Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort

BACKGROUND

Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling.

METHODS

Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification.

RESULTS

The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition.

CONCLUSIONS

Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.

Predictors of germline status for hereditary melanoma: 5 years of multi-gene panel testing within the Italian Melanoma Intergroup

BACKGROUND

The incidence of cutaneous melanoma is increasing in Italy, in parallel with the implementation of gene panels. Therefore, a revision of national genetic assessment criteria for hereditary melanoma may be needed. The aim of this study was to identify predictors of susceptibility variants in the largest prospective cohort of Italian high-risk melanoma cases studied to date.

MATERIALS AND METHODS

From 25 Italian centers, we recruited 1044 family members and germline sequenced 940 cutaneous melanoma index cases through a shared gene panel, which included the following genes: CDKN2A, CDK4, BAP1, POT1, ACD, TERF2IP, MITF and ATM. We assessed detection rate according to familial status, region of origin, number of melanomas and presence and type of non-melanoma tumors.

RESULTS

The overall detection rate was 9.47% (5.53% analyzing CDKN2A alone), ranging from 5.14% in sporadic multiple melanoma cases (spoMPM) with two cutaneous melanomas to 13.9% in familial cases with at least three affected members. Three or more cutaneous melanomas in spoMPM cases, pancreatic cancer and region of origin predicted germline status [odds ratio (OR) = 3.23, 3.15, 2.43, P < 0.05]. Conversely, age > 60 years was a negative independent predictor (OR = 0.13, P = 0.008), and was the age category with the lowest detection rate, especially for CDKN2A. Detection rate was 19% when cutaneous melanoma and pancreatic cancer clustered together.

CONCLUSIONS

Gene panel doubled the detection rate given by CDKN2A alone. National genetic testing criteria may need a revision, especially regarding age cut-off (60) in the absence of strong family history, pancreatic cancer and/or a high number of cutaneous melanomas.

Germline ATM variants predispose to melanoma: a joint analysis across the GenoMEL and MelaNostrum consortia

PURPOSE

Ataxia-Telangiectasia Mutated (ATM) has been implicated in the risk of several cancers, but establishing a causal relationship is often challenging. Although ATM single-nucleotide polymorphisms have been linked to melanoma, few functional alleles have been identified. Therefore, ATM impact on melanoma predisposition is unclear.

METHODS

From 22 American, Australian, and European sites, we collected 2,104 familial, multiple primary (MPM), and sporadic melanoma cases who underwent ATM genotyping via panel, exome, or genome sequencing, and compared the allele frequency (AF) of selected ATM variants classified as loss-of-function (LOF) and variants of uncertain significance (VUS) between this cohort and the gnomAD non-Finnish European (NFE) data set.

RESULTS

LOF variants were more represented in our study cohort than in gnomAD NFE, both in all (AF = 0.005 and 0.002, OR = 2.6, 95% CI = 1.56-4.11, p < 0.01), and familial + MPM cases (AF = 0.0054 and 0.002, OR = 2.97, p < 0.01). Similarly, VUS were enriched in all (AF = 0.046 and 0.033, OR = 1.41, 95% CI = 1.6-5.09, p < 0.01) and familial + MPM cases (AF = 0.053 and 0.033, OR = 1.63, p < 0.01). In a case-control comparison of two centers that provided 1,446 controls, LOF and VUS were enriched in familial + MPM cases (p = 0.027, p = 0.018).

CONCLUSION

This study, describing the largest multicenter melanoma cohort investigated for ATM germline variants, supports the role of ATM as a melanoma predisposition gene, with LOF variants suggesting a moderate-risk.

Abstract P4-06-16: Analysis of tumor infiltrating lymphocytes in three age categories of luminal B-like breast cancer patients and its correlation with lymph node involvement and systemic immunosenescence/frailty markers

BACKGROUND Immunosenescence, the age-related decrease in immune competence, which is characterized by decreased adaptive immunity and increased low-grade inflammation. It may lead to altered tumor immunity. However, immunosenescence markers have not been correlated yet with tumor infiltrating leukocytes (TILs) nor with clinical frailty.

METHODS This is the first study that investigates how age affects the relation between systemic immunity and tumor microenvironment in early luminal B-like breast cancer (BC) in function of age. Luminal B-like BC was defined as grade II-III, ER+, HER2- on core biopsies at inclusion. Three distinct age categories of BC patients were chosen: 35-45 years (y) (N=15), 55-65y (N=19), ≥70y (N=31). Stromal TILs (sTILs) % were assessed according to published guidelines, on representative tumor sections. Further characterization of the TILs by immunohistochemistry, using the antibodies against CD3, CD4, CD8, CD5, CD20, CD68 and FOXP3, is currently ongoing. Immunosenescence was evaluated by looking at eleven inflammatory plasma cytokines and chemokines, circulating insulin-like growth factor-1 (IGF-1), T-cell p16INK4a expression, PBMC subset profiles and expression levels of twenty immune-related microRNAs. In the old age category, geriatric assessment was performed.

RESULTS With increasing age, sTILs % significantly decreased, concomitant with significantly increased plasma levels of several inflammatory cytokines (IL-1α, IL-6) and chemokines (IP-10, IL-8, MCP-1), intermediate monocytes, as well as T-cell p16INK4a expression. Significant age-related decrease was seen for plasma IGF-1, naïve CD8+ T-cells and CD8+ T-cells expressing CD27 and/or CD28. Four immune-related microRNAs showed significantly different expression levels between the age groups: miR-18a decreased with age, miR-155 increased with age, miR-19b and miR-20a peaked in the middle group. As expected, various correlations exist between the different blood immunosenescence markers. The % of sTILs showed weak negative correlations with IL-6, IL-8, IL-1α, MCP-1 and the % of regulatory T-cells. Additionally the % of sTILs and several makers of immunosenescence (MCP-1, miR-20a, miR-155, intermediate monocytes) correlated with components of the geriatric assessment (activities of daily living (ADL), mini nutritional assessment (MNA), mini–mental state examination (MMSE)) and with the Leuven oncogeriatric frailty score (LOFS) in the oldest group. Conversely, lymph node involvement was not associated with the % of sTILs nor with any blood aging biomarker.

CONCLUSION sTILs % and several blood immunosenescence markers significantly differ between young and older luminal B-like BC patients. Some of these markers correlated with markers of clinical frailty as well. These findings suggest that interactions between tumor cells and immune/inflammatory cells differ with age and therefore applicable immune biomarkers and approaches for immunotherapy may vary depending on patients' age.

Citation Format: Berben L, Hatse S, Kenis C, Dalmasso B, Smeets A, Vos H, Neven P, Floris G, Wildiers H. Analysis of tumor infiltrating lymphocytes in three age categories of luminal B-like breast cancer patients and its correlation with lymph node involvement and systemic immunosenescence/frailty markers [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 P4-06-16.

Abstract P4-07-08: Age-related microRNAs and their biomarker potential in chemotherapy-treated older breast cancer patients

BD and SH contributed equally to this study.

Background

MicroRNAs (miRNAs) are important regulators of cellular function and have been associated with both aging and cancer, while the impact of chemotherapy on miRNAs has barely been studied.

Patients and Methods

To examine whether chemotherapy accelerates the aging process, we have monitored age-related circulating miRNAs in 89 older breast cancer patients (≥70y), receiving adjuvant chemotherapy (N= 46; chemo group, ChG) or no chemotherapy (N= 43; control group, CoG). Patients and associated blood samples belonged to the cohort of our recently published study (Brouwers et al., Oncotarget. 2016.) All patients underwent geriatric assessment at inclusion (T0), after 3 months (T1) and 1 year (T2). At each timepoint we analysed the serum expression of nine age-related miRNAs (miR-20a, miR-30b, miR-34a, miR-106b, miR-191, miR-301a, miR320b, miR374a, miR-378a).

Our primary aim was to assess miRNA changes during the study period, including differences between groups. Secondary endpoints included association of microRNAs with: chronological age, clinical geriatric assessment parameters and aging biomarkers assessed in the above-mentioned study. We then investigated the predictive role of miRNAs at T0 on: decline in functionality and quality of life, toxicity and unexpected hospitalization during or after chemotherapy. We also performed clustering of patients according to specific miRNA signatures.

Results

Except for miR-106b, which appeared to behave slightly different in ChG compared to CoG, all other miRNAs underwent moderate fluctuations during the study course with no significant differences between both groups. Also within the older cohort, several age-related miRNAs significantly (p&lt;0.05) correlated with clinical aging/frailty (miR-106b, miR-191, miR-301a, miR-320b, miR-374a), as well as with other biomarkers of aging. In particular, miR-106b, miR-374a and miR-378a were associated with IL-6 (slope= -0.34, -0.30 and 0.30 respectively, p&lt;0.05), whereas miR-301a and miR-378a showed a relevant correlation with MCP-1 (slope= -0.18 and 0.27 respectively, p&lt; 0.05).

Moreover, based on their 'aging miRNA' profiles, patients clustered into two distinct groups, cluster A (CA) and cluster B (CB), exhibiting significantly different results for several biological/clinical aging parameters. CA (N=43, miR-20a, miR-30b, miR-191, miR-301a and miR-374a underexpressed, miR-378a overexpressed) was characterized by older age, higher geriatric risk profile, as well as elevated IL-6, TNFα and MCP-1 levels compared to CB (N=45, inverse expression pattern). Moreover, 31.9% of CA patients but only 7.4% of CB patients experienced decline in quality of life after chemotherapy (p=0.051).

Conclusions

These results further corroborate our recent findings, stating that adjuvant chemotherapy does not significantly boost aging progression in elderly breast cancer patients. Our data also endorsed specific age-related miRNAs as promising aging/frailty biomarkers in oncogeriatric populations.

Citation Format: Dalmasso B, Hatse S, Brouwers B, Laenen A, Berben L, Kenis C, Smeets A, Neven P, Schöffski P, Wildiers H. Age-related microRNAs and their biomarker potential in chemotherapy-treated older breast cancer patients [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 P4-07-08.