Abstract P4-03-07: Analysis of hereditary cancer syndromes by using a panel of genes: Novel and multiple pathogenic mutations

BACKGOUND: Hereditary cancer predisposition syndromes are believed to be responsible for approximately 5-10% of all diagnosed cancer cases. In the past, single genes analysis of certain high risk genes was used for the determination of the genetic cause of cancer heritability in certain families. The selection of genes was mainly based on the family history of the individuals analyzed and included only highly associated genes (e.g. the BRCA1 and BRCA2 genes for families with breast cancer history. Nowadays though, the application of Next Generation Sequencing (NGS) technology has facilitated multigene panel analysis and is widely used in clinical practice, for the identification of individuals with cancer predisposition gene mutations.

AIM: The aim of this study was to investigate the extent and nature of mutations in 36 genes implicated in hereditary cancer predisposition in individuals referred for testing in our lab.

MATERIALS & METHODS: In total, 1197 individuals were referred for testing in our lab in the past four years from Greece, Romania and Turkey. The analysis of genes involved in hereditary cancer predisposition was performed using two NGS approaches. The first 451 individuals were analyzed using an amplicon based sequencing method (26 gene panel), while the following 746 individuals were analyzed using a capture based method (33 gene panel). Genomic DNA was enriched for targeted regions of 36 genes involved in hereditary predisposition to cancer included in both versions of the panel (APC, BMPR1A, BRCA1, BRCA2, CDH1, CDK4, CDKN2A, EPCAM, MEN1, MLH1, MSH2, MSH6, MUTYH, PALB2, PMS2, PTEN, RET, SMAD4, STK11, TP53, VHL, ATM, BRIP1, CHEK2, NBN, RAD51C, RAD51D, BARD1, BLM, CHEK1, ABRAXAS1 (FAM175A), MRE11 (MRE11A), NF1, RAD50, RAD51B, XRCC2). Sequencing was carried out using the Illumina NGS technology. Reads were aligned to the reference sequence (GRCh37), and sequence changes were identified and interpreted in the context of a single clinically relevant transcript. The presence of large genomic rearrangements was investigated by computational analysis of NGS results and the use of MLPA for 13 genes. All clinically significant observations were confirmed by orthogonal technologies.

RESULTS: In total, a pathogenic mutation was identified in 259 of the 1197 individuals (21.6%) analyzed while a VUS was identified in 35.7% of the cases. Clinically significant mutations were identified in 29 of the genes analyzed. Concerning the mutation distribution among individuals with positive findings, 44.7% of them were located in BRCA1/2 genes whereas 20.9%, 19.9%, and 14.5% in high, moderate and low risk genes respectively. In addition to BRCA1 and BRCA2 genes other highly mutated genes were CHEK2 (10.6%), PALB2 (7.1%), MUTYH (7.1%) and ATM (4.3%). Of note is that 25 of the 259 positive individuals (9.7%) carried clinically significant mutations in two different genes and 5.8% had a large genomic rearrangement (LGR).

CONCLUSIONS: Our results support the clinical significance of analysis of a panel of genes involved in hereditary cancer predisposition. In our cohort, analysis of this panel allowed for the identification of 8.3% additional pathogenic variants in moderate/low risk genes, enabling personalized management of these individuals.

Citation Format: Tsoulos N, Tsaousis GN, Papadopoulou E, Agiannitopoulos K, Pepe G, Kambouri S, Apessos A, Diamantopoulos N, Floros T, Iosifidou R, Katopodi O, Koumarianou A, Markopoulos C, Papazisis K, Venizelos V, Xanthakis I, Xepapadakis G, Banu E, Eniu DT, Negru S, Stanculeanu DL, Ungureanu A, Ozmen V, Tansan S, Tekinel M, Yalcin S, Nasioulas G. Analysis of hereditary cancer syndromes by using a panel of genes: Novel and multiple pathogenic mutations [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-03-07.

Abstract P3-04-04: Germline and somatic mutation status in tissues from BRCA1/2 carriers

Background – aim: In carriers of BRCA1/2 pathogenic mutations (mut), it is expected that the germline mut is present in all tissues, particularly in normal; the somatic mut status in normal tissues from these patients is usually not addressed. We investigated the mut status in normal and tumor tissues in a real-life cohort of BRCA1/2 carriers who underwent prophylactic surgery.

Methods: All 53 women had known BRCA1/2 germline mut that had been assessed independently; 42 had previous cancer manifestation (PCM); all had prophylactic mastectomy; 22 had prophylactic hystero-salpingo-oophorectomy. By using a 60-gene NGS panel, we examined the mut status of 231 samples, 39 peripheral blood and 192 paraffin tissues (FFPE: 46 tumors, out of which 43 breast; 97 normal breast [NB]; 49 normal ovary and salpinx [NGYN]). Germline mut status was interrogated in tissues with the above panel, Sanger sequencing and a multiplex PCR protocol for large exonic deletions, along with extensive FFPE DNA quality control (QC) to exclude false negatives.

Results: Eight patients carried germline BRCA2 and 45 BRCA1 mut (29 in the BRCT-domain; 31 substitutions/indels). We identified somatic mut in 85% of the tumors and in 64% of the normal samples; mut were found significantly more often (p=0.003) and in higher numbers (p<0.001) in NGYN than in NB. In NB and NGYN, top 3 genes with somatic mut were BRCA2 (28%), BRCA1 (17%), TP53 (7%). In tumors, somatic mut were most frequent in TP53 (49%; p<0.001) and BRCA1 (38%; p=0.039). Among all tissue types, the 5 tumors post-neoadjuvant treatment had the highest and NB the lowest mut load (p=0.001). In NB and NGYN, mut load was not affected by PCM or BRCA1 mut domain but it was higher in BRCA1 vs. BRCA2 carriers (p=0.027) and in those with BRCA1 substitutions/indels vs. exon deleting and skipping mut (p<0.001). In tumors, germline BRCA1 substitutions/indels were associated with higher mut load (p=0.014). We validated germline mut status in all blood samples and in 111 tissue samples that passed FFPE DNA QC from 40 patients. The germline mut was not found in 14 samples (4 breast tumors; 3 NB; 7 NGYN) from 10 (25%) patients, all BRCA1 carriers, 9 with germline mut in the BRCT-domain. The only non-BRCT domain germline mut that was lost in one breast tumor, p.V1234fs, was replaced by the R1751* (validated), again in the BRCT domain. In normal tissues, those with lost germline mut had significantly less somatic mut compared to those with preserved germline mut (p<0.001).

Conclusions: In BRCA1/2 carriers, somatic mut in BRCA genes and TP53 are present in normal breast and GYN tissues, more frequently in the latter, and seem associated with the mutated gene and with the type of mut in the germline. The mut status of normal breast tissue does not seem to be affected by neoadjuvant chemotherapy for breast cancer. The observed BRCA1 germline mut loss, particularly in normal tissues, may be approached as a negative selection for the inherited mut; similarly to the described germline mut reversion after chemotherapy, tissues may react to deleterious effects of haploinsufficiency, which needs functional validation.

Citation Format: Kotoula V, Demiri E, Fostira F, Vrettou E, Papadopoulou K, Tikas I, Papazisis K, Zaramboukas T, Asimaki-Vlachopoulou A, Miliaras S, Fountzilas E, Ananiadis A, Chrisafi S, Poulios C, Natsiopoulos I, Tsiftsoglou A, Fountzilas G. Germline and somatic mutation status in tissues from BRCA1/2 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 P3-04-04.

Adverse event management in patients with advanced cancer receiving oral everolimus: focus on breast cancer

BACKGROUND

Everolimus, an orally administered rapamycin analogue, inhibits the mammalian target of rapamycin (mTOR), a highly conserved intracellular serine-threonine kinase that is a central node in a network of signaling pathways controlling cellular metabolism, growth, survival, proliferation, angiogenesis, and immune function. Everolimus has demonstrated substantial clinical benefit in randomized, controlled, phase III studies leading to approval for the treatment of advanced renal cell carcinoma, advanced neuroendocrine tumors of pancreatic origin, renal angiomyolipoma and subependymal giant-cell astrocytoma associated with tuberous sclerosis complex, as well as advanced hormone-receptor-positive (HR(+)) and human epidermal growth factor receptor-2-negative advanced breast cancer.

MATERIALS AND METHODS

We discuss clinically relevant everolimus-related adverse events from the phase III studies, including stomatitis, noninfectious pneumonitis, rash, selected metabolic abnormalities, and infections, with focus on appropriate clinical management of these events and specific considerations in patients with breast cancer.

RESULTS

The majority of adverse events experienced during everolimus therapy are of mild to moderate severity. The safety profile and protocols for toxicity management are well established. The class-effect adverse event profile observed with everolimus plus endocrine therapy in breast cancer is (as expected) distinct from that of endocrine therapy alone, but is similar to that observed with everolimus in other solid tumors. Information gained from the experience in other carcinomas on prompt diagnosis and treatments to optimize drug exposure, treatment outcomes, and patients' quality of life also applies to the patient population with advanced breast cancer.

CONCLUSIONS

As with all orally administered agents, education of both physicians and patients in the management of adverse events for patients receiving everolimus is critical to achieving optimal exposure and clinical benefit. Active monitoring for early identification of everolimus-related adverse events combined with aggressive and appropriate intervention should lead to a reduction in the severity and duration of the event.

Development and validation of a prognostic model in patients with metastatic renal cell carcinoma treated with sunitinib: a European collaboration

BACKGROUND

Accurate prediction of outcome for metastatic renal cell carcinoma (mRCC) patients receiving targeted therapy is essential. Most of the available models have been developed in patients treated with cytokines, while most of them are fairly complex, including at least five factors. We developed and externally validated a simple model for overall survival (OS) in mRCC. We also studied the recently validated International Database Consortium (IDC) model in our data sets.

METHODS

The development cohort included 170 mRCC patients treated with sunitinib. The final prognostic model was selected by uni- and multivariate Cox regression analyses. Risk groups were defined by the number of risk factors and by the 25th and 75th percentiles of the model's prognostic index distribution. The model was validated using an independent data set of 266 mRCC patients (validation cohort) treated with the same agent.

RESULTS

Eastern Co-operative Oncology Group (ECOG) performance status (PS), time from diagnosis of RCC and number of metastatic sites were included in the final model. Median OS of patients with 1, 2 and 3 risk factors were: 24.7, 12.8 and 5.9 months, respectively, whereas median OS was not reached for patients with 0 risk factors. Concordance (C) index for internal validation was 0.712, whereas C-index for external validation was 0.634, due to differences in survival especially in poor-risk populations between the two cohorts. Predictive performance of the model was improved after recalibration. Application of the mRCC International Database Consortium (IDC) model resulted in a C-index of 0.574 in the development and 0.576 in the validation cohorts (lower than those recently reported for this model). Predictive ability was also improved after recalibration in this analysis. Risk stratification according to IDC model showed more similar outcomes across the development and validation cohorts compared with our model.

CONCLUSION

Our model provides a simple prognostic tool in mRCC patients treated with a targeted agent. It had similar performance with the IDC model, which, however, produced more consistent survival results across the development and validation cohorts. The predictive ability of both models was lower than that suggested by internal validation (our model) or recent published data (IDC model), due to differences between observed and predicted survival among intermediate and poor-risk patients. Our results highlight the importance of external validation and the need for further refinement of existing prognostic models.

Maximising the duration of disease control in metastatic renal cell carcinoma with targeted agents: an expert agreement

With six targeted agents approved (sorafenib, sunitinib, temsirolimus, bevacizumab [+interferon], everolimus and pazopanib), many patients with metastatic renal cell carcinoma (mRCC) will receive multiple therapies. However, the optimum sequencing approach has not been defined. A group of European experts reviewed available data and shared their clinical experience to compile an expert agreement on the sequential use of targeted agents in mRCC. To date, there are few prospective studies of sequential therapy. The mammalian target of rapamycin (mTOR) inhibitor everolimus was approved for use in patients who failed treatment with inhibitors of vascular endothelial growth factor (VEGF) and VEGF receptors (VEGFR) based on the results from a Phase III placebo-controlled study; however, until then, the only licensed agents across the spectrum of mRCC were VEGF(R) inhibitors (sorafenib, sunitinib and bevacizumab + interferon), and as such, a large body of evidence has accumulated regarding their use in sequence. Data show that sequential use of VEGF(R) inhibitors may be an effective treatment strategy to achieve prolonged clinical benefit. The optimal place of each targeted agent in the treatment sequence is still unclear, and data from large prospective studies are needed. The Phase III AXIS study of second-line sorafenib vs. axitinib (including post-VEGF(R) inhibitors) has completed, but the data are not yet published; other ongoing studies include the Phase III SWITCH study of sorafenib-sunitinib vs. sunitinib-sorafenib (NCT00732914); the Phase III 404 study of temsirolimus vs. sorafenib post-sunitinib (NCT00474786) and the Phase II RECORD 3 study of sunitinib-everolimus vs. everolimus-sunitinib (NCT00903175). Until additional data are available, consideration of patient response and tolerability to treatment may facilitate current decision-making regarding when to switch and which treatment to switch to in real-life clinical practice.

Abstract P2-09-18: High VEGFR1 and VEGFR3 Protein Expression Is Associated with Improved Response to the Combination of Paclitaxel (P) and Bevacizumab (Bev) Therapy in Patients with HER2-Negative Metastatic Breast Cancer (MBC)

Background: Treatment with weekly P and 2-weekly Bev has been established as an active 1st line treatment in patients with MBC. However, robust predictive or prognostic biomarkers for this treatment have not been identified as yet.

Patients and Methods: In this retrospective analysis, we evaluated the activity of this combination in patients with HER2-negative MBC. Further, we explored the role of a panel of biomarkers on patients’ outcome. VEGF-A, VEGF-C, VEGFR1, VEGFR2, and VEGFR3 were centrally assessed by immunohistochemistry (IHC) in 70 tissue blocks. P was administered either weekly 90 mg/m2 x12 with 2-weekly Bev 10 µg/kg (86 patients) or 3-weekly 175 mg/m2 x6 with 3-weekly Bev 15µg/kg (38 patients). Bev was administered until progression in the majority of the patients.

Results: The ORR did not differ significantly between the weekly or 3-weekly P schedule (55.8% vs 55.3%). In contrast to the published literature with P monotherapy, median PFS was significantly longer in the 3-weekly compared to the weekly P schedule (20.4 months vs 10.2 months, p=0.029). Median survival has not been reached yet. 2-year survival was 76.1% and 67.3%, respectively (p=0.085). High VEGFR1 and VEGFR3 protein expression, assessed by IHC, was associated with higher response rates (p=0.010 and p=0.039, respectively).

Conclusions: This retrospective analysis confirmed the activity of P and Bev in patients with HER2-negative MBC. Protein expression of VEGFR1 and VEGFR3 was found to be of predictive value. These findings need to be validated in a larger cohort of patients treated with this combination. VEGF polymorphisms (VEGF-2578 and VEGF-1154) are currently assessed in peripheral blood DNA from our patients for possible predictive value.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-09-18.