Characterization of small (<4cm) solid renal masses by computed tomography and magnetic resonance imaging: Current evidence and further development

Diagnosis of renal cell carcinomas (RCC) subtypes on computed tomography (CT) and magnetic resonance imaging (MRI) is clinically important. There is increased evidence that confident imaging diagnosis is now possible while standardization of the protocols is still required. Fat-poor angiomyolipoma show homogeneously increased unenhanced attenuation, homogeneously low signal on T2-weighted MRI and apparent diffusion coefficient (ADC) map, may contain microscopic fat and are classically avidly enhancing. Papillary RCC are also typically hyperattenuating and of low signal on T2-weighted MRI and ADC map; however, their gradual progressive enhancement after intravenous administration of contrast material is a differentiating feature. Clear cell RCC are avidly enhancing and may show intracellular lipid; however, these tumors are heterogeneous and are of characteristically increased signal on T2-weighted MRI. Oncocytomas and chromophobe tumors (collectively oncocytic neoplasms) show intermediate imaging findings on CT and MRI and are the most difficult subtype to characterize accurately; however, both show intermediately increased signal on T2-weighted with more gradual enhancement compared to clear cell RCC. Chromophobe tumors tend to be more homogeneous compared to oncocytomas, which can be heterogeneous, but other described features (e.g. scar, segmental enhancement inversion) overlap considerably between tumors. Tumor grade is another important consideration in small solid renal masses with emerging studies on both CT and MRI suggesting that high grade tumors may be separated from lower grade disease based upon imaging features.

Abstract P2-05-08: Mucinous breast carcinomas: A genomically distinct subtype of estrogen receptor-positive invasive breast cancers

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.

Abstract P2-05-03: Novel driver genetic alterations in MYB-NFIB-negative breast adenoid cystic carcinomas

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.

Abstract PD1-15: The landscape of somatic genetic alterations in breast cancers from ATM germline mutation carriers

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.

Abstract PD8-09: Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics and functional analysis

Background: BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in the hereditary breast and ovarian cancer (HBOC) syndrome. Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact in breast and other cancers remains to be fully elucidated. Here we took a combined genomic and functional approach to identify the role of mutations in HR-related genes and their impact on HR DNA repair.

Methods: Whole-exome sequencing and Affymetrix SNP6 array data from 8,178 tumors, comprising 24 different cancer types including breast cancer, were retrieved from The Cancer Genome Atlas (TCGA). We identified the prevalence of missense and pathogenic (frame-shift, nonsense, start/stop codon and splice site variants) somatic and germline mutations in 102 HR-related genes curated from the literature. For each mutation, we determined if the alterations were bi-allelic. We evaluated genomic signatures of HR-deficiency in each tumor using large-scale state transitions (LSTs) and a mutational signature of HR-deficiency (signature 3). An independent set of 24 fresh sporadic breast cancer tissue specimens from our institution was subjected to i) an ex-vivo assay that assesses the ability of cancer cells to form RAD51 foci in response to ex-vivo irradiation (IR), and ii) whole exome-sequencing to define whether RAD51 deficient tumors would display LSTs, signature 3 and bi-allelic inactivation of HR-related genes.

Results: 13% and 5% of all TCGA cases displayed pathogenic mono- and bi-allelic alterations of HR-related genes, respectively. Of the biallelic alterations, only 45% occurred in traditional BRCA1/2 associated hereditary cancers (HBOCs, namely breast, ovarian and prostate cancer). Bi-allelic, but not mono-allelic, pathogenic genetic alterations in HR-related genes were significantly associated with genomic evidence of HR deficiency across cancer types, in HBOCs and within breast cancer. In HBOCs, bi-allelic alterations in HR-related genes were mutually exclusive (p=0.02). In breast cancer, bi-allelic inactivation of HR DNA repair-related genes was observed in 9.8%, of which 7.8% involved a germline pathogenic mutation and 2.0% were solely somatic. In breast cancer, in addition to BRCA1 and BRCA2, bi-allelic inactivation of PALB2 (0.2%), ATM (1.1%) and POLQ (0.3%) were found to be associated with genomic features of HR deficiency. In the 24 additional breast cancers, 9 were classified by the functional ex-vivo RAD51 assay as HR-deficient, 8 of which displayed bi-allelic inactivation of one HR-related gene, whereas only 1 of the 15 HR-proficient breast cancers harbored bi-allelic inactivation of HR-related genes (p&lt;0.001).

Conclusion: Bi-allelic germline and somatic alterations of HR-related genes in addition to BRCA1 and BRCA2 are present in breast and other cancer types. Irrespective of the gene, these bi-allelic alterations are associated with HR deficiency as defined by genomic methods and functional assays, expanding the potential opportunities for therapies targeting HR DNA repair defects.

Citation Format: Riaz N, Blecua P, Lim RS, Shen R, Higginson DS, Weinhold N, Norton L, Weigelt B, Powell SN, Reis-Filho JS. Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics 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 PD8-09.

Impact of primary tumor side (TS) on outcomes of once-every-2-weeks (q2w) cetuximab + first-line (1L) FOLFOX or FOLFIRI in patients with RAS wild-type (wt) metastatic colorectal cancer (mCRC) in the phase 2 APEC trial

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Background: In the RAS wt population of APEC, q2w cetuximab combined with 1L FOLFOX or FOLFIRI achieved a best confirmed overall response rate (BORR), median progression-free survival (PFS), and median overall survival (OS) similar to those reported in prior 1L pivotal studies involving weekly (qw) cetuximab. In this hypothesis-generating subgroup analysis, we evaluated the impact of TS in APEC study patients with RAS wt mCRC. Methods: APEC was a nonrandomized phase 2 trial conducted in the Asia-Pacific region, with BORR as the primary endpoint. Patients with KRAS exon 2 wt tumors received q2w cetuximab + investigator’s choice of FOLFOX or FOLFIRI; subsequent analyses considered patients who were RAS wt ( KRAS/ NRAS, exons 2-4). TS was categorized in evaluable patients with RAS wt tumors (left [L]-sided = splenic flexure, descending colon, sigmoid colon, and rectum; right [R]-sided = appendix, cecum, ascending colon, hepatic flexure, and transverse colon). Results: Among 167 patients with RAS wt mCRC, 159 were evaluable for TS; 130 (81.8%) had L-sided and 29 (18.2%) had R-sided mCRC. Baseline characteristics in the TS subgroups reflected the known differences between L- and R-sided mCRC. Efficacy data for the TS subgroups are summarized in the table. Conclusions: Consistent with prior 1L pivotal studies involving qw cetuximab, a prognostic effect of TS in patients receiving 1L q2w cetuximab was confirmed in APEC. BORR remained ≥50% in patients with R-sided mCRC, in line with prior evidence that use of cetuximab may be appropriate when tumor shrinkage/cytoreduction is the goal. These hypothesis-generating data also raise the possibility of synergy between cetuximab and, in particular, irinotecan for PFS and OS in patients with R-sided tumors, although numbers are small. Clinical trial information: NCT00778830. [Table: see text]

Multidisciplinary retroperitoneal and pelvic soft-tissue sarcoma case conferences: the added value that radiologists can provide

Clinical Vignette: A 50-year-old woman presents to the emergency department with increasing abdominal pain. Abdominal computed tomography imaging reveals an expanded inferior vena cava-filling defect that is suspicious for a retroperitoneal sarcoma, possibly a primary leiomyosarcoma of the inferior vena cava. The surgery team discusses the case with the radiologist, and all agree that there are multiple challenges with obtaining a tissue diagnosis and determining resectability. Thus, it is decided that this patient should be discussed at a multidisciplinary case conference. In the present article, we feature a case-based scenario focusing on the role of the radiologist in this type of multidisciplinary team.

Abstract P1-05-03: The genomic landscape of breast metaplastic carcinoma

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.

Abstract S4-04: Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes

Introduction: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of invasive breast cancer. We sought to determine the genomic landscape of LCIS and the mutational processes involved in the clonal evolution and progression from LCIS to ductal carcinoma in situ (DCIS) and invasive lobular carcinoma (ILC).

Methods: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, DCIS, ILC, invasive ductal carcinomas (IDC)) and subjected to microdissection and DNA/RNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 and data were aligned to the reference human genome and processed using GATK. Single nucleotide variants (SNVs) and small insertions/deletions were identified using MuTect and Varscan, respectively. Purity and ploidy estimates were calculated using ABSOLUTE. Clonal frequencies were estimated using Pyclone and the clonal structure of each sample was reconstructed using SubcloneSeeker. Shannon index and Simpson index metrics were used to calculate heterogeneity levels. Mutational signatures were defined according to their mutational trinucleotide context, and the expression levels of APOBEC gene family members were assessed by quantitative reverse transcription (qRT)-PCR.

Results: 30 LCIS, 10 ILCs, 7 DCIS and 5 IDCs from 15 patients qualified for data analysis. CDH1 was the most frequently mutated gene and found to be targeted by mutations in 26 LCIS samples (23 somatic, 3 germline). The repertoire of somatic mutations in LCIS was similar to that of luminal A breast cancers, with the exception of the significantly higher frequency of CDH1 mutations and the lower prevalence of TP53 mutations. ILCs were clonally related to at least one LCIS in 10 patients, and in 3/7 patients, DCIS was clonally related to at least one LCIS. Clonal composition analysis revealed that the presence of a minor clone(s) in LCIS, and the levels of intra-tumor genetic heterogeneity were significantly higher in LCIS clonally related with DCIS/ILC than in LCIS unrelated to DCIS/ILC. In two cases, a minor LCIS subclone constituted the major clone in the associated DCIS/ILC. A comparative analysis of the mutational signatures in the truncal and branch mutations of these cases revealed that whilst the truncal mutations displayed an aging signature, branch mutations were enriched for the APOBEC signature. qRT-PCR analysis demonstrated that cases displaying the APOBEC signature also harbored significantly higher levels of APOBEC3B expression than samples with the aging signature.

Conclusions: LCIS displays intra-lesion genetic heterogeneity, and the progression from LCIS to DCIS or ILC may involve the selection of clones resulting from distinct mutational processes during clonal evolution. Our findings also suggest that cytodine deamination driven by the overexpression of APOBEC3B may drive the progression of LCIS to DCIS/ILC in a subset of cases.

Citation Format: Reis-Filho JS, Schizas M, Piscuoglio S, Sakr RA, Ng CKY, Lim RS, Carniello JVS, Towers R, Martelotto L, Giri DD, de Andrade VP, Viale A, Solit DB, Weigelt B, King TA. Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S4-04.

Abstract P6-03-10: Genomic and transcriptomic heterogeneity in metaplastic breast carcinomas

Introduction: Metaplastic breast carcinoma (MBC) is a rare form of triple-negative breast cancer (TNBC), accounting for approximately 0.2%-5% of all invasive breast cancers. These tumors are characterized by the presence of neoplastic cells displaying differentiation towards squamous epithelium or mesenchymal elements. MBCs are reported to have an aggressive clinical behavior, to exhibit a worse prognosis and to respond less frequently to conventional chemotherapy regimens than common forms of TNBCs. In this study, we sought to define whether morphologically distinct subgroups of MBCs would be underpinned by distinct gene expression or copy number profiles, and whether MBCs, akin to other special histologic types of TNBC (e.g. secretory carcinoma and adenoid cystic carcinoma), would be underpinned by a highly recurrent fusion gene.

Methods: RNA and DNA samples were extracted from microdissected frozen MBCs (5 squamous, 5 spindle and 7 chondroid) and subjected to gene expression profiling using the Illumina Human HT-12 v4 platform and gene copy number profiling using the Affymetrix Human SNP 6.0 arrays, respectively. Genes differentially expressed between MBC subtypes were identified using SAM, and functional annotation of these genes was performed using Ingenuity Pathway Analysis. Intrinsic molecular subtypes were determined using the PAM50 and claudin-low intrinsic gene lists. In addition, all cases were subjected to paired-end massively parallel RNA-sequencing (Illumina GAIIx). Putative expressed fusion transcripts were identified using a validated algorithm (i.e. ChimeraScan), and confirmed by means of RT-PCR.

Results: MBCs with spindle cell morphology were all classified as of claudin-low intrinsic subtype, whereas MBCs with chondroid or squamous cell metaplasia were classified as of normal breast-like, basal-like or claudin-low subtypes, suggesting that these morphologic subgroups are heterogeneous. Unsupervised analysis of microarray and RNA-sequencing gene expression data further demonstrated that MBCs with spindle cell differentiation displayed distinctive transcriptomic profiles, and formed clusters distinct from those enriched for MBCs with chondroid and squamous cell metaplasia. MBCs with spindle cell morphology preferentially expressed regulators of epithelial-to-mesenchymal transition including lower expression of E-cadherin and EpCAM. At the genomic level, MBC subtypes displayed patterns of gene copy number alterations similar to those of common forms of TNBCs from The Cancer Genome Atlas, and no significant differences were found among the distinct MBC subtypes. Nine in-frame fusion genes, TBL1XR1-PIK3CA, WAPL-CDHR1, MAP2K3-HMGCLL, PARG-BMS1, FN1-ICAM1, TNKS1BP1-SPARC, AAK1-ARNT2, MBTPS1-TCEANC2 and PSMA6-SHMT1 were identified and validated in the index cases, however none of these was found to be recurrent in the cases analyzed in this study.

Conclusion: MBC subtypes, despite harboring similar patterns of gene copy number alterations, display significant transcriptomic differences, which may account for their distinct histologic features. Our findings also demonstrate that unlike other histologic special types of TNBC, MBCs are not underpinned by a highly recurrent expressed fusion gene.

Citation Format: Piscuoglio S, Ng CKY, Cowell CF, Mariani O, Martelotto L, Natrajan R, Lim RS, Maher CA, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Genomic and transcriptomic heterogeneity in metaplastic breast carcinomas. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-10.

Abstract P2-01-02: Capturing intra-tumor genetic heterogeneity in cell-free plasma DNA from patients with oligometastatic breast cancer

Background: The analysis of cell-free tumor DNA (ctDNA) from plasma has been heralded as a non-invasive technique for disease monitoring and as a means to overcome the challenges posed by intra-tumor genetic heterogeneity. ctDNA levels have been shown to correlate with tumor burden in breast cancer patients. Hence, we sought to define whether massively parallel sequencing of cell-free plasma DNA would capture the entire repertoire of somatic mutations present in the primary tumors and/ or metastases from patients with oligometastatic breast cancer.

Methods: Frozen diagnostic biopsies from primary tumors and their distant metastases were obtained from five prospectively accrued treatment-naïve patients with stage IV breast cancer at presentation (1 estrogen receptor (ER)+/HER2+, 2 ER+/HER2-, 2 ER-/HER2+). A second, independent formalin-fixed paraffin-embedded (FFPE) diagnostic biopsy was obtained from the primary tumor and metastasis from 4 patients. Plasma samples were obtained from all patients. DNA samples from microdissected frozen tumors and peripheral blood, as well as plasma from one patient, were subjected to high-depth whole exome sequencing. DNA samples from all biopsies (frozen/FFPE), plasma and peripheral blood were subjected to targeted capture massively parallel sequencing, with baits for all somatic mutations detected by whole exome sequencing and all exons of the 100 genes most frequently mutated in breast cancer. Driver mutations were defined by state-of-the-art bioinformatic methods and literature search.

Results: We identified and confirmed a median of 54 (range 25-75) and 53 (range 26-85) non-synonymous mutations in the primary tumors and metastases from the 5 cases analyzed, respectively. By sequencing the plasma DNA to a median depth of 248x (range 92-431x), state-of-the-art mutation callers revealed 0-4 mutations (0%-8% of mutations) per patient, and direct interrogation of the sequencing data, based on prior knowledge of the mutations present in the lesions, resulted in the identification of 2-18 mutations (3%-38% of mutations) per patient. Of the bona fide driver mutations, 2/3 TP53 mutations, 0/1 PIK3CA hotspot mutation, 0/1 BRCA2 frameshift mutation, 0/1 GATA3 frameshift mutation and 0/1 ERBB3 activating mutation were captured in the plasma DNA. A SMAD4 pathogenic mutation and a TCF7L2 truncating mutation were found in two diagnostic biopsies of metastatic lesions but not in two biopsies of the primary tumors in one patient each. Whilst the SMAD4 mutation was detected in the plasma DNA from the respective patient, the TCF7L2 mutation was not. Of the 62 mutations restricted to the primary tumors (0-42 per patient) and 74 restricted to the metastatic tumors (1-41 per patient), 4 and 7, respectively, were captured in the plasma DNA.

Conclusions: Massively parallel sequencing assessment of plasma DNA allows for the identification of mutations found in primary tumors and/ or their metastases, however, only a subset of these could be detected at up to 431x depth. These observations suggest that current approaches for whole exome or targeted massively parallel sequencing may not be sufficient to capture the genetic heterogeneity of breast cancers in patients with oligometastatic disease.

Citation Format: Ng CKY, Bidard F-C, Piscuoglio S, Lim RS, Pierga J-Y, Cottu P, Vincent-Salomon A, Viale A, Norton L, Sigal B, Weigelt B, Reis-Filho JS. Capturing intra-tumor genetic heterogeneity in cell-free plasma DNA from patients with oligometastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-01-02.

Final analysis of the phase 2 APEC study: Overall survival (OS) data and biomarker subanalyses for first-line FOLFOX or FOLFIRI with cetuximab (cet) once every 2 weeks in patients (pts) with KRAS or RAS (KRAS and NRAS, exons 2-4) wild-type (wt) metastatic colorectal cancer (mCRC)

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Background: The Asia-Pacific, multicenter, nonrandomized, phase II APEC study previously reported that first-line therapy for pts with KRAS ex 2 wt mCRC consisting of C once every 2 weeks combined with FOLFOX or FOLFIRI achieved efficacy and safety profiles comparable to those reported in analogous pivotal studies involving weekly C. This final analysis presents OS data from the KRAS wt intent-to-treat (ITT) population, as well as subgroup efficacy analyses stratified by BRAF, PIKC3A, and all RAS mutation status. Methods: Eligible pts received C once every 2 weeks (day 1 of each cycle, 500 mg/m2) with FOLFOX or FOLFIRI (investigator’s choice). Study treatment continued until disease progression, dose-limiting toxicity or consent withdrawal. The primary endpoint was best confirmed overall response as assessed by RECIST 1.0; progression-free survival (PFS) and OS were secondary endpoints. In the evaluable populations, the status of BRAF, PIK3CA, and all RAS mutations was assessed retrospectively by pyrosequencing. Results: 42 months after the last patient was enrolled, median OS in the KRAS wt population was 26.8 months (Table). There were no unexpected safety findings. Additional biomarker results—including objective response rate (ORR), PFS, and OS subgroup analyses stratified on BRAF, PIKC3A, and all RAS mutation status—will be presented. Conclusions: The observed median OS of 26.8 months in the KRAS wt population is comparable to that reported in prior pivotal studies involving weekly C plus FOLFOX or FOLFIRI in the first line. These results suggest that C plus FOLFOX or FOLFIRI in a once-every-2-weeks regimen is active and tolerable as first-line therapy in this Asia-Pacific study population and a convenient alternative to weekly administration. Clinical trial information: NCT00778830. [Table: see text]

Postoperative bladder and sexual function in patients undergoing surgery for rectal cancer: a systematic review and meta-analysis of laparoscopic versus open resection of rectal cancer

There have been conflicting opinions regarding the superiority of open and laparoscopic surgery in preserving bladder and sexual function after rectal cancer surgery. This systematic review and meta-analysis aims to pool the available data comparing the impact of surgical approaches on postoperative sexual and urinary function. A search of Pubmed, Medline, Cochrane and Embase was undertaken and studies from January 2000 to February 2013 were identified. We included, in our meta-analysis, both prospective and retrospective studies that compared laparoscopic surgery and open surgery for rectal cancer. A total of 876 patients undergoing rectal cancer surgery (lap n = 468, open n = 408) were examined. In men, postoperative ejaculatory function and erectile dysfunction evaluated from two studies comprising of 74 patients showed no difference between groups. The rate of overall sexual dysfunction evaluated from five studies comprising of 289 patients revealed a rate of 34 % in both the open and lap groups. Postoperative urinary function evaluated from five studies comprising of 312 patients showed no difference between groups. In women, postoperative sexual and urinary function were evaluated from five studies comprising of 321 patients. Three studies (n = 219) reported no difference in sexual function between groups. Postoperative urinary function evaluated from four studies comprising of 212 patients was found to be comparable. The available data are limited, but suggest that neither form of surgical approach be it laparoscopy or open surgery demonstrate superiority in preservation of sexual and bladder function. Further research into the technical aspects of surgery and evaluating newer minimally invasive technologies such as the robot may prove to be useful in improving functional outcomes of rectal cancer patients.

Efficacy and safety of every-2-weeks cetuximab combined with FOLFOX or FOLFIRI as first-line therapy in patients with KRAS wild-type metastatic colorectal cancer (mCRC): An Asia-Pacific nonrandomized phase II study (APEC)

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Background: Randomized studies have shown that weekly cetuximab added to first-line FOLFOX or FOLFIRI improves clinical outcome in patients (pts) with KRAS wild-type (wt) mCRC. This Asia-Pacific multicenter study investigated FOLFOX or FOLFIRI + every 2 weeks cetuximab (C) as first-line therapy in pts with KRAS wt mCRC. Methods: Eligible pts received every 2 weeks cetuximab (d1 500 mg/m2 q14d) with, based on investigator’s choice, either FOLFOX (oxaliplatin 100 mg/m2, folinic acid [FA] 200 mg/m2 L-form or 400 mg/m2 racemic, then 5-fluorouracil [5-FU], as a 400 mg/m2 iv bolus and a 2400 mg/m2 infusion over 46 h) or FOLFIRI (irinotecan 180 mg/m2, FA 200 mg/m2 L-form, or 400 mg/m2 racemic, then 5-FU, as a 400 mg/m2 iv bolus and a 2400 mg/m2infusion over 46 h), until disease progression, unacceptable toxicity or consent withdrawal. Primary endpoint was tumor response; assessed radiologically (RECIST 1.0) every 8 weeks. Results: Data cut-off was 86 weeks after the date of last patient included. The ITT/safety population comprised 289 pts; 65.1% received FOLFOX + C and 34.9% FOLFIRI + C. Baseline characteristics were generally well balanced. Leukocyte count >10000/mm3was more frequent (16.5% vs 7.9%) and prior adjuvant treatment less frequent (21.3% vs 46.5%) in pts receiving FOLFOX + C. Response (CR or PR) was observed in 170 (58.8%) pts. The overall R0 resection rate was 10.0%. Survival data are not mature. Cetuximab dose intensity was >80% in 77.7% (FOLFOX + C) and 74.3% (FOLFIRI + C) of pts. Most frequent grade 3/4 adverse events (>10% in either arm) were neutropenia, diarrhea, hypokalemia, neuropathy (FOLFOX + C only) and skin reactions. Conclusions: Efficacy and safety profiles of every 2 weeks cetuximab combined with FOLFOX or FOLFIRI were similar to those reported for either chemotherapy plus weekly cetuximab in pivotal studies. Clinical trial information: NCT00778830. [Table: see text]

Pharmacodynamic effects of regorafenib in metastatic colorectal carcinoma (mCRC)

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Background: Regorafenib, an oral multikinase inhibitor of VEGFR2/3, PDGFRb, KIT, FGFR, RET, RAF and TIE2, is efficacious in refractory mCRC but its mechanism of action is unclear and predictive biomarkers are lacking. Methods: We assessed tumor and circulatory biomarkers in a phase 2 study of regorafenib in refractory mCRC patients. Regorafenib was administered orally at 160mg/d for 3 out of 4 weeks. Post cycle 2 response was assessed by RECIST 1.1. Subjects were scheduled for FDG PET-CT scans (pre + D15) and paired core needle tumor biopsies for IHC analysis (pre + D21) in cycle 1. Archival tumor mutations were evaluated using Sequenom MassARRAY OncoCarta Panel V1.0 assay. Results: 35 patients were treated; 49% received > 4 prior therapies and 43% had prior bevacizumab. Median PFS was 3.45 mths (95% CI: 3.40-3.49), ORR was 3% and disease control rate [DCR] (PR + SD at 8 wks) was 57%. Early PET responses (EORTC criteria) were seen in 49%, but did not predict for DCR (p=1.0). Fatigue, hand foot skin reaction (HFSR), voice change and diarrhea occurred in > 30% of subjects. Grade 3-5 toxicities occurred in 46%, the commonest being HFSR and rash (17% each). Median relative dose intensity was 92%; 43% required > 1 dose reduction, 60% required > 1 dose interruption. KRAS (29%), BRAF (9%), EGFR (9%), NRAS (6%) KIT (3%), PIK3CA (3%), PDGFRA (3%) and CDK (3%) mutations were detected in archival tumors. None predicted for ORR or DCR; PFS was identical in KRAS mutant vs wt patients (3.45 mths, p=0.39) and similar in BRAF mutant vs wt patients (3.48 vs 3.45 mths, p=0.10). The patient with the longest PFS (12.6 mths) had a BRAF mutation. Amongst the 10 paired tumor samples available, IHC markers upregulated in >50% cases were pMEK, pERK, pJun and pJNK, whilst those downregulated/ unchanged in >50% were pKIT, pVEGFR2, CD31 [vascular endothelial cells (ECs)] and podoplanin (lymphatic ECs). The greatest change was observed in podoplanin expression, corresponding to a 60% reduction in lymphatic vessel density. Conclusions: FDG-PET responses in cycle 1 did not predict for regorafenib clinical benefit in mCRC patients. Targeting lymphatic/vascular ECs in the tumor microenvironment may be a more significant antitumor mechanism of regorafenib than MAP kinase pathway inhibition. Clinical trial information: NCT01189903.

Sarcocystis spp infection in Philippine water buffaloes (Bubalus bubalis)

In a survey of sarcocysts in muscle tissues obtained from 142 water buffaloes, 65% of the carcasses had sarcocysts. Macroscopic and two forms of microscopic sarcocysts, the spindle-shaped or fusiform sarcocysts commonly occurring in the muscles of the esophagus, throat and limbs, and the globular to oval-shaped sarcocysts which were the dominant form in the diaphragm and cervical muscle tissues were noted. Ultrastructural analysis of macroscopic and microscopic sarcocysts and their cyst wall revealed two distinct species of Sarcocystis: the macroscopic species, Sarcocystis fusiformis which has been previously reported in Philippine carabaos possessing highly dendritic cauliflower-like projections emanating from the primary cyst wall, with annulated microfilaments and numerous electron dense granules: and the Sarcocystis levinei (Dissanaike and Kan, 1978) Huong, Dubey and Uggla. 1997 exhibiting a cyst wall with undulating and hair-like villar protrusions with expanded or dome-shaped base, intermediate finger-like, and distal tapering segments which at some points join to form conical tufts. Our findings represent the first report of S. levinei in the country supported with ultrastructural analysis of the sarcocysts and cyst wall, and likewise refute earlier published reports that all microscopic sarcocysts in Philippine carabaos are developing forms of the macroscopic species, S. fusiformis. Histopathological changes such as displacement and necrosis of the surrounding host muscle tissue were observed with macroscopic sarcocysts and histologically processed tissue samples containing microscopic fusiform sarcocysts. Necrotic myofibrils and mitochondria were evident in ultrathin sections.

The t(4;14) translocation in myeloma dysregulates both FGFR3 and a novel gene, MMSET, resulting in IgH/MMSET hybrid transcripts

Previously we reported that a karyotypically silent t(4;14)(p16. 3;q32.3) translocation is present in about 25% of multiple myeloma (MM) tumors, and causes overexpression of FGFR3, which is 50 to 100 kb telomeric to the 4p16 breakpoints. Frequent FGFR3 kinase activating mutations in MM with t(4;14) translocations substantiate an oncogenic role for FGFR3. We now report that the 4p16 breakpoints occur telomeric to and within the 5' introns of a novel gene, MMSET (Multiple Myeloma SET domain). In normal tissues, MMSET has a complex pattern of expression with a short form (647 amino acids [aa]) containing an HMG box and hath region, and an alternatively spliced long form (1365 aa) containing the HMG box and hath region plus 4 PHD fingers and a SET domain. Although t(4;14) translocation results in IgH/MMSET hybrid transcripts, overexpression of MMSET also occurs from endogenous promoters on 4p16. Given the homology to HRX/MLL1/ALL1 at 11q23 that is dysregulated by translocations in acute leukemia, we hypothesize that dysregulation of MMSET contributes to neoplastic transformation in MM with t(4;14) translocation. This is the first example of an IgH translocation that simultaneously dysregulates two genes with oncogenic potential: FGFR3 on der(14) and MMSET on der(4).

Epidemic polyarthritis in South Australia 1979-1980

During the past season, a further outbreak of Ross River epidemic polyarthritis occurred in South Australia. Significant differences in the epidemiology occurred, which support the hypothesis that the virus is brought to the area by wild birds.