P03.08.B Proton Therapy and recurrent Lower Grade Glioma: clinical and radiological aspects, intraoperative findings and histo-pathological features

Background

Radiation therapy (RT) plays a central role in management of central nervous system disease, in particular in the multimodality management of low(er) and high-grade CNS gliomas. New strategy that involved Proton Therapy (PT) have been experienced in the last years. No data are available about re-surgery of lesion irradiated with protons.

Material and Methods

We reviewed our single Unit experience of re-surgery of Lower-Grade Glioma patients that received, in their neuro-oncological history, a treatment with PT. We collect clinical data, intra-operative findings, histopathological features and oncological and clinical outcome after surgery.

Results

We collected three cases of young with an IDH1-mutated tumor that underwent to Proton Therapy (PT). In two cases PT was performed due to progression of disease, in one case as adjuvant therapy after first surgical treatment. In all cases we performed surgery within three years after PT. All patients complained drug resistant epilepsy after PT with symptom relief after surgery and one patient complained a spine fracture due to corticosteroids intake to control radionecrosis’s symptoms after PT. In the pre-operative work-up all patient performed a 11-C-Methionin PET scan that revealed an increase of tracer uptake in the suspected area of tumor progression. In one case advanced MRI protocol with PWI was performed to further distinguish and sample area of pseudoprogression and tumor progression. In two patients area of gliosis and necrosis was find at the histological examination.

Conclusion

Our experience, although limited to three case, provided a clinical and radiological example of the small cohort of patients that performed surgery after a Prothon Radiotherapy. Clinical presentation was heterogenous except a poor seizure control. Despite time elapsed since PT, areas of radionecrosis were found in the histopathological samples of 2/3 of patients. Moreover, we need to collect more data to draw a complete picture in this complex field.

P07.08.B Surgical management of recurrent lower-grade gliomas: analysis of oncological and functional outcomes and associated factors

Background

Presently, there are no clear evidence-based recommendations for the surgical management of progressive or recurrent lower-grade gliomas (LGGs). In our work, we evaluated the oncological (PFS, OS) and functional (neurological, neuropsychological, quality of life evaluation) outcomes of a series of LGGs treated in a 5-year period. The aim was to identify clinical, imaging, and molecular factors, associated with better outcomes, to be implemented in the treatment decision making process.

Material and Methods

In our retrospective analysis, 738 recurrent LGGs were included (follow-up 7.9 years; IQR:6-9); 550 were surgically treated, 495 with open resection (with brain mapping techniques), and 55 with tumor biopsy (with frameless stereotactic technique).

Results

Overall, 521 patients (70.6%) recurred. Of those treated with open resection 63.5% relapsed. Tumor progression was histologically confirmed in 72.5% of cases, no valuable tumor (effect of treatment) in 27.5% of cases (particularly in cases previously treated with RT and CHT), histo-molecular conversion (astrocytoma instead of oligodendroglioma diagnosis) in 7.5% of cases, malignant transformation in 38.7% of cases. Among the clinical (patient functional status, previous PFS, previous EOR, previous CHT and duration of CHT, previous RT), imaging (type of recurrence, i.e. typical versus atypical, speed of growth, contrast enhancement), and molecular (IDH, codeletion, ATRX, MGMT, tumor grade, CDNK status) factors analyzed, longest PFS of recurrent tumors was associated with patient functional status, previous PFS, previous EOR, speed of growth (>6 mm/year), atypical type of recurrence, tumor grade, presence of codeletion, and CDNK status. Best functional outcome associated with surgical resection, EOR, and tumor grade; worst functional outcome with RT and malignant transformation. Longest OS associated with previous EOR, surgical resection, tumor grade, presence of co-deletion. Malignant transformation was associated to previous EOR. Among patients submitted solely to tumor biopsy, changes in MGMT methylation status and in IDH status were observed in 65.3% and 5% of cases, respectively. Modification in IDH status was associated with atypical (distant) type of recurrence. New histo-molecular profile helped in the treatment decision making process.

Conclusion

Surgical resection of recurrent LGGs is associated with longer PFS and OS. Tumor biopsy should be considered, when surgery considered unfeasible, to tailor adjuvant treatment.

P01.14.B Visuospatial selective attention deficit after resection of right hemisphere gliomas: a multivariate lesion symptom mapping and diffusion tractography study

Background

The ability to select relevant information to current behavioural goals despite concomitant distractors (i.e. selective attention) is crucial for daily life. Despite the implication of fronto-parietal network in sustaining visuospatial selective attention has been considered crucial, the role of subcortical structures is still unclear. Aim of this study was to evaluate the impact of neurosurgical removal of right gliomas on visuospatial selective attention performances.

Material and Methods

The visuospatial selective attention domain was assessed pre- and postoperatively (1 month follow-up) in 73 patients operated for right hemisphere gliomas. Support-vector-regression lesion-symptom mapping and disconnectome analysis (Lesion Quantification Toolkit, HCP 1065 data) were used to evaluate the relationship between the resection cavities and the postoperative performance on a standardized selective attention test. To test and refine the atlas-based results, in a subset of 17 patients with preoperative diffusion tractography, the postoperative outcome was correlated with the percentage of disconnection for different white matter tracts.

Results

Results showed that resection of a cluster enclosing the SMA-complex and the surrounding white matter was significantly associated with a decline in visuospatial selective attention performances (p<.05). Disconnectome analysis at population level revealed that the deficit was significantly correlated with the resection of superior cortico-striatal fibres, superior thalamic radiations, corticopontine projections, callosal connections and fibres of the frontal aslant tract. Within all the cortico-subcortical terminations of these tracts, disconnection of streamlines of the SMA-complex was the most associated with selective attention deficits. Tractography in single patients confirmed the population level results and suggested that ventro-lateral resections in case of inferior frontal or insular tumours significantly disconnecting the frontal aslant tract but sparing superior projection fibres were not associated with any postoperative disturbances.

Conclusion

Results show converging evidence to support a critical role for the SMA/preSMA and its projections in maintaining efficiency of attentive control. The present results reveal the importance of a fronto-medial descending connectivity in mediating the voluntary control of visuospatial selective attention. From a surgical standpoint, to avoid postoperative deficits, it seems crucial to preserve SMA projection pathways, while the disconnection of the frontal aslant tract is feasible without any postoperative decline.

P01.19.A The temporo-parieto-occipital junction in the non-dominant hemisphere as a challenging hub for glioma surgery: functional and oncological outcomes

Background

The temporo-parieto-occipital junction (TPOJ) in the non-dominant hemisphere is a complex region intersected by multiple white matter bundles (Optic radiations, Inferior-fronto-occipital tract, inferior-longitudinalis-tract, superior-longitudinalis-tract, vertical-occipital-tract, medial-dorsal-longitudinal-tract, parietal-aslant-tract), subserving several high-level neurological functions such as spatial recognition, visual agnosia, visual field, attention and working memory. Few data are available on the optimum brain mapping strategy to be adopted for resecting tumors involving this area. Ideally it should allow surgeon to effectively identify several tracts and safely preserve all functions.

Material and Methods

We developed a proper protocol to approach this complex area integrating, in awake condition, intraoperative visual test (iVT) to mapping visual field, semantic association test (SRAT) to prevent visual agnosia and preserve working memory, hand manipulation task (hMT) to preserve spatial abilities. We reviewed its efficacy in a series of 38 patients with tumors involving non-dominant TPOJ, looking to functional (neurologic-neuropsychological) and oncological (EOR) outcomes. we perform a lesion symptom map and a disconnectome analysis to evaluate what region predict a decline in neuropsychological function and which tract of white brain matter are correlated in the decline of performance.

Results

Feasibility was high and all patients were able to perform and complete the protocol, which lasted, on the average11 min cortically and 25 min subcortically. Specificity was >95%. Immediate post-operative deficits were documented in 87.4% of patients, permanent in 3.9% (visual field, visual spatial abilities). Attentive and emotional domains were those mostly affected in the neuropsychological evaluation. Lesion symptom mapping and disconnectomic analysis showed that the postoperative decrease in neuropsychological performance was associated with resection of a cluster of voxels corresponding to the anterior portion of the temporo-parietal junction. The white matter tracts mainly involved were the anterior and posterior segment of the middle longitudinal fasciculus (aMdLF and pMdLF) and the parietal aslant tract (PAT).

Conclusion

Effective and safe resection of tumors involving non-dominant TPOJ is feasible. The adoption of a specific brain mapping protocol in awake setting is recommended to achieve a full functional preservation and extend tumor resection. Further analysis should be performed to assess the role of this subcortical tracts.

OS07.7.A Rate and type of recurrence of lower-grade gliomas submitted to functional neurosurgical approach: the impact of the extent of resection

Background

In the last decade, different published studies enlightened the extent-of-resection (EOR) as an independent factor for progression-free-survival (PFS) in patients with lower-grade gliomas (LGG). Aim of this study was to evaluate the impact of resections extending beyond FLAIR MRI abnormalities (supratotal), and eventual predictive factors and characteristics of recurrences.

Material and Methods

We retrospectively analysed 460 patients submitted to surgery between 2007 and 2016 with a presumptive diagnosis of LGG, i.e., harbouring a mass lesion with no enhancement on contrast-administered T1-weighted MRI-sequences. All resections were performed according to functional boundaries determined by brain mapping/monitoring technique, without any patient or tumor a priori selection. The EOR was defined by analyzing pre- and post-operative volumetric FLAIR images.

Results

The median pre-operative tumor volume was 43,7 cm3. A supratotal resection (SPR) was achieved in 31.4%, a gross-total (GTR) in 41.1%, a subtotal (STR) in 27.5%. WHO grade II/III gliomas were diagnosed in 347 cases (319 IDH-mutant, 28 IDH-wildtype). Median follow-up was 60 months. SPR versus other EOR was associated to increased PFS (log rank test, p=.000) and malignant PFS (p=.000). Data were confirmed also after IDH status stratification. Rate of immediate and permanent post-op deficits among different EOR were comparable. Pre-op tumor volume, parietal and insular sites, eloquent location and dominant hemisphere tumors, and astrocytoma histology were associated to recurrence (p<.05). In 95.1% of cases recurrences were peri-cavitary. Lesions invading the corpus callosum presented minor rate of relapse; recurrences were most frequently diffuse and at distant sites. After SPR most common radiological appearance of recurrence was solid, while after GTR and STR percentages of solid and diffuse patterns were similar. Occurrence of distant recurrences, away from the resection cavity, were most associated to SPR.

Conclusion

Our preliminary data suggests the dramatic impact in LGG of resections extending beyond FLAIR abnormalities on PFS and malignant PFS and on the characteristics of tumor recurrence.

MLH1 deficiency leads to deregulated mitochondrial metabolism

The DNA mismatch repair (MMR) pathway is responsible for the repair of base-base mismatches and insertion/deletion loops that arise during DNA replication. MMR deficiency is currently estimated to be present in 15-17% of colorectal cancer cases and 30% of endometrial cancers. MLH1 is one of the key proteins involved in the MMR pathway. Inhibition of a number of mitochondrial genes, including POLG and PINK1 can induce synthetic lethality in MLH1-deficient cells. Here we demonstrate for the first time that loss of MLH1 is associated with a deregulated mitochondrial metabolism, with reduced basal oxygen consumption rate and reduced spare respiratory capacity. Furthermore, MLH1-deficient cells display a significant reduction in activity of the respiratory chain Complex I. As a functional consequence of this perturbed mitochondrial metabolism, MLH1-deficient cells have a reduced anti-oxidant response and show increased sensitivity to reactive oxidative species (ROS)-inducing drugs. Taken together, our results provide evidence for an intrinsic mitochondrial dysfunction in MLH1-deficient cells and a requirement for MLH1 in the regulation of mitochondrial function.

[Eating disorders]

Anorexia and bulimia are part of eating disorders which are defined in the diagnostic and statistical manual as mental health disorders. Screening tools exist and there are different types of treatment which are generally multi-disciplinary. The nurse, as well as the family or immediate circle, are essential players in the care. Specialist units and the development of research are improving the understanding, treatment and support of these complex disorders.

The sexual dimorphism of anticardiolipin autoantibodies in acute Q fever patients

OBJECTIVES

Q fever is a zoonotic disease caused by Coxiella burnetii which affects men more than women (sex ratio men/women: 2.2). Acute Q fever complications are associated with elevation of anticardiolipin (aCL) antibodies. Here, we investigate the sexual dimorphism of aCL antibodies during acute C. burnetii infection.

METHODS

IgG aCL antibodies were evaluated at the time of Q fever serological diagnosis with enzyme-linked immunosorbent assay. Results were analysed according to sex.

RESULTS

Among the 1323 patients with Q fever tested for aCL, 1013 had acute Q fever (692 men/321 women) and 310 had persistent focalized infection (226 men/84 women). In cases of acute Q fever, men presented a significantly higher proportion of positive aCL antibodies (351/692, 50.7%) than women (113/321, 35.2%) (p <0.05). In addition, men had significantly higher aCL antibodies levels than women (p <0.001).

CONCLUSIONS

We highlight a relationship between sex and markers of autoimmunity during Q fever. Further investigations are necessary to better understand the mechanisms of this sexual dimorphism.

Viral load, tissue distribution and histopathological lesions in goats naturally and experimentally infected with the Small Ruminant Lentivirus Genotype E (subtype E1 Roccaverano strain)

Small Ruminant Lentivirus (SRLV) subtype E1, also known as Roccaverano strain, is considered a low pathogenic virus on the basis of natural genetic deletions, in vitro properties and on-farm observations. In order to gain more knowledge on this atypical lentivirus we investigated the in vivo tropism of Roccaverano strain in both, experimentally and naturally infected goats. Antibody responses were monitored as well as tissue distribution and viral load, evaluated by real time PCR on single spliced (gag/env) and multiple spliced (rev) RNA targets respectively, that were compared to histopathological lesions. Lymph nodes, spleen, alveolar macrophages and mammary gland turned out to be the main tissue reservoirs of genotype E1-provirus. Moreover, mammary gland and/or mammary lymph nodes acted as active replication sites in dairy goats, supporting the lactogenic transmission of this virus. Notably, a direct association between viral load and concomitant infection or inflammatory processes was evident within organs such as spleen, lung and testis. Our results validate the low pathogenicity designation of SRLV genotype E1 in vivo, and confirm the monocyte-macrophage cell lineage as the main virus reservoir of this genotype. Accordingly, SRLV genotype E displays a tropism towards all tissues characterized by an abundant presence of these cells, either for their own anatomical structure or for an occasional infectious/inflammatory status.

Abstract MIP-056: CONSTITUTIVELY ACTIVE ESTROGEN RECEPTOR–ALPHA LIGAND BINDING DOMAIN (ERA–LBD) MUTATIONS IN OVARIAN CARCINOMA

OBJECTIVES: Mutations in ESR1 that are acquired following treatment with aromatase inhibitors commonly underlie resistance to endocrine therapy in breast cancer. ERa-LBD mutations, especially at ESR1 Y537 and D538, confer constitutive activity and partial resistance to selective estrogen receptor modulators (SERMs), such as tamoxifen, and degraders (SERDs) such as fulvestrant in transcription assays. Some ovarian tumors also respond to anti-hormone therapy, and a subset which initially respond subsequently become resistant. The mechanisms of resistance to hormone therapy in ovarian cancer have not been previously described. Comprehensive genomic profiling (CGP) of ovarian tumors was used to analyze ESR1 and correlate responsiveness to aromatase inhibitors in a subset of these patients.

METHODS: DNA was extracted from tumor specimens and sequenced using hybridization-capture (FoundationOne) targeting up to 315 genes, plus select introns frequently rearranged in cancer. Demographic and clinicopathologic data will be presented for a subset of patients whose tumors harbor ERa-LBD mutations associated with activation and resistance..

RESULTS: CGP of 3,641 ovarian and peritoneal carcinomas revealed 31 (0.9%) samples with amplification of ESR1 and 16 (0.4%) samples with acquired or de novo mutations affecting the ERa-LBD: Y537S (10), Y537N (1), D638G (4), and S341L (1). Within the 16 samples, ovarian serous carcinoma (10), ovarian endometrioid adenocarcinoma (3), ovarian epithelial carcinoma NOS (2), and peritoneal serous carcinoma (1) were represented. In cases of acquired mutations following prior hormone therapy, there was evidence of clinical benefit to SERM/SERDs.

CaseAgeDiseaseESR1 MutationPrior HRTAcquiredSERM/SERD (*post mut if acquired)Clinical Benefit SERM/SERD159Ov serousY537SYYNN/A258Papillary serousY537NNNYY344Endometrioid ov adenoY537SNNYY445HG ov serousD538GNUYU564Endometrioid ov adenoY537SYUNU646LG ov serousY537SYUYU739Papillary serousY537SYUNN/A827LG ov serousY537SYYYY

CONCLUSIONS: Acquired activating mutations in ESR1, previously described in breast cancer, can occur in ovarian serous carcinomas and endometrioid carcinomas initially responsive to hormone therapy and suggest a similar mechanism for acquired aromatase inhibitor resistance. However, ERa mutations can occur in gynecologic malignancies even in the absence of prior endocrine therapy. Tumors harboring these mutations may remain responsive to SERM/SERDs.

Citation Format: J. A. Elvin, L. Gay, G. Colon-Otero, M. Jorgensen, L. Havrilesky, D. Zajchowski, L Shawver, F. A. Valea, S Aithal, J. S. Ross, M. Markman, S. Gaillard. CONSTITUTIVELY ACTIVE ESTROGEN RECEPTOR–ALPHA LIGAND BINDING DOMAIN (ERA–LBD) MUTATIONS IN OVARIAN CARCINOMA [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr MIP-056.

Comprehensive genomic profiling of salivary mucoepidermoid carcinomas reveals frequent BAP1, PIK3CA, and other actionable genomic alterations

Background

We sought to identify genomic alterations (GAs) in salivary mucoepidermoid carcinomas.

Patients and methods

DNA was extracted from 48 mucoepidermoid carcinomas. Comprehensive genomic profiling (CGP) including the calculation to tumor mutational burden (TMB) was performed on hybridization-captured adaptor ligation-based libraries of 315 cancer-related genes plus introns from 28 genes frequently rearranged for cancer and evaluated for all classes of GAs.

Results

A total of 183 GAs were found in 80 unique genes. High-grade tumors had more GAs (mean 5 ± 3.8) compared with low (2.3 ± 1.4) or intermediate (2.6 ± 1.5) (P = 0.019). TP53 GAs were seen in all tumor grades (41.7%) but were most common in high-grade malignancies (56%) (P = 0.047). CDKN2A GAs were seen in 41.6% of tumors. PI3K/mTOR pathway activation, including PI3KCA mutations, were more common in high grade (52%) than in low- and intermediate-grade tumors (4.3%) (P = 0.007). BAP1 GAs were observed in 20.8% of tumors and BRCA1/2 GAs present in 10.5% of specimens. ERBB2 amplifications were seen in only 8.3% of tumors. The TMB for this patient group was relatively low with only 5 (10%) of cases having greater than 10 mutations/megabase of sequenced DNA.

Conclusion

CGP of salivary mucoepidermoid carcinomas revealed diverse GAs that may lead to customized treatment options for patients with these rare tumors.

Abstract P3-07-02: Are we missing actionable targets in breast cancer? Novel insights into recurrent Ret alterations

Background: Recurrent gene fusions in breast cancer have been rarely reported suggesting that they either are not present or are not easily detected by standard sequencing methods. Comprehensive genomic profiling (CGP) by hybrid capture-based, high depth next-generation sequencing approaches, can be used to detect recurrent rearrangements and other genomic alterations involving target genes. We found that CGP can identify recurrent alterations involving RET, a known oncogenic tyrosine receptor kinase, in a subset of breast cancer.

Methods: CGP using FoundationOne platform was performed interrogating the entire coding region for up to 315 cancer-related genes and introns of up to 28 genes involved in rearrangements at a depth of 500-1000X in formalin-fixed, paraffin embedded tumor tissue (Foundation Medicine, MA). Engineered representative RET fusion vectors were synthesized and expressed in non-tumorigenic cell lines (breast MCF10A and mouse 3T3 fibroblasts), and cells were evaluated for RET kinase signaling, drug response, and tumorigenicity. Patient-derived xenografts (PDX) generated from two triple negative breast cancers (TNBCs) were used in an ex vivo assay (Response3DXTM, Molecular Response LLC, San Diego, CA).

Results: Twenty-two RET rearrangements were identified in 8119 (0.27%) breast cancer cases. Of these, 5 rearrangements were activating RET fusions including CCDC6-RET (n=4) and NCOA4-RET (n=1), that have been described in other cancer types. Five other cases had clear evidence of genomic rearrangement involving RET, but the 5' partners could not be definitively identified. The remaining twelve cases had complex rearrangements of RET including internal duplications. RET amplification was also observed, both in TNBC and in a HER2+ breast cancer at onset of resistance to HER2-targeted therapy.

Both NCOA4-RET and a novel RASGEF1A-RET fusion were characterized in vitro. Non-tumorigenic cells engineered to stably overexpress either RET fusions demonstrated transformed phenotypes. The fusions were constitutively active, as shown by endogenous phosphorylation of the kinase domain, and drove activation of downstream signaling as shown by increased phosphorylation of ERK and AKT. Cells transformed by RET-fusions were exquisitely sensitive to treatment with RET inhibitors. Interestingly, a PDX model of RET-amplified TNBC was sensitive to treatment with a PIK3CA inhibitor. An index case of ER+/PR-/HER2+, metastatic breast cancer that had radiographic evidence of disease progression while on trastuzumab, pertuzumab, and anastrazole was found to have a NCOA4-RET fusion by CGP. Subsequent treatment with with cabozantinib plus anastrazole led a rapid clinical and radiographic response.

Conclusions: CGP can identify recurrent RET rearrangements in breast cancer that act as primary oncogenic drivers and can be therapeutically targeted. RET alterations may also play a role in acquired resistance to HER2-targeted therapies, suggesting a role for combined RET and HER2-targeted therapy in this setting. Our data demonstrate that RET alterations can be identified by clinical-grade CGP and are promising candidates as therapeutic targets in selected breast cancer patients.

Citation Format: Hirshfield KM, Paratala BS, Hindoyan A, Dolfi SC, Yilmazel B, Schrock A, Gay L, Ali SM, Ross JS, Williams CB, Nair P, Ganesan S, Leyland-Jones B. Are we missing actionable targets in breast cancer? Novel insights into recurrent Ret alterations [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 P3-07-02.

Abstract P2-12-01: Comprehensive genomic profiling of 34 cases of breast angiosarcoma

Background: Angiosarcoma of the breast (BAS) is a rare but lethal neoplasia, either arising de novo or secondary to radiation therapy, with incidence of the latter disease increasing. We queried a database of more than 70,000 advanced cancer patients assayed with comprehensive genomic profiling (CGP) in the course of clinical care to uncover the frequency, type and associated genomic alterations (GA) in BAS and to highlight possible routes to benefit from targeted therapy.

Methods: CGP was performed for 34 BAS cases using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of &gt;500X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes. RNA sequencing for 265 genes was also performed for 24 cases. Limited clinical histories from submitted pathology reports were reviewed under IRB permission.

Results: Clinical specimens from 34 BAS patients, all females, were assayed. The cases harbored 87 total GA for a mean of 2.59 per case, 25% of which were copy number amplifications. The most commonly altered genes were MYC (41%, 14/34), PIK3CA (26%, 9/34), and KDR (26%, 9/34). All MYC alterations were amplifications with a mean copy number of 39, and alterations in other MYC family members (MYCN and MYCL1) were not observed. KDR was recurrently altered as T771R (7/9) and T771K (1/9) and amplified in one case (1/9).

MYC and KDR alterations were mutually exclusive (p&lt;0.0001). 6/14 MYC amplified cases had prior histories of breast carcinoma, with 3/6 noted as being treated with radiation therapy. For the remainder of MYC amplified cases (8/14), no relevant clinical history was available.

Two cases harboring gene fusions were identified including CIC-MEGF8 and NTRK1-PEAR1. Two rearrangements of potential functional significance including CIC-DEDD2 and HT-ALK (exon1 HT - exon5-29 ALK including kinase domain) were also observed. The case harboring HT-ALK also had MYC amplification and known prior radiation therapy. Two other MYC amplified cases also harbored targetable kinase alterations, including FLT4 amplification (described as targetable in Ravi et al JNCCN 2016) and FGFR3 S249C, a known activating mutation.

Conclusions: MYC amplification defines over 40% (14/34) of advanced BAS cases. Of MYC amplified cases, 28% (4/14) harbored targetable alterations of tyrosine kinases including a potential novel ALK fusion. FLT4 amplification only co-occurred with MYC amplification, but this result was not statistically significant in this small series. KDR and MYC alteration were mutually exclusive, and 45% of non-MYC altered cases (9/20) harbored KDR alterations, which were predominantly mutations of T771. Further clinico-pathologic correlation, particularly history of radiation therapy, will be explored in this series, as well defining BAS that harbor neither MYC nor KDR alterations.

Citation Format: Ravi V, Madison R, Schrock AB, Cote G, Millis S, Alvarez R, Choy E, Katz D, Chung J, Gay L, Miller VA, Ross JS, Ali SM, Schnitt S. Comprehensive genomic profiling of 34 cases of breast angiosarcoma [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 P2-12-01.

Tumour Cell Heterogeneity

The population of cells that make up a cancer are manifestly heterogeneous at the genetic, epigenetic, and phenotypic levels. In this mini-review, we summarise the extent of intra-tumour heterogeneity (ITH) across human malignancies, review the mechanisms that are responsible for generating and maintaining ITH, and discuss the ramifications and opportunities that ITH presents for cancer prognostication and treatment.

Polymorphisms near TBX5 and GDF7 are associated with increased risk for Barrett's esophagus

BACKGROUND & AIMS

Barrett's esophagus (BE) increases the risk of esophageal adenocarcinoma (EAC). We found the risk to be BE has been associated with single nucleotide polymorphisms (SNPs) on chromosome 6p21 (within the HLA region) and on 16q23, where the closest protein-coding gene is FOXF1. Subsequently, the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) identified risk loci for BE and esophageal adenocarcinoma near CRTC1 and BARX1, and within 100 kb of FOXP1. We aimed to identify further SNPs that increased BE risk and to validate previously reported associations.

METHODS

We performed a genome-wide association study (GWAS) to identify variants associated with BE and further analyzed promising variants identified by BEACON by genotyping 10,158 patients with BE and 21,062 controls.

RESULTS

We identified 2 SNPs not previously associated with BE: rs3072 (2p24.1; odds ratio [OR] = 1.14; 95% CI: 1.09-1.18; P = 1.8 × 10(-11)) and rs2701108 (12q24.21; OR = 0.90; 95% CI: 0.86-0.93; P = 7.5 × 10(-9)). The closest protein-coding genes were respectively GDF7 (rs3072), which encodes a ligand in the bone morphogenetic protein pathway, and TBX5 (rs2701108), which encodes a transcription factor that regulates esophageal and cardiac development. Our data also supported in BE cases 3 risk SNPs identified by BEACON (rs2687201, rs11789015, and rs10423674). Meta-analysis of all data identified another SNP associated with BE and esophageal adenocarcinoma: rs3784262, within ALDH1A2 (OR = 0.90; 95% CI: 0.87-0.93; P = 3.72 × 10(-9)).

CONCLUSIONS

We identified 2 loci associated with risk of BE and provided data to support a further locus. The genes we found to be associated with risk for BE encode transcription factors involved in thoracic, diaphragmatic, and esophageal development or proteins involved in the inflammatory response.

Next-generation sequencing of adrenocortical carcinoma reveals new routes to targeted therapies

Aims

Adrenocortical carcinoma (ACC) carries a poor prognosis and current systemic cytotoxic therapies result in only modest improvement in overall survival. In this retrospective study, we performed a comprehensive genomic profiling of 29 consecutive ACC samples to identify potential targets of therapy not currently searched for in routine clinical practice.

Methods

DNA from 29 ACC was sequenced to high, uniform coverage (Illumina HiSeq) and analysed for genomic alterations (GAs).

Results

At least one GA was found in 22 (76%) ACC (mean 2.6 alterations per ACC). The most frequent GAs were in TP53 (34%), NF1 (14%), CDKN2A (14%), MEN1 (14%), CTNNB1 (10%) and ATM (10%). APC, CCND2, CDK4, DAXX, DNMT3A, KDM5C, LRP1B, MSH2 and RB1 were each altered in two cases (7%) and EGFR, ERBB4, KRAS, MDM2, NRAS, PDGFRB, PIK3CA, PTEN and PTCH1 were each altered in a single case (3%). In 17 (59%) of ACC, at least one GA was associated with an available therapeutic or a mechanism-based clinical trial.

Conclusions

Next-generation sequencing can discover targets of therapy for relapsed and metastatic ACC and shows promise to improve outcomes for this aggressive form of cancer.

The genetic architecture of sexual conflict: male harm and female resistance in Callosobruchus maculatus

Males harm females during mating in a range of species. This harm is thought to evolve because it is directly or indirectly beneficial to the male, despite being costly to his mate. The resulting sexually antagonistic selection can cause sexual arms races. For sexually antagonistic co-evolution to occur, there must be genetic variation for traits involved in female harming and susceptibility to harm, but even then intersexual genetic correlations could facilitate or impede sexual co-evolution. Male Callosobruchus maculatus harm their mates during copulation by damaging the female's reproductive tract. However, there have been no investigations of the genetic variation in damage or in female susceptibility to damage, nor has the genetic covariance between these characters been assessed. Here, we use a full-sib/half-sib breeding design to show that male damage is heritable, whereas female susceptibility to damage is much less so. There is also a substantial positive genetic correlation between the two, suggesting that selection favouring damaging males will increase the prevalence of susceptible females. We also provide evidence consistent with intralocus sexual conflict in this species.

Negative phenotypic and genetic associations between copulation duration and longevity in male seed beetles

Reproduction can be costly and is predicted to trade-off against other characters. However, while these trade-offs are well documented for females, there has been less focus on aspects of male reproduction. Furthermore, those studies that have looked at males typically only investigate phenotypic associations, with the underlying genetics often ignored. Here, we report on phenotypic and genetic trade-offs in male reproductive effort in the seed beetle, Callosobruchus maculatus. We find that the duration of a male's first copulation is negatively associated with subsequent male survival, phenotypically and genetically. Our results are consistent with life-history theory and suggest that like females, males trade-off reproductive effort against longevity.

Myocardial Adenomatoid Tumor in Eight Cattle: Evidence for Mesothelial Origin of Bovine Myocardial Epithelial Inclusions

The adenomatoid tumor is an uncommon benign lesion, thus far described only in humans. Adenomatoid tumors typically arise in the genital tract, exceptionally in the heart, and usually represent an incidental finding. Microscopically, they are constituted by epithelioid cells that form tubular structures and anastomosing channels within a fibrous stroma. Mesothelial origin of these lesions is suggested by their immunohistochemical characteristics. In cattle, previously reported myocardial epithelial inclusions are morphologically similar in that the cells are immunoreactive for both cytokeratins and vimentin, and bear surface microvilli. Myocardial lesions found incidentally at slaughter in 8 cattle histologically resembled the so-called bovine myocardial epithelial inclusions and had morphologic and immunohistochemical features consistent with human adenomatoid tumor. All lesions were in the left ventricular myocardium, adjacent to the epicardium, and composed of epithelioid cells that formed cords and tubules, and were immunoreactive for pan-cytokeratins, cytokeratin 5/6, vimentin, calretinin, Wilms' tumor 1 suppressor gene, and CD30 antigen. By electron microscopy, numerous long slender microvilli were associated with desmosomes and tonofibrils. The immunohistochemical and ultrastructural features were considered consistent with mesothelial origin. These lesions, corresponding to the previously described myocardial epithelial inclusions in cattle, might be considered embryologic rests and could represent the bovine counterpart of the human adenomatoid tumor.

Does reproductive isolation evolve faster in larger populations via sexually antagonistic coevolution?

Sexual conflict over reproductive investment can lead to sexually antagonistic coevolution and reproductive isolation. It has been suggested that, unlike most models of allopatric speciation, the evolution of reproductive isolation through sexually antagonistic coevolution will occur faster in large populations as these harbour greater levels of standing genetic variation, receive larger numbers of mutations and experience more intense sexual selection. We tested this in bruchid beetle populations (Callosobruchus maculatus) by manipulating population size and standing genetic variability in replicated lines derived from founders that had been released from sexual conflict for 90 generations. We found that after 19 generations of reintroduced sexual conflict, none of our treatments had evolved significant overall reproductive isolation among replicate lines. However, as predicted, measures of reproductive isolation tended to be greater among larger populations. We discuss our methodology, arguing that reproductive isolation is best examined by performing a matrix of allopatric and sympatric crosses whereas measurement of divergence requires crosses with a tester line.

Sperm competition and maternal effects differentially influence testis and sperm size in Callosobruchus maculatus

The evolutionary factors affecting testis size are well documented, with sperm competition being of major importance. However, the factors affecting sperm length are not well understood; there are no clear theoretical predictions and the empirical evidence is inconsistent. Recently, maternal effects have been implicated in sperm length variation, a finding that may offer insights into its evolution. We investigated potential proximate and microevolutionary factors influencing testis and sperm size in the bruchid beetle Callosobruchus maculatus using a combined approach of an artificial evolution experiment over 90 generations and an environmental effects study. We found that while polyandry seems to select for larger testes, it had no detectable effect on sperm length. Furthermore, population density, a proximate indicator of sperm competition risk, was not significantly associated with sperm length or testis size variation. However, there were strong maternal effects influencing sperm length.

Speciation with gene flow in the large white-headed gulls: does selection counterbalance introgression?

We investigated the role of selection in generating and maintaining species distinctness in spite of ongoing gene flow, using two zones of secondary contact between large gull species in Europe (Larus argentatus and Larus cachinnans) and North America (Larus glaucescens and Larus occidentalis). We used the pattern of neutral genetic differentiation at nine microsatellite loci (F(ST)) as an indicator of expected changes under neutral processes and compared it with phenotypic differentiation (P(ST)) for a large number of traits (size, plumage melanism and coloration of bare parts). Even assuming very low heritability, interspecific divergence between L. glaucescens and L. occidentalis in plumage melanism and orbital ring colour clearly exceeded neutral differentiation. Similarly, melanism of the central primaries was highly divergent between L. argentatus and L. cachinnans. Such divergence is unlikely to have arisen randomly and is therefore attributed to spatially varying selection. Variation in plumage melanism in both transects agrees with Gloger's rule, which suggests that latitude (and associated sun and humidity gradients) could be the selective pressure shaping differentiation in plumage melanism. We suggest that strong species differentiation in orbital ring colour results from sexual selection. We conclude that these large gull species, along with other recently diverged species that hybridize after coming into secondary contact, may differ only in restricted regions of the genome that are undergoing strong disruptive selection because of their phenotypic effects.

Molecular and morphological patterns of introgression between two large white-headed gull species in a zone of recent secondary contact

Incomplete reproductive isolation promotes gene flow between diverging taxa. However, any gene encoding for traits involved in the reproductive barriers will be less prone to introgression than neutral markers. Comparing introgression rates among loci is thus informative of the number and functions of loci involved in the reproductive barriers. This study aimed at identifying possible mechanisms of restriction to gene flow across a zone of recent secondary contact between Larus argentatus and Larus cachinnans by comparing introgression patterns for nine microsatellite loci, a fragment of mitochondrial DNA and a set of phenotypic traits. The low linkage disequilibrium between neutral nuclear markers indicated introgression without any barrier to gene flow. However, asymmetric introgression of mitochondrial DNA suggested that interspecific crosses may be more successful in one direction. The introgression rate for phenotypic traits was variable and low compared to neutral molecular markers. This was particularly evident in colouration of bare parts: individuals with intermediate colouration were scarcer in sympatry than expected if the genomes recombined freely. We hypothesized that one of these variables, the orbital ring colour, may play a role in mate choice, acting as an incomplete premating barrier through assortative mating. This study emphasizes that multilocus approaches are useful to discriminate among possible mechanisms responsible for the maintenance of hybrid zones.

The DNA sequence and biological annotation of human chromosome 1

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Phylogeography of a game species: the red-crested pochard (Netta rufina) and consequences for its management

Western European populations of red-crested pochard (Netta rufina) are characterized by low size and high fragmentation, which accentuate their sensitivity to hunting. Uncertainties regarding the demographic trends of these populations highlight the need for pertinent hunting regulations. This requires identification of the limits of the populations under exploitation, i.e. delimiting a management unit. We used the left domain of the mitochondrial control region and seven nuclear loci (four microsatellites and three introns) to assess the level of genetic structure and demographic independence between the fragmented Western European and the large Central Asian populations. The second objective was to investigate the colonization history of the Western European populations. This study demonstrated that the Western European populations of red-crested pochard constitute a separate demographic conservation unit relative to the Asian population as a result of very low female dispersal (mitochondrial DNA: PhiST = 0.152). A morphometric analysis further suggested that Central Asian and Western European specimens of both sexes originate from different pools of individuals. Male dispersal seems higher than female dispersal, as suggested by the lack of clear genetic structure for the nuclear markers at this continental scale. Genetic data, in conjunction with historical demographic data, indicate that the current Western European populations probably originate from a recent colonization from Central Asia. As numbers of red-crested pochards in Western Europe cannot be efficiently supplemented by immigration from the larger Asian populations, a management plan regulating the harvest in Western Europe is required.

Apolipoprotein E gene polymorphism and colorectal cancer: gender-specific modulation of risk and prognosis

Apolipoprotein E ( ApoE ) gene polymorphism is a major factor in lipid metabolism. It has been suggested that this polymorphism can modulate colorectal tumour risk. We tested this hypothesis for colorectal cancer (CRC). ApoE genotype was determined in 206 patients with CRC and 353 healthy controls from the East Anglia region of the U.K. Compared with individuals possessing the most common epsilon 3/epsilon 3 genotype, those with the epsilon 2/epsilon 3 genotype had an increased risk of colon cancer [odds ratio (OR) = 1.91; 95% confidence interval 1.05-3.45]. However, this association was strongly affected by gender. Separate analysis of male and female subjects revealed a highly significant association in men (OR = 2.71; 95% confidence interval 1.30-5.65), but no association in women (OR = 1.01; 95% confidence interval 0.37-2.77). Likewise, the proportion of male patients with more advanced tumours (Dukes' C&D) was significantly increased among those with the ApoE epsilon 2/epsilon 3 genotype (OR = 4.16; 95% confidence interval 1.36-12.75). No significant effect of the presence of the epsilon 4 allele on CRC risk was found; however, there were no epsilon 4/epsilon 4 homozygotes among patients with proximal colon cancers. The ApoE epsilon 3/epsilon 3 majority genotype appeared to be associated with the lowest risk of CRC. These results suggest that ApoE genotype can influence both CRC risk and prognosis of the existing disease in a gender-dependent manner.