Oncogenic Alterations Research Articles

MEK inhibitor-based therapy in metastatic pancreatic adenocarcinoma with KRAS G12R alteration.

725 Background: Pancreatic ductal adenocarcinoma (PDAC) is largely driven by oncogenic alterations in the KRAS , TP53 , CDKN2A/B , and SMAD4 genes. KRAS G12R accounts for nearly 20% of KRAS alterations in PDAC, is biologically unique, and offers the potential for improved response to MEK inhibitor (MEK-inh)-based therapy. As part of the MCW-Master-PREDICT (NCT05802069) observational study, we evaluated the efficacy of MEK-inh-based therapy matched to the unique molecular alterations in the tumor of each patient as recommended by the molecular tumor board. Methods: From March 2022 to December 2023, 8 patients with metastatic PDAC were treated with MEK-inh-based therapy. Molecular profiling was performed by Tempus (648 genes) in 7 patients, and FoundationOne (324 genes) in 1 patient. Description of molecular alterations, matched therapies, and efficacy of treatment are provided. Results: The median age of patients starting MEK inhibitor-based therapy was 69 years, with 62% of them being female. The molecular characteristics and matched therapies are summarized (Table). MEK-inh-based therapy was administered to 3 (37.5%) patients as a first or second-line treatment, and to 5 (62.5%) patients as a third to fifth-line treatment for metastatic PDAC. The overall survival and progression free survival (PFS) on MEK-inh-based therapy was 8.4 and 4.9 months, respectively. Four patients had PFS beyond 4 months (4.9, 5.5, 5.6 and 6.9 months). Conclusions: Individualized MEK-inh-based therapy demonstrated efficacy in late-line treatment of metastatic PDAC with KRAS G12R alterations. Using this approach earlier in the treatment course and in combination with RAS inhibitors or cytotoxic systemic therapies may further enhance outcomes. Tumor alterations and matched therapies. Gene altered Number of patients (%) Number of patients matched (%) Drug family matched KRAS G12R 8 (100) 8/8 (100) MEK inhibitor TP53 7 (87.5) 4/7 (57) VEGF/VEGR inhibitor* CDKN2A 4 (50) 4/4 (100) CDK4/6 inhibitor** SMAD4 2 (25) 2/2 (100) MEK inhibitor + (EGFR or Pan-HER inhibitor)*** *PMID: 27466356; **PMID: 33472910; ***PMID: 36127339, PMID: 24625091.

MEK inhibitor-based therapy in metastatic pancreatic adenocarcinoma with KRAS G12D or KRAS G12V alteration.

726 Background: Up to 95% of pancreatic ductal adenocarcinomas (PDAC) are driven by oncogenic alterations in the KRAS gene, with KRAS G12D (40%) and KRAS G12V (30%) mutations being the most common. However, in most cases, KRAS alterations are accompanied by alterations in other tumor suppressors such as TP53 , CDKN2A/B , and SMAD4 . Therefore, targeting KRAS alone may not be sufficient for effective treatment of PDAC . As part of the MCW-Master-PREDICT (NCT05802069) observational study, we evaluated the effectiveness of MEK inhibitor (MEK-inh)-based therapy, tailored to the unique molecular alterations of each patient’s tumor, in treating metastatic PDAC (mPDAC) with KRAS G12D or KRAS G12V alterations. Methods: From April 2022 to December 2023, 19 patients ( KRAS G12D=10 (53%), KRAS G12V=9 (47%)) were treated with MEK-inh-based therapy. Comprehensive genomic profiling was performed using Tempus xT (648 genes) in 15 patients (79%), FoundationOne (324 genes) in 4 patients (21%), and STRATA (429 genes) in 1 patient. The genomic characteristics, matched therapies, and treatment outcomes are provided (Table). Results: Of the 19 patients, 11 (58%) were female. The median age at the initiation of MEK-inh-based therapy was 67 years. Six (32%) patients received MEK-inh-based therapy as first or second-line treatment, while 13 (68%) patients were treated in the third to fifth-line. Among the 19 patients, the median overall survival (mOS) and median progression-free survival (mPFS) from the initiation of MEK-inh-based therapy were 5 and 2 months, respectively. The mOS from the time of MEK-inh-based therapy was 5.1 months for KRAS G12D, and 4.7 months for KRAS G12V (P=0.87). The mPFS from the time of MEK-inh-based therapy was 2.3 months for KRAS G12D and 1.4 months for KRAS G12V (P=0.12). Among all 19 patients, 4 (21%) patients had mPFS above 4 months ( KRAS G12V=1, KRAS G12D=3; 4.1, 4.3, 4.7, 9.9 months). Conclusions: The efficacy of MEK-inh-based therapy was limited in the late-line treatment of mPDAC for patients with KRAS G12D and KRAS G12V mutations. The potential role of MEK inhibitors in earlier lines of therapy, and their combination with KRAS inhibitors, requires further prospective evaluation. Tumor alterations and matched therapies. Altered gene KRAS G12V(N=9) KRAS G12D(N=10) Patients matched(N=19) Type of matched therapy KRAS G12D/V 9 (100%) 10 (100%) 19 (100%) MEK inhibitor TP53 7 (78%) 8 (80%) 8 (42%) VEGF/VEGR inhibitor* CDKN2A/B 8 (89%) 5 (50%) 9 (47%) CDK4/6 inhibitor** SMAD4 3 (33%) 4 (40%) 4 (21%) MEK inhibitor + (EGFR or pan-HER inhibitor) *** *PMID: 27466356; **PMID: 33472910; ***PMID: 36127339, PMID: 24625091. N= number of patients.

Molecular and clinical determinants of targeted therapy (TT) outcomes in biliary tract cancer (BTC): Analysis of a prospectively maintained next generation sequencing (NGS) biorepository.

555 Background: BTCs are genomically diverse. TT have established antitumor activity in a subset of pts that harbour actionable alterations; however, most patients (pts) do not respond to or experience acquired resistance on TT. We sought to explore genomic mechanisms of response across the spectrum of BTCs. Methods: We leveraged a prospectively maintained cohort of pts with histologically confirmed BTC who underwent molecular profiling using an FDA authorized, targeted, NGS assay. Additional clinicopathologic information was retrospectively extracted with an aim to describe the genomic profile and clinical actionability using OncoKB, to explore outcomes for pts treated with TT, and to nominate innate and acquired genomic mechanisms of resistance. Results: N = 1254 pts had molecular profiling: 61.2% intrahepatic (iCCA), 16.8% extrahepatic cholangiocarcinoma (eCCA), 22.1% gallbladder cancer (GBC). MSI high was observed in 2.1% and the median TMB was 3.3 (range: 0-74.6 muts/mb). Among MSS tumors, the most frequently altered genes were TP53 (36%), CDKN2A (21%), ARID1A (18%), KRAS (17%), and IDH1/2 (16%). Genomic profiles differed significantly based on anatomic subsite. Oncogenic drivers were mostly clonal except for ERBB2 amplifications and mutations, which were subclonal in 19%, and 28% of cases respectively. OncoKB level 1/2 events observed in 32.2% (iCCA 40%, eCCA 15%, and GBC 22%). Progression-free survival (PFS) for pts with these oncogenic drivers: IDH , FGFR2 , ERBB2, BRAF V600E , MSI high , and TMB high from start of matched TT (N=164) is listed in the table. Clinical factors or co-occurring genomic alterations did not impact outcomes. Profiling of paired pre- and post-progression samples (N=25) nominated pathway reactivation in FGFR2 , BRAF , NTRK, and ERBB2 driven tumors with emergence of recurrent oncogenic FGFR2 , RAS , MEK , and MET alterations, respectively, as well as off target MYC amplification and CDKN2A loss. Loss of the oncogenic driver at progression was only observed for ERBB2 driven tumors. Conclusions: Acknowledging the limitations of the study design, matched TT in a real-world, prospectively maintained cohort offers meaningful PFS, most notably in those pts with MSI high BTC treated with immunotherapy. In those with acquired resistance to TT, alterations predicted to reactivate the primary oncogenic pathway were identified. ERBB2 heterogeneity and loss is predicted to be a mechanism of resistance to HER2 targeted therapy. Outcomes for BTC treated with matched TT. Target Median PFS, months (95% CI) IDH1/2 (N = 72) 4.2 (2.9-6.8) FGFR2 (N=37) 7.4 (6.5-9.4) ERBB2 (N =22) 8.2 (2.95-16.7) MSI high (N = 14) NR (10.15-NR) TMB high (N=12) 2.69 (1.64-NR) BRAF V600E (N=7) 16.6 (3.7-NR)

Efficacy of PD-1 blockade plus chemotherapy in patients with oncogenic-driven non-small-cell lung cancer

BackgroundPD-1 blockade plus chemotherapy has become the first-line standard of care for patients with advanced non-small-cell lung cancer (NSCLC) without oncogenic drivers. Oncogenic-driven advanced NSCLC showed limited response to PD-1 blockade monotherapy or chemotherapy alone. Whether NSCLC patients with oncogenic drivers could benefit from PD-1 blockade plus chemotherapy remains undetermined.MethodsThree hundred twelve NSCLC patients with at least one oncogenic driver alteration received PD-1 plus chemotherapy or each monotherapy were retrospectively identified. Objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) were compared to evaluate the therapeutic outcomes differences among patients with different oncogenic drivers.ResultsOne hundred sixty-two patients received PD-1 blockade plus chemotherapy, 57 received PD-1 blockade monotherapy and 93 received chemotherapy alone were included. Oncogenic driver mutations including KRAS (31.4%), EGFR (28.8%), HER2 (14.7%), BRAF (10.6%), RET (7.4%), and other mutations (7.1%) were identified. Patients with oncogenic drivers who received PD-1 blockade plus chemotherapy had significantly better outcomes compared to those received PD-1 blockade or chemotherapy alone (ORR: 51% vs. 18% vs. 25%, P < 0.001; median PFS: 10.0 [95% CI: 8.9–12.6] vs. 3.7 [95% CI: 2.9–5.1] vs. 5.3 [95% CI: 4.5–6.2] months, P < 0.001; median OS: 26.0 [95% CI: 23.0–30.0] vs. 14.3 [95% CI: 9.6–19.8] vs. 16.1 [95% CI: 11.6–21.9] months, P < 0.001). The superior efficacy was consistently found in separate analyses for patients received first-line and second/third line treatments. Among individual gene alterations, patients with KRAS, EGFR, or BRAF mutations treated with PD-1 blockade plus chemotherapy achieved markedly improved PFS and OS than those received PD-1 blockade or chemotherapy alone. Multivariate Cox regression analysis revealed that PD-1 blockade plus chemotherapy was independently associated with better PFS and OS.ConclusionPD-1 blockade plus chemotherapy demonstrated superior efficacy than PD-1 blockade monotherapy or chemotherapy alone in patients with oncogenic-driven advanced NSCLC, particularly in KRAS, EGFR and BRAF subgroups. These findings suggest that PD-1 blockade plus chemotherapy may be considered as an optional treatment option for patients without available targeted therapies.

Buparlisib and Paclitaxel in Patients with Head and Neck Squamous Cell Carcinoma: Immunogenomic Biomarkers of Efficacy from the BERIL-1 Study.

BERIL-1 was a randomized phase 2 study that studied paclitaxel with either buparlisib, a pan-class I PIK3 inhibitor, or placebo in patients with recurrent or metastatic (R/M) head and neck squamous cell cancer (HNSCC). Considering the therapeutic paradigm shift with immune checkpoint inhibitors (ICIs) now approved in the first-line setting, we present an updated immunogenomic analysis of patients enrolled in BERIL-1, including patients with immune-infiltrated tumors. The objective of this study was to identify biomarkers predictive of treatment efficacy in the context of the post-ICI therapeutic landscape. Genomic analyses were performed at baseline on tumor and/or plasma circulating DNA (ctDNA) samples, and immunohistochemistry (IHC) studies, including immune infiltration [tumor-infiltrating lymphocytes (TILs) and CD8 expression], were performed on tumor samples. Immunogenomic biomarkers were correlated to overall survival (OS). Among 158 patients enrolled in BERIL-1, either tumor (53.2%; n = 84) or ctDNA samples (70.8%; n = 112) were available in 85.4% (n = 135). The most commonly mutated genes were TP53 (57.0%), NOTCH1 (23.7%), and PIK3CA (22.2%). In the IHC studies, 98.6% (n = 68/69) of patients were TILs positive in the buparlisib arm versus 94.4% (n = 68/72) in the placebo arm. In patients with TILs-positive tumors, enrichment for clinical benefit on the buparlisib arm was seen in those with PIK3 pathway activation [25.0% (n = 17/68)] with a hazard ratio (HR) for death of 0.43 [95% confidence interval (CI) 0.21-0.87, p = 0.016]. Similarly, improved OS was seen in patients on the buparlisib arm and NOTCH pathway activation [20.5% (n = 14/68)] with a HR for death of 0.40 (95% CI 0.18-0.90, p = 0.022). Both associations were absent in the placebo group. TP53 and tumor mutational burden (TMB) did not correlate with OS in the buparlisib or placebo arms. In this immunogenomic analysis of BERIL-1, improved HRs for OS were seen in patients with tumor immune infiltration and selected oncogenic alterations, including PIK3 and NOTCH pathway activation (NCT01852292).

The continually evolving landscape of novel therapies in oncogene-driven advanced non-small-cell lung cancer.

Non-small-cell lung cancer (NSCLC) is a highly heterogeneous disease that is frequently associated with a host of known oncogenic alterations. Advances in molecular diagnostics and drug development have facilitated the targeting of novel alterations such that the majority of NSCLC patients have driver mutations that are now clinically actionable. The goal of this review is to gain insights into clinical research and development principles by summary, analysis, and discussion of data on agents targeting known alterations in oncogene-driven, advanced NSCLC beyond those in the epidermal growth factor receptor (EGFR) and the anaplastic lymphoma kinase (ALK). A search of published and presented literature was conducted to identify prospective trials and integrated analyses reporting outcomes for agents targeting driver gene alterations (except those in EGFR and ALK) in molecularly selected, advanced NSCLC. Clinical efficacy data were extracted from eligible reports and summarized in text and tables. Findings show that research into alteration-directed therapies in oncogene-driven, advanced NSCLC is an extremely active research field. Ongoing research focuses on the expansion of new agents targeting both previously identified targets (particularly hepatocyte growth factor receptor (MET), human epidermal growth factor receptor 2 (HER2), and Kirsten rat sarcoma viral oncogene homolog (KRAS)) as well as novel, potentially actionable targets (such as neuregulin-1 (NRG1) and phosphatidylinositol 3-kinase (PI3K)). The refinement of biomarker selection criteria and the development of more selective and potent agents are allowing for increasingly specific and effective therapies and the expansion of clinically actionable alterations. Clinical advances in this field have resulted in a large number of regulatory approvals over the last 3 years. Future developments should focus on the continued application of alteration therapy matching principles and the exploration of novel ways to target oncogene-driven NSCLC.

Genomic characterization and histologic analysis of uterine leiomyosarcoma arising from leiomyoma with bizarre nuclei.

Leiomyoma with bizarre nuclei (LM-BN) is a rare variant of leiomyoma with a benign clinical course. In contrast, leiomyosarcoma (LMS) is a high-grade, malignant neoplasm characterized by high recurrence rates and poor survival. While LM-BN and LMS show distinct morphologies, they share similar immunoprofiles and molecular alterations, with both considered 'genomically unstable'. Rare cases of LM-BN associated with LMS have been reported; however, the histogenesis and molecular relationship between these two tumors remains unclear. In this study, we assessed 11 cases of LMS arising in conjunction with LM-BN confirmed by histology and immunohistochemistry (IHC), further analyzed by clinical, histologic, and molecular characteristics of these distinct components. LM-BN and LMS had similar p16 and p53 IHC patterns, but LMS had a higher Ki-67 index and lower estrogen and progesterone eceptor expression. Digital image analysis based on cytologic features revealed spatial relationships between LMS and LM-BN. Genomic copy number alterations (CNAs) demonstrated the same clonal origin of LMS arising from existing LM-BN through conserved CNAs. LMS harbored highly complex CNAs and more frequent losses of the TP53, RB1, and PTEN genomic regions than LM-BN (p = 0.0031), with CDKN2A/B deletion identified in LMS only. Mutational profiling revealed many shared oncogenic alterations in both LM-BN and LMS; however, additional mutations were present within LMS, indicative of tumor progression through progressive genomic instability. Analysis of spatial transcriptomes defined uniquely expressed gene signatures that matched the geographic distribution of LM-BN, LMS, and other cell types. Our findings indicate for the first time that a subset of LMS arises from an existing LM-BN, and highly complex genomic alterations could be potential high risks associated with disease progression in LM-BN. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

The genomic landscape of cutaneous squamous cell carcinoma in Japan.

Comprehensive studies of the genetic profiles of cutaneous squamous cell carcinoma (cSCC) in Japanese patients have been lacking, although an understanding of these profiles is crucial for improving treatment outcomes. Since 2019, comprehensive genomic profiling (CGP) has been covered by Japan's health insurance, and the resulting data have been compiled into a comprehensive database by the country's Center for Cancer Genomics and Advanced Therapeutics (C-CAT). In this retrospective study, we used CGP data from the C-CAT database to analyze genomic characteristics of cSCC in Japanese patients. The patients' clinical and genomic data, including the chemotherapy regimens, tumor mutational burden (TMB), and survival status, were obtained. We analyzed the cases of 152 patients, with only those evaluated by the FoundationOne® CDx included for accuracy. Among the 152 patients, the most common gene oncogenic alterations were observed in TP53 (67%), CDKN2A (54%), TERT (49%), CDKN2B (33%), and NOTCH1 (18%). TMB-high (≥10 mut/Mb) was observed in 27% (n = 41) of the patients, with a median age of 75 years for this group. TMB-low (<10 mut/Mb) was observed in 73% (n = 111) of the patients; their median age was 67 years.

Comment on 'Oncogenic alterations in KIR3DL1 in cutaneous acral CD8+ lymphoproliferative disorder' by Wobser et al.

Comment on 'Oncogenic alterations in KIR3DL1 in cutaneous acral CD8+ lymphoproliferative disorder' by Wobser et al.

Serous-like breast carcinomas: immunophenotypic, genetic, and clinicopathologic characterization of a morphologically distinct group of tumours.

Unusual morphologic patterns of breast carcinomas can raise diagnostic consideration for metastasis or special breast cancer subtypes with management implications. We describe rare invasive breast cancers that mimic serous carcinoma of the gynaecologic tract (serous-like breast carcinomas, SLBC) and characterize their clinicopathologic, immunophenotypic, and genetic features. All patients were female (n = 15, median age 49 years) without a history of gynaecologic malignancy. SLBC were characterized histologically by angulated, branched, sometimes anastomosing glands with micropapillary and/or pseudopapillary luminal projections in desmoplastic stroma. Most SLBC were triple-negative (TN, n = 10) or HER2-positive (n = 2) and grade 2 or 3, while some were oestrogen receptor (ER) low-positive/HER2-negative and low-grade (n = 3). CK5/6 was positive irrespective of grade or receptor status (10/10). All SLBC expressed GATA3 (14/15), TRPS1 (7/7), and/or mammaglobin (4/13). SOX10 was positive in most TN (9/10) and all ER low-positive (3/3) cases, but negative in HER2-positive tumours. WT1 was universally negative, and PAX8 was focal in one mammaglobin-positive tumour. All ER-negative SLBC were p53-aberrant and 9/11 were p16-aberrant, whereas ER-positive tumours were wildtype for both markers (3/3). TP53 was the only frequently mutated gene, altered in all ER-negative (10/10) but no ER-positive (0/4) tumours. Clinical behaviour was variable. Only 1/6 patients achieved pathologic complete response to neoadjuvant chemotherapy. SLBC is a rare morphologic pattern of invasive breast carcinoma that mimics metastatic serous gynaecologic carcinoma, a potential diagnostic pitfall. SLBC are heterogeneous with respect to grade, receptor profile, and oncogenic driver alterations, without specific genetic underpinnings identified. Additional studies are warranted to further evaluate the clinical behaviour of these tumours.

Molecular landscape and classification of vascular anomalies.

Vascular malformations, which result from anomalies in angiogenesis, include capillary, lymphatic, venous, arteriovenous, and mixed malformations and affect specific vessel types. Historically, treatments such as sclerotherapy and surgery have shown limited efficacy in complicated cases. Most vascular malformations occur sporadically, but some can be inherited. They result from mutations similar to oncogenic alterations, activating pathways such as PI3K-AKT-mTOR or Ras-MAPK-ERK. Recognizing these parallels, we highlight the potential of targeted molecular inhibitors, repurposing anticancer drugs for the treatment of vascular malformations. This case-based review explores recent developments in precision medicine for slow-flow and fast-flow vascular malformation.

Targeted RNA sequencing in diagnostically challenging head and neck carcinomas identifies novel MON2::STAT6, NFATC2::NUTM2B, POC5::RAF1, and NSD3::NCOA2 gene fusions.

Although molecular tests developed for a growing list of oncogenic alterations have significantly aided in the classification of head and neck carcinomas, tumours in which prototypical histologic and immunophenotypic features are lacking or only partially developed continue to pose diagnostic challenges. Searching for known diagnostic and therapeutic targets by clinical next-generation sequencing (NGS) assays can often lead to new discoveries. We present our institutional experience in applying targeted RNA NGS in 36 head and neck carcinomas that were morphologically difficult to classify between 2016 and 2023. The patients ranged in age from 5 to 83 years (median, 64), with the majority of tumors occurring in the major salivary glands and the sinonasal tract. Overall, seven (19%) cases showed unusual gene rearrangements, including five novel alterations: MON2::STAT6 in a hard palate adenocarcinoma with mucinous features, POC5::RAF1 in apocrine intraductal carcinoma of the lacrimal gland, EWSR1::CDADC1 fusion in a basaloid carcinoma of the submandibular gland, NFATC2::NUTM2B in myoepithelial carcinoma, and NSD3::NCOA2 fusion in a peculiar high-grade carcinoma with a peritheliomatous growth pattern, and focal myogenic differentiation. Potential therapeutic actionability was identified in three cases (RAF1 and FGFR2 fusions). These findings broaden the current spectrum of gene rearrangements in head and neck carcinomas and support the utility of clinical NGS in identifying unusual, actionable alterations in diagnostically challenging cases.

First Insight into the Mutational Landscape of BRAF and KRAS Genes in Lung Cancer Patients from Morocco

Background: Lung cancer (LC) is a lethal malignancy with a late diagnosis and poor prognosis. During the last decade, the identification of oncogenic driver alterations has noticeably changed the therapeutic landscape and contributed to the emergence of the “oncogene addiction” concept and precision medicine in oncology. Among these alterations, the spotlight has turned to driver mutations in the KRAS and BRAF genes, which have garnered significant attention due to the emergence of targeted therapies and the potential for personalized treatment strategies. Objective: Hence, the present study aimed to evaluate the mutational landscape of the KRAS and BRAF genes in LC Moroccan patients along with their frequencies and their correlation with clinicopathological features. Methods: A total of 60 fresh biopsies were collected from patients with primary LC and were subjected to PCR-DNA sequencing of exon 2 of KRAS and exon 15 of BRAF genes in order to detect the most common mutations known by their implication in response to targeted therapies. Results: Sequencing analysis revealed that mutations in KRAS and BRAF genes represented respectively 8.3% and 6.7% of cases; one patient had two KRAS mutations (G12A and K5E), and none had simultaneous BRAF and KRAS mutations. The vast majority of patients harboring KRAS mutations were men, formal smokers with adenocarcinomas, and at advanced stage (stage III). BRAF mutations were mainly detected in men and nonsmokers with adenocarcinoma. Statistical analyses showed no significant correlation between KRAS and BRAF substitutions and clinico-pathological features (p&gt;0.05). Conclusion: The presence of these mutations will be used as a valuable molecular biomarker to select potential candidates eligible for effective personalized medicine using available agents targeting these mutations. Much effort is needed to identify other druggable mutations to generalize personalized LC therapy for better management of this devastating disease.

Biomarker analyses from the phase III randomized CLEAR trial: lenvatinib plus pembrolizumab versus sunitinib in advanced renal cell carcinoma.

In CLEAR, lenvatinib+ pembrolizumab (L+ P) significantly improved efficacy versus sunitinib in first-line treatment of patients with advanced renal cell carcinoma (aRCC). We report results from CLEAR biomarker analyses. Programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) and next-generation sequencing assays (whole exome sequencing/RNA sequencing) were carried out on archival tumor specimens. For IHC-derived/RNA sequencing analyses, a continuous analysis was carried out adjusting by Karnofsky performance status (KPS) score for: PD-L1 combined positive score (CPS) versus best overall response (BOR)/progression-free survival (PFS); and each gene signature score [T-cell inflamed gene expression profile (TcellinfGEP)/non-TcellinfGEP signatures including proliferation and angiogenesis] versus BOR/PFS. Association between mutation status of RCC driver genes and PFS were analyzed for genes for which ≥20 patients per arm had oncogenic alterations. Association of molecular subtypes with outcome was evaluated with baseline KPS adjustments. The set of biomarkers evaluated and statistical significance criteria for PD-L1 CPS, gene signature scores, and molecular subtypes were prespecified. Within-arm analyses using continuous values showed no association between PD-L1 levels and BOR/PFS for either treatment. PFS hazard ratios between arms were similar regardless of the mutant or wild-type subgroups of RCC driver genes (VHL, PBRM1, SETD2, BAP1, KDM5C). No associations between PFS and gene signature scores were observed for L+ P. With sunitinib, high proliferation and MYC signature scores showed shorter PFS; high angiogenesis and microvessel density signature scores showed longer PFS. Six new molecular subtypes were defined. Tumors of patients with favorable/intermediate risk were enriched in angiogenesis and angiogenesis/stromal clusters; those with poor risk were enriched in proliferative and unclassified (low-TcellinfGEP/low-angiogenesis/low-proliferation) clusters. No association between molecular subtypes and PFS for L+ P/sunitinib was observed (after adjustment for KPS and gene signatures that were individually associated with PFS). Improvements in objective response rate and PFS for L+ P versus sunitinib in aRCC were observed consistently across a range of biomarker subgroups defined using RCC driver mutations, PD-L1, gene expression signatures, and molecular subtypes.

Actionable non-small cell lung cancer mutation identification by comprehensive genomic profiling for clinical trial enrollment: the European Program for the ROutine testing of Patients with Advanced lung cancer (EPROPA).

To reduce the gap about the relevant heterogeneity of molecular testing and cancer care across Europe, Women Against Lung Cancer in Europe (WALCE) promoted the European Program for ROutine testing of Patients with Advanced lung cancer (EPROPA) and provided a free-of-charge molecular profiling platform for non-small cell lung cancer sample characterization with the aim of increasing the detection of targetable drivers and improving patients' access to clinical trials. From January 2021 to December 2023, 20 centres located at 5 different European countries (Greece, Slovenia, Romania, Albania and Italy) joined EPROPA, with 555 advanced NSCLC patients registered into the program. Anonymized patients' clinical-pathological data were shared through the EPROPA web platform and tissue samples were collected to the Molecular Pathology Unit of the Reference Center (University of Turin) for molecular analyses. A comprehensive genomic profiling by targeted next-generation sequencing approach has been performed and molecular reports have been discussed within the molecular tumour board (MTB) in order to assess patients' eligibility for clinical trials. The average turnaround time was 8 days, with only 30 out of 555 (6%) tissue samples not suitable for molecular analysis. Among the 525 analyzed samples, a total of 570 molecular alterations have been identified, including 264 pathogenic targetable oncogenic alterations and 113 cases with co-occurring mutations. A total of 18 molecular alterations with potential germline and hereditary cancer syndrome implications have been reported. The identification of a clinical trial was considered for 205 patients. After MTB discussion, 30 patients were enrolled and treated in clinical studies available in Europe. Survival outcome were significantly improved in patients with targetable molecular alterations receiving a matched targeted therapy. This data confirmed the feasibility and usefulness of the program in the real-world practice scenario, supporting the implementation of NGS-based molecular characterization of NSCLC samples, in order to reduce the unequal access to tests, drugs and clinical trials in Europe.

Alternative lengthening of telomere-based immortalization renders H3G34R-mutant diffuse hemispheric glioma hypersensitive to PARP inhibitor combination regimens

Abstract Background Diffuse hemispheric glioma, H3 G34R/V-mutant (DHG-H3G34) is characterized by poor prognosis and lack of effective treatment options. DHG-H3G34R further harbor deactivation of alpha-thalassemia/mental retardation syndrome X-linked protein (ATRX; DHG-H3G34R_ATRX) suggesting a unique interaction of these 2 oncogenic alterations. In this study, we dissect their cell biological interplay, investigate the impact on telomere stabilization, and consequently validate a targeted therapy approach. Methods We characterized patient-derived primary pediatric high-grade glioma (pHGG) models for telomere-maintenance mechanisms, DNA damage stress (including protein expression, pH2AX/Rad51 foci, cell-cycle arrest) and their sensitivity towards poly-ADP ribose polymerase inhibitor (PARPi) combinations. Human induced pluripotent stem cells (iPSCs) were used for modeling the disease. The anticancer activity of PARPi combinations in vivo was studied in Chorioallantoic Membrane (CAM) and orthotopic in vivo experiments. Finally, we treated a DHG-H3G34R_ATRX patient with PARPi combination therapy. Results We elaborate that alternative lengthening of telomeres (ALT) is a key characteristic of DHG-H3G34R_ATRX. A dominant cooperative effect between H3G34R and ATRX loss in ALT activation also became apparent in iPSCs, which endogenously exert telomerase activity. In both, patient-derived DHG-H3G34R_ATRX models and H3G34R+/ATRX- iPSCs, the ALT-phenotype was associated with increased basal DNA damage stress, mediating synergistic susceptibility towards PARPi (talazoparib, niraparib) combinations with topoisomerase-I inhibitors (topotecan, irinotecan). In a first-of-its-kind case, treatment of a DHG-H3G34R_ATRX patient with the brain-penetrant PARP inhibitor niraparib and topotecan resulted in significant tumor reduction. Conclusions Our preclinical and clinical data strongly support the further development of PARPi together with DNA damage stress-inducing treatment regimens for DHG-H3G34R_ATRX.

BIOM-48. UTILITY OF CIRCULATING TUMOR DNA (CTDNA) FROM CEREBROSPINAL FLUID (CSF) FOR PROGNOSIS OF PATIENTS WITH RECURRENT HIGH-GRADE GLIOMA

Abstract High-grade gliomas (HGGs) are the most aggressive primary brain tumors, and molecular characterization is vital for their diagnosis and treatment. Due to their location, tumor sampling is often challenging. Therefore, developing minimally invasive diagnostic methods is urgently needed. Here we report that circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) can identify key genomic alterations and track clonal evolution in HGGs. Detection of CSF ctDNA correlates with leptomeningeal disease and overall survival, indicating its potential for integration into clinical decision-making. Our study includes 313 samples from 253 patients with recurrent glioma treated at MSKCC who underwent CSF collection using the MSK-IMPACT targeted sequencing assay. 37% of genomic alterations were detected using our less stringent variant calling criteria and Gaussian Mixture Model to call copy number events. CSF ctDNA positivity was determined by the presence of at least one oncogenic disease-defining alteration or any shared alteration with the tumor. We found 212 CSF ctDNA positive (68%) and 101 CSF ctDNA negative (32%) samples. CSF ctDNA positivity was the highest amongst histone mutant tumors (96%). We noticed 44% of alterations shared between the tumor and the CSF, additionally, we noted considerable tumor evolution particularly within the growth signaling pathways (e.g. PDGFRA). Our cohort demonstrated that patients with positive CSF ctDNA had a significantly shorter overall survival compared to those who were CSF ctDNA negative (4.83 months vs 14.14 months, HR 2.4, p &amp;lt; 0.001). Radiographic findings such as enhancing disease and contact of the tumor with the ventricular space were positively associated with CSF ctDNA positivity. Additionally, CSF ctDNA was associated with positive cytology in 12/12 cases (100%). With our improved pipeline, we hypothesize CSF ctDNA may be used as a prognostic biomarker for survival, but confirmation requires further validation in a prospective study.

PATH-30. CLINICAL OUTCOMES AND PREDICTIVE BIOMARKERS FOR IDH-WILDTYPE GLIOBLASTOMAS DEVELOPING HYPERMUTATION FOLLOWING TEMOZOLOMIDE TREATMENT

Abstract Current standard of care for IDH-wildtype glioblastoma (GBM) includes maximal safe resection, adjuvant radiation, and chemotherapy with the alkylating agent temozolomide. A subset of gliomas treated with temozolomide develop somatic hypermutation with a predominance of C&amp;gt;T transitions due to the alkylation effects on DNA. However, the frequency of occurrence, clinical ramifications, and predictive biomarkers for developing temozolomide-induced hypermutation (TMZ-HM) in GBM are unknown. Here we performed comprehensive histopathologic, genomic, and epigenomic evaluation of paired initial and recurrent GBM from 106 patients. Seven patients (7%) developed hypermutation at time of first recurrence, while an additional five patients (5%) developed hypermutation at a subsequent recurrence. Patients who developed TMZ-HM had a significantly longer interval between initial surgery and first recurrence (27.8 vs. 9.9 months, p&amp;lt;0.001). In contrast to IDH-mutant gliomas where TMZ-HM is associated with poor prognosis, those patients with IDH-wildtype GBM who developed TMZ-HM had significantly longer overall survival from both initial surgery (67.9 vs. 20.3 months, p&amp;lt;0.001) and from time of recurrence after development of hypermutation (30.9 vs. 9.5 months, p=0.001). There was no difference in oncogenic alteration frequency in initial GBM that subsequently developed TMZ-HM. However, 4 specific CpG sites out of 12 total interrogated sites in the promoter region of MGMT (a DNA repair enzyme) and 5 specific CpG sites in the promoter region of KCNQ1DN (a negative regulator of c-Myc) were significantly more hypermethylated in those GBM that developed TMZ-HM. We then generated a weighted risk score across these CpG sites that can be used to prospectively identify GBM likely to develop TMZ-HM associated with favorable survival. In summary, patients with GBM that develop TMZ-HM follow a more favorable clinical course, and specific MGMT and KCNQ1DN promoter hypermethylation patterns could serve as a biomarker to identify these patients who may potentially benefit from extended alkylating chemotherapy treatment.

TMOD-13. IDENTIFYING MOLECULAR SIGNATURES OF PPM1D-MUTANT DIPGS

Abstract Diffuse Intrinsic Pontine Glioma (DIPGs) are universally fatal pediatric tumors with a median survival of only 9-12 months. PPM1D-truncating mutations (PPM1Dtr), which promote its phosphatase activity and suppress TP53 function, are found in approximately 15% of DIPG tumors. PPM1Dtr are mutually exclusive to TP53 mutations, and present unique therapeutic opportunities to reactivate wild-type TP53. Another distinct feature of PPM1Dtr DIPGs is the co-occurrence of PI3K/AKT/mTOR pathway alterations, such as PIK3CA. There is an unmet need to elucidate the underlying molecular mechanisms of DIPG and identify novel therapeutic vulnerabilities that will improve outcomes of this devastating tumor. We hypothesize that PPM1D-mutant DIPGs can be therapeutically targeted by reactivating the p53 signaling pathway and other complementary pathways which cooperate with PPM1Dtr. To investigate this, we have generated Trp53- and Ppm1d-mutant isogenic DIPG murine models to determine how specific oncogenic alterations function in DIPG formation, growth and treatment sensitivity. Current studies aim to examine differences in sensitivity to standard of care treatment modalities and leverage next generation sequencing techniques to uncover additional vulnerabilities. We found notable differences upon addition of PIK3CA mutations in the context of PPM1Dtr DIPG tumor formation, growth, survival, and lineage identity. Ongoing studies using whole genome transcriptomics to compare tumor models will provide insight into the molecular signals and cell state changes driven by individual genetic alterations. Furthermore, by comparing isogenic TP53 and PPM1Dtr mutant DIPG models, we aim to further delineate the molecular mechanisms that drive differential sensitivity of TP53 wild-type tumors. The immune-competent nature of our murine models also provides us with a unique opportunity to delineate tumor immune microenvironment changes. Leveraging this information and our novel murine models, our long-term goal is to develop combinatorial therapeutic strategies to improve outcomes for this deadly disease.

PATH-08. MOLECULAR DIVERGENCE RATES DIFFER BETWEEN BRAIN METASTASES AND EXTRACRANIAL DISEASE SITES ACROSS PRIMARY TUMOR HISTOLOGIES

Abstract Genomic alterations and molecular subgroups between extracranial disease sites and brain metastases often differ, yet the prevalence and clinical significance of divergent evolution in brain metastases is not fully understood. This study examined genomic alterations and molecular subgroup divergence rates between matched brain metastases and extracranial disease sites. A retrospective, two-center study was conducted on patients who underwent resection of brain metastases between 2014-2022 with clinical and matched genomic data and/or molecular markers available. The overall cohort comprised 256 patients with matched tumors from multiple cancer types, most commonly from breast (n=108, 42.2%), melanoma (n=83, 32.4%), and NSCLC (n=43, 16.8%). Targeted next-generation sequencing of over 500 oncogenes was performed on resected tumors as part of clinical care (n=41 patients with matched specimens). Molecular subgroups for breast, melanoma, and non-small cell lung cancer were also assessed by immunohistochemistry to evaluate rates of molecular subgroup discordance between sites. Subgroup discordance by immunohistochemistry was observed most frequently across breast cancer (22.2%, n=24/108) with loss of the estrogen receptor (ER) and progesterone receptor (PR) and gain of HER2 most frequently observed within brain metastases. Molecular subgroup discordance was rare within melanoma (7.3%, n=6/82) and NSCLC (14.0%, n=6/43) patients. When evaluating oncogenomic alterations from targeted DNA sequencing in 41 patients with matched specimens, 80.5% (33/41) of brain metastases demonstrated a unique oncogene alteration profile compared to an extracranial disease site. Fourteen patients (34.1%) had a gain of at least 1 targetable alteration within a brain metastasis that was not observed in an extracranial disease site. Brain metastases demonstrated high rates of genomic divergence compared to primary and extracranial metastatic disease sites. This data supports obtaining brain metastasis tissue and conducting molecular profiling of this tissue to help select optimal CNS penetrant systemic therapies for each patient.