, p & gt;0.05). As compared to common forms of ER+/HER2- IBC, MCBs had a lower frequency of PIK3CA mutations (7% vs 42%, p & lt;0.001) and a higher frequency of GATA3 mutations (27% vs 12%, p=0.04). Mucinous B MCBs had a higher frequency of KMT2C mutations than ER+/HER2- IBCs (25% vs 6%, p=0.04). Most MCBs displayed the mutational signature 1 (aging-related; 20/30, 67%), and no differences in the frequency of specific mutational signatures according to the type of MCBs were observed. Concurrent 1q gains and 16q losses, which are the hallmark genetic alterations of low-grade ER+/HER2- breast cancers, were not observed in pure MCBs, but were found in three of the five mixed MCBs analyzed. The mucinous and ductal components of all five mixed MCBs shared a median of 58% of somatic mutations (range 42%-64%), including clonal GATA3 frameshift mutations in two of them, as well as a similar pattern of copy number alterations, supporting their clonal relatedness. Additional somatic mutations found to be restricted to the ductal or mucinous components of all mixed MCBs analyzed were identified, including clonal missense mutations in PIK3C2B and PIK3R2 in the ductal component of one case, and a PIK3R5 missense mutation in the mucinous component of another case. Conclusions: The repertoire of somatic mutations in MCBs is distinct from that of common forms of ER+/HER2- IBCs. These differences include the lack of concurrent 1q gains/16q losses, a lower frequency of PIK3CA mutations and a higher frequency of GATA3 mutations in pure MCBs. Citation Format: Pareja F, Geyer FC, Piscuoglio S, Selenica P, Kumar R, Lim RS, Guerini-Rocco E, Marchio C, Mariani O, Ng CKY, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Mucinous breast carcinomas: A genomically distinct subtype of estrogen receptor-positive invasive breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-05-08.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 4_Supplement ( 2017-02-15), p. S2-02-S2-02
    Abstract: Introduction: Women carrying BRCA1 or BRCA2 germline mutations have a 45-80% lifetime risk of developing breast cancer (BC). BRCA1 and BRCA2 are perceived as bona fide tumor suppressor genes, whereby bi-allelic inactivation in tumor cells is required for tumorigenesis. Recent studies have indicated that loss of heterozygosity (LOH) of the wild-type allele of BRCA1 may be heterogeneous and constitute a late event. Therefore, additional somatic events prior to full BRCA1/2 inactivation may be required for tumorigenesis. Given that the somatic events that result in the development of BRCA1/2-BCs and their chronology are not understood, here we sought to define the genomic landscape of BRCA1/2-BCs and whether LOH of BRCA1/2 wild-type allele and/or mutations affecting additional tumor suppressor genes would be clonal or subclonal in these cancers. Methods: We retrieved 29 BRCA1-BCs and 10 BRCA2-BCs from the Pathology Departments of the authors' institutions. DNA extracted from microdissected tumor and normal breast samples was subjected to targeted capture massively parallel sequencing using either the MSK-IMPACT assay or an assay targeting all exons of 254 genes recurrently mutated in BC or related to DNA repair. Somatic single nucleotide variants, small insertions and deletions and copy number alterations affecting genes present in both sequencing assays (111 genes) were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to define clonal (i.e. present virtually in 100% of the cancer cells of a given case) and subclonal mutations and the presence of LOH of the BRCA1 and BRCA2 wild-type alleles. Results: Our analysis revealed bi-allelic inactivation of BRCA1 in 28 of 29 BRCA1-BCs (93% harbored LOH of the BRCA1 wild-type allele and 3% harbored a second somatic BRCA1 pathogenic mutation). The only BRCA1-BC lacking bi-allelic inactivation of BRCA1 was an estrogen receptor-positive lobular carcinoma, lacking genomic features consistent with homologous recombination DNA repair defects, diagnosed at 62 years of age. Bi-allelic inactivation of BRCA2 was found in all cases (100% of harbored LOH of the BRCA2 wild-type allele). A clonal somatic 'second hit' resulting in bi-allelic inactivation of BRCA1 or BRCA2 was detected in 76% and 100% of BRCA1-BCs and BRCA2-BCs, respectively. In BRCA1-BCs, TP53 mutations were detected in 76% of cases, and these mutations were found to be clonal in 58% of cases. The repertoire of somatic mutations affecting BRCA1-BCs included clonal somatic mutations or homozygous deletions of known tumor suppressor genes, such as PTEN, RB1, CDKN2A and NF1. In contrast, only 10% of the BRCA2-BCs harbored TP53 somatic mutations. Though clonal somatic mutations in several cancer genes were detected, 40% of BRCA2-BCs had no mutations affecting the cancer genes analyzed. Conclusions: Bi-allelic inactivation of BRCA1 and BRCA2 are frequent events in BRCA1-BCs and BRCA2-BCs, respectively. In a subset of BRCA1-BCs, however, the second 'hit' appeared to be subclonal, whereas mutations affecting TP53 and other tumor suppressor genes were clonal, supporting the notion that at least in a subset of these tumors, loss of the wild-type allele of BRCA1 may be preceded by inactivation of another tumor suppressor gene. Citation Format: Geyer FC, Burke KA, Macedo GS, Piscuoglio S, Ng CK, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson M, Wen YH, Weigelt B, Schnitt SJ, Tung N, Reis-Filho JS. The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-02.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 4_Supplement ( 2018-02-15), p. PD1-15-PD1-15
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 4_Supplement ( 2018-02-15), p. PD1-15-PD1-15
    Abstract: Introduction:Pathogenic and/or founder germline variants in the ataxia-telangiectasia mutated (ATM) gene confer an increased breast cancer (BC) risk. The protein kinase ATM plays a central role inDNA double-strand break-repair and in the activation of downstream targets such as p53 and BRCA1. We sought to define the repertoire of somatic genetic alterations of BCs from patients with pathogenic germline ATM mutations and whether somatic loss of heterozygosity (LOH) of ATM would be present in these cancers. Methods: 21 BCs from ATM germline mutation carriers were microdissected. Tumor and normal DNA samples were subjected to whole-exome sequencing (WES, n=12) or massively parallel sequencing targeting all coding regions and selected intronic and regulatory regions of 410 key cancer genes (n=9). Somatic mutations, copy number alterations, cancer cell fractions, large-scale state transitions (LSTs) and mutational signatures were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to assess LOH of the wild-type allele of ATM. Results: Of the patients included in this study, 71%, 24% and 5% of cases harbored ATM missense (all but one p.V2424G), frame-shift and nonsense germline mutations, respectively. All tumors were ER-positive and four (19%) were HER2-positive. The median age of the patients was 46 years (32–79 years). Our analyses revealed biallelic inactivation of ATM through LOH of the wild-type allele in 16 of 21 cases (76%), and second somatic ATM mutations were not found. The median number of non-synonymous somatic mutations was 38 (range 15-113) and 2 (range 0-8)in tumors subjected to WES and targeted sequencing, respectively. The repertoire of somatic genetic alterations of ATM-associated BCs was found to be heterogeneous, including clonal PIK3CA mutations (24%), GATA3 mutations (19%), FANCI amplifications (19%) and CCND1 amplifications (14%). Importantly, however, no somatic mutations affecting TP53 were found. Analysis of the WES data revealed that 5 (42%) ATM-associated BCs displayed high LST scores, all of which harbored bi-allelic ATM inactivation. In contrast to BRCA1- and BRCA2-associated BCs, which frequently display the mutational signature 3 associated with defective homologous recombination DNA repair, the ATM-associated BCs studied displayed the ageing mutational signature (i.e. signature 1). Comparison of the mutational profiles of the ATM--associated BCs subjected to WES (n=12) with those of BRCA1- (n=11) and BRCA2-associated (n=10) BCs from The Cancer Genome Atlas revealed that TP53 was more frequently mutated in BCs from BRCA1 germline mutation carriers (0% vs 72%, P & lt;0.001), while no differences with BRCA2-associated BCs were found. Conclusion: ATM-associated BCs frequently display bi-allelic ATM inactivation through LOH of the wild-type allele and a subset of these cases displayed high levels of LSTs. These findings suggest that at least in a subset of ATM-associated BCs, biallelic inactivation of ATM rather than a dominant negative effect of the germline mutation may be the mechanism of inactivation of this tumor suppressor gene. The repertoire of somatic genetic alterations of ATM-associated BCs is heterogeneous, with a noticeable lack of TP53 somatic mutations. Citation Format: Weigelt B, Bi R, Kumar R, James PA, Thorne H, Couch FJ, Eccles DM, Blows F, Geyer FC, Li A, Selenica P, Lim RS, Blecua P, Shen R, Wen H, Robson ME, Reis-Filho JS, Chenevix-Trench G. The landscape of somatic genetic alterations in breast cancers from ATM germline mutation carriers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD1-15.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 4_Supplement ( 2018-02-15), p. PD4-13-PD4-13
    Abstract: Introduction:Adenomyoepithelioma (AME) of the breast is a rare biphasic tumor, characterized by epithelial and myoepithelial differentiation. Although AMEs have an indolent clinical course, a subset may progress to carcinoma and metastasize. We sought to define the mutational landscape of AMEs and investigate the functional impact of recurrent pathogenic mutations identified in these tumors. Methods: Thirty-one AMEs were subjected to whole-exome sequencing (WES, n=8) or massively parallel sequencing targeting all coding regions of 410 key cancer genes and intronic and regulatory regions of selected genes (n=23). Somatic genetic alterations were defined using state-of-the-art bioinformatics algorithms. In an additional set of 12 AMEs, Sanger sequencing analysis of HRAS, PIK3CA and AKT1 was performed. Non-tumorigenic estrogen receptor (ER)-negative mammary epithelial cells (i.e. MCF10A, MCF10A with a PIK3CA H1047R mutation knock-in and MCF12A) were utilized for functional studies using both conventional monolayer and three-dimensional (3D) culture assays. Results: 27 (63%) and 16 (37%) AMEs were ER-positive and ER-negative, respectively. ER-negativity was significantly associated with histologic features predictive of a more aggressive behavior, with a higher number of mutations and copy number alterations, and with a distinct mutational profile as compared to ER-positive AMEs. Of the 27 ER-positive AMEs, 12 cases (44%) harbored PIK3CA hotspot mutations, and 5 PIK3CA wild-type cases displayed E17K AKT1 hotspot mutations. By contrast, of the 16 ER-negative AMEs, 9 (56%), 9 (56%) and 3 (19%) harbored HRAS, PIK3CA (mostly E545K and H1047R hotspots) and PIK3R1 mutations, respectively. Strikingly, all HRAS mutations were restricted to ER-negative AMEs, affected the hotspot codon Q61 (Q61R/K), and all but one co-occurred with PIK3CA or PIK3R1 mutations. In addition, HRAS Q61 hotspot mutations were significantly associated with necrosis (p=0.01) and high mitotic rates (p=0.03). CDKN2A homozygous deletions were also detected only in ER-negative AMEs (19%) and found to be significantly associated with progression to carcinoma (p=0.001). Forced expression of HRAS Q61R in MCF10A and MCF12A cells resulted in i) increased proliferation and transformation, ii) an irregular growth pattern in 3D organotypic cell cultures, iii) partial loss of the epithelial phenotype, and iv) acquisition of myoepithelial differentiation, which was more overt in PIK3CA-mutant MCF10A cells. HRAS Q61Rinduced hyperactivation of the PI3K pathway, but both PI3K and MAPK pathways likely contributed to the RAS-mediated proliferation, which was completely arrested by combined AKT and MEK inhibition. Conclusion: AMEs are phenotypically and genetically heterogeneous. Whilst pathogenic mutations in PI3K pathway-related genes occur across the spectrum of lesions, HRAS Q61 hotspot mutations are restricted to ER-negative AMEs. Our genomic and functional analyses indicate that HRAS Q61 mutations are driver events in the pathogenesis of ER-negative AMEs and, in conjunction with mutant PIK3CA, may lead to the acquisition of myoepithelial differentiation in breast epithelial cells. Citation Format: Geyer FC, Li A, Papanastasiou AD, Smith A, Selenica P, Burke KA, Edelweiss M, Wen H-C, Piscuoglio S, Schultheis AM, Martelotto LG, Pareja F, Kumar R, Brandes A, Lozada J, Macedo GS, Muenst S, Terracciano LM, Jungbluth A, Foschini MP, Wen HY, Brogi E, Palazzo J, Rubin BP, Ng CKY, Norton L, Varga Z, Ellis IO, Rakha E, Chandarlapatty S, Weigelt B, Reis-Filho JS. Estrogen receptor-negative breast adenomyoepitheliomas are driven by co-occurring HRAS hotspot and PI3K pathway gene mutations: A genetic and functional analysis [abstract] . In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-13.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 4_Supplement ( 2017-02-15), p. P1-05-04-P1-05-04
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 4_Supplement ( 2017-02-15), p. P1-05-04-P1-05-04
    Abstract: Introduction: Metaplastic breast carcinoma (MBC) is characterized by the presence of neoplastic cells displaying squamous and/or mesenchymal differentiation. Morphologic intra-tumor heterogeneity is frequent in MBCs and reported to be reflected at the transcriptomic level: whilst squamous and chondroid MBCs are preferentially of basal-like subtype, spindle cell MBCs are of claudin-low subtype. Likewise, histologically distinct components within MBCs have been shown to display distinct focal copy number alterations. Here we sought to investigate whether histologically distinct components within MBCs would be underpinned by different mutational profiles and mutational signatures. Methods: Ten MBCs with two histologically distinct components (spindle, chondroid, osseous, squamous and/ or ductal) were retrieved from the Department of Pathology of the authors' institution. The distinct components of each case and, in two cases, two regions of the same component were separately microdissected. DNA extracted from tumor samples (n=22) and matched normal tissues was subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. Somatic mutations were classified as clonal (i.e., present virtually in all tumor cells) or subclonal using ABSOLUTE and FACETS. Mutational signatures were defined using non-negative matrix factorization. Results: Medians of 146 (56-290) somatic mutations and 108 non-synonymous somatic mutations (39-222) per tumor component were identified. The histologically distinct components of each case harbored identical clonal TP53 mutations. Additional recurrent mutations in cancer genes included those affecting PI3K pathway genes (PIK3CA, 2 cases; PIK3R1, 2 cases). Shared mutations between components of each case ranged from 34% to 99% of all mutations, with a median of 84%, of which 24% (12%-53%) were truncal (i.e., shared by and clonal in both components). Private mutations (i.e., found in only one component) ranged from 1% to 66%, with a median of 16%, of which 72% (0-100%) were non-synonymous and 1% (0-52%) were clonal. In two cases, the comparison of two histologically similar regions revealed less heterogeneity, with 94% (87%-100%) of shared mutations, whereas in these samples the median of private mutations was 6% (0-13%), of which 70% (0-100%) were non-synonymous and none were clonal. Private non-synonymous mutations affecting cancer genes included those in PIK3R1, MED12 and NOTCH1. The mutational signatures (e.g. aging or BRCA) were concordant between distinct components of each case; however, differences in the mutational signatures were observed between truncal somatic mutations and mutations restricted to individual components. Conclusions: MBCs display substantial genetic intra-tumor heterogeneity, which is more overt between histologically distinct components than between regions of similar histology. Our data suggest a genotypic-phenotypic correlation and corroborate the notion that distinct components within MBCs, although clonally related, may be driven by distinct somatic genetic alterations. Citation Format: Geyer FC, Burke KA, Papanastatiou AD, Macedo GS, Brogi E, Norton L, Wen YH, Weigelt B, Reis-Filho JS. Intra-tumor genetic heterogeneity and histologic heterogeneity within metaplastic breast cancers: Genotypic-phenotypic correlations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-04.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 4_Supplement ( 2018-02-15), p. P2-05-03-P2-05-03
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 4_Supplement ( 2018-02-15), p. P2-05-03-P2-05-03
    Abstract: Introduction: Breast adenoid cystic carcinoma (AdCC) is a rare type of triple-negative breast cancer associated with an indolent clinical behavior. AdCCs provide a clear example of genotypic-phenotypic correlation with the majority harboring the MYB-NFIB fusion gene. In this study, we sought to identify alternative driver genetic alterations in breast AdCCs lacking the MYB-NFIB fusion gene. Methods: Nucleic acids obtained from four breast AdCCs lacking the MYB-NFIB fusion gene as defined by reverse transcription (RT)-PCR and/or fluorescence in situ hybridization (FISH) were subjected to RNA-sequencing (n=3), whole-genome (n=2) and/or targeted (n=1) massively parallel sequencing. Sequencing data were analyzed using state-of-the-art bioinformatics algorithms, and potential alternative driver genetic alterations were validated using orthogonal sequencing and molecular pathology methods. Results: RNA-sequencing revealed the presence of MYBL1-ACTN1 or MYBL1-NFIB fusion genes in two breast AdCCs, which were validated by whole-genome sequencing and/or MYBL1 FISH analysis. Both MYBL1 fusion gene-positive cases were found to overexpress MYBL1 as defined by quantitative RT-PCR analysis. In the third MYB-NFIB-negative breast AdCC studied, a high-level MYB gene amplification coupled with overexpression of MYB at the mRNA and protein levels was identified. In the fourth breast AdCC, which expressed high levels of MYB, whole-genome and RNA-sequencing revealed no definite alternative driver alteration, however, a MYBL2 intronic mutation was found in this case, which was associated with high levels of MYBL2 mRNA expression. In this case, single sample gene set enrichment analysis revealed activation of pathways similar to those activated in AdCCs harboring the MYB-NFIB or MYBL1 fusions genes. Conclusion: We demonstrate that in breast AdCCs lacking the MYB-NFIB fusion gene MYBL1 rearrangements and MYB amplification are likely alternative driver genetic events. Given that activation of MYB/MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification or other yet to be validated mechanisms (e.g. MYBL2 non-coding mutations), our findings further suggest that breast AdCCs constitute a convergent phenotype. Citation Format: Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. Novel driver genetic alterations in MYB-NFIB-negative breast adenoid cystic carcinomas [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-05-03.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 4_Supplement ( 2017-02-15), p. P1-05-03-P1-05-03
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 4_Supplement ( 2017-02-15), p. P1-05-03-P1-05-03
    Abstract: Introduction: Metaplastic breast carcinoma (MBC) is a rare histologic type of triple-negative breast cancer (TNBC), characterized by the presence of cells displaying squamous and/or mesenchymal differentiation. The transcriptomic profiles of MBCs have been reported to vary according to the type of metaplastic elements. The somatic genetic alterations that underpin this breast cancer subtype remain to be fully characterized. Here we sought to define the genomic landscape of MBCs, whether different subtypes of MBC would be driven by distinct constellations of genetic alterations, and to investigate functionally the impact of mutations affecting WNT pathway genes using non-malignant breast epithelial cells. Methods: Thirty-five MBCs were retrieved from the pathology department of the authors' institutions and classified into the MBC histologic subtypes. All but one of the MBCs were of triple-negative phenotype. DNA was extracted from microdissected tumor-normal pairs and subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. The genomic profiles of MBCs were compared to those of 69 common type TNBCs from The Cancer Genome Atlas. Overall mutation rates were compared using the Mann Whitney U test, and the frequency of mutations in each gene was compared using Fisher's exact test. RNA was extracted from a subset of MBCs and subjected to WNT signaling pathway activation analysis with the RT2 Profiler PCR Array. Triple-negative non-malignant breast epithelial cells (MCF10A and MCF12A) and cancer cell lines were utilized for 2D and 3D functional studies. Results: Whole-exome analysis revealed that MBCs displayed a median of 103 (15-344) somatic mutations, which did not differ from the median number of somatic mutations in common type TNBCs (76, range 14-233). The most frequent recurrently mutated cancer genes included TP53 (69%) and PIK3CA (29%). MBCs more frequently harbored mutations in PI3K pathway genes than common type TNBCs (57% vs 22%, P & lt;0.05), including mutations affecting PIK3CA (29% vs 7%), PIK3R1 (11% vs 0) and PTEN (11% vs 1%). MBCs also more frequently harbored mutations affecting WNT signaling pathway genes (46% vs 26%, P & lt;0.05), including AXIN1 (6% vs 1%), WNT5A (6% vs 0) and APC (3% vs 0). MBC subtype analysis revealed that PIK3CA mutations were only detected in non-chondroid MBCs (53% vs 0), CHERP mutations were only found in chondroid MBCs (25% vs 0), whereas USP5 mutations only found in squamous MBCs (33% vs 0). MBCs with somatic mutations in WNT pathway genes had significantly higher WNT pathway activation than MBCs lacking mutations in these genes (P=0.0244). Consistent with the mesenchymal phenotype frequently exhibited by MBCs, in vitro experiments provided functional evidence that aberrant WNT pathway activation induces an epithelial-to-mesenchymal transition (EMT) phenotype, with downregulation of epithelial markers and upregulation of EMT transcriptional inducers. Conclusions: MBCs are significantly enriched for mutations affecting PI3K and WNT pathways, highlighting the importance of the dysregulation of the WNT pathway in MBC carcinogenesis. Moreover, our findings suggest that specific mutations are significantly associated with distinct histologic subtypes of MBCs. Citation Format: Geyer FC, Ng CK, Piscuoglio S, Wen YH, Wen H-C, Pareja F, Eberle CA, Burke KA, Lim RS, Natrajan R, Mariani O, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. The genomic landscape of breast metaplastic carcinoma [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-03.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 4_Supplement ( 2017-02-15), p. P2-03-01-P2-03-01
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 4_Supplement ( 2017-02-15), p. P2-03-01-P2-03-01
    Abstract: Background: The PALB2 gene encodes the partner and localizer of the BRCA2 protein, which participates in homologous recombination during DNA repair via an interaction with BRCA1 and BRCA2. Germline mutations in PALB2 are associated with an increased risk of breast cancer, with a cumulative risk of 35% by age 70 in female PALB2 mutant carriers. The aims of this project were to characterize the genomic landscape of PALB2 breast cancers and define the differences in the repertoire of somatic genetic alterations and mutational signatures between PALB2, BRCA1 and BRCA2 breast cancers. Methods: Representative samples from fourteen breast cancers from patients with known PALB2 germline mutations (seven frame-shift (2 H1170fs, 3 K346fs, 1 T841fs and 1 L531fs), five truncating (3 W1038* and 2 Q775*) and two missense (W1140G and L35P)) were microdissected to ensure a tumor cell content of & gt;70%. DNA samples from microdissected tumors and their matched normal counterparts were subjected to whole exome sequencing on an Illumina HiSeq2000 to a median depth of 118x (range 33-193x). Somatic single nucleotide variations were detected using MuTect, and small insertions and deletions were identified using Strelka and Varscan2. Using ABSOLUTE and FACETS, we investigated the presence of loss of heterozygosity (LOH) of the PALB2 wild-type allele in these tumors. In addition, the mutational signatures and large scale state transitions (LSTs) were defined. The repertoire of somatic mutations identified in PALB2 breast cancers was compared to that of breast cancers from BRCA1 (n=11) and BRCA2 (n=10) germline mutation carriers from The Cancer Genome Atlas study. Results: PALB2 breast cancers were found to harbor a median of 80 somatic mutations (range 22-286) and one somatic mutation (range 0-13) affecting known cancer genes. Somatic loss of the PALB2 wild-type allele was found in five cases, and in three additional cases, a second PALB2 somatic mutation likely constituted the second 'hit' (two with truncating mutations, Q479* and Q61*, and one with a Q921fs frameshift mutation). Six PALB2 breast cancers displayed the BRCA mutations signature; of these, five had PALB2 bi-allelic inactivation (three LOH of the wild-type allele and two a second PALB2 somatic mutation). 71% of the samples were found to have LSTs, including all cases with a BRCA mutational signature. A significant association between PALB2 bi-allelic inactivation and concurrent BRCA signature and high LST was observed (p=0.015). Breast cancers from PALB2 mutation carriers had fewer somatic TP53 mutations than BRCA1 breast cancers (3/14, 21% vs 9/11, 82%, p=0.004), but no difference in the repertoire of somatic mutations compared to that of BRCA2 breast cancers. Conclusions: PALB2 breast cancers were found to harbor pathogenic mutations in driver genes, including TP53, PIK3CA, NF1 and NCOR1, however lacked highly recurrent somatic mutations. Unlike BRCA1/2 breast cancers, the majority of breast cancers from PALB2 germline mutation carriers lacked LOH of the PALB2 wild-type allele. Importantly, however, an association between PALB2 bi-allelic inactivation and the BRCA mutational signature and LSTs was observed, providing additional evidence for a homologous recombination-deficient phenotype at least in a subset of PALB2 cancers. Citation Format: Burke KA, Berman S, Geyer FC, Piscuoglio S, Ng CK, Wen YH, Mannermaa A, Peterlongo P, Tondini C, Janatova M, Soo Hwang T, Ng P-S, Looi LM, Chenevix-Trench G, Southey MC, Weigelt B, Foulkes W, Tischkowitz M, Reis-Filho JS, PALB2 Interest Group. Mutational landscape of breast cancers from PALB2 germline mutation carriers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-03-01.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2019
    In:  Cancer Research Vol. 79, No. 4_Supplement ( 2019-02-15), p. P2-01-02-P2-01-02
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 4_Supplement ( 2019-02-15), p. P2-01-02-P2-01-02
    Abstract: Introduction: Ductal carcinoma in situ (DCIS) is a bona fide non-obligate precursor of invasive carcinoma. Single cell sequencing studies have revealed intra-lesion genetic heterogeneity in DCIS and shown that progression to invasive ductal carcinoma (IDC) may occur through different mechanisms, including the selection of a subpopulation of tumor cells, acquisition of new genetic alterations or multi-clonal invasion. Here, we sought to investigate the genetic heterogeneity of DCIS, and to document further the clonal selection process accompanying progression to IDC. Materials and methods: Synchronous DCIS (n=16) and IDC (n=15) samples from 14 patients were microdissected separately, and DNA samples of tumor and matched normal tissues were subjected to whole-exome sequencing (WES; n=27) or massively parallel targeted sequencing of all coding regions of ≥410 cancer-related genes (n=4). Somatic genetic alterations and mutational signatures were identified using state-of-the-art bioinformatics algorithms. PyClone was employed to define the clonal architecture of each DCIS and IDC and infer the clonal shifts accompanying progression from DCIS to IDC. Results: DCIS were found to harbor recurrent somatic mutations affecting PIK3CA (50%), GATA3 (44%), TP53 (38%), CBFB (19%), PTEN (13%), and AKT1 (13%), which are genes known to be significantly mutated in invasive breast cancers. Despite the genomic similarities between matched DCIS and IDCs, NOTCH2 and MYC were found to be amplified solely in the IDC component of two cases, and PPM1D amplification was restricted to the DCIS component of another case. The mutational signature ascribed to aging (i.e. signature 1) was the predominant mutational signature in the DCIS and IDCs analyzed. PyClone analysis revealed that all synchronous DCIS and IDC studied here were clonally related and confirmed the previous observation that DCIS displays intra-lesion genetic heterogeneity. Evidence of clonal selection in the progression from DCIS to IDC was observed in three cases, whereby a minor DCIS subclone likely constituted the substrate for the development of IDC. In one of these cases, from a patient with a BRCA1 germline pathogenic mutation, we observed a shift from the mutational signature associated with defective homologous recombination DNA repair (i.e. signature 3) to the APOBEC-related mutational signatures (i.e. signatures 2 and 13) in the progression from DCIS to IDC. Conclusion: Intra-lesion genetic heterogeneity is a common feature in DCIS synchronously diagnosed with IDC. Our findings corroborate the notion that DCIS is a direct non-obligate precursor of IDC, and that clonal selection in the progression of DCIS to IDC may be present in a subset of cases, but is unlikely to constitute the most frequent mechanism of progression. Citation Format: Lee JY, Bi R, Pareja F, Geyer FC, Brown D, Wen HY, Norton L, Hicks J, Weigelt B, Reis-Filho JS. Whole exome sequencing analysis of the progression from ductal carcinoma in situ to invasive ductal carcinoma [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 P2-01-02.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2019
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 4_Supplement ( 2019-02-15), p. P3-07-02-P3-07-02
    Abstract: Introduction: Metaplastic breast carcinomas (MBCs) and uterine carcinosarcomas (UCSs) are histologically similar, being often characterized by an admixture of adenocarcinoma areas with areas displaying sarcomatoid differentiation. We sought to investigate whether their histologic similarities would be paralleled by similar patterns of genetic alterations, and to determine whether the different histologic components of MBCs and UCSs would be clonally related. Methods: Whole exome sequencing (WES) data from 35 MBCs previously analyzed by our group and 57 UCSs from The Cancer Genome Atlas (TCGA) study were reanalyzed. Somatic single nucleotide variants were detected with MuTect and indels with Strelka, Varscan2, Scalpel and Lancet. Copy number alterations were inferred using FACETS and functional annotation of the non-synonymous somatic mutations, amplifications or homozygous deletions was performed. We further microdissected the histologically distinct components of 11 MBCs and six UCSs and subjected each component to WES. Clonal decomposition was performed using PyClone. Results: The most frequent somatic mutations identified in MBCs were TP53 (69%), PIK3CA (29%), FAT3 (26%) and PTEN (14%), whereas the most frequently mutated genes in UCSs were TP53 (84%), FBXW7 (35%), PIK3CA (29%), PTEN (15%) and PPP2R1A (15%). MBCs displayed a significantly higher frequency of mutations targeting FAT3 (26% vs 4%, P & lt;0.01), FAT1 (11% vs 0%, P & lt;0.05) and CHERP (11% vs 0%, P & lt;0.05) than UCSs. UCSs more frequently harbored mutations affecting FBXW7 (35% vs 0%; P & lt;0.01) and PPP2R1A (15% vs 0%, P & lt;0.05) than MBCs. MBCs and UCSs displayed similar copy number alteration profiles, with frequent gains/ amplification of 8q, 3q and 1q, and losses of 8p. Pathway analysis based on the genes targeted by somatic genetic alterations revealed that both MBCs and UCSs were underpinned by genetic alterations resulting in activation of similar pathways, including PI3K, p53, Wnt and Notch signaling. Analysis of the separate components of MBCs and UCSs revealed that the histologically distinct components of MBCs and UCSs are clonally-related, with a median of 71% (range 26%-93%) and 78% (range 30%-93%) of somatic mutations being shared by the distinct components in MBCs and UCSs, respectively. In MBCs, clonal TP53, NOTCH3, KMT2D, FAT4 and PIK3CA mutations and several copy number alterations were shared by the histologically distinct components. Mutations private to each of the histologically distinct components included PIK3R1, CHERP and MAPK14 mutations. The carcinomatous and sarcomatous components of UCSs shared clonal TP53, PIK3CA, CDKN2A, ITGB7 and FGFR2 mutations. Private KMT2B mutations were identified in the UCS carcinomatous components. PyClone analysis revealed that the clonally-related histologically distinct components of each case harbored intra-component genetic heterogeneity coupled with parallel evolution. Conclusions: Our findings support the contention that UCSs constitute the uterine counterpart of MBCs due to their similar histology and patterns of genetic alterations affecting the same signaling pathways (i.e. TP53, PI3K, Wnt and Notch). In each MBC and UCS analyzed here, the histologically distinct components were found to be clonally related. Citation Format: Da Cruz Paula A, Brown D, Geyer FC, Smith E, Pareja F, Papanastasiou AD, Fusco N, Marchio C, Brogi E, Wen HY, Vincent-Salomon A, Norton L, Weigelt B, Reis-Filho JS. Metaplastic breast carcinomas and uterine carcinosarcomas are histologically and genetically related [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 P3-07-02.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2019
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages