Targetable Alterations Research Articles

Abstract 6127: MDM2 inhibition in combination with MEK inhibition in pre-clinical models of lung adenocarcinomas with MDM2 amplification

Abstract The eventual development of resistance to single-agent targeted therapies in lung adenocarcinomas (LUAD) is inevitable, and new strategies are needed. We hypothesize that combination therapies aimed at a known driver and a distinct targetable alteration could prolong time on oral targeted therapy. In an analysis of 7636 patients with LUAD who underwent MSK-IMPACT large panel NGS testing, 5.5% (416/7636) harbored MDM2 amplification (MDM2amp), a known mechanism of TP53 inactivation. MDM2amp was over-represented among tumors with alterations in METex14 (34.4%, p<0.001), EGFR (10%, p<0.001), RET (11%, p<0.05), and ALK (9.9%, p<0.002). The small molecule MDM2 inhibitor milademetan (mila) caused growth inhibition as a single-agent in MDM2amp patient-derived cell lines with concurrent kinase alterations including ECLC5-GLx (MDM2amp/TRIM33::RET/TP53 wildtype (WT)) and LUAD12c (MDM2amp/METex14/KRASG12S/TP53 WT). Mila also caused growth inhibition in a cell line with KRASG12C and WT TP53 without MDM2amp (SW1573 (KRASG12C/TP53WT)), but not in cell lines with TP53 mutations (LUAD-002AS1 (KIF5B::RET/TP53P128fs, H1792 (KRASG12C/TP53 splice site mut)). Treatment of ECLC5-GLx and LUAD12c with mila resulted in restoration of ERK phosphorylation, confirming a previous report of ERK activation upon MDM2 inhibition. At 48 hours, ERK phosphorylation was suppressed by concurrent mila and MEK inhibition using trametinib (tram). In contrast, ERK phosphorylation was not suppressed by concurrent mila and KIF5B::RET inhibition using selpercatinib (in ECLC5-GLx) or MET inhibition using capmatinib (in LUAD12c). The combination of mila+tram was synergistic in slowing growth of ECLC5-GLx, LUAD12c, and SW1573 cells, and increased expression of pro-apoptotic proteins PUMA and BIM, beyond that achieved by either agent alone. In ECLC5-GLx, mila+tram also caused increased apoptotic cells measured by Annexin-V compared to either agent alone (combination p<0.01 compared to mila, p<0.001 compared to tram). In vivo, combination mila+tram was more effective than mila or tram alone in ECLC5-GLx (p<0.0001 and p<0.0001, respectively), LX-285 (EGFRex19del/MDM2amp) (p<0.0001 and p<0.0001, respectively), and L-13BS1 (model resistant to capmatinib) (METex14/MDM2amp) (p<0.05 and p<0.0001, respectively). These results suggest that combined MDM2/MEK inhibition is effective in patient-derived LUAD models harboring MDM2amp. This combination, potentially applicable to LUADs with a wide variety of oncogenic driver mutations and kinase fusions will be investigated as part of a phase 1/2 clinical trial. Citation Format: Arielle Elkrief, Vladimir Markov, Álvaro Quintanal-Villalonga, Rebecca Caeser, Pawel Sobczuk, Emily Cheng, Alexander Drilon, Gregory J. Riely, William W. Lockwood, Elisa de Stanchina, Charles M. Rudin, Igor Odintsov, Romel Somwar. MDM2 inhibition in combination with MEK inhibition in pre-clinical models of lung adenocarcinomas with MDM2 amplification [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 6127.

Abstract 938: Outcomes of molecular tumor board recommendations for cancer patients with progression on standard of care therapies in Saudi Arabia

Abstract Introduction: Molecular Tumor Boards (MTB) are essential in Precision Oncology Programs. Gaps, however, remain in interpreting comprehensive genomic profiling (CGP) results, and determining their actionability. Our MTB, established in October 2020 and conducted at a tertiary cancer center in Saudi Arabia, focused on discussing patients with complex CGP results and recommending genomic based therapies. Meetings occurred virtually, every month, with oncologists, pathologists and genomicists attending. Methods: This is a retrospective cohort study of patients discussed in our MTB from October 2020 till October 2022. We report the outcomes of these patients who had progressive disease on standard of care (SOC) therapies, and have had non Tier 1 alterations (ESCAT classification) in their CGP reports. We chose an FDA approved, commercially available CGP, which tests 324 genes (FoundationOne CDX). We present the demographics, clinical characteristics, CGP results, recommendations of the MTB, and patient outcomes. Results: Sixty patients fitting the criteria above have been discussed. Median number of prior systemic therapy lines was 2 (range 0-8). The most common primary diagnosis was soft tissue sarcoma (25%), followed by liver and pancreato-biliary cancers (20%), followed by head and neck cancers (15%) and skin cancers (8%). Of the 60 patients, 48 patients had response evaluations. Thirty five patients (out of 48, 73%) have had recommendations for genomic based therapies based on their CGP results. Only 16 patients (out of 35, 46%) received MTB recommended therapies. Eight patients (out of 16, 50%) have remained progression free and on MTB recommended genomic therapy for 6 months and above. The commonest reasons for not receiving MTB recommended therapy were patient clinical deterioration or death (9 patients, 47%) followed by patients responding on current line of therapy (7 patients, 37%). Most common pathogenic targetable alterations were CDKN2A/B mutations (6 patients), followed by alterations in FGFR (5 patients), PTEN (4 patients), BRAF (4 patients), PIK3CA (2 patients) and ERBB2 (2 patients) followed by others (will be presented). Conclusion: Following recommendations, of the first MTB in Saudi Arabia, resulted in improved outcomes of cancer patients who had progressive disease on SOC therapies. Consideration of performing CGP and discussing patients early in their cancer journey may allow them to receive, and benefit from recommended genomic therapies earlier. Citation Format: Kanan Alshammari, Fouad Sabatin, Mehlika Hazar-Rethinam, Faizah Alotaibi, Reham Ajina, Hussam Shehata, Mohammad Alkhayyat, Abdullah Alsaleh, Mohammed Algarni. Outcomes of molecular tumor board recommendations for cancer patients with progression on standard of care therapies in Saudi Arabia [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 938.

Optical Genome Mapping in Routine Cytogenetic Diagnosis of Acute Leukemia

Cytogenetic aberrations are found in 65% of adults and 75% of children with acute leukemia. Specific aberrations are used as markers for the prognostic stratification of patients. The current standard cytogenetic procedure for acute leukemias is karyotyping in combination with FISH and RT-PCR. Optical genome mapping (OGM) is a new technology providing a precise identification of chromosomal abnormalities in a single approach. In our prospective study, the results obtained using OGM and standard techniques were compared in 29 cases of acute myeloid (AML) or lymphoblastic leukemia (ALL). OGM detected 73% (53/73) of abnormalities identified by standard methods. In AML cases, two single clones and three subclones were missed by OGM, but the assignment of patients to cytogenetic risk groups was concordant in all patients. OGM identified additional abnormalities in six cases, including one cryptic structural variant of clinical interest and two subclones. In B-ALL cases, OGM correctly detected all relevant aberrations and revealed additional potentially targetable alterations. In T-ALL cases, OGM characterized a complex karyotype in one case and identified additional abnormalities in two others. In conclusion, OGM is an attractive alternative to current multiple cytogenetic testing in acute leukemia that simplifies the procedure and reduces costs.

Small Cell Lung Cancer in Light/Never Smokers - A Role for Molecular Testing?

This report describes the management of small cell lung cancer (SCLC) transformation in a patient with untreated ALK-mutated advanced disease and a minimal smoking history, and a separate case of a de novo SCLC in a lifelong nonsmoker found to have a potentially targetable ERBB2 alteration. In the first case, chemotherapy followed by a targeted inhibitor was chosen due to the presence of the ALK rearrangement, as well as a somewhat discordant response to induction chemotherapy, suggesting possible progression of the ALK inhibitor-sensitive component. Molecular testing for the identification of driver mutations should be considered in patients with SCLC who have light/never smoking histories in order to help understand the incidence and ultimate optimal management strategies.

MP41-15 DIFFERENCES IN SOMATIC AND GERMLINE VARIATIONS IN HISPANIC AND NON-HISPANIC PATIENTS WITH RENAL CELL CARCINOMA

You have accessJournal of UrologyCME1 Apr 2023MP41-15 DIFFERENCES IN SOMATIC AND GERMLINE VARIATIONS IN HISPANIC AND NON-HISPANIC PATIENTS WITH RENAL CELL CARCINOMA Peris Castaneda, Eric Lo, John Heard, Michael Nazmifar, Michael Kheshvadjian, and Michael Ahdoot Peris CastanedaPeris Castaneda More articles by this author , Eric LoEric Lo More articles by this author , John HeardJohn Heard More articles by this author , Michael NazmifarMichael Nazmifar More articles by this author , Michael KheshvadjianMichael Kheshvadjian More articles by this author , and Michael AhdootMichael Ahdoot More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003279.15AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Among patients with renal cell carcinoma (RCC), those of Hispanic ethnicity have worse disease burden. Hispanic patients (HP) are diagnosed at a younger age and have higher stage disease at diagnosis. Although some of the disparity is due to social factors, studies have shown differences in RCC histologic subtype between HP and non-Hispanic white patients. This suggests a potential molecular component conferring greater pre-treatment disease. HP have been underrepresented in molecular genomic studies of RCC and data on gene variation are lacking. Here, we aim to determine differences in germline and somatic alterations in HP and non-Hispanic patients (NHP) with RCC. METHODS: We queried a multi-institutional pan-cancer database of >5 million patients for patients aged ≥18 diagnosed with RCC. Demographic factors and disease-specific factors were compared between HP and NHP to assess for statistical significance (p<0.05). Frequency and type of germline and somatic alterations were compared. RESULTS: We identified 558 HP and 4829 NHP with RCC. No difference in gender distribution was observed. HP were younger at diagnosis (57.3 years vs 61.4 years in NHP) (p<0.001) and more likely to be diagnosed at or before age 46 (20% vs 11% in NHP) (p<0.001). Fifty-seven percent of HP reported being never smokers compared to 40% of NHP (p<0.001). A higher proportion of HP presented with T4 or T3 disease (75%, compared to 43% of NHP). Overall, somatic variant information was available for 166 HP and 667 NHP; germline variant information was available for 38 HP and 667 NHP. The most common somatic and germline variants in HP and NHW are shown in Figure 1. Overall, somatic alterations appeared commensurate with the general RCC population. HP showed higher rates of germline alterations in CHEK2, MSH6, FH, and FLCN compared to NHP. CONCLUSIONS: Differences in germline alterations are observed between HP and NHP with RCC. Further genomic studies that include HP are needed to better identify targetable genetic alterations and improve treatment decisions. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e561 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Peris Castaneda More articles by this author Eric Lo More articles by this author John Heard More articles by this author Michael Nazmifar More articles by this author Michael Kheshvadjian More articles by this author Michael Ahdoot More articles by this author Expand All Advertisement PDF downloadLoading ...

MP63-08 CLINICAL AND GENOMIC RISK FEATURES OF HIGH GRADE T1 NON-MUSCLE INVASIVE BLADDER CANCER

You have accessJournal of UrologyCME1 Apr 2023MP63-08 CLINICAL AND GENOMIC RISK FEATURES OF HIGH GRADE T1 NON-MUSCLE INVASIVE BLADDER CANCER Carissa Chu, Jessica Chen, Manuel DE Jesus Escano, Karissa Whiting, Irina Ostrovnaya, Song Jiang, Wesley Yip, Sari Khaleel, Andrew Lenis, Timothy Clinton, Goh Alvin, CHA Eugene, Timothy Donahue, Guido Dalbagni, Gopa Iyer, David Solit, Judy Sarungbam, Hikmat AL-Ahmadie, Bernard Bochner, and Eugene Pietzak Carissa ChuCarissa Chu More articles by this author , Jessica ChenJessica Chen More articles by this author , Manuel DE Jesus EscanoManuel DE Jesus Escano More articles by this author , Karissa WhitingKarissa Whiting More articles by this author , Irina OstrovnayaIrina Ostrovnaya More articles by this author , Song JiangSong Jiang More articles by this author , Wesley YipWesley Yip More articles by this author , Sari KhaleelSari Khaleel More articles by this author , Andrew LenisAndrew Lenis More articles by this author , Timothy ClintonTimothy Clinton More articles by this author , Goh AlvinGoh Alvin More articles by this author , CHA EugeneCHA Eugene More articles by this author , Timothy DonahueTimothy Donahue More articles by this author , Guido DalbagniGuido Dalbagni More articles by this author , Gopa IyerGopa Iyer More articles by this author , David SolitDavid Solit More articles by this author , Judy SarungbamJudy Sarungbam More articles by this author , Hikmat AL-AhmadieHikmat AL-Ahmadie More articles by this author , Bernard BochnerBernard Bochner More articles by this author , and Eugene PietzakEugene Pietzak More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003321.08AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: High grade non-muscle invasive bladder cancer invading the lamina propria (HG T1) exhibits variable clinical behavior. Existing risk stratification approaches by clinicopathologic alone are limited in determining who will benefit most from immediate radical cystectomy (RC) versus BCG. We report contemporary outcomes of patients managed with BCG or immediate RC and comparative mutational landscape across the spectrum of HG T1 disease. METHODS: This was a single-center retrospective cohort study of patients newly diagnosed with HG T1 non-muscle invasive bladder cancer between 2014 and 2020>18 months of follow up. All included patients underwent restaging TURBT with confirmed T1 by TURBT/EUA/imaging. Targeted exome sequencing with MSK-IMPACT was performed on 139 HG T1 tumors and 191 T2 tumors. RESULTS: 390 patients were included with median follow up time of 35 months (IQR 19-59 months). 308 were managed with intravesical BCG and 82 immediate RC. Patients selected for immediate RC were younger (median age 66 vs 69, p<0.001) and had higher rates of concurrent CIS (78 vs 53%, p<0.001), deep lamina propria invasion (37 vs 17%, p<0.001), lymphovascular invasion (7 vs 0.3%, p<0.001), and larger tumor size (4.3 cm vs 3.3 cm, p=0.007). Of the 82 patients who immediate radical cystectomy (BCG naïve), 32 (40%) were upstaged to pT2 and/or N+disease at RC. Persistent pT1 disease at re-resection and the presence of variant histology were associated with pathologic upstaging (p<0.01), while tumor size, concurrent CIS, bladder neck involvement, or prostatic urethra involvement were not. Compared to patients without additional risk factors, patients with CIS and at least one additional risk (e.g . “very high risk” T1 disease) harbored more TP53, ERBB2/Her2, and RB1 mutations and fewer FGFR3 mutations and a genomic profile more similar to T2 tumors than NMIBC (Figure 1). CONCLUSIONS: Very high risk T1 tumors are genomically similar to muscle-invasive tumors and are enriched in targetable alterations including ERBB2/Her2. Integration of genomic sequencing with clinical and pathologic features of HG T1 disease may improve risk stratification and treatment selection. Source of Funding: Ruth L. Kirschstein National Research Service Award T32CA082088 American Society of Clinical Oncology Young Investigator Award (YIA) Award © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e874 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Carissa Chu More articles by this author Jessica Chen More articles by this author Manuel DE Jesus Escano More articles by this author Karissa Whiting More articles by this author Irina Ostrovnaya More articles by this author Song Jiang More articles by this author Wesley Yip More articles by this author Sari Khaleel More articles by this author Andrew Lenis More articles by this author Timothy Clinton More articles by this author Goh Alvin More articles by this author CHA Eugene More articles by this author Timothy Donahue More articles by this author Guido Dalbagni More articles by this author Gopa Iyer More articles by this author David Solit More articles by this author Judy Sarungbam More articles by this author Hikmat AL-Ahmadie More articles by this author Bernard Bochner More articles by this author Eugene Pietzak More articles by this author Expand All Advertisement PDF downloadLoading ...

Pathogenic genomic alterations in Chinese pancreatic cancer patients and their therapeutical implications.

Approximately 90% of pancreatic ductal adenocarcinoma (PDAC) cases are driven by the untargetable non-G12C KRAS mutations, and only a small subset of patients are eligible for FDA-approved precision therapies. The practice of precision therapy in pancreatic cancer was limited by the paucity of targetable genetic alterations, especially in the Asian population. To explore therapeutic targets in 499 Chinese PDAC patients, a deep sequencing panel (OncoPanscan™, Genetron health) was used to characterize somatic alterations including point mutations, indels, copy number alterations, gene fusions as well as pathogenic germline variants. We performed genomic profiling in 499 Chinese PDAC patients, which revealed somatic driver mutations in KRAS, TP53, CDKN2A, SMAD4, ARID1A, RNF43, and pathogenic germline variants (PGVs) in cancer predisposition genes including BRCA2, PALB2, and ATM. Overall, 20.4% of patients had targetable genomic alterations. About 8.4% of patients carried inactivating germline and somatic variants in BRCA1/2 and PALB2, which were susceptible to platinum and PARP inhibitors therapy. Patients with KRAS wild-type disease and early-onset pancreatic cancer (EOPC) harbored actionable mutations including BRAF, EGFR, ERBB2, and MAP2K1/2. Compared to PGV-negative patients, PGV-positive patients were younger and more likely to have a family history of cancer. Furthermore, PGVs in PALB2, BRCA2, and ATM were associated with high PDAC risk in the Chinese population. Our results demonstrated that a genetic screen of actionable genomic variants could facilitate precision therapy and cancer risk reduction in pancreatic cancer patients of Asian ethnicity.

Real-World Data of Combined Immunochemotherapy in Patients With Nonsquamous Advanced NSCLC. A Single-Center Retrospective Study

IntroductionOn the basis of the landmark trial KEYNOTE-189 (KN-189), pembrolizumab plus chemotherapy has become the standard-of-care first-line treatment for patients with advanced nonsquamous NSCLC without oncogenic driver alterations.KN-189 included a selected patient population and lacks external validity. In clinical practice, many patients do not meet the inclusion criteria of KN-189, although they are treated accordingly. It is unknown whether these patients benefit equally as the trial population. MethodsWe retrospectively analyzed all patients with advanced nonsquamous NSCLC without targetable oncogenic alterations who received the KN-189 treatment regimen between April 2018 and May 2021 at the University Hospital Basel, Switzerland. Patients were grouped into those who retrospectively met the inclusion criteria of KN-189 (group A) and those who did not (group B). Outcome parameters included progression-free survival (PFS), overall survival (OS), and objective response rate. Multivariate subgroup analyses were performed. ResultsWe identified 75 patients, including 29 patients in group A and 46 patients in group B. Median PFS was 9.2 and 4.6 months in group A and B, respectively (p = 0.12). Median OS was 16.5 and 6.5 months in group A and B, respectively (p = 0.11). Objective response rate was 59% in group A and 33% in group B (p = 0.03). Eastern Cooperative Oncology Group performance status greater than or equal to 2 and active infections were significantly associated with shorter PFS and OS. ConclusionsWe report real-world data for patients treated according to the KN-189 regimen with inferior outcomes in patients who did not meet the KN-189 inclusion criteria. Better treatment options for this vulnerable patient population are needed.

Interview: Timothy Clinton

Interview: Timothy Clinton

Real-world treatment patterns and outcomes of patients with metastatic nonsquamous non-small cell lung cancer after progression on standard-of-care therapy in the United States

ObjectivesData to guide treatment selection in metastatic nonsquamous (mNSq) non-small cell lung cancer (NSCLC) after progression on current standard-of-care (SoC) treatment are limited. We investigated patterns of treatment and clinical outcomes following one or more disease progressions on SoC. Materials and methodsElectronic medical records in the ConcertAI Patient360 NSCLC database were analyzed for US adults with mNSq NSCLC who initiated treatment between 2016 and 2021. Analyses were conducted separately for patients who had ≥1 prior lines of therapy and progression(s) without (Cohort 1) or with (Cohort 2) evidence of targetable genetic alterations (EGFR, ALK, or ROS1). Outcomes included real-world progression-free survival (rwPFS) and overall survival (rwOS). ResultsCohorts 1 and 2 included 281 and 109 patients, respectively. In Cohort 1, subsequent treatment was most often with docetaxel monotherapy (18.5%) or docetaxel + ramucirumab (32.4%). Most patients in Cohort 2 received platinum-based doublet chemotherapy with (22.9%) or without (34.9%) immunotherapy. Median rwPFS and rwOS were 2.9 and 7.2 months, respectively, in Cohort 1, and 3.2 and 10.4 months in Cohort 2. Neither the addition of ramucirumab to docetaxel in Cohort 1 nor the addition of immunotherapy to chemotherapy in Cohort 2 was associated with a marked improvement in additional survival. ConclusionPatients with progressive mNSq NSCLC most commonly received later-line docetaxel for cancer without driver mutations, or platinum-based chemotherapy (following one or more lines of tyrosine kinase inhibitor therapy) for cancer with driver mutations, consistent with guideline recommendations. Median survival was poor regardless of subsequent treatment, highlighting the need for more effective options.

Paired Comparison of Routine Molecular Screening of Patient Samples with Advanced Non-Small Cell Lung Cancer in Circulating Cell-Free DNA Using Three Targeted Assays.

Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancers. Approximately 10-50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors. Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay. In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay. The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.

Abstract P5-14-10: Targetable alterations and genomic signatures within breast cancer brain metastases: Data from comprehensive genomic profiling of 761 breast cancer brain metastases

Abstract Background: Breast cancer brain metastasis (BCBM) represents an area of unmet clinical need. We previously demonstrated the genomic differences between primary BC and BCBM. In this study we examined the genomic differences between BCBM by BC subtypes and the potential actionable targets that might be taken forward for each subtype in clinical trials. Material and Methods: A total of 761 BCBMs were analyzed by comprehensive genomic profiling (CGP) for alterations in up to 395 genes (Foundation Medicine, USA). The samples were classified by immunohistochemistry (IHC) of the BCBM to ER+ (ER+/HER2-, ER+/HER2+), ER-/HER2+ and ER-/HER2-. Homologous recombination deficiency (HRD-gLOH; cutoff 16%), tumour mutational burden (TMB; cutoff 10 mutations/Mb), microsatellite instability (MSI) and PD-L1 prevalence and expression by IHC using the VENTANA SP142 assay (Immune Cell Score [IC] cutoff 1%) were also investigated. Results: For all BC subtypes the most enriched gene alterations in BCBM (&amp;gt;20% prevalence) were: TP53, MYC and PIK3CA. ESR1 and ERBB2 were more prevalent in ER+ and HER2+ tumours respectively, with ESR1 alterations significantly enriched in ER+/HER2- BCBMs (p&amp;lt; 0.0001). Frequently altered genes by BCBM subtype were: ER+/HER2-: CDH1 (8%) and BRCA2 (7%); ER+/HER2+: PIK3C2B (11%), MDM4 (11%), TBX3 (9%) and AKT2 (8%); ER-/HER2+: LYN (9%). Significantly enriched genes (p&amp;lt; 0.01) by BCBM subtype were: HER2+: CDK12 (15%); ER-/HER2-: BRCA1 (14%), CCND3 (9%), VEGFA, JAK2 (8% each) and the immune checkpoint inhibition (ICPI) biomarkers PDCD1LG2 (PDL2), CD274 (PDL1) (7% each). HRD-gLOH was high in ER+/HER2-: (43%) and ER-/HER2-: (70%). TMB and MSI were present in 10%-21% and 1-3% of BCBM respectively, whereas PDL1 protein expression by subtypes was: ER+/HER2- 23%, ER+/HER2+ 27%, ER-/HER2+ 57% , ER-/HER2- 48%. Table 1 summarizes the proportion of BCBMs with actionable alterations and selected clinical trials in BCBM. Conclusion: Clinically-relevant genomic alterations were identified across all BCBM subtypes. High HRD-gLOH, TMB and MSI were observed across all the BCBMs subtypes whereas PDL1/PDL2 alterations were a distinctive feature of ER-/HER2- BCBM. These data highlight the need to assess the genomic landscape of BCBM to enable rational treatment decisions with targeted agents, as well as to enable enrichment of relevant populations within clinical trials. Table 1. Selected studies with targeted therapy and/or immunotherapy in breast cancer brain metastases. The percentage (%) of actionable alterations by ER and HER2 status is summarized. ND: Not Detectable. Citation Format: Athina Giannoudis, Ethan Sokol, Shakti Ramkissoon, Talvinder Bhogal, Jeff Ross, Kimberly McGregor, Evangelia Razis, Rupert Bartsch, Richard S. Huang, Carlo Palmieri. Targetable alterations and genomic signatures within breast cancer brain metastases: Data from comprehensive genomic profiling of 761 breast cancer brain metastases [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-14-10.

Abstract P5-03-05: Distinct molecular differences between African American/Black and White women with Triple Negative Breast Cancer

Abstract Introduction: Triple-negative breast cancer (TNBC) is an aggressive disease that lacks well-defined molecular targets. It accounts for 15-20% of all breast cancers and disproportionately affects women of color due to both limited access to treatment and genetic variation. Recent studies identified BRCA1(or 2) and the PIK3CA/AKT1/PTEN axis as targets for treatment, but these studies neglected to account for genetic variations between race. Here, we present molecular differences between African American/Black (AA) and White (W) women with TNBC to highlight the importance of accounting for race to develop effective therapy and improve long-term outcomes. Methods: This study utilized the TCGA Firehose Legacy Breast Carcinoma dataset on cBioPortal. Subjects with breast cancer and negative ER, PR, and HER2 scores were stratified into AA (n=32) and W (n=69) subgroups. Data was analyzed to compare the most altered genes, copy number variation (CNV), and survival rates between the subgroups. The logrank test was used to obtain the hazard rate. The GISTIC2 model was used to assess CNV and G-scores (G; amplitude of aberration x frequency of occurrence). Results: The main genetic differences were in PIK3CA and BRCA1(or 2) genes. PIK3CA was detected as one of the ten most altered genes in TNBC, but this alteration was found in less than 10% of the TNBC cases. Of the 10%, PIK3CA was altered in 19% of W and 9% of AA subgroup. BRCA1(2) were altered in 10%(7%) of W but 0%(3%) of AA. Additionally, structural differences in chromosomes contributed to different survival outcomes. Both groups had co-amplification in 8q, but a significant hazard rate difference (z = 5.32, p &amp;lt; 0.001) was found for the W compared to the AA for the MYC gene. Further, the W had significantly higher amplification at 3q (G = 0.8 in W; 0.45 in AA). It is important to note that the PIK3CA gene lies in the 3q.26 region, meaning this gene is amplified significantly in the W subgroup. The AA group had a significant deletion at 8p.23 (G=0.5 in W; 0.8 in AA). Deletion of 8p causes MYC amplification, a targetable alteration. Conclusion: Our analysis reveals critical differences between AA and W subgroups with TNBC. Thus, it is clear that targeting the PIK3CA or BRCA1(2) gene benefits the W more than the AA population. To alleviate the disproportionate burden that AA women with TNBC face, more effort must be geared to find solutions specific to the AA subgroup. A greater sample size will help determine whether MYC amplification is unique to the AA subgroup, and if so, it could be targeted to improve outcomes of AA women with TNBC. Nevertheless, more data and research is needed to understand causes and decrease the rate of disparate outcomes in patients with TNBC. Citation Format: So Hyeon Park, Roy Khalife, Evan White, Anthony Magliocco. Distinct molecular differences between African American/Black and White women with Triple Negative Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-03-05.

A molecular guide to systemic therapy in salivary gland carcinoma.

Salivary gland carcinomas (SGC) are a rare and variable group of head and neck cancers with historically poor response to cytotoxic chemotherapy and immunotherapy in the recurrent, advanced, and metastatic settings. In the last decade, a number of targetable molecular alterations have been identified in SGCs including HER2 upregulation, androgen receptor overexpression, Notch receptor activation, NTRK gene fusions, and RET alterations which have dramatically improved treatment outcomes in this disease. Here, we review the landscape of precision therapy in SGC including current options for systemic management, ongoing clinical trials, and promising future directions.

Clinical management of molecular alterations identified by high throughput sequencing in patients with advanced solid tumors in treatment failure: Real-world data from a French hospital.

In the context of personalized medicine, screening patients to identify targetable molecular alterations is essential for therapeutic decisions such as inclusion in clinical trials, early access to therapies, or compassionate treatment. The objective of this study was to determine the real-world impact of routine incorporation of FoundationOne analysis in cancers with a poor prognosis and limited treatment options, or in those progressing after at least one course of standard therapy. A FoundationOneCDx panel for solid tumor or liquid biopsy samples was offered to 204 eligible patients. Samples from 150 patients were processed for genomic testing, with a data acquisition success rate of 93%. The analysis identified 2419 gene alterations, with a median of 11 alterations per tumor (range, 0-86). The most common or likely pathogenic variants were on TP53, TERT, PI3KCA, CDKN2A/B, KRAS, CCDN1, FGF19, FGF3, and SMAD4. The median tumor mutation burden was three mutations/Mb (range, 0-117) in 143 patients with available data. Of 150 patients with known or likely pathogenic actionable alterations, 13 (8.6%) received matched targeted therapy. Sixty-nine patients underwent Molecular Tumor Board, which resulted in recommendations in 60 cases. Treatment with genotype-directed therapy had no impact on overall survival (13 months vs. 14 months; p = 0.95; hazard ratio = 1.04 (95% confidence interval, 0.48-2.26)]. This study highlights that an organized center with a Multidisciplinary Molecular Tumor Board and an NGS screening system can obtain satisfactory results comparable with those of large centers for including patients in clinical trials.

New established cell lines from undifferentiated pleomorphic sarcoma for in vivo study

As a high-grade soft-tissue sarcoma(STS), undifferentiated pleomorphic sarcoma(UPS) is highly recurrent and malignant. UPS is categorized as a tumor of uncertain differentiation and has few options for treatment due to its lack of targetable genetic alterations. There are also few cell lines that provide a representative model for UPS, leading to a dearth of experimental research. Here, we established and characterized new cell lines derived from two recurrent UPS tissues. Cells were obtained from UPS tissues by mincing, followed by extraction or dissociation using enzymes and culture in a standard culture environment. Cells were maintained for several months without artificial treatment, and some cell clones were found to be tumorigenic in an immunodeficient mouse model. Interestingly, some cells formed tumors in vivo when injected after aggregation in a non-adherent culture system for 24 h. The tissues from in vivo study and tissues from patients shared common histological characteristics. Pathways related to the cell cycle, such as DNA replication, were enriched in both cell clones. Pathways related to cell-cell adhesion and cell-cell signaling were also enriched, suggesting a role of the mesenchymal-to-epithelial transition for tumorigenicity in vivo. These new UPS cell lines may facilitate research to identify therapeutic strategies for UPS.

Circulating tumor DNA–based genomic landscape of KRAS wild-type pancreatic adenocarcinoma.

747 Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer deaths. KRAS is a primary oncogenic driver in the majority of PDAC patients. KRAS wild-type (wt) PDAC (~10%) is a molecularly heterogeneous subgroup that may harbor alternate drivers and targetable alterations. In this study, we sought to characterize the circulating tumor DNA (ctDNA) landscape of alterations in PDAC patients harboring KRAS mutations ( KRAS mut) compared to KRAS wt. Methods: We analyzed ctDNA samples from 2000 patients ( N= 1000 each for KRAS mut and KRAS wt) collected prospectively between 2019-2022 using a 74-83 gene next generation sequencing panel (Guardant360). KRAS mutation not detected was used as a proxy for KRAS wt. To limit bias from low tumor shed, samples were excluded if they did not have maximum variant allele fraction (VAF) &gt; 0.34% and if the only maximum VAF &gt; 0.34% was within putative germline range (40-60%). Statistical analyses were performed using Fisher’s exact test or t-test. Results: No significant gender differences were noted between KRAS wt and KRAS mut patients. Median age was 72yo in KRAS wt and 69yo in KRAS mut patients. Overall, KRAS wt patients had higher frequency of alterations in ATM, BRAF, ERBB2, FGFR2, JAK3, MET and NOTCH1 compared to KRAS mut (all p &lt; 0.05). Meanwhile, KRAS wt patients had lower frequency of alterations in CDKN2A, SMAD4, CDK6, ARID1A, and TP53 compared to KRAS mut (all p &lt; 0.05). The most frequently mutated gene in KRAS wt PDAC was TP53 (46%), followed by ATM (26%) and EGFR (11%). The most common currently targetable alterations identified in KRAS wt patients were ATM (26%), BRCA1/2 (12%), EGFR (11%; 70% mutations, 30% amplifications), FGFR1/2 (9%), BRAF (8%; 91% mutations, 9% amplifications), PIK3CA (7%), MET (7%; 80% mutations, 20% amplifications) and ERBB2 (5.8%; 79% mutations, 21% amplifications) among others. Median tumor mutational burden for KRAS wt patients was higher than KRAS mut (10.0 vs. 7.77 mut/Mb, p = 0.035). There were no significant differences in rates of MSI-H between KRAS wt and KRAS mut patients (1.9% vs. 1.3%, p = 0.37). KRAS wt patients harbored higher number of oncogenic gene fusions compared to KRAS mut (1.6% vs 0.2%, p = 0.0013). The most common fusion partners among KRAS wt patients included FGFR2 (0.4%), BRAF (0.4%), ALK (0.2%), NTRK (0.2%), RET (0.2%), FGFR3 (0.1%) and EGFR (0.1%). Potential germline variants (pathogenic/likely pathogenic) were detected in both KRAS wt and mut patients, most commonly in the DNA-damage repair genes, including ATM (3.5%), BRCA2 (1.8%) and BRCA1 (0.6%). Conclusions: Targetable alterations and oncogenic rearrangements are enriched in KRAS wt PDAC compared to KRAS mut. These analyses provide additional therapeutic options and may improve outcomes for KRAS wt patients, warranting blood-based ctDNA genomic profiling in PDAC, especially when a tissue biopsy is not feasible or sufficient for comprehensive genomic profiling.

Pembrolizumab plus pemetrexed-carboplatin combination in first-line treatment of advanced non-squamous non-small cell lung cancer: a multicenter real-life study (CAP29).

Pembrolizumab combined with chemotherapy is now first-line standard of care in advanced non-small cell lung cancer. This real-life study aimed to assess efficacy and safety of carboplatin-pemetrexed plus pembrolizumab in advanced non-squamous non-small cell lung cancer. CAP29 is a retrospective, observational, multicenter real-life study conducted in 6 French centers. We evaluated efficacy of first-line setting chemotherapy plus pembrolizumab (November 2019 to September 2020) in advanced (stage III-IV) non-squamous non-small cell lung cancer patients without targetable alterations. Primary endpoint was progression-free survival. Secondary endpoints were overall survival, objective response rate and safety. With a median follow-up of 4.5 months (0 to 22 months), a total of 121 patients were included. Baseline characteristics were: median age of 59.8 years with 7.4% ≥75 years, 58.7% of males, 91.8% PS 0-1, 87.6% of stage IV with ≥3 metastatic sites in 62% of cases. Patients had brain and liver metastases in 24% and 15.7% of cases, respectively. PD-L1 was <1% (44.6%), 1-49% (28.1%) and ≥50% (21.5%). Median progression-free survival and overall survival achieved 9 and 20.6 months, respectively. Objective response rate was 63.7% with 7 prolonged complete responses. Survival benefit seemed to be correlated with PD-L1 expression. Brain and liver metastases were not statistically associated with decreased overall survival. Most common adverse events were asthenia (76%), anemia (61.2%), nausea (53.7%), decreased appetite (37.2%) and liver cytolysis (34.7%). Renal and hepatic disorders were the main causes of pemetrexed discontinuation. Grade 3-4 adverse events concerned 17.5% of patients. Two treatment-related deaths were reported. First-line pembrolizumab plus chemotherapy confirmed real-life efficacy for patients with advanced non-squamous non-small cell lung cancer. With median progression-free survival and overall survival of 9.0 and 20.6 months, respectively and no new safety signal, our real-life data are very close to results provided by clinical trials, confirming the benefit and the manageable toxicity profile of this combination.

Genomic profiling to provide new treatment opportunities in ampullary carcinoma.

582 Background: Ampullary carcinoma (AC) is a rare heterogeneous group of diseases with an abysmal prognosis. Treatment options are limited, and the molecular landscape of this disease and its therapeutic implications have been incompletely explored. Here, we aim to provide a clinical and genomic characterization of AC and explore opportunities for precision oncology. Methods: Patients diagnosed with AC and treated at a single tertiary institution between 2010 and 2022 were reviewed. Molecular profiles were analyzed by applying an in-house exome-targeted panel or the FoundationOne CDx panel. Gene mutations were categorized into molecular pathways and potentially targetable alterations were classified according to the ESCAT scale. Overall survival (OS) and disease-free survival (DFS) were estimated by using the Kaplan-Meier method. Results: We included 64 patients with a median age of 66 years, 51.6% were women, most were classified as pancreatobiliary tumours (PB, 58.3%), followed by intestinal (INT, 33.3%) and mixed histologies (8.3%). 18.8%, 23.4%, 32.8% and 25.0% of the patients were diagnosed at stage I, II, III and IV, respectively. 81.2% of the patients were treated with surgery. The INT subtype was enriched in WNT pathway alterations (28.6 vs 6.2%, p=0.02) and showed a non-significant enrichment in the apoptotic pathway (57.1 vs 34.4%, p=0.08). Conversely, BP showed a non-significant enrichment in HRR pathway alterations (16.7 vs 54.5%, p=0.3). The frequency of KRAS mutations were similar in both subtypes (38.1 vs 37.5%). Potentially actionable molecular alterations were found in 46.7% of the patients (9 ERBB2, 8 HRD, 8 PI3KCA, 2 MSI, 2 BRAF, 2 PTEN and 1 KRAS G12C). Importantly, KRASwt tumours were enriched in potentially targetable alterations (ESCAT I-IIIA), including 20% ERBB2 amplification/mutations, 6% MSI and 3% BRCA1. 6 patients received matched targeted therapies during their disease course, 66% of which responded and 100% stable disease, with a median TTD of 7 months. Conclusions: More than 45% of AC harbor potentially targetable genomic alterations that may provide novel therapeutic opportunities and enhance personalized medicine in this rare disease entity.

Genomic landscape of acquired resistance to targeted therapies in metastatic colorectal cancer (mCRC).

190 Background: Therapies targeting oncogenic driver mutations have radically altered the treatment paradigm for mCRC and improved outcomes. New selective inhibitors aim to expand the portion of mCRC with targetable alterations. However, these drugs are limited by a relatively short duration of response before the emergence of acquired resistance. We hypothesized that both the putative resistance mechanism (mutations (MUT) versus copy number alterations (CNA)) and the clonality of the emergent mutations may influence time to resistance. Methods: We screened the MSKCC IMPACT dataset of 5,403 MSS (microsatellite stable) CRC patient samples (3,704 primary sequenced, 1669 metastatic site sequenced) for patients (pts) who had been treated with targeted therapies against EGFR, BRAF, KRAS G12C, or HER2 with tissue or liquid biopsy samples profiled at progression. Clinicopathological features and acquired genomic changes emerging at resistance were assessed. Results: 42 pts were identified with targeted oncogenic drivers consisting of BRAF V600E (17 pts), EGFR (12 pts), KRAS G12C (11 pts), and HER2 (2 pts). Progression specimens analyzed consisted of tissue biopsies in 17 pts (40%) and circulating free DNA (cfDNA) in 21 pts (50%), 4 pts had both tissue and cfDNA analyzed at progression. Median time on targeted therapy (TOT) was 7.1 months (95% CI: 5.6-8.5). Putative resistance alterations were identified in 33 pts (79%) (18 cfDNA, 11 tissue, 4 both cfDNA and tissue) and consisted of MUT alone in 30%, MUT+CNA or rearrangement 70%. Concurrent PIK3CA mutations in pre-treatment tissues were identified in 17 pts (40%) and did not associate with TOT (p=0.68); acquired PI3K pathway alterations were identified in 5 pts (12%), including 2 pts who had baseline tumor PIK3CA mutation. Number of putative resistance alterations ranged from 0-13, with multiple resistance alterations identified in 18 pts (15 ctDNA, 3 tissue), and these could be categorized into three groups: one alteration (15/33; 45%), 2-4 alterations (8/33; 24%), and ≥5 alterations (10/33; 30%). Evaluating TOT by type of alteration: MUT only: 9.8 months, MUT+ CNA+/- rearrangement: 6.6 months (p=0.0079). Evaluating TOT by number of alterations: &gt;4 alterations: 6.1 months versus 1-4 alterations: 8.9 months (p=0.012), or 1 alteration: 8.0 months versus &gt;1 alteration: 6.7months (p= 0.5). There was no significant difference in TOT when evaluating by clonality of mutations, where subclonal was defined as &lt;5% of highest variant allelic fraction (clonal vs subclonal, 9.7 vs 6.7 months, p= 0.09). Fusions identified at time of resistance (involving BRAF in 2 pts, MET in 1 pt, RET in 1 pt) occurred with ≥5 alterations in 3 of 4 pts. Conclusions: Presence of CNA and ≥5 new alterations at resistance were associated with shorter TOT, and there was a trend for subclonal alterations and shorter TOT. New approaches that target underlying mechanisms for these changes may extend TOT.