Genomic landscape of liquid biopsy mutations in TP53 and DNA damage genes in cancer patients

Next-generation sequencing (NGS) assays based on plasma cell-free DNA (cfDNA) are increasingly used for clinical trials inclusion. Their optimized limit of detection applied to a large number of genes leads to the identification of mutations not confirmed in tissue. It becomes essential to describe the characteristics and consequences of these liquid biopsy-only mutations. In the STING protocol (Gustave Roussy, NCT04932525), 542 patients with advanced solid cancer had cfDNA-based and tissue-based NGS analysis (performed by FoundationOne® Liquid CDx and FoundationOne CDx™, respectively). Mutations identified in the liquid biopsy but not in the paired tissue were considered as liquid biopsy-only mutations irrespective of their variant allelic frequency (VAF). Out of 542 patients, 281 (51.8%) harbored at least one liquid biopsy-only mutation. These patients were significantly older, and more heavily pretreated. Liquid biopsy-only mutations occurring in TP53, and in DDR genes (ATM, CHEK2, ATR, BRCA2, and BRCA1) accounted for 90.8% of all the mutations. The median VAF of these mutations was generally low (0.37% and 0.40% for TP53 and DDR genes respectively). The variant type repartition depended on the gene. Liquid biopsy-only mutations affected hotspot in TP53 codon 273, 125, 195, 176, 237 or 280 and ATM codon 2891 and 3008. In a subset of 37 patients, 75.0%, 53.5% and 83.3% of the liquid biopsy-only mutations occurring respectively in ATM, TP53, and CHEK2 were confirmed in the matching whole blood sample. Although liquid biopsy-only mutations makes the interpretation of liquid biopsy results more complex, they have distinct characteristics making them more easily identifiable.

Clinical utility of plasma ctDNA sequencing in metastatic urothelial cancer

BACKGROUND

Genomic stratification may help improve the management of patients with metastatic urothelial cancer (mUC), given the recent identification of targetable alterations. However, the collection of tissue samples remains challenging. Here, we assessed the clinical utility of plasma circulating tumour DNA (ctDNA) sequencing in these patients.

METHODS

Patients with mUC were prospectively enroled in the STING trial (NCT04932525), in which ctDNA was profiled using the Foundation One Liquid CDx Assay (324 genes, blood tumour mutational burden [bTMB], microsatellite instability status). Each genomic report was reviewed by a multidisciplinary tumor board (MTB).

RESULTS

Between January 2021 and June 2022, 140 mUC patients underwent molecular profiling. The median time to obtain the assay results was 20 days ((confidence interval) CI95%: [20,21]). The ctDNA analysis reproduced the somatic genomic landscape of previous tissue-based cohorts. Concordance for serial ctDNA samples was strong (r = 0.843 CI95%: [0.631-0.938], p < 0.001). At least one actionable target was detected in 63 patients (45%) with a total of 35 actionable alterations, including bTMB high (≥10 mutations/Mb) (N = 39, 21.1%), FGFR3 (N = 20, 10.8%), and Homologous recombination deficiency (HRD) alterations (N = 14, 7.6%). MTB recommended matched therapy in 63 patients (45.0%). Eight patients (5.7%) were treated, with an overall response rate of 50% (CI95%: 15.70-84.30) and a median progression-free survival (PFS) of 5.2 months (CI95%: 4.1 - NR). FGFR3 alterations were associated with a shorter PFS in patients treated with immunotherapy.

CONCLUSION

Overall, we demonstrated that genomic profiling with ctDNAs in mUC is a reliable and feasible approach for the timely initiation of genotype-matched therapies.

Homologous recombination deficiency (HRD) testing on cell-free tumor DNA from peritoneal fluid

BACKGROUND

Knowing the homologous recombination deficiency (HRD) status in advanced epithelial ovarian cancer (EOC) is vital for patient management. HRD is determined by BRCA1/BRCA2 pathogenic variants or genomic instability. However, tumor DNA analysis is inconclusive in 15-19% of cases. Peritoneal fluid, available in > 95% of advanced EOC cases, could serve as an alternative source of cell-free tumor DNA (cftDNA) for HRD testing. Limited data show the feasibility of cancer panel gene testing on ascites cfDNA but no study, to date, has investigated HRD testing.

METHODS

We collected ascites/peritoneal washings from 53 EOC patients (19 from retrospective cohort and 34 from prospective cohort) and performed a Cancer Gene Panel (CGP) using NGS for TP53/HR genes and shallow Whole Genome Sequencing (sWGS) for genomic instability on cfDNA.

RESULTS

cfDNA was detectable in 49 out of 53 patients (92.5%), including those with limited peritoneal fluid. Median cfDNA was 3700 ng/ml, with a turnaround time of 21 days. TP53 pathogenic variants were detected in 86% (42/49) of patients, all with HGSOC. BRCA1 and BRCA2 pathogenic variants were found in 14% (7/49) and 10% (5/49) of cases, respectively. Peritoneal cftDNA showed high sensitivity (97%), specificity (83%), and concordance (95%) with tumor-based TP53 variant detection. NGS CGP on cftDNA identified BRCA2 pathogenic variants in one case where tumor-based testing failed. sWGS on cftDNA provided informative results even when tumor-based genomic instability testing failed.

CONCLUSION

Profiling cftDNA from peritoneal fluid is feasible, providing a significant amount of tumor DNA. This fast and reliable approach enables HRD testing, including BRCA1/2 mutations and genomic instability assessment. HRD testing on cfDNA from peritoneal fluid should be offered to all primary laparoscopy patients.

Circulating tumor DNA landscape and prognostic impact of acquired resistance to targeted therapies in cancer patients: a national center for precision medicine (PRISM) study

BACKGROUND

Despite the effectiveness of the various targeted therapies currently approved for solid tumors, acquired resistance remains a persistent problem that limits the ultimate effectiveness of these treatments. Polyclonal resistance to targeted therapy has been described in multiple solid tumors through high-throughput analysis of multiple tumor tissue samples from a single patient. However, biopsies at the time of acquired resistance to targeted agents may not always be feasible and may not capture the genetic heterogeneity that could exist within a patient.

METHODS

We analyzed circulating tumor DNA (ctDNA) with a large next-generation sequencing panel to characterize the landscape of secondary resistance mechanisms in two independent prospective cohorts of patients (STING: n = 626; BIP: n = 437) with solid tumors who were treated with various types of targeted therapies: tyrosine kinase inhibitors, monoclonal antibodies and hormonal therapies.

RESULTS

Emerging alterations involved in secondary resistance were observed in the plasma of up 34% of patients regardless of the type of targeted therapy. Alterations were polyclonal in up to 14% of patients. Emerging ctDNA alterations were associated with significantly shorter overall survival for patients with some tumor types.

CONCLUSION

This comprehensive landscape of genomic aberrations indicates that genetic alterations involved in secondary resistance to targeted therapy occur frequently and suggests that the detection of such alterations before disease progression may guide personalized treatment and improve patient outcome.

Targetable Molecular Alterations in the Treatment of Biliary Tract Cancers: An Overview of the Available Treatments

Biliary tract cancers (BTCs) are rare tumours, most often diagnosed at an unresectable stage, associated with poor prognosis, with a 5-year survival rate not exceeding 10%. Only first- and second-line treatments are well codified with the combination of cisplatin-gemcitabine chemotherapy and immunotherapy followed by 5-FU and oxaliplatin chemotherapy, respectively. Many studies have shown that BTC, and more particularly intrahepatic cholangiocarcinoma (iCCA), have a high rate of targetable somatic alteration. To date, the FDA has approved several drugs. Ivosidenib targeting IDH1 mutations, as well as futibatinib and pemigatinib targeting FGFR2 fusions, are approved for pre-treated advanced CCA. The combination of dabrafenib and trametinib are approved for BRAFV600E mutated advanced tumours, NTRK inhibitors entrectinib and larotrectinib for tumours bearing NTRK fusion and prembrolizumab for MSI-H advanced tumours, involving a small percentage of BTC in these three settings. Several other potentially targetable alterations are found in BTC, such as HER2 mutations or amplifications or KRASG12C mutations and mutations in genes involved in DNA repair mechanisms. This review aims to clarify the specific diagnostic modalities for gene alterations and to summarize the results of the main trials and developments underway for the management of advanced BTC with targetable alterations.

Resistance to Selective FGFR Inhibitors in FGFR-Driven Urothelial Cancer

Several fibroblast growth factor receptor (FGFR) inhibitors are approved or in clinical development for the treatment of FGFR-driven urothelial cancer, and molecular mechanisms of resistance leading to patient relapses have not been fully explored. We identified 21 patients with FGFR-driven urothelial cancer treated with selective FGFR inhibitors and analyzed postprogression tissue and/or circulating tumor DNA (ctDNA). We detected single mutations in the FGFR tyrosine kinase domain in seven (33%) patients (FGFR3 N540K, V553L/M, V555L/M, E587Q; FGFR2 L551F) and multiple mutations in one (5%) case (FGFR3 N540K, V555L, and L608V). Using Ba/F3 cells, we defined their spectrum of resistance/sensitivity to multiple selective FGFR inhibitors. Eleven (52%) patients harbored alterations in the PI3K-mTOR pathway (n = 4 TSC1/2, n = 4 PIK3CA, n = 1 TSC1 and PIK3CA, n = 1 NF2, n = 1 PTEN). In patient-derived models, erdafitinib was synergistic with pictilisib in the presence of PIK3CA E545K, whereas erdafitinib-gefitinib combination was able to overcome bypass resistance mediated by EGFR activation.

SIGNIFICANCE

In the largest study on the topic thus far, we detected a high frequency of FGFR kinase domain mutations responsible for resistance to FGFR inhibitors in urothelial cancer. Off-target resistance mechanisms involved primarily the PI3K-mTOR pathway. Our findings provide preclinical evidence sustaining combinatorial treatment strategies to overcome bypass resistance. See related commentary by Tripathi et al., p. 1964. This article is featured in Selected Articles from This Issue, p. 1949.

Abstract 3418: Alterations in PIK3CA/PTEN as resistance mechanisms in lung cancer patients progressing on first-line next generation EGFR/ALK tyrosine kinase inhibitors

Introduction: Advent of targeted therapies has deeply changed treatment of advanced oncogene-addicted non-small cell lung cancer (NSCLC), but development of resistance remains a main issue. Given the efficacy of next generation tyrosine kinase inhibitors (TKIs) against on-target mutations, their first-line administration could increase the relevance of off-target resistance mechanisms. Activating PIK3CA mutations and PTEN loss have been described as putative off-target resistance mechanisms across generations of EGFR TKIs. The role of these alterations in the development of resistance to ALK TKIs has been less described.

MATCH-R trial (NCT02517892) is an ongoing prospective study whose objective is to understand mechanisms of acquired resistance to cancer therapies and develop strategies to overcome it.

Materials and methods: We collected clinical and molecular data of patients (pts) with NSCLC enrolled in the molecular target group (MTG) of MATCH-R trial. We identified pts with EGFR mutations or ALK rearrangements who developed PIK3CA/PTEN alterations in tissue biopsy and/or circulating tumor DNA upon progression to first-line osimertinib/alectinib. We established patient-derived cell lines (PDCL) from the identified MATCH-R pts and we engineered commercial cell lines (CCL) harboring EGFR mutation (PC9) or ALK fusion (H3122) to constitutively express PIK3CA mutations and/or to have a permanent loss of PTEN. Cell viability assays and Western blot studies with different EGFR/ALK/PI3K/mTOR inhibitors were performed.

Results: Of the 186 pts with advanced NSCLC included in the MTG of MATCH-R, 110 (59.1%) harbored EGFR mutations (EGFR+) and 27 (14.5%) ALK rearrangements (ALK+). Among them, 19 received first-line osimertinib and seven first-line alectinib. Five and two pts developed PIK3CA/PTEN alterations in the EGFR+ and ALK+ groups, respectively. In the EGFR+ group, PIK3CA E545K (n=2), R108H, N345K and R357Q mutations were detected. PTEN mutations (F437fs*5 and Y27C) were concomitant with E545K and R357Q mutations, respectively. In both ALK+ pts, a PIK3CA E545K mutation was identified, together with PTEN exon 5 splicing in one case. We confirmed on CCL that PIK3CA E545K mutation, alone or in combination with PTEN loss, confers resistance to second-/third-generation EGFR/ALK TKIs. PTEN loss alone had a moderate

impact on TKIs sensitivity. Overcoming strategies combining EGFR/ALK TKIs with PIK3CA/mTOR inhibitors are being evaluated and will be disclosed at the meeting.

Conclusions: Activating PI3KCA mutations and molecular events leading to PTEN loss are frequent events at resistance to first-line EGFR/ALK TKIs, and can be detected concomitantly. Functional assays confirmed that these alterations act as resistance mechanisms. These observations are of interest as PI3KCA/mTOR inhibitors may have a role in overcoming resistance.

Citation Format: Giorgia Guaitoli, Francesco Facchinetti, Juan David Flórez-Arango, Floriane Braye, Hayato Mizuta, Santiago Ponce-Aix, Damien Vasseur, Ken André Olaussen, Stefan Michiels, Mihaela Aldea, Jordi Remon, Fabrice Barlesi, Benjamin Besse, David Planchard, Luc Friboulet. Alterations in PIK3CA/PTEN as resistance mechanisms in lung cancer patients progressing on first-line next generation EGFR/ALK tyrosine kinase inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3418.

Abstract 3361: Clinical and genomic correlates of liquid biopsy (LB) derived variant allele frequency (VAF) in advanced NSCLC patients

Background: Initially developed as an alternative to tissue-based molecular assessment, LB is expanding its role in cancer care, with quantitative measure of blood ctDNA being tested for response prediction, response assessment and minimal residual disease detection. Its use for molecular classification has been extensively validated, but little is known about determinants of shedding parameters such as VAF. While it is correlated with tumor burden, characteristics of the tumor such as site of metastasis or particular mutations may have a role. Scope of this study is to elucidate these factors.

Methods: Data from advanced NSCLC patients included in two prospective cohorts who received a LB with 36-genes InVisionFirst-Lung (INI) and the 324-gene FoundationOne Liquid CDx (FMI) assays were reviewed and patients with available 18F FDG positron emission tomography scan (PET) performed within 30 days from LB were included. Total Metabolic Tumor Volume was calculated for each PET with a 42% SUVmax threshold. The higher VAF (mVAF) was calculated for each LB, excluding germline mutations and clonal hematopoiesis-related variants. Patients should be either untreated or with progressive disease at the time of LB. Regression analysis was performed according to a rank-based estimation model.

Results: Overall 301 LB were included, 119 with InVisionFirst-Lung and 182 with FoundationOne Liquid CDx. LB were contributive in 154 (85%) FMI and 102 (86%) INI. MaxVAF was correlated with tMTV in FMI ( rho 0.3571, p 0.0004) and IVI (rho 0.3387, p = 0.0003) cohort. In FMI cohort, median mVAF was higher for TP53 mutant vs wt (n= 111, mVAF 21.1 % vs 8.0%, p &lt; 0.0001), RB1 mutant (n = 11, mVAF 26.3% vs 4.7%, p 0.0103) and in those with liver metastasis ( p 0.0089). LDH was correlated to mVAF (rho 0.280, p = 0.0037). In multivariate model, tMTV (p &lt; 0.0001), TP53 mutation ( p 0.0039), RB1 mutation (p 0.0003) and liver metastasis ( p 0.0371) remained significantly associated with mVAF. When LDH was added to the model (LDH available for 119 pts), tMTV lost its significance (p 0.561). In INI cohort, median mVAF was also higher in patients with TP53 mutation ( 7.1% vs 3%, p 0.0038), in patients with liver metastasis ( 10.1% vs 4.6%, p 0.0299), and it was correlated with tMTV (rho 0.502, p &lt; 0.0001). It was confirmed in a multivariate model (p &lt; 0.0001 for tMTV and 0.0049 for TP53). Correlation between mVAF and LDH was also seen (LDH available for 54 pts, rho 0.591, p &lt; 0.0001). Among patients with liver metastasis, mVAF was correlated with MTV of liver lesions in FMI (n = 30, rho = 0.212, p = 0.0069) and INI cohort (n= 26, rho 0.204, p 0.0313). Overall, in patients with LDH &lt; ULN, 18/103 were non contributive, vs 4/70 in those with LDH &gt; ULN.

Conclusion: In patients with aNSCLC, mVAF depends on disease burden, on the molecular characteristics of the disease and on the presence and extent of liver disease. LDH levels above ULN predict the presence of ctDNA and percentage of mVAF.

Citation Format: Filippo Gustavo Dall'Olio, Damien Vasseur, Camilo Garcia, Arianna Marinello, Mihaela Aldea, Laura Mezquita, Jordi Remon, Anas Gazzah, Marco Tagliamento, Kristi Beshiri, Pernelle Lavaud, Maud Ngocamus, David Planchard, Etienne Rouleau, Antoine Italiano, Benjamin Besse. Clinical and genomic correlates of liquid biopsy (LB) derived variant allele frequency (VAF) in advanced NSCLC patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3361.

Abstract 1034: Clinical utility of liquid biopsy for molecular characterization and resistance detection in patients with advanced NSCLC and ALK, ROS1 or RET fusions

Introduction Liquid biopsy (LB) is increasingly used in non-small cell lung cancer (NSCLC) for molecular diagnosis or resistance detection. Due to its non-invasive nature, it is often preferred over tissue biopsies, especially when sequential biopsies are warranted. Here, we report the clinical utility of liquid biopsy in patients with advanced NSCLC and ALK, ROS1 or RET fusions and its relevance to detect resistance after targeted therapy.

Methods Between December 2020 and June 2022, 597 patients with advanced lung cancer had at least one liquid biopsy assessed by Foundation One CDx Liquid (panel of 324 genes) in a single institution. Plasma collection was performed in treatment-naïve patients and/or at time of progression. Clinical and molecular data were collected from patients with known fusions (ALK, ROS1, RET). LB were defined as “positive” if the fusion or resistance mutations were identified and “negative” in the absence of circulating-tumor DNA. The clinical utility of LB was evaluated as the proportion of positive results. The clinical relevance for resistance detection was defined as the proportion of LB that identified a putative resistance mechanism after targeted therapy.

Results A total of 68 patients (29 ALK+, 22 RET+ and 17 ROS1+) with 83 LB were included. Patients were females in 50% of cases, had no smoking history in 58% of cases and had adenocarcinoma in 91% of cases. LB was positive in 55/83 (66%) cases overall, in 14/15 (93%) treatment-naïve patients and in 39/66 (59%) pre-treated patients. Factors significantly associated with a negative LB were limited disease progression (brain- or thoracic-only, p&lt;0.001) and ongoing treatment at time of LB collection (p&lt;0.05). Out of 47 LB performed at progression after targeted therapies, 7 (15%) found on-target resistance, 10 (21%) by-pass resistance, 10 (21%) no explainable resistance and 20 (43%) were negative. By-pass alterations included KRAS p.G12C/A mutations (N=2, ALK+), PIK3CA p.E545K/Q (N=3, ALK+), PTEN splice-site mutation (N=1, RET+), MYC amplifications (N=3, ALK+/RET+) and MET amplification (N=1, ROS1+).

Conclusion LB was able to detect resistance mechanisms in one third of NSCLC patients with ALK, RET or ROS1 fusions. However, LB frequently failed to detect circulating-tumor DNA especially in patients with limited disease progression or with ongoing treatment at time of sample collection.

Citation Format: Mihaela Aldea, Arianna Marinello, Marco Tagliamento, Filippo Dall'Olio, Damien Vasseur, Arnaud Bayle, Anas Gazzah, Miruna Grecea, Claudio Nicotra, Ludovic Lacroix, Santiago Ponce, Luc Friboulet, Fabrice Barlesi, Fabrice Andre, David Planchard, Etienne Rouleau, Antoine Italiano, Benjamin Besse. Clinical utility of liquid biopsy for molecular characterization and resistance detection in patients with advanced NSCLC and ALK, ROS1 or RET fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1034.

Abstract 4526: Molecular landscape of clonal hematopoiesis in patients with lung cancer: First results of the CHIC study

Introduction: CHIC (Clonal Hematopoiesis In Lung Cancer) is a retro-prospective study that aims to describe the characteristics of clonal hematopoiesis (CH) in patients with non-small cell lung cancer (NSCLC). We present preliminary results from the retrospective cohort.

Experimental procedures: A retrospective analysis conducted in patients with metastatic or recurrent NSCLC included in the MATCH-R study (NCT02517892) at Gustave Roussy (Villejuif, France). CH was evaluated by a 74-gene targeted NGS panel (HaloPlex - Agilent) performed on DNA extracted by isolated-by-blood leukocytes. The variant allele frequency (VAF) threshold of detection was set at 1%.

Results: 108 consecutive patients with advanced NSCLC included from October 2015 to July 2019 were evaluated, irrespective of the tumor molecular profile. 46% of the patients were female, 67% were former or current smokers. 82% of the patients had adenocarcinoma and 44%, 23%, 33% had bone, liver and/or brain metastases, respectively. Patients had received a median of 2 lines of systemic therapy and 81% were on active anticancer treatment at the time of CH assessment. At least one CH mutation was found in 38 out of 108 patients (35% prevalence), with an increasing with age trend. Patients carrying CH were older as compared to those without CH and had in 29% vs. 11% of cases tumor histology other than adenocarcinoma (p=0.009). No difference in overall survival was observed according to CH detection (log rank p=0.318). We found 64 mutations in 19 different genes: 63% of the patients carried a single mutation, while co-occurrence of two, three, four or five mutations, within the same gene or in more than one, was found in seven (18%), four (11%), one (3%) and two patients (5%), respectively. Epigenetic modifiers (DNMT3A, TET2, ASXL1) were the most frequently mutated genes: 38 mutations with a median VAF of 6.5% detected in 32 patients. DNA repair genes (PPM1D, TP53, CHEK2, ATM) were the second most frequently mutated: 11 mutations at a median VAF of 4% were detected in 9 patients. 7 mutations in genes encoding for the cohesin complex (SMC3, SMC1A, RAD21, STAG2) were found in 6 patients, with a median VAF of 5%. A non-simultaneous cfDNA sequencing by FoundationOne Liquid CDx assay (324-gene panel) was performed in 9 patients for tumor profiling. In 2 out of 3 tested cases the presence of CH was confirmed in plasma liquid biopsy. 4 patients with no detectable CH by the targeted blood sequencing subsequently were found having CH mutations in plasma NGS, on average 45 months apart. To note, as many as 5 out of the 19 detected mutated genes (PPM1D, SMC3, SMC1A, PRPF8, ZRSR2) are not part of the FDA-approved NGS panel used for cfDNA profiling in solid tumors.

Conclusion: We found a consistent prevalence of CH in patients with NSCLC by using a sequencing approach targeted for hematologic disorders. Prognostic implications of CH are under investigation and will be evaluated in the full cohort.

Citation Format: Marco Tagliamento, Christophe Marzac, Mihaela Aldea, Damien Vasseur, Arnaud Bayle, Anas Gazzah, Maud Ngocamus, Claudio Nicotra, Julieta Rodriguez, Antonin Levy, Capucine Baldini, Santiago Ponce, Felix Blanc-Durand, Etienne Rouleau, Antoine Italiano, Ludovic Lacroix, Luc Friboulet, David Planchard, Fabrice Barlesi, Yohann Loriot, Jean-Baptiste Micol, Benjamin Besse. Molecular landscape of clonal hematopoiesis in patients with lung cancer: First results of the CHIC study. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4526.

Liquid Biopsies for Circulating Tumor DNA Detection May Reveal Occult Hematologic Malignancies in Patients With Solid Tumors

PURPOSE

High-risk clonal hematopoiesis (CH) is frequently incidentally found in patients with solid tumors undergoing plasma cell-free DNA sequencing. Here, we aimed to determine if the incidental detection of high-risk CH by liquid biopsy may reveal occult hematologic malignancies in patients with solid tumors.

MATERIALS AND METHODS

Adult patients with advanced solid cancers enrolled in the Gustave Roussy Cancer Profiling study (ClinicalTrials.gov identifier: NCT04932525) underwent at least one liquid biopsy (FoundationOne Liquid CDx). Molecular reports were discussed within the Gustave Roussy Molecular Tumor Board (MTB). Potential CH alterations were observed, and patients referred to hematology consultation in the case of pathogenic mutations in JAK2, MPL, or MYD88, irrespective of the variant allele frequency (VAF), or in DNMT3A, TET2, ASXL1, IDH1, IDH2, SF3B1, or U2AF1 with VAF ≥ 10%, while also considering patient cancer-related prognosis. TP53 mutations were discussed case-by-case.

RESULTS

Between March and October 2021, 1,416 patients were included. One hundred ten patients (7.7%) carried at least one high-risk CH mutation: DNMT3A (n = 32), JAK2 (n = 28), TET2 (n = 19), ASXL1 (n = 18), SF3B1 (n = 5), IDH1 (n = 4), IDH2 (n = 3), MPL (n = 3), and U2AF1 (n = 2). The MTB advised for hematologic consultation in 45 patients. Overall, 9 patients of 18 actually addressed had confirmed hematologic malignancies that were occult in six patients: two patients had myelodysplastic syndrome, two essential thrombocythemia, one a marginal lymphoma, and one a Waldenström macroglobulinemia. The other three patients were already followed up in hematology.

CONCLUSION

The incidental findings of high-risk CH through liquid biopsy may trigger diagnostic hematologic tests and reveal an occult hematologic malignancy. Patients should have a multidisciplinary case-by-case evaluation.

Clinical utility of circulating tumor DNA sequencing with a large panel: a National Center for Precision Medicine (PRISM) study

BACKGROUND

Circulating tumor DNA (ctDNA) sequencing is a promising approach for tailoring therapy in patients with cancer. We report hereby the results from a prospective study where we investigated the impact of comprehensive molecular profiling of ctDNA in patients with advanced solid tumors.

PATIENTS AND METHODS

Genomic analysis was performed using the FoundationOne Liquid CDx Assay [324 genes, tumor mutational burden (TMB), microsatellite instability status]. Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumor board (MTB). Actionable targets were classified by ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) tier leading to molecular-based treatment suggestions wherever it was possible.

RESULTS

Between December 2020 and November 2021, 1772 patients with metastatic solid tumors underwent molecular profiling. Median time to assay results was 12 days. Results were contributive for 1658 patients (94%). At least one actionable target was detected in 1059 patients (64%) with a total of 1825 actionable alterations including alteration of the DNA damage repair response pathway (n = 336, 18%), high TMB (>16 mutations/Mb; n = 243, 13%), PIK3CA mutations (n = 150, 8%), ERBB family pathway alterations (n = 127, 7%), PTEN alterations (n = 95, 5%), FGFR alterations (n = 67, 4%) and MET activations (n = 13, 0.7%). The MTB recommended a matched therapy for 597 patients (56%) with a total of 819 therapeutic orientations: clinical trials (n = 639, 78%), off-label/compassionate use (n = 81, 10%), approved drug (n = 51, 6%), and early access program (n = 48, 6%). In total, 122 patients (21%) were treated. Among the assessable patients (n = 107), 4 (4%) had complete response, 35 (33%) had partial response, 27 (25%) had stable disease, and 41 (38%) a progressive disease as best response. The median progression-free survival and median overall survival were 4.7 months (95% confidence interval 2.7-6.7 months) and 8.3 months (95% confidence interval 4.7-11.9 months) respectively.

CONCLUSIONS

ctDNA sequencing with a large panel is an efficient approach to match patients with advanced cancer with targeted therapies.

RET-MAP: An International Multicenter Study on Clinicobiologic Features and Treatment Response in Patients With Lung Cancer Harboring a RET Fusion

INTRODUCTION

Nearly 1% to 2% of NSCLCs harbor RET fusions. Characterization of this rare population is still incomplete.

METHODS

This retrospective multicenter study included patients with any-stage RET positive (RET+) NSCLC from 31 cancer centers. Molecular profiling included DNA/RNA sequencing or fluorescence in situ hybridization analyses. Clinicobiological features and treatment outcomes (per investigator) with surgery, chemotherapy (CT), immune checkpoint blockers (ICBs), CT-ICB, multityrosine kinase inhibitors, and RET inhibitors (RETis) were evaluated.

RESULTS

For 218 patients included between February 2012 and April 2022, median age was 63 years, 56% were females, 93% had adenocarcinoma, and 41% were smokers. The most frequent fusion partner was KIF5B (72%). Median tumor mutational burden was 2.5 (range: 1-4) mutations per megabase, and median programmed death-ligand 1 expression was 10% (range: 0%-55%). The most common metastatic sites were the lung (50%), bone (43%), and pleura (40%). Central nervous system metastases were found at diagnosis of advanced NSCLC in 21% of the patients and at last follow-up or death in 31%. Overall response rate and median progression-free survival were 55% and 8.7 months with platinum doublet, 26% and 3.6 months with single-agent CT, 46% and 9.6 months with CT-ICB, 23% and 3.1 months with ICB, 37% and 3 months with multityrosine kinase inhibitor, and 76% and 16.2 months with RETi, respectively. Median overall survival was longer in patients treated with RETi versus no RETi (50.6 mo [37.7-72.1] versus 16.3 mo [12.7-28.8], p < 0.0001).

CONCLUSIONS

Patients with RET+ NSCLC have mainly thoracic and bone disease and low tumor mutational burden and programmed death-ligand 1 expression. RETi markedly improved survival, whereas ICB may be active in selected patients.

Abstract 75: Highly multiplexed EGFR mutation detection from liquid biopsy samples using the 6-color Crystal Digital PCR™

Liquid biopsies are a minimally invasive sampling approach to overcome the heterogeneity of tumors and represent a valuable source of circulating tumor DNA (ctDNA) for oncological biomarker analysis. ctDNA measurements require a highly sensitive and reliable detection technology to quantify often low-level genetic aberrations within a high background of wild-type sequences. Digital PCR emerged as a powerful technology for the next-generation analysis of liquid biopsies. Stilla Technologies' 6-color naica® system is an ultrasensitive, easy-to-use digital PCR platform capable of simultaneously and precisely quantifying high numbers of biomarkers in a single reaction.

Non-small cell lung cancer (NSCLC) is a leading cause of cancer mortality worldwide. Epidermal growth factor receptor (EGFR) is frequently mutated in NSCLC. A handful of anti-EGFR Tyrosine Kinase Inhibitor therapies are approved by the FDA; however, most patients develop resistance over time to these treatments. Both monitoring primary EGFR mutations to predict treatment response and precociously detecting resistance mutations to adapt treatments promptly through ctDNA analysis stand to improve the effectiveness of NSCLC patient management.

Stilla has developed a highly multiplexed 6-color Crystal Digital PCR EGFR kit detecting more than 90% of EGFR mutations described in NSCLC from ctDNA. The assay detects 32 common and rare somatic EGFR mutations in exons 18, 19, 20, and 21, including both activating and resistant mutations.

In this work, we evaluated the sensitivity, precision and specificity of the EGFR 6-color Crystal Digital PCR assay highly specific and sensitive for the detection of EGFR mutations, with a Limit of Detection in a high background of wild-type DNA ranging from 0.30 to 0.46 cp/μL (with observed MAFs ranging from 0.06 to 0.09%). Moreover, a high concordance was observed between those EGFR results obtained for NSCLC ctDNA samples using 6-color Crystal Digital PCR and other technologies. With a rapid time to results and straightforward ctDNA analysis workflow, Crystal Digital PCR on the naica system promises ultrasensitive, highly multiplexed 6-color mutation detection, maximizing the information obtained from precious samples.

Citation Format: Cécile Jovelet, Myrtille Remy, Noémie Pata-Merci, Damien Vasseur, Ludovic Lacroix, Claudia Labrador-Rached, Allison C. Mallory. Highly multiplexed EGFR mutation detection from liquid biopsy samples using the 6-color Crystal Digital PCR™ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 75.

Abstract 3413: Clinical utility of circulating tumor DNA sequencing with a large panel: The experience of Gustave Roussy/National Center for Precision Medicine (PRISM)

Background: Circulating tumor DNA (ctDNA) sequencing is a promising approach for testing gene alterations and tailoring therapy in cancer patients given, its limited invasiveness, high sensitivity and potential to comprehensively represent tumor heterogeneity. Here, we report the results from a single-center study conducted at Gustave Roussy (Villejuif, France) where we investigated the impact of comprehensive molecular profiling of ctDNA in patients with advanced solid tumors.

Methods: Genomic analysis was performed using the Foundation One Liquid CDx Assay (324 genes, tumor mutational burden [TMB], microsatellite instability status). Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumor board (MTB) dedicated to precision medicine, attended by experts in clinical oncology, molecular biology, and clinical genetics. Actionable targets were defined by the MTB according to the existing level of evidence (classified by ESCAT tier), and molecular-based treatment suggestions were proposed where possible.

Results: Between December 2020 and November 2021, 1772 patients with metastatic solid tumors underwent molecular profiling. Median time to assay results was 12 days. Results were contributive for 1658 patients (94%). At least one actionable target was detected in 1059 patients (64%) with a total of 1825 theragnostic alterations including : high blood TMB (&gt; 16 mutations/Mb) (N= 243, 13%), alteration of the DNA damage repair response pathway (N=336, 18%), PIK3CA mutations (N=150, 8%), FGFR alterations (N= 67, 4%), MET activations (N=13, 0.7%), ERBB family pathway alterations (N=127, 7%) and PTEN mutations (N=95, 5%). Overall, the MTB recommended a matched therapy for 597 patients (56%) with a total of 819 therapeutic orientations: clinical trials (N= 639, 78%), off label/compassionate use (N=81, 10%), drug with a market authorization (N=51, 6%) and drug within an early access program (N=48, 6%). MTB did not recommend treatment for 462 patients (44%) with targetable molecular alterations for the following reasons: no clinical trial (N=421, 65%), matched treatment was already received (N=169, 26%), worsening of performance status (N= 49, 8%).

Conclusions: This large-scale study demonstrates that liquid biopsy with a large NGS ctDNA panel is an efficient approach to match patients to genomically directed clinical trials/targeted therapies. Outcomes of patients treated with matched therapy will be presented at the meeting.

Citation Format: Arnaud Bayle, Laila Belcaid, Miha Aldea, Florent Peyraud, Patricia Martin Romano, Félix Blanc-Durand, Rebecca Clodion, Santiago Ponce, Claudio Nicotra, Antoine Hollebecque, Yohann Loriot, Benjamin Besse, Damien Vasseur, Ludovic Lacroix, Etienne Rouleau, Jean-Charles Soria, Fabrice Barlesi, Geoffrey R. Oxnard, Fabrice Andre, Antoine Italiano. Clinical utility of circulating tumor DNA sequencing with a large panel: The experience of Gustave Roussy/National Center for Precision Medicine (PRISM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3413.

Abstract 4019: RET-MAP: An international multi-center study of patients with advanced non-small cell lung cancer and RET fusions

Introduction: RET fusions (RET+) are identified in nearly 1% of advanced NSCLC (aNSCLC). We evaluated characteristics and outcomes of patients (pts) with RET+ aNSCLC.

Methods: This is an international, multicenter, retrospective study evaluating clinical, biological, pathological and radiological data of pts with RET+ aNSCLC. Objective response rates (ORR), duration of response (DOR) and progression-free survival (PFS) were evaluated under double or single agent chemotherapy (CT), immunotherapy (ICI), CT-ICI, multityrosine kinase inhibitors (MTKi) and RET inhibitors (RETi). Overall survival (OS) was calculated from the start of first line therapy and compared between pts treated or not by RETi, after stratification by number of treatment lines.

Results: A total of 71 pts was included from 11 centers. Median age was 60 [IQR 47-69], 58% were female, 93% had adenocarcinoma, 2 pts (3%) had squamous and 2 (3%) neuroendocrine carcinoma, 38 (53.5%) were tobacco consumers (median 18.5 PY [7.8-31.3]), 50 (70%) had stage IV disease at diagnosis. Fusion partners were KIF5B (35/49, 71%), CCDC6 (9/49, 18%), others (5/49, 10%). Median TMB was 2.76 [2.0-8.5], median PD-L1 5% [0-29]. The most frequent co-mutation was TP53 (18/58 cases, 31%). Median number of metastatic sites was 2 [1-3], most commonly lung (48%), bone (45%), pleura (41%) and nodes (35%). Brain metastases were found in 18% of cases at diagnosis and in 31% at last follow-up or death. Table reports outcomes by treatment. mOS was 50.6 months [95%CI 37.6 - NR]. Fifty-two pts received 1st generation RETi. The use of RETi improved OS in pts treated with ≤2 lines of therapy (NR vs 17.8 months, p=0.024) and in those receiving &gt;2 lines (50.6 vs 12.7 months, p=0.0037). Pts responding to ICI had a median PD-L1 of 85% [15.5-90].

Conclusions: Pts with RET+ aNSCLC have mainly thoracic and bone disease. Despite smoking history, median TMB and PD-L1 expression are low. ICI may have a significant activity in selected cases. RETi improve OS.

Outcomes by treatment First use of Doublet CT (N=46) Single agent CT (N=12) CT-ICI (N=9) ICI (N=19) MTKi (N=9) RETi (N=52) Line of treatment (median, range) 1 [1-1] 2 [2-3] 1 [1-2] 2 [2-3] 3 [1.5-3.5] 2 [1-3] ORR (N,%) 25/40 (62.5%) 3/12 (25%) 3/9 (33%) 7/17 (41%) 4/8 (50%) 36/45 (80%) mPFS (months, 95%CI) 7.89 [6.18-14] 2.81 [2.43-NR] 5.62 [2.79-NR] 3.71 [2.99-11.5] 2.76 [1.51-NR] 24.7 [16.2-NR] mDOR (months,95%CI) 11.83 [7.06-15.6] 8.90 [4.21-NR] 14.47 [10.25-NR] 20.47 [11.3-NR] 8.18 [1.64-NR] 24.74 [17.12-NR] Stopped for toxicity (N,%) 7/46 (15%) 1/12 (8%) 2/9 (22%) 4/18 (22%) 1/9 (11%) 14/50 (28%)

Citation Format: Mihaela Aldea, Arianna Marinello, Wael Zrafi, Fabrizio Tabbo, Florian Guisier, Damien Vasseur, Vincent Fallet, Clarisse Audigier-Valette, Laura Mezquita, Antonio Calles, Giannis Mountzios, Marco Tagliamento, Judith Raimbourg, Safae Terrisse, Silvia Novello, Maria-Rosa Ghigna, Fabrice Barlesi, David Planchard, Benjamin Besse. RET-MAP: An international multi-center study of patients with advanced non-small cell lung cancer and RET fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4019.

Abstract 3414: Systematic comparison of ctDNA vs tissue sequencing with a large panel to guide therapy in patients with advanced cancer: A study from the French National Center for Precision Medicine (PRISM)

Background: Genomic profiling with tissue sequencing is still considered as the gold standard despite several limitations including screening failures due to limited tissue availability, and inability to capture intratumor spatial and temporal heterogeneity, which may impair accurate treatment selection. Several studies have demonstrated the potential of circulating tumor DNA (ctDNA) to detect genomic alterations at high accuracy compared with tissue analysis. However, no studies have comprehensively evaluated differences between tissue and ctDNA by using a large panel in the same cohort.

Methods: Genomic analysis was performed for each patient by using the Foundation One Liquid CDx Assay and the Foundation One CDx Assay (324 genes, tumor mutational burden [TMB], microsatellite instability). Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumor board (MTB). Actionable targets were defined by the MTB according to the existing level of evidence (ESCAT tiers) and molecular-based treatment suggestions were proposed where possible.

Results: Between Dec 2020 and Nov 2021, 1021 patients (median age: 62 years) with advanced cancer underwent both tissue and ctDNA NGS. Five most frequent tumor types were colorectal (N=137,13%), NSCLC (N=130,13%), breast (N=120, 12%), prostate (N=82, 8%) and pancreas (N=65, 6%). Median time elapsed between request and assay results was 12 days for ctDNA and 46 days for tissue. Testing failure was 15% for tissue and 3.9% for ctDNA. Overall, 824 (81%) patients had evaluable results for both tissue and liquid. Total number of cancer-related alterations and variants of unknown significance were 4704 and 11673 vs 4645 and 7481 for ctDNA and tissue, respectively. Proportion of patients with a higher number of cancer alterations identified in ctDNA compared with tissue increased in parallel with the time elapsed between the tissue and ctDNA sampling (45% vs 33% for a delay &gt; 26 months or &lt; 8 months). MSI and TMB status were concordant for 71% and 64% of patients, respectively. MSI status was evaluable for 97% of patients through ctDNA vs 90% through tissue. Number of actionable alterations was similar in 346 (42%) of cases, whereas it was higher in tissue for 289 (35%) and in liquid for 189 (23%) patients. ctDNA profiling allowed the identification of an ESCAT I/II or III or IV alteration not present in tissue for 74 (9%), 113 (14%) and 52 (6%) patients, respectively. Overall, MTB recommended a matched therapy for 430 patients (52%). Such a recommendation would not have been made without the results of ctDNA for 120 patients (15%).

Conclusion: This systematic comparison of ctDNA vs tissue sequencing demonstrates the capacity of ctDNA for capturing clinically relevant alterations to guide therapy in cancer patients with high accuracy and rapid turnover results.

Citation Format: Arnaud Bayle, Florent Peyraud, Laila Belcaid, Maxime Brunet, Miha Aldea, Rebecca Clodion, Paul Dubos, Damien Vasseur, Claudio Nicottra, Santiago Ponce, Isabelle Soubeyran, Emmanuel Khalifa, Yohann Loriot, Benjamin Besse, Ludovic Lacroix, Etienne Rouleau, Geoffrey Oxnard, Fabrice Barlesi, Fabrice Andre, Antoine Italiano. Systematic comparison of ctDNA vs tissue sequencing with a large panel to guide therapy in patients with advanced cancer: A study from the French National Center for Precision Medicine (PRISM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3414.

Abstract 2975: RAS precision medicine transatlantic partnership: Exploration of RAS and NF1 co-mutations in NSCLC

Background: RAS is the most commonly mutated oncogene in cancer, with KRAS mutated in ~30% of non-small cell lung cancer (NSCLC). RAS is a small GTPase cycling between GTP-bound ‘ON’ state and GDP-bound ‘OFF’ state. KRAS oncoproteins cycle between these states via hydrolysis and nucleotide exchange with the aid of GAPs, including NF1, and GEFs. Given the ’inactive state’ inhibition of recently developed KRAS G12C inhibitors on the GDP-bound state, this has highlighted the continued reliance of KRAS-mutants upon cycling, and the potential for mutants to retain dependence upon upstream influences, including NF1, for pathogenicity.

Methods: 474 patients with advanced RAS- and/or NF1-mutant NSCLC were retrospectively identified from four tertiary cancer centers between 2008 -2021. DNA from archival FFPE samples, serum or combination underwent targeted NGS panels to identify mutations. Molecular, clinical, pathological and treatment outcome data were collected. Online resources including cBioPortal and Project Achilles were used to assess the functional role of any findings.

Results: KRAS mutations were identified in 416/474 patients and NF1-mutations in 63/474 patients, eight of whom harbored two NF1-mutations. 24/63 (38%) of NF1-mutant cancers had a concomitant KRAS-mutation. We identified that KRAS G13D was more prevalent in NF1 mutant cancers vs. NF1 wildtype (NF1 MT: 6/24, 25%; vs. NF1 WT: 4/281, 1.4%; p&lt;0.0001). KRAS G12C was identified in 11/24 (45.8%) of the double mutants vs. 109/282 (38.7%) of the NF1 WT patients (p=0.52). Those with G13D/NF1 co-mutation had a predicted pathogenic NF1-mutation in 5/6 (83%) of cases. Functional analysis of NF1 KO in G13D mutant lung cancer cell lines identified that NF1 was more essential in G13D mutant cell lines, with median Chronos score -0.26 G13D vs. -0.04 G12C (p=0.02). mRNA expression data identified a range of mRNA expression Z-scores relative to all samples for NF1-mutant cancers, ranging from lowest expression at -4.54 to +1.63, median -0.51. A higher mRNA expression was identified for NF1 missense mutations of unknown significance compared to truncating mutations with likely pathogenic, loss of function.

Conclusions: These results highlight the co-mutational landscape of KRAS G13D with NF1 in NSCLC, suggesting functional importance conferred by NF1 loss, and highlight NF1 mutations as an additional pathogenic even when combined with KRAS mutation. The genomic landscape of KRAS and NF1 mutant NSCLC will be explored further through Whole Genome Sequencing data from the 100,000 Genomes Project (Genomics England).

Citation Format: Helen M. Adderley, Mihaela Aldea, Jaqueline Aredo, Mathew Carter, Matthew Church, Pantelis Nicola, Jamie Weaver, Aisha Ghaus, Damien Vasseur, Matthew Krebs, Nicola Steele, Fiona Blackhall, Heather Wakelee, Benjamin Besse, Colin Lindsay. RAS precision medicine transatlantic partnership: Exploration of RAS and NF1 co-mutations in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2975.

Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test

FDA-approved next-generation sequencing assays based on cell-free DNA offers new opportunities in a molecular-tumor-board context thanks to the noninvasiveness of liquid biopsy, the diversity of analyzed parameters and the short turnaround time. It gives the opportunity to study the heterogeneity of the tumor, to elucidate complex resistance mechanisms and to adapt treatment strategies. However, lowering the limit of detection and increasing the panels' size raise new questions in terms of detection of incidental germline alterations, occult malignancies and clonal hematopoiesis of indeterminate potential mutations. In this review, after a technological discussion and description of the common problematics encountered, we establish recommendations in properly using these FDA-approved tests in a molecular-tumor-board context.

Genomic landscape of acquired resistance to targeted therapies in patients with solid tumors: A study from the National Center for Precision Medicine (PRISM)

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Background: Despite the effectiveness of the various targeted therapies currently approved in solid tumors, acquired resistance remains a persistent problem that limits the ultimate effectiveness of these treatments. Polyclonal resistance to targeted therapy has been described in multiple solid tumors through high throughput analysis of multiple tumor tissue samples from a single patient. However, biopsies at the time of acquired resistance to targeted agents may not always be feasible and may not capture the genetic heterogeneity that could exist within a patient. We used here sequencing of circulating tumor DNA (ctDNA) to characterize the landscape of secondary resistance mechanisms in a large cohort of patients with solid tumors. Methods: This study enrolled patients with advanced cancer from two institutional molecular profiling program STING (NCT04932525, sponsor: Gustave Roussy) or BIP (NCT02534649sponsor: Institut Bergonié). Genomic analysis was performed for each patient by using the Foundation One Liquid CDx Assay (324 genes, tumor mutational burden [TMB], microsatellite instability status). Results: 3435 patients with metastatic disease entered the study. Among them 992 patients (29%) received a targeted therapy matched to a specific molecular alteration before ctDNA. The main tumor types were: prostate cancer (349, 35%), luminal breast cancer (236, 24%), oncogene-addicted non-small cell lung cancer (129, 13%), KRAS-wild type colorectal cancer (126, 13 %). The most frequent class of targeted agents were androgen receptor pathway inhibitor (n = 350, 35%), aromatase inhibitor (236, 24%), anti- EGFR monoclonal antibodies (166, 17%), anti- EGFR tyrosine kinase inhibitors (83, 8%). ctDNA sequencing revealed DNA aberrations involved in secondary resistance in 308 patients (31%). The most frequent aberrations were AR mutations/amplifications, ESR1 point mutations, KRAS point mutations, EGFR point mutations. Among patients with resistance mutation, polyclonal aberrations were identified in 123 patients (40%). The median number of polyclonal aberrations per patient was 2 (range: 2-16). Polyclonal aberrations involved at least 2 different genes in 32 patients (10%). Preliminary results suggest that patients with polyclonal aberrations had worse outcome in comparison with patients with one or no detected aberration and final data will be presented at the time of the congress. Conclusions: We report here the first comprehensive landscape of genomic aberrations in ctDNA involved in resistance to targeted therapies in cancer patients. Polyclonal secondary genomic aberrations represent a frequent clinical resistance mechanism that may explain the poor rate of sustained complete remission observed with targeted therapies and must guide the development of future combinatorial strategies.

Minimal residual disease (MRD) in patients with resected stage I NSCLC: Results of the prospective adjuvant IFCT-0703 trial

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Background: MRD aims to detect circulating biomarkers of micrometastatic disease and ultimately predict recurrences. The IFCT-0703 randomized phase II trial failed to show a benefit of 6 months adjuvant pazopanib (P) vs. placebo after resection of stage I NSCLC (7th TNM edition). The outcome of pts based on their MRD status has been evaluated. Methods: Blood samples were collected in EDTA tubes (Becton Dickinson Company) after surgery (T0), after 3 months (T3) of P or placebo and at the end of treatment (T6). Plasmas were obtained after double centrifugation of total blood. Total nucleic acid was extracted using the Maxwell RSC LV plasma kit (Promega) according to the manufacturer’s protocol. Samples were quantified using the QuBit dsDNA HS Assay kit on a QuBit 3.0 flurometer (Thermo Fisher Scientific). Molecular analysis was performed by next generation sequencing using the Oncomine Lung cfDNA Assay (ThermoFisher Scientific). Two MRD definitions were tested : 1) high level of DNA in the blood or 2) any mutation detected by the standard bioinformatic pipeline was considered present, whatever the allelic fraction. Results: 143 pts were randomized in 29 centers between March 2009 and August 2012, 71 and 72 in the placebo and P arms respectively. Among the 119 pts with evaluable T0 samples, 27 pts recurred and 14 died. Median DNA concentration ([DNA]) was 6.6 ng/ml and an increase of [DNA] of 10 ng/ml was found prognostic of poor DFS and OS, HR=1.4, 95%CI [1.14-1.72], p=0.0016 and HR=1.62, 95%CI [1.15-2.30], p=0.0057 respectively. In 81 pts with available T0-T6 samples, [DNA] variation had no different impact on DFS and OS, in the P arm and the placebo arm. ctDNA mutations (ctDNA+) were detected in 31/119 pts. ctDNA+ were more frequent in samples with high DNA quantity (p=0.0002). Genes mutated at T0 were TP53 in 16, NRAS in 6, MAP2K1 in 2, KRAS in 1, EGFR in 5, BRAF in 1, ALK in 2. 29 pts had 1 mutation, 2 had 2 mutations. DFS and OS were similar between pts with or without ctDNA+ : HR= 1.038 (95%CI 0.438-2.456, p=0.93) and 1.193 (95% CI 0.367-3.882, p=0.77) respectively. Among 27 pts with ctDNA+ at T0 and available sample at T6, 23 had no more mutations at T6. Two pts had a ctDNA+ only at T6 (not at T3), one of them had a recurrence at 7 months. Conclusions: Post-operative ctDNA mutations are found in 26.0% of the pts but their positivity had no impact on DFS or OS. In contrast, DFS and OS were poorer in pts with increased plasma DNA concentration. ctDNA mutations status do not recapitulate the complexity of MRD characterization. NGS will be performed on matched tissues in order to refine MRD definition. Clinical trial information: NCT00775307.

Meningeal "Lazarus Response" to Lorlatinib in a ROS1-Positive NSCLC Patient Progressing to Entrectinib

Background

ROS1 tyrosine kinase inhibitors (TKIs) have showed activity and efficacy in ROS1-rearranged non-small cell lung cancer (NSCLC). In the clinical practice, besides the utilization of crizotinib, less is known about the best treatment strategies involving additional, new-generation TKIs for the sequential treatment of ROS1-positive NSCLC patients.

Case Presentation

A patient suffering from a ROS1-rearranged lung adenocarcinoma, after receiving cisplatin-pemetrexed chemotherapy, was treated with entrectinib, a new-generation ALK/ROS1/NTRK inhibitor. After 16 months, central nervous system (CNS) metastases appeared, without extra-cerebral disease progression. Stereotactic brain radiotherapy was performed and entrectinib was maintained, due to the global systemic disease control. Approximately one month after radiotherapy, thoracic and meningeal progressions were detected, the latter highly symptomatic with neurocognitive disorders, visual hallucinations and worsening of psycho-motor impairment. A lumbar puncture was positive for tumor cells and for an EZR-ROS1 fusion. The administration of lorlatinib (a third-generation ALK/ROS1 inhibitor) prompted an extremely rapid improvement of clinical conditions, anticipating the positive results observed at radiologic evaluation that confirmed the disease response still ongoing after nine months since treatment start.

Discussion

With the expanding availability of targeted agents with differential activity on resistance mechanism and on CNS disease, choosing wisely the best treatment strategies is pivotal to assure the best clinical outcomes in oncogene-addicted NSCLC patients. Here we have reported lorlatinib reverted an almost fatal meningeal carcinomatosis developing during entrectinib in a ROS1-positive NSCLC patient.

Chronic Plasma Exposure to Kinase Inhibitors in Patients with Oncogene-Addicted Non-Small Cell Lung Cancer

Simple Summary

In this study, we measured the plasmatic concentration of Kinase inhibitors (KI) among a population with non-small cell lung cancer (NSCLC) harboring driver genetic alterations. They received erlotinib, gefitinib, osimertinib, crizotinib, or dabrafenib (with or without trametinib) for at least three months. The results were measured by ultra-performance liquid chromatography coupled with tandem mass spectrometry and compared to previously published data. Between November 2013 and February 2019, fifty-one samples were analyzed. The main outcome was the rate of samples with suboptimal KI plasma concentrations. Suboptimal plasma concentrations were observed in 51% (26/51) of cases and might contribute to treatment failure.

Abstract

Kinase inhibitors (KI) have dramatically improved the outcome of treatment in patients with non-small cell lung cancer (NSCLC), which harbors an oncogene addiction. This study assesses KI plasma levels and their clinical relevance in patients chronically exposed to KIs. Plasma samples were collected in NSCLC patients receiving erlotinib, gefitinib, osimertinib, crizotinib, or dabrafenib (with or without trametinib) for at least three months between November 2013 and February 2019 in a single institution. KI drug concentrations were measured by ultra-performance liquid chromatography coupled with tandem mass spectrometry and compared to published data defining optimal plasma concentration. The main outcome was the rate of samples with suboptimal KI plasma concentrations. Secondary outcomes included its impact on T790M mutation emergence in patients receiving a first-generation epidermal growth factor receptor (EGFR) KI. Fifty-one samples were available from 41 patients with advanced NSCLC harboring driver genetic alterations, including EGFR, v-Raf murine sarcoma viral oncogene homolog B (BRAF), anaplastic lymphoma kinase (ALK) or ROS proto-oncogene 1 (ROS1), and who had an available evaluation of chronic KI plasma exposure. Suboptimal plasma concentrations were observed in 51% (26/51) of cases. In EGFR-mutant cases failing first-generation KIs, EGFR exon 20 p.T790M mutation emergence was detected in 31% (4/13) of samples in optimal vs. none in suboptimal concentration (0/5). Suboptimal plasma concentrations of KIs are frequent in advanced NSCLC patients treated with a KI for at least three months and might contribute to treatment failure.