Abstract P5-13-01: Comprehensive tumor analysis by NGS in metastatic breast cancer patients

Background: Comprehensive tumor analysis by Next Generation Sequencing (NGS) is imperative for targeted and immunotherapy related biomarkers’ analysis in metastatic breast cancer enabling personalization of cancer treatment in these patients. In parallel with targeted therapies, immunotherapies are also evolving, revolutionizing cancer therapy. Thus, biomarkers such as. Microsatellite Instability (MSI), and Tumor Mutational Burden (TMB) are commonly employed in NGS analysis due to their correlation to Immune Checkpoint inhibitors treatment.Methods: In the present study, tumor molecular profile analysis was performed in 73 metastatic breast cancer patients using a broad NGS assay, which analyzes more than 500 unique cancer related genes and is able to detect relevant single nucleotide variations (SNVs), indels, copy number variations (CNVs) and gene fusions, in addition to TMB and MS) simultaneously. Results: An actionable alteration was detected in 79.45% of the patients. 35.62% of them had at least one alteration with an on label treatment associated and 10.96% received information related to an off-label treatment (Tiers 1A.1 and 2C.1 respectively). Additionally, 31.51% of the tumors harbored an alteration that could be used for clinical trial inclusion (Table 1). The most prevalent altered gene in these patients was the PIK3CA gene, with 27.40% mutation rate. Moreover, in 11 cases (15.07%) the mutation detected was in a gene involved in the Homologous recombination (HR) pathway, with evidence of response to PARP inhibitors. BRCA1/2 genes were as expected the most prominent HR mutated genes (5 out of 11 HR mutations), while the remaining HR mutations involved other HR genes (ATM, BLM, CHEK2, FANCM, RAD50). 24.66% of the tumors had a TMB value >10muts/MB and thus were eligible for ICI treatment. The addition of TMB to targeted biomarkers’ analysis increased the number of patients with an on-label treatment recommendation by 8.22%. Conclusions: Tumor molecular profile analysis using NGS, in real world samples, is a first-tier method for metastatic breast cancer and provides important information for decision making in the treatment of such patients. Importantly, simultaneous analysis for targeted therapy and immunotherapy biomarkers could lead to better tumor characterization and offered actionable information in 9 out of 10 patients tested. However, appropriate interpretation of results from such analysis is essential for implementation in clinical practice and accurate refinement of the treatment strategy..

Table 1.Biomarker's summary in the 73 patients included in the studyPercentage of patients with Tier1 variantsPercentage of patients with 2C.1 variantsPercentage of patients with 2C.2/2D variantsPercentage of patients with Tier 3 variantsPercentage of patients with TMB>10muts/MBMEDIAN TMBPercentage of MSI-High patients35.62% (26/73)10.96% (8/73)12.33% (9/73)0% (0/73)24.66% (18/73)5.050% (0/73)

Citation Format: Eirini Papadopoulou, Nikolaos Tsoulos, Vasiliki Metaxa-Mariatou, Aikaterini Tsantikidi, Georgios Kapetsis, Chrysiida Florou-Chatzigiannidou, Sonia Maravelaki, Evgenia Bourkoula, Dimitrios Fotiou, Georgios Tsaousis, Nikolaos Touroutoglou, Dimitrios Trafalis, Ioannis Boukovinas, Ioannis Varthalitis, Zacharenia Saridaki, Charalampos Zoublios, Eleni Galani, George Papatsibas, Christos Papadimitriou, Tania Zlatintsi, Polixenia Iorga, Bülent Orhan, Sualp Tansan, Tahsin Özatlı, George Nasioulas. Comprehensive tumor analysis by NGS in metastatic breast cancer patients [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-13-01.

Comprehensive tumor molecular profile analysis in clinical practice

Background

Tumor molecular profile analysis by Next Generation Sequencing technology is currently widely applied in clinical practice and has enabled the detection of predictive biomarkers of response to targeted treatment. In parallel with targeted therapies, immunotherapies are also evolving, revolutionizing cancer therapy, with Programmed Death-ligand 1 (PD-L1), Microsatellite instability (MSI), and Tumor Mutational Burden (TMB) analysis being the biomarkers employed most commonly.

Methods

In the present study, tumor molecular profile analysis was performed using a 161 gene NGS panel, containing the majority of clinically significant genes for cancer treatment selection. A variety of tumor types have been analyzed, including aggressive and hard to treat cancers such as pancreatic cancer. Besides, the clinical utility of immunotherapy biomarkers (TMB, MSI, PD-L1), was also studied.

Results

Molecular profile analysis was conducted in 610 cancer patients, while in 393 of them a at least one biomarker for immunotherapy response was requested. An actionable alteration was detected in 77.87% of the patients. 54.75% of them received information related to on-label or off-label treatment (Tiers 1A.1, 1A.2, 2B, and 2C.1) and 21.31% received a variant that could be used for clinical trial inclusion. The addition to immunotherapy biomarker to targeted biomarkers’ analysis in 191 cases increased the number of patients with an on-label treatment recommendation by 22.92%, while an option for on-label or off-label treatment was provided in 71.35% of the cases.

Conclusions

Tumor molecular profile analysis using NGS is a first-tier method for a variety of tumor types and provides important information for decision making in the treatment of cancer patients. Importantly, simultaneous analysis for targeted therapy and immunotherapy biomarkers could lead to better tumor characterization and offer actionable information in the majority of patients. Furthermore, our data suggest that one in two patients may be eligible for on-label ICI treatment based on biomarker analysis. However, appropriate interpretation of results from such analysis is essential for implementation in clinical practice and accurate refinement of treatment strategy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-021-00952-9.

Abstract P1-03-08: Different genomic rearrangements account for 17% of BRCA1/2 mutations in Greece

AIM: The aim of this study was to further delineate the extent and nature of mutations in the BRCA1 and BRCA2 genes, responsible for hereditary breast and ovarian cancer in Greek families.

MATERAILS & METHODS: Genomic DNA was isolated from whole peripheral blood of patients referred to our center for mutation analysis of the BRCA1 and BRCA2 genes. Patients were included on the basis of affected family members, types of cancer present in the family and age at diagnosis of breast cancer in the proband. Families were subdivided into high, medium and low risk depending on the number of affected family members, types of cancer diagnosed in the family and age at diagnosis of affected family members. In total, 675 families have been analyzed by our group in the past 4 years. Mutation analysis in all cases included sequencing of the coding region and the splice sites of the two genes. In addition, MLPA analysis was carried in 585 of the patients.

RESULTS: In total, a pathogenic mutation has been identified in 12% of the 675 patients analyzed. Of the 78 mutations identified in total, 13 (17%) were large genomic rearrangements. These were deletions of exons 8, 20, 23, 23-24 and the entire BRCA1 gene, in addition to a duplication of exons 3-8 of the BRCA1 gene. As far as BRCA2 is involved deletions of exons 3, 15 and the entire BRCA2 gene were detected. All deletions were confirmed by use of other MLPA probe sets and/or relative quantitation by Real Time PCR. Of the rearrangements identified, two, namely deletions of exon 20 and exons 23-24 of the BRCA1 gene were identified in more than one unrelated families. In addition, the recurrent mutations 5382insC and G1738R, which have been previously identified as founder mutations in the Greek population, were identified in multiple unrelated analyzed families.

CONCLUSIONS: Our results indicate that different large genomic rearrangements account for an important proportion (17%) of the mutations in the BRCA1 and BRCA2 genes, in Greek families at risk of carrying a germline mutation as judged by family / personal history. The use of the available technologies for the identification of such mutational events is therefore necessary when carrying out complete analysis of the genes in high risk families of Greek background.

Citation Format: Angela Apessos, Eirini Papadopoulou, Vassiliki Metaxa-Mariatou, Konstantinos Agiannitopoulos, Christos Markopoulos, Vasileios Venizelos, Grigorios Xepapadakis, Maria Vasilaki-Antonatou, Antonios Keramopoulos, Nikolaos Bredakis, Aristeidis Tsiftsoglou, Georgios Kesisis, Stylianos Kakolyris, Nikolaos Touroutoglou, Ioannis Natsiopoulos, Konstantinos Papazisis, Georgios Nasioulas. Different genomic rearrangements account for 17% of BRCA1/2 mutations in Greece [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P1-03-08.

KRAS, NRAS and BRAF mutations in Greek and Romanian patients with colorectal cancer: a cohort study

OBJECTIVES

Treatment decision-making in colorectal cancer is often guided by tumour tissue molecular analysis. The aim of this study was the development and validation of a high-resolution melting (HRM) method for the detection of KRAS, NRAS and BRAF mutations in Greek and Romanian patients with colorectal cancer and determination of the frequency of these mutations in the respective populations.

SETTING

Diagnostic molecular laboratory located in Athens, Greece.

PARTICIPANTS

2425 patients with colorectal cancer participated in the study.

PRIMARY AND SECONDARY OUTCOME MEASURES

2071 patients with colorectal cancer (1699 of Greek and 372 of Romanian origin) were analysed for KRAS exon 2 mutations. In addition, 354 tumours from consecutive patients (196 Greek and 161 Romanian) were subjected to full KRAS (exons 2, 3 and 4), NRAS (exons 2, 3 and 4) and BRAF (exon 15) analysis. KRAS, NRAS and BRAF mutation detection was performed by a newly designed HRM analysis protocol, followed by Sanger sequencing.

RESULTS

KRAS exon 2 mutations (codons 12/13) were detected in 702 of the 1699 Greek patients with colorectal carcinoma analysed (41.3%) and in 39.2% (146/372) of the Romanian patients. Among the 354 patients who were subjected to full KRAS, NRAS and BRAF analysis, 40.96% had KRAS exon 2 mutations (codons 12/13). Among the KRAS exon 2 wild-type patients 15.31% harboured additional RAS mutations and 12.44% BRAF mutations. The newly designed HRM method used showed a higher sensitivity compared with the sequencing method.

CONCLUSIONS

The HRM method developed was shown to be a reliable method for KRAS, NRAS and BRAF mutation detection. Furthermore, no difference in the mutation frequency of KRAS, NRAS and BRAF was observed between Greek and Romanian patients with colorectal cancer.

Ibandronate reduces radiotherapy-resistant metastatic bone pain in patients with solid tumors: A comparison of i.v. and oral formulations

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Background: Bisphosphonates are used to treat metastatic bone disease (MBD). However, some bisphosphonates are associated with renal toxicity. Ibandronate (IA) is a single-nitrogen, noncyclic bisphosphonate with a renal safety profile similar to placebo in phase III trials. This study compares the effects of i.v. IA 6mg and oral IA 50mg on bone pain, analgesic intake and renal safety. Methods: Recruited patients fulfilled the following criteria: age ≥18, solid tumors with at least one bone lesion, normal renal (serum creatinine ≤1.5mg/dL) and hepatic function, WHO performance status 0, I or II, life expectancy ≥6 months, normal serum calcium or asymptomatic hypercalcemia. Patients were excluded if they were pregnant or lactating, taking nephrotoxic drugs or osteoclast activity modulators. Eligible patients (n=52) were recruited for a two-arm study, with 26 patients per group treated over 6 months. Groups were matched for age, gender, weight, height, blood pressure, site of primary tumor, site and number of bone metastases and number of irradiated sites. Intravenous IA 6mg was administered over 15 minutes every 4 weeks. Oral IA 50mg was administered as a single, daily tablet before breakfast. Studies were ceased on occurrence of new bone events. Primary endpoint was reduction in bone pain and reduced analgesic use. Results: There were no significant differences in patient demographics between the two treatment arms. The percentage of patients receiving i.v. IA that achieved stable or progressive disease was 15.4%; those receiving oral IA attained 11.5% stable or progressive disease. Pain (Brief Pain Inventory questionnaire) and analgesic intake were assessed at baseline, 3 and 6 months. Both i.v. and oral IA caused a significant and sustainable decrease in each of the pain indices (p<0.0005) with no significant difference between i.v. and oral groups. Both i.v. and oral IA treatment led to a trend in decrease of analgesic use. Conclusions: Oral and i.v. ibandronate have comparable efficacy for palliation of bone pain in MBD patients.

No significant financial relationships to disclose.

Polymorphisms in FcγRIIIA (CD16) Receptor Expression Are Associated With Clinical Response to Rituximab in Waldenström’s Macroglobulinemia

Purpose

Rituximab is an important therapeutic for Waldenström’s macroglobulinemia (WM). Polymorphisms in FcγRIIIA (CD16) receptor expression modulate human immunoglobulin G1 binding and antibody-dependent cell-mediated cytotoxicity, and may therefore influence responses to rituximab.

Patients and Methods

Sequence analysis of the entire coding region of FcγRIIIA was undertaken in 58 patients with WM whose outcomes after rituximab were known.

Results

Variations in five codons of FcγRIIIA were identified. Two were commonly observed (FcγRIIIA-48 and FcγRIIIA-158) and predicted for amino acid polymorphisms at FcγRIIIA-48: leucine/leucine (L/L), leucine/arginine (L/R), and leucine/histidine (L/H). Polymorphisms at FcγRIIIA-158 were phenylalanine/phenylalanine (F/F), phenylalanine/valine (F/V), and valine/valine (V/V). A clear linkage between these polymorphisms was detected and all patients with FcγRIIIA-158F/F were always FcγRIIIA-48L/L, and patients with either FcγRIIIA-L/R or -L/H always expressed at least one valine at FcγRIIIA-158 (P ≤ .001). The response trend was higher for patients with FcγRIIIA-48L/H (38.5%) versus -48L/R (25.0%) and LL (22.0%), and was significantly higher for patients with FcγRIIIA-158V/V (40.0%) and -V/F (35%) versus -158F/F (9.0%; P = .030). Responses for patients with FcγRIIIA-48L/L were higher when at least one valine was present at FcγRIIIA-158 (P = .057), thereby supporting a primary role for FcγRIIIA-158 polymorphisms in predicting rituximab responses. With a median follow-up of 13 months, no significant differences in the median time to progression and progression-free survival were observed when patients were grouped according to their FcγRIIIA-48 and -158 polymorphisms.

Conclusion

The results of these studies therefore support a predictive role for FcγRIIIA-158 polymorphisms and responses to rituximab in WM.

Clinical results of a pharmacodynamically-based strategy for higher dosing of gemcitabine in patients with solid tumors

BACKGROUND

The long intracellular half-life of gemcitabine's active metabolite, difluorodeoxycytidine triphosphate (dFdCTP), suggested that small increases in peak intracellular dFdCTP levels would have a profound effect on its intracellular area under the curve (AUC). Previous studies had shown that a dose rate of 10 mg/m2/min that achieved plasma gemcitabine concentrations of 15-20 mumol/l maximized the intracellular rate of accumulation of dFdCTP. This phase I study was therefore designed to evaluate the clinical feasibility of this pharmacologically-based strategy; assessing the toxic effects and anticancer activity of high weekly doses of gemcitabine administered at a fixed dose rate of 10 mg/m2/min.

PATIENTS AND METHODS

Thirty one patients with solid tumor malignancies received 103 courses of gemcitabine. Twenty nine patients had received prior treatment. Weekly doses were escalated from 1200 mg/m2 administered intravenously over 120 minutes to 2800 mg/m2 over 280 minutes for three weeks every four weeks.

RESULTS

The first-course MTD was 2250 mg/m2. The dose-limiting toxicity was myelosuppression with thrombocytopenia and granulocytopenia quantitatively more important than anemia. However, cumulative myelosuppression was documented suggesting that a lower MTD of 1800 mg/m2 was more appropriate with a recommended phase II starting dose of 1500 mg/m2. There was no neurologic toxicity. Nonhematologic toxicity was minimal and included fatigue, nausea, and skin rash, but was not dose dependent. Three objective responses were documented.

CONCLUSIONS

Escalated doses of gemcitabine designed to maximize intracellular dFdCTP levels can be safely administered using a fixed dose rate. The encouraging anticancer effects documented in patients with refractory malignancies suggests that short gemcitabine infusions based on well-established cellular pharmacologic principles may improve the therapeutic index of this agent. Comparison with standard 30-minute bolus dosing will be evaluated in subsequent randomized phase II trials.

Thymidylate synthase inhibitors

Folate analogues that inhibit thymidylate synthase (TS) selectively were developed based on TS and folate molecular structures and properties. The structure-activity relationship, preclinical and clinical development, and issues of potential importance in the future success of these TS inhibitors are reviewed herein. Properties of these new compounds depend mainly on the use of the reduced folate carrier (RFC) proteins for cellular entry and on intracellular polyglutamation, which augments TS inhibitory function and cellular retention. CB3717 [Zeneca (formerly ICI Pharmaceuticals), Macclesfield, United Kingdom], the first selective TS inhibitor developed, demonstrated antineoplastic activity in Phase I trials, but its development was abandoned due to nephrotoxicity. ZD1694 (Tomudex; Zeneca), a water-soluble, nonnephrotoxic quinazoline, demonstrated activity in colorectal, breast, and pancreatic cancer. Phase III trials of Tomudex in advanced colorectal cancer were completed recently. LY231514 (Eli Lilly Research Labs, Indianapolis, IN) uses the RFC and polyglutamation to exert its selective TS inhibitory action. Phase I trials of this compound have been completed. ZD9331 (Zeneca), currently in preclinical studies, was designed to obviate the use of the RFC for cellular entry. 1843U89 (Glaxo-Wellcome, Research Triangle Park, NC), currently in Phase I trial, does not require the RFC; polyglutamation of this potent TS inhibitor leads to its higher cellular retention without augmenting its TS inhibitory activity. Currently in clinical trials, AG337 (p.o. and i.v. forms) and AG331 (both by Agouron, La Jolla, CA) are lipophilic potent TS inhibitors with action independent of the RFC and polyglutamation. Multiple mechanisms through which cells may overcome TS inhibition have been described. Combining TS inhibitors with other agents that affect TS, interfere with TS gene and mRNA regulation, or inhibit salvage mechanisms of thymidylate depletion may potentially enable greater clinical utility of this class of compounds.

Testicular lymphoma: late relapses and poor outcome despite doxorubicin-based therapy

PURPOSE

To determine the significance of the International Prognostic Index (IPI) score in adults with testicular lymphoma treated with doxorubicin-based regimens.

PATIENTS AND METHODS

Untreated adults with testicular lymphoma who presented between 1969 and 1993 were studied. Those with Ann Arbor stages III and IV were included if they had a testicular mass at presentation.

RESULTS

We identified 22 patients, 21 with intermediate-grade and one with high-grade lymphoma. All 10 patients with an IPI score < or = 1 had Ann Arbor stage I disease, whereas the 12 with an IPI score more than 1 had Ann Arbor stage II to IV disease. Complete remission (CR) was achieved in 73% of patients. At 153 months, 22% of all complete responders and 40% and 0% of those with IPI scores < or = 1 and more than 1, respectively, remained in CR (P = .01). With a median follow-up time of 113 months for survivors, the failure-free survival (FFS) rate at 153 months was 16% for all patients or 32% and 0% for those with IPI scores < or = 1 and more than 1, respectively (P = .02). The CNS or contralateral testis were involved in all patients who failed to respond to primary therapy and in 50% of those who relapsed from CR.

CONCLUSION

The prognosis of patients with testicular lymphoma appears poor despite doxorubicin-based chemotherapy. On the basis of failures in the CNS and contralateral testis, we recommend prophylactic intrathecal chemotherapy and scrotal radiotherapy for all patients. Those with an IPI score < or = 1 can be treated with conventional doxorubicin-based regimens, but those with an IPI score more than 1 should be considered for investigational systemic therapy.