Actionable Alterations Research Articles

Genomic Landscape of NSCLC in the Republic of Ireland

IntroductionThe identification of genomic “targets” through next-generation sequencing (NGS) of patient’s NSCLC tumors has resulted in a rapid expansion of targeted treatment options for selected patients. This retrospective study aims to identify the proportion of patients with advanced NSCLC in the Republic of Ireland whose tumors harbor actionable genomic alterations through broad NGS panel testing. MethodsInstitutional review board approval was obtained before study initiation. Patients with NSCLC whose tumors underwent genomic testing through the largest available NGS panel at a nationally funded Cancer Molecular Diagnostics laboratory (St. James’s Hospital) between June 2017 and June 2022 were identified. Patient demographics and tumor-related data were collected by retrospective review from all cancer centers in Ireland, referring to the Cancer Molecular Diagnostics laboratory. A total of 203 (9%) tumor samples were excluded due to insufficient neoplastic cell content. Genomic data were collected through retrospective search of Ion Reporter software. The spectrum and proportion of patients with oncogenic driver mutations were evaluated using descriptive statistics (SPSS version 29.0). ResultsIn total, 2052 patients were identified. Patients were referred from 23 different hospital sites and all four geographic regions (Leinster = 1091, 53%; Munster = 763, 37.2%; Connacht = 191, 9.3%; Ulster = 7, 0.3%). Median age was 69 (range: 26–94) years; 53% were male. The most common tumor histologic subtype was adenocarcinoma (77%, n = 1577). An actionable genomic alteration was identified in 1099 cases (53%), the most common of which was KRAS (n = 657, 32%). Less frequently, NSCLC tumors harbored the following: MET exon 14 skipping (n = 53, 2.6%), MET amplification (n = 26, 1.3%), EGFR (n = 181, 8.8%), HER2 (n = 35, 1.7%), and BRAF (n = 72, 3.5%) mutations. Fusions were detected in 76 patients (3.7%) including ALK (n = 44, 58%), RET (n = 11, 14.5%), ROS1 (n = 16, 21%), and FGFR3 (n = 5, 6.6%), whereas no NTRK fusion was identified. Co-alterations were detected in 114 patients (5.6%), the most common of which was KRAS/PIK3CA (n = 19, 17%), EGFR/PIK3CA (n = 10, 8.5%), and KRAS/IDH1 (n = 9, 8%). Other co-alterations of interest identified included KRAS G12A/ROS1 fusion (n = 1) and KRAS G12C/BRAF G469A (n = 2). ConclusionsThis is the first retrospective study to comprehensively characterize the genomic landscape of NSCLC in Ireland, using the broadest available NGS panel. Actionable alterations were identified in 53.4% of the patients, and KRAS was the most common oncogenic driver alteration. Our study revealed a lower prevalence of patients whose tumor harbors ALK, ROS1, and RET fusions, compared with similar data sets.

Platform trial for off-label oncology drugs using comprehensive genomic profiling under the universal public healthcare system: the BELIEVE trial

BackgroundPrecision medicine has transformed cancer treatment by focusing on personalized approaches based on genomic abnormalities. However, comprehensive genomic profiling (CGP) and access to targeted therapies are limited in Japan. This study investigates the BELIEVE trial, which aims to improve drug accessibility for patients with actionable genetic abnormalities through off-label drug administration.MethodsThe BELIEVE trial is a platform trial with a single master protocol, conducted under the Clinical Trials Act and the patient-proposed health services (PPHS) scheme. Eligible patients with solid tumors exhibiting actionable alterations were enrolled, and CGP tests covered by national health insurance were employed. Treatment selection, study drugs from collaborating pharmaceutical companies, and treatment schedules adhered to predefined protocols. Primary and secondary endpoints were evaluated, and statistical analysis was conducted based on patient response rates.ResultsThe BELIEVE trial offered treatment opportunities for patients with relapse/refractory disease who lacked standard therapies or clinical trial options. This study addresses unmet medical needs and contributes to the establishment of precision medicine systems. Similar trials like NCI-MATCH and TAPUR are being conducted globally. The BELIEVE trial provides a platform for off-label drug administration, collects essential clinical data, and contributes to drug approval applications.ConclusionThe BELIEVE trial provides hope for patients with actionable genetic abnormalities by facilitating access to targeted therapies through off-label drug administration. It establishes a regulatory framework and promotes collaboration between industry and academia by expanding organ-specific and cross-organ biomarker-based treatments.

Role of Tumor Molecular Profiling With FoundationOne®CDx in Advanced Solid Tumors: A Single-Centre Experience From Romania.

Background In the field of precision oncology, comprehensive genomic profiling tests play a very important role by providing a complex understanding of the molecular characteristics of malignant tumors. Therefore, next-generation sequencing (NGS) has become a valuable tool in various aspects of cancer care from diagnosis and monitoring to treatment selection and personalized cancer treatment. Our aim was to evaluate the role of tumor molecular profiling in tailored treatment selection. Methods In our study, we conducted a retrospective analysis to assess the practicality of utilizing NGS testing in patients with metastatic solid tumors. The genomic testing was performed on blood or tissue samples from a fresh biopsy, less than six months old, and the expression of programmed death-ligand 1 was evaluated by immunohistochemistry. Results A total of 75 tests were performed on 66 patients between 2019 and 2022, with a success rate of 80%. The most common pathologies were gastro-intestinal tract cancer (26%), breast cancer (14%), non-small cell lung cancer (11%), and pancreatic cancer(11%). There were 9% liquid biopsies and 91% tissue biopsies.From all 66 patients tested, 55 had at least one genetic alteration. The most frequent genetic alteration found was TP53 (n=32) followed by KRAS (n=15) and BRCA1/2 (n=12) mutations. There were nine patients tested (14%) that presented a high tumor mutational burden, and only one patient presented high microsatellite instability.There were 37 patients (56%) with actionable alterations found from which 14 received matched therapy and four patients were enrolled in clinical trials. The NGS testing played a significant role in determining the next therapeutic strategy in 20 out of 66 patients (30.3%). Conclusion From all the patients included in our analysis, 83% had at least one mutation that is known to be of pathogenic significance but only 23% received treatment selected by the analysis of the tumor's genome, and only 6% were included in a clinical trial. This moderate success of personalized medicine using NGS testing highlights the importance of evaluating the factors that could lead to further improvement.

Precision medicine for KRAS wild-type pancreatic adenocarcinomas

BackgroundKRAS mutation is the most common molecular alteration in pancreatic adenocarcinoma (PDAC), and around 10% of patients harbor KRAS wild-type tumors (KRASWT). MethodsA retrospective chart review of clinical/molecular data was performed including all PDAC patients with a determined KRAS status (tumor molecular profiling on tissue or liquid biopsy). Results342 patients were included with 54 KRASWT PDAC (16%) compared to 288 patients with KRASm PDAC. Median age was 61 years [IQR:54.0;67.0] and 164 pts (48%) were female. At diagnosis, KRASWT patients (63%) were more frequently diagnosed at a non-metastatic stage compared to KRASm patients (41%) (p = 0.003). Regarding metastatic sites, liver was less frequent in KRASWT (39%, p < 0.0001).Median overall survival (mOS) from initial diagnosis was significantly higher in the KRASWT group compared to KRASm (50.8 months, CI95% [32.0-NR] vs 21.1 months, CI95% [18.9–23.4] (p < 0.004 after adjustment on age, ECOG and stage at diagnosis). In first-line systemic treatment, (mostly FOLFIRINOX) progression-free survival (PFS) was also higher in KRASWT.Based on ESCAT classification, a putative actionable alteration (ESCAT I-III) was identified in 19 (36%) KRASWT pts and 46 (16%) KRASm patients (p < 0.0001) with more alterations in FGFR2, BRAF(V600E), NRTK and more MSI tumors. KRASWT harbored also fewer alterations in TP53, CDKN2A, and SMAD4. 12 KRASWT patients received a molecularly-matched treatment with clinical benefit and improved outcomes compared to KRASm patients. ConclusionsKRASWT patients display distinct disease characteristics and outcomes with prolonged overall survival. KRASWT patients also harbor more actionable molecular alterations, leading to higher survival rates after receiving molecularly matched treatments.

Psilocybin-induced default mode network hypoconnectivity is blunted in alcohol-dependent rats

Alcohol Use Disorder (AUD) adversely affects the lives of millions of people, but still lacks effective treatment options. Recent advancements in psychedelic research suggest psilocybin to be potentially efficacious for AUD. However, major knowledge gaps remain regarding (1) psilocybin’s general mode of action and (2) AUD-specific alterations of responsivity to psilocybin treatment in the brain that are crucial for treatment development. Here, we conducted a randomized, placebo-controlled crossover pharmaco-fMRI study on psilocybin effects using a translational approach with healthy rats and a rat model of alcohol relapse. Psilocybin effects were quantified with resting-state functional connectivity using data-driven whole-brain global brain connectivity, network-based statistics, graph theory, hypothesis-driven Default Mode Network (DMN)-specific connectivity, and entropy analyses. Results demonstrate that psilocybin induced an acute wide-spread decrease in different functional connectivity domains together with a distinct increase of connectivity between serotonergic core regions and cortical areas. We could further provide translational evidence for psilocybin-induced DMN hypoconnectivity reported in humans. Psilocybin showed an AUD-specific blunting of DMN hypoconnectivity, which strongly correlated to the alcohol relapse intensity and was mainly driven by medial prefrontal regions. In conclusion, our results provide translational validity for acute psilocybin-induced neural effects in the rodent brain. Furthermore, alcohol relapse severity was negatively correlated with neural responsivity to psilocybin treatment. Our data suggest that a clinical standard dose of psilocybin may not be sufficient to treat severe AUD cases; a finding that should be considered for future clinical trials.

The landscape of actionable genomic alterations in lung adenocarcinomas in India.

Lung adenocarcinoma (LUAD), the most prevalent form of non-small cell lung cancer (NSCLC), remains a leading cause of cancer-related death globally, including in India, with a 5-year survival rate below 10%. Despite these grim statistics, recent advances in the use of next-generation sequencing (NGS) for identifying genetic alterations and the emergence of targeted therapies have opened new possibilities for personalized treatment based on distinct molecular signatures. To understand the molecular pattern of NSCLC, a retrospective study was conducted with 53 Indian LUAD patient samples, using a targeted NGS panel of 46 cancer-relevant oncogenes to identify clinically relevant variants. Pathogenic or likely pathogenic variants were detected in 94% of the 53 cases. Non-synonymous mutations, rearrangements, copy number alterations, insertions, and deletions of functional relevance were observed in 31 out of 46 genes. The most frequently mutated genes included TP53 (52.8%) and EGFR (50.9%), followed by RET, PIK3CA and ERBB2; some patients had multiple alterations in the same gene. Gender-based enrichment analysis indicated that ALK and IDH2 alterations were more prevalent in females, while TP53 and PTEN were more common in males. No significant correlation was found between mutations and other clinicopathological attributes, such as age, stage, and subtype. A higher prevalence of EGFR, RET, PIK3CA, ERBB2 and ALK mutations were observed compared to previous LUAD genetic studies coupled with a lower frequency of KRAS mutations. Clinically actionable variants were annotated using OncoKB and categorized into the four therapeutic levels based on their clinical evidence. Seventy-nine percent of cases had at least one clinically actionable alteration. Most patients (39.6%) had the highest level of actionability (Level 1) wherein an FDA-approved drug is available specifically for the observed mutation in lung cancer patients. EGFR Exon19 in-frame deletions and EGFR L858R were the most frequent among targetable variants (20.7%). These findings emphasize the importance of a selective NGS panel in enabling personalized medicine approaches by identifying actionable molecular alterations and informing the choice of targeted therapy for more effective treatment options in Indian NSCLC patients.

Time to Deliver on Promises: The Role of ERBB2 Alterations as Treatment Options for Colorectal Cancer Patients in the Era of Precision Oncology.

Receptor tyrosine kinase erythroblastic oncogene B2 (ERBB2), also known as human epidermal growth factor receptor 2 (HER2), represents an oncogenic driver and has been effectively targeted in breast and gastric cancer. Recently, next-generation sequencing (NGS) discovered ERBB2 as a promising therapeutic target in metastatic colorectal cancer (mCRC), where it is altered in 3-5% of patients, but no therapies are currently approved for this use. Herein, we present the experience of a single center in diagnosing actionable genetic ERBB2 alterations using NGS and utilizing the latest therapeutic options. Between October 2019 and December 2022, a total of 107 patients with advanced CRC underwent molecular analysis, revealing actionable ERBB2 mutations in two patients and ERBB2 amplifications in two other patients. These findings correlated with immunohistochemical (IHC) staining. Of these four patients, two were treated with trastuzumab-deruxtecan (T-DXd). We present two exemplary cases of patients with actionable ERBB2 alterations to demonstrate the effectiveness of T-DXd in heavily pretreated ERBB2-positive mCRC patients and the need for early molecular profiling. To fully exploit the potential of this promising treatment, earlier molecular profiling and the initiation of targeted therapies are essential.

Latest trends in cancer clinical trials using genomics

Background: Recent advances in molecular biology and genomics have revolutionized the understanding of the intricate molecular underpinnings of cancer. Next-generation sequencing analysis now allows identification of specific actionable genetic alterations. This breakthrough has paved the way for precision medicine in oncology, redefining the conventional clinical trial landscape and enabling personalized approaches to cancer treatment.Current Concepts: The shift toward precision medicine involves a fundamental departure from the traditional Phases 1–4 clinical trial protocols. Instead of using uniform treatment pathways, personalized therapies are designed based on the genetic profiles of individual patients. Tumor-agnostic clinical trials are becoming as a prominent concept, encompassing innovative adaptive designs that adapt treatments to specific genetic variations. Master protocols such as umbrella studies, basket trials, platform studies, and master observational trials exemplify this transformation.Discussion and Conclusion: International precision medicine research is characterized by exemplar studies such as the NCI-MATCH study in the United States, the Drug Rediscovery Protocol study in the Netherlands, and the Targeted Agent and Profiling Utilization Registry study in the United States. Korean oncology research also contributed to the international effort in precision medicine through initiatives like K-MASTER and the Korean Precision Medicine Networking Group, which is making commendable contributions to the global precision medicine movements.

Druggable genomic landscapes of high-grade gliomas.

Despite the putatively targetable genomic landscape of high-grade gliomas, the long-term survival benefit of genomically-tailored targeted therapies remains discouraging. Using glioblastoma (GBM) as a representative example of high-grade gliomas, we evaluated the clonal architecture and distribution of hotspot mutations in 388 GBMs from the Cancer Genome Atlas (TCGA). Mutations were matched with 54 targeted therapies, followed by a comprehensive evaluation of drug biochemical properties in reference to the drug's clinical efficacy in high-grade gliomas. We then assessed clinical outcomes of a cohort of patients with high-grade gliomas with targetable mutations reviewed at the Johns Hopkins Molecular Tumor Board (JH MTB; n = 50). Among 1,156 sequence alterations evaluated, 28.6% represented hotspots. While the frequency of hotspot mutations in GBM was comparable to cancer types with actionable hotspot alterations, GBMs harbored a higher fraction of subclonal mutations that affected hotspots (7.0%), compared to breast cancer (4.9%), lung cancer (4.4%), and melanoma (1.4%). In investigating the biochemical features of targeted therapies paired with recurring alterations, we identified a trend toward higher lipid solubility and lower IC50 in GBM cell lines among drugs with clinical efficacy. The drugs' half-life, molecular weight, surface area and binding to efflux transporters were not associated with clinical efficacy. Among the JH MTB cohort of patients with IDH1 wild-type high-grade gliomas who received targeted therapies, trametinib monotherapy or in combination with dabrafenib conferred radiographic partial response in 75% of patients harboring BRAF or NF1 actionable mutations. Cabozantinib conferred radiographic partial response in two patients harboring a MET and a PDGFRA/KDR amplification. Patients with IDH1 wild-type gliomas that harbored actionable alterations who received genotype-matched targeted therapy had longer progression-free (PFS) and overall survival (OS; 7.37 and 14.72 respectively) than patients whose actionable alterations were not targeted (2.83 and 4.2 months respectively). While multiple host, tumor and drug-related features may limit the delivery and efficacy of targeted therapies for patients with high-grade gliomas, genotype-matched targeted therapies confer favorable clinical outcomes. Further studies are needed to generate more data on the impact of biochemical features of targeted therapies on their clinical efficacy for high-grade gliomas.

Abstract A113: National multidisciplinary tumor board improves diagnostic stratification and therapeutic management in cancers of unknown primary

Abstract Introduction: With the increasing complexity of current diagnostic investigations, the integration of clinical, pathological and genomic characteristics is crucial for the management of patients (pts) with cancers of unknown primary (CUP). A national multidisciplinary tumor board (NatCUPMTB) was created in July 2020 in France to discuss the diagnostic and therapeutic management of CUP pts. The objective of this study was to evaluate the diagnostic, prognostic and therapeutic impact of this NatCUPMTB after 30 months of activity. Methods: This was a multicenter retrospective study with prospective follow-up. All pts discussed at least once in the NatCUPMTB between July 2020 and January 2023 were included. Pts and tumors characteristics, pathological and genomic analyses including WGS, WES and transcriptome analysis performed on the two PFMG2025 (French Genomic Medecine Plan 2025) national sequencing laboratories, multidisciplinary tumor board (MTB) conclusions, and follow-up after MTB were collected. Results: 151 pts were included. The median age at diagnosis was 58 yo, 55% were female, and the majority of patients had an OMS status &amp;lt;2. The median number of metastatic sites at diagnosis was 2, with a majority located in the lymph nodes (63%). The median time between diagnosis and first MTB presentation was 4 months (1-20). At the time of analysis, NatCUPMTB conclusions and long-term follow up (30 months) were available for 93 pts alive at the second MTB presentation. MTB investigations enabled to identify a likely primary origin in 62/93 (67%) pts, the most frequent being renal carcinoma (N=10), lung carcinoma (N=9) and breast carcinoma (N=8). The most frequently molecular alterations found were in TP53 (37%), KRAS (19%), CDKN2A (18%), NF2 (12%), KMT2C (10%), CDKN2B (9%), PBRM1 (9%) genes. MTB diagnoses were based on the combination of clinical, pathological and genomic investigations in 34/93 (37%) of pts. The others were based on pathological and genomic investigations in 15/93 pts (16%), genomic in 4/93 pts (4%), clinical and genomic in 3/93 pts (3%), clinical and pathological in 3/93 pts (3%) and pathological in 3/93 pts (3%). After a median follow-up of 11.2 months, the median overall survival (OS) was 11.9 months from the 2nd MTB presentation. Importantly, a personalized therapeutic strategy was recommended by NatCUPMTB in 79/93 (85%) of pts. Among these recommendations, 38/79 (49%) were based on the diagnosis of tissue of origin (TOO), 12/79 (15%) on an actionable molecular alteration, 24/79 (30%) on both the TOO and an actionable molecular alteration, and 5/79 (6%) were based on an unguided clinical trial. Conclusion: NatCUPMTB provides significant diagnostic and therapeutic benefit in 85% of pts with CUP. Early presentation of pts at NatCUPMTB as soon as CUP diagnosis is suspected should be recommended. Citation Format: Ivan Bieche, Maud Kamal, Nicolas Jacquin, Célia Dupain, Isabelle Guillou, Etienne Rouleau, Julien Masliah Planchon, Isabelle Soubeyran, Christelle De La Fouchardière, Camille Tlemsani, Hélène Blons, Laëtitia Marisa, Anna Patrikidou, Fabienne Escande, Pierre Blanc, Jennifer Wong, Pierre Saintigny, Sandrine Boyault, Adrien Buisson, Yves Allory, Anne Vincent-Salomon, Vincent Cockenpot, Janick Selves, Christophe Le Tourneau, Sarah Watson. National multidisciplinary tumor board improves diagnostic stratification and therapeutic management in cancers of unknown primary [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A113.

Abstract C019: Inactivating TSC1 and TSC2 alterations, co-mutations, and genomic instability in advanced cancers: Analysis of a real-world (RW) patient (pt) population using the Foundation Medicine genomic database

Abstract Background Tumor suppressor genes tuberous sclerosis complex subunit 1 and 2 (TSC1, TSC2) are critical negative regulators of mTOR activity. In the exploratory biomarker analysis (AMPECT, NCT02494570) and an Expanded Access Program (NCT03817515), pts with inactivating alterations in TSC1 or TSC2 demonstrated responses with the mTOR inhibitor, nab-sirolimus. While these alterations are observed in most cancer histologies, characterization and distribution of TSC1 and TSC2 alterations across tumor types are not well understood. PRECISION I (NCT05103358), a currently enrolling tumor-agnostic study, will assess the clinical benefit of nab-sirolimus in pts with cancer who harbor inactivating TSC1 and TSC2 alterations. To appreciate the potential for TSC1 and TSC2 as therapeutic biomarkers, we analyzed TSC1 and TSC2 mutational data from a RW genomic database. Methods Next-generation sequencing (NGS) data from Foundation Medicine’s genomic database of pts primarily with advanced cancer were analyzed using the FoundationInsights™ web-based platform. Frequency and actionability of TSC1 and TSC2 alterations were assessed. Known or likely pathogenic inactivating TSC1 and TSC2 alterations (ie, indel, rearrangement, frameshift, biallelic loss, nonsense, and some missense mutations) were further characterized for co-mutations, tumor mutational burden (TMB), and microsatellite instability status. Results As of 29 Mar 2022, 438,974 pts with advanced cancer in the Foundation Medicine genomic database had tumor tissue NGS data available. Known/likely inactivating alterations in TSC1 and TSC2 were identified in 8464 (1.9%) pts; 4.3% had variants of unknown significance, primarily missense (~89%), that were not known to be inactivating. Of the inactivating alterations, 52.1% were TSC1 and 48.6% TSC2, including short variants, defined as base substitutions and short indels (85.0%), rearrangements (10.8%), and copy number deletions (17.9%). Alterations were most frequently identified in urinary bladder (8.6%), kidney and renal pelvis (5.8%), corpus and uterus (3.4%), soft tissue (including heart; 2.4%), and liver and intrahepatic bile duct (2.3%) cancers. The most frequently co-occurring mutations included TP53 (62.2%), CDKN2A (26.2%), and TERT (22.2%). TMB was low (&amp;lt;6 mutations per megabase) in 51.6% of pts with inactivating alterations in TSC1 and TSC2. Samples were mostly microsatellite stable (MSS; 82.2%) across tumor types. Conclusion In a large RW database of pts with advanced cancer, inactivating TSC1 and TSC2 variants occurred in 1.9% of pts. These occurred across common tumor types at rates as high as 8.6% (urinary bladder tumors). A majority of pts had low TMB and/or MSS status, suggesting that these are actionable alterations and not passenger events (Bennett et al, Mod Pathol 2022). Common co-mutations also have limited clinical actionability. These observations suggest cancers with TSC1 and TSC2 alterations may be candidates for targeted therapy; this hypothesis is being tested in the currently enrolling PRECISION I (NCT05103358) study. Citation Format: David J. Kwiatkowski, Norma A. Palma, Willis H. Navarro, Gopa Iyer. Inactivating TSC1 and TSC2 alterations, co-mutations, and genomic instability in advanced cancers: Analysis of a real-world (RW) patient (pt) population using the Foundation Medicine genomic database [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C019.

Abstract A123: Circulating tumor DNA (ctDNA) genomic and epigenomic profiling (GuardantINFINITY) for diagnosis of DNA damage repair (DDR) loss of function (LOF) and response monitoring in the TRESR and ATTACC trials

Abstract Background First-generation panel-based ctDNA sequencing is widely used to identify actionable genomic alterations, but limited coverage and sensitivity hinder broader clinical utility, especially in cancers driven by DDR LOF. Further, tissue-free, variant-based approaches for response monitoring have several challenges, including the limited number and low variant allele frequencies (VAF) of monitorable variants and contamination from non-tumor-derived sources (eg, clonal hematopoiesis [CH]). Newer panels may address these challenges with broader coverage, optimized bioinformatics, and the integration of epigenetic analysis for molecular response (MR). Methods Blood samples were collected from 2 phase 1 studies (TRESR; NCT04497116 and ATTACC; NCT04972110) of the ataxia telangiectasia and Rad3-related (ATR) inhibitor camonsertib in combination with gemcitabine or PARPi (talazoparib, niraparib, or olaparib). Cell-free DNA and PBMCs were sequenced using the combined genomic (&amp;gt;800 genes) and methylation (15Mb) GuardantINFINITY platform. Results The study included 117 patients (pts) with ovarian (n=29), breast (n=18), pancreatic (n=18), prostate (n=16) and other (n=36) cancers, enrolled with pathogenic alterations in BRCA2 (n=41), ATM (n=32), BRCA1 (n=23), PALB2 (n=8) and other genes (n=13). Enrollment alterations identified by local NGS were confirmed in 83% (94/114) of pts excluding 3 enrolled by protein loss. 50% (5/10) of complex alterations (large deletions or rearrangements) with sufficient circulating tumor fraction (cTF) were confirmed. Among pts with breast, ovarian, prostate, or pancreatic cancers previously treated with PARPi and/or platinum and harboring BRCA1/2 or PALB2 alterations, reversions were detected in 31% (17/54), with 6 pts reverted by 1 or more large intragenic deletions. A CRC pt with a clonal biallelic sATM alteration had 2 missense reversions in cis, an event not previously reported to occur in ATM. In pts with matched PBMCs, confirmed CH alterations were detected in 79% (44/56), including 59% (33/56) with at least 1 CH variant over 1% VAF. 106 pts had evaluable paired samples at baseline and on-treatment (taken between 2-12 weeks on-treatment [median, 3 weeks]). Using mVAF of the Guardant360 74-gene subset or methylation-based cTF, 72% or 86% were monitorable, respectively. In the subset of evaluable pts with matched PBMC sequencing (n=54), after PBMC-informed CH filtering, monitorability was reduced from 69% to 61% between G360 mVAF and G360 mVAF-CH, respectively. PBMC-informed CH filtering improved the correlation between variant-based and methylation-based monitoring (G360 mVAF, R=0.89, p=1.1e-11 vs G360 mVAF-CH, R=0.95, p=3e-15; Pearson correlation). Correlation of ctDNA monitoring metrics with clinical outcomes is ongoing. Conclusions Broad panel coverage enabled accurate diagnosis of complex DDR LOF and detection of reversion alterations. Methylation-based cTF allows monitoring of most pts in this cohort and consistent with previous observations may avoid signal contamination from CH for robust MR analysis. Citation Format: Ezra Rosen, Joseph D Schonhoft, Ian M Silverman, Arielle Yablonovitch, Sunantha Sethuraman, Parham Nejad, Danielle Ulanet, Julia Yang, Insil Kim, Kezhen Fei, Yi Xu, Errin Lagow, Shile Zhang, Mingyang Cai, Maria Koehler, Benedito A Carneiro, Stephanie Lheureux, Michael Cecchini, Benjamin Herzberg, Jorge S Reis-Filho, Victoria Rimkunas, Timothy A Yap. Circulating tumor DNA (ctDNA) genomic and epigenomic profiling (GuardantINFINITY) for diagnosis of DNA damage repair (DDR) loss of function (LOF) and response monitoring in the TRESR and ATTACC trials [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A123.

Molecular targeted and systemic therapy for intrahepatic cholangiocarcinoma: a multi-disciplinary approach.

Most patients with intrahepatic cholangiocarcinoma (ICC) are diagnosed with advanced disease. For individuals with resectable tumors, R0 resection with lymphadenectomy is the best potentially curative-intent treatment. After resection, adjuvant therapy with capecitabine is the current standard of care. For patients with unresectable or distant metastatic disease, doublet chemotherapy with gemcitabine and cisplatin is the most utilized first-line regimen, but recent studies using triplet regimens and even the addition of immunotherapy have begun to shift the paradigm of systemic therapy. Molecular therapies have recently received US FDA approval for second-line treatment for patients harboring actionable genomic alterations. This review focuses on the multidisciplinary approach to the treatment of ICC with an emphasis on molecular targeted and systemic therapy.

Clinical Practice Recommendations for the Use of Next-Generation Sequencing in Patients with Solid Cancer: A Joint Report from KSMO and KSP.

In recent years, next-generation sequencing (NGS)-based genetic testing has become crucial in cancer care. While its primary objective is to identify actionable genetic alterations to guide treatment decisions, its scope has broadened to encompass aiding in pathological diagnosis and exploring resistance mechanisms. With the ongoing expansion in NGS application and reliance, a compelling necessity arises for expert consensus on its application in solid cancers. To address this demand, the forthcoming recommendations not only provide pragmatic guidance for the clinical use of NGS but also systematically classify actionable genes based on specific cancer types. Additionally, these recommendations will incorporate expert perspectives on crucial biomarkers, ensuring informed decisions regarding circulating tumor DNA panel testing.

High Throughput Microfluidics Platform to Assess Synthetic Lethality and Novel Therapeutic Drug Combinations

Molecularly targeted therapies have reshaped cancer treatment in recent decades; however, not all patient cancers are eligible for or effectively treated by such approaches. In addition, resistance mechanisms (both pre-existing and acquired) limit clinical benefit. To these ends, combination therapies involving targeted agents are increasingly being developed for their potential to induce potent synthetic lethalities, bypass drug resistance, promote durable responses, limit adverse side effects via reduced dosing, and expand treatment options. In the context of acute myeloid leukemia (AML) specifically, several efficacious combination therapies have been approved for specific patient subsets, such as all-trans retinoic acid (ATRA) plus arsenic trioxide in the PML-RARA fusion acute promyelocytic subtype and Midostaurin plus Cytarabine and Daunorubicin in FLT3-mutant AML. Despite the availability of these and other therapies, there remains an unmet need for treatments against AML subtypes lacking actionable driver alterations or for which current therapies are insufficient. A major hurdle limiting novel combination therapy discovery is the sheer combinatorics associated with mixing two or more agents (e.g., screening all possible pairs of 100 drugs in a single cell line requires nearly 5,000 combination experiments). Thus, there is a practical need for methodologies that prioritize test compounds among broad candidate sets and high throughput technologies for rapid and efficient screening. We have developed a combination drug screening workflow that integrates machine learning-based predictions of potentially synergistic compound pairs with a droplet microfluidics-based screening platform. Our physical platform, termed the FlowMatrix, contains a series of nano wells arrayed in a 96 x 96 grid (for 9,216 total wells) in which cells are incubated and compounds delivered via emulsified droplets. To facilitate drug combination screening, the FlowMatrix is loaded column-wise with a 96-element library and subsequently loaded a second time along its rows with either the same or an independent drug library. In our current setup, one FlowMatrix can capture complete data for up to 100 unique drug pairs, which includes control, single-agent, and 4x4 dose combination measurements for each pair. Following multi-day incubation, viability for each well is assessed by the number of live cells imaged with fluorescence microscopy. Combinations with high scoring synergy based on Bliss independence criteria are then pushed to validation and further characterization pipelines. We are currently focused on identifying novel combination therapies for AML. Using small molecule libraries of diverse compound classes and machine learning to prioritize initial screening candidates, we have to-date profiled &amp;gt;8,500 AML cell line-drug combinations in our system. This encompasses &amp;gt;2,900 unique drug combinations profiled in 7 distinct AML cell lines. Among ~270 hits that emerged from these screens are established clinical and preclinical AML combination therapies, in addition to candidates that, to the best of our knowledge, are novel in the context of AML. Strong established hits in our screen include ATR inhibition plus Gemcitabine treatment as well as several combinations involving the BCL-2 inhibitor Venetoclax with chemotherapies (Decitabine and Daunorubicin), Quizartinib, Idasanutlin, and mTOR inhibitors. Thus, we have developed an efficient and cost-effective high throughput drug combinations profiling system that has uncovered candidate therapies that may expand treatment options for patients afflicted by AML.

Emerging Precision Medicine Approaches for Lung Neuroendocrine Tumors

Well-differentiated lung neuroendocrine tumors (LNETs) are heterogeneous cancers that are increasing in incidence. Treatment options for LNETs have expanded in recent years, and our knowledge of the molecular subtypes has also advanced. Multidisciplinary teams have an established role in personalizing the best treatment for individual patients. Other precision medicine approaches for the treatment of LNETs have lagged behind those for non-small-cell lung cancer, with only rare actionable molecular alterations identified and few established predictive factors to guide therapy selection. However, as summarized in this review, there is increasing potential for personalized treatment of patients with LNETs. In particular, advances in radiotheragnostics may allow us to tailor the treatment of individual patients with NETs in the coming years. These advances may soon deliver the promise of more effective, less toxic treatments and better outcomes for patients with these increasingly common cancers.

Real-World Outcomes of Immunotherapy in Second- or Later-Line Non-Small Cell Lung Cancer with Actionable Genetic Alterations.

While the efficacy of immune checkpoint inhibitors (ICIs) in treating non-small cell lung cancer (NSCLC) patients with actionable genetic alterations (AGAs) is modest, certain patients demonstrate improved survival. Thus, this study aimed to evaluate the benefits of ICIs in NSCLC patients with diverse AGAs and verify the predictive biomarkers of ICI efficacy. From January 2018 to July 2022, this study compared the progression-free survival (PFS) of NSCLC patients with different AGAs treated with ICI monotherapy as second- or later-line therapy at Samsung Medical Center. To ascertain the predictors of ICIs efficacy, we adjusted ICIs' effects on PFS in terms of clinical and molecular biomarkers. EGFR (46.0%) was the most prevalent mutation in 324 patients. In multivariate analysis, PD-L1 positivity (tumor proportion score (TPS) ≥ 1%) (HR = 0.41) and the use of steroids for immune-related adverse events (HR = 0.46) were positive factors for ICI therapy in the AGAs group. Co-existing mutation of STK11 with KRAS mutation (HR = 4.53) and TP53 with MET mutation (HR = 9.78) was negatively associated with survival. The efficacy of ICI treatment varied across AGA subtypes, but patients with KRAS, MET, and BRAF mutations demonstrated relatively long-duration benefits of ICI therapy. PD-L1 was a significant positive predictive biomarker in all AGA groups.

CNSC-16. MOLECULAR PROFILING AND ACTIONABLE MUTATIONS IN ADULT PATIENTS WITH IDH WILD TYPE GLIOMAS AND GLIONEURONAL AND NEURONAL TUMORS

Abstract BACKGROUND Next generation sequencing (NGS) assays enable the identification of genetic alterations that may guide a personalized treatment in glioma patients. Material and METHODS From July 2021 to May 2023 a NGS analysis (Myriapod® NGS Cancer DNA and RNA panels) was performed in a cohort of 211 adults IDH wild type (wt) gliomas or circumscribed astrocytoma or glioneuronal/neuronal tumors. The aim was to identify actionable molecular alterations and provide targeted therapy at recurrence accordingly. RESULTS NGS analysis was available in 211 patients (95.5%), while NGS was not feasible in 10 patients (4.5%). 188/211 (89.1%) had an IDH wt glioblastoma (GBM) (median age 61 years), 6 (2.8%) had IDH wt lower grade gliomas (LGG) (median age 63 years), and 17 (8.1%) had circumscribed astrocytoma or glioneuronal/neuronal tumor (median age 37 years). Overall, actionable molecular alterations were found in 13/211 patients (6.2%). 7/211 patients (3.3%) had BRAF V600E mutation (3 IDH wt GBM, 1 IDH wt LGG, and 3 circumscribed/glioneuronal and neuronal tumor), 4/211 patients (1.9%) had FGFR3-TACC3 fusion (all GBM), 1/211 patients (0.5%) had PIK3CA mutation (GBM), and 1/211 patients (0.5%) had NTRK1 fusion (glioneuronal tumor). Other molecular mutations, including ALK, ERBB2, MET, KIT, KRAS, PDGFRA, and RET have not been detected. Three patients recurred after first-line therapy: 1 with BRAF mutated GBM, 1 with GBM harboring FGFR3-TACC3 fusion, and 1 with NTRK1 fusion positive glioneuronal tumor received specific BRAF/MEK inhibitor (dabrafenib/trametinib), FGFR inhibitor (pemigatinib), and NTRK inhibitor (larotrectinib), respectively. A remarkable activity of BRAF/MEK and NTRK inhibitors was observed (9 and 6 months, respectively *), while FGFR inhibitor did not display an activity to control disease (9 weeks). * ongoing CONCLUSION The incidence of actionable molecular alterations in IDH wt gliomas and glioneuronal/neuronal tumors was low. However, the use of targeted therapies may lead to significant impact on the outcome.

PATH-01. COMPARATIVE EVALUATION OF THE DIAGNOSTIC AND PROGNOSTIC PERFORMANCE OF CNSIDE™ VERSUS STANDARD CYTOLOGY FOR LEPTOMENINGEAL DISEASE

Abstract OBJECTIVE We compared the real-world performance of the cerebrospinal fluid (CSF) CNSide™ versus cytology assays in diagnosing leptomeningeal disease (LMD). METHODS Consecutive patients with suspected LMD from January 2020 to December 2022 who underwent lumbar punctures for CSF cytology and CNSide™ analyses were reviewed. LMD diagnosis was defined by EANO criteria. We used descriptive statistics, confusion matrix, Kaplan Meier curves, and Cox proportional regression methods to analyze outcomes. RESULTS 87 patients with median age of 63 years (range:23-93) were evaluated, of which 82 (94%) met EANO positive (possible, probable, or confirmed criteria) cohort. Of the EANO cohort, 33 (40%) had uncontrolled systemic disease and 25 (46%) were on systemic therapy with medium/high CNS penetrance. The median time from initial cancer diagnosis to LMD was 31 months (range:21-43). LMD was diagnosed by CSF cytology (EANO confirmed) in 23 cases, all identified by CNSide™. CNSide™ identified an additional 13 cases, increasing diagnostic yield by 56.5%. Commonest primary histologies in the EANO cohort were breast (36, 44.0%) and lung (34, 41.5%); 18 (53.0%) of lung cancers harbored actionable molecular alterations, while breast cancers expressed hormone receptors in 27 (75%) and HER2 alterations in 8 (22%). Median overall survival (OS) for the CNSide™ cohort was 19.5 weeks (95%CI:11.0-28.0) and 31 weeks (95%CI:21-43) for EANO positive cases. Median OS for breast patients in CNSide™ cohort was 42 (R: 15-65) weeks, about 7-fold that of lung (median 6.5, R: 2-20). There was no correlation between OS and cell density by CNSide™ (HR:1.000, 95%CI:0.999-1.001, p=0.909). OS was higher for cases treated with intrathecal chemotherapy (HR:0.189, 95%CI:0.053-0.672, p=0.010), but not statistically different by radiotherapy modality (HR, 0.583, 95%CI:0.264-1.287, p=0.181). CONCLUSIONS This retrospective, single-institution, real-world analysis of CNSide™ showed increased sensitivity versus cytology and provided clinically relevant, cell-based molecular CSF analyses.

Second-Line Chemotherapy for Intrahepatic Cholangiocarcinomas: What Is the Real Gain?

The presence of actionable alterations in advanced biliary tract cancer patients opened new therapeutic possibilities for second-line treatments. However, for around 60% of the patients, chemotherapy remains the only therapeutic option. The aim of our study was to evaluate outcomes and prognostic parameters in patients with intrahepatic cholangiocarcinomas treated with second-line chemotherapy. A total of 255 consecutive metastatic intrahepatic cholangiocarcinoma (ICC) patients were retrospectively reviewed and clinicopathologic and survival data were collected. Fourty-four percent of ICC patients underwent second-line chemotherapy. In particular, younger ICC patients with better ECOG PS status, and with disease control after first-line chemotherapy were those who were treated with second-line treatments. Median progression-free survival in the patients treated with second-line chemotherapy was 3 months. Finally, the patients affected by intrahepatic cholangiocarcinoma with better ECOG PS, with prior surgical resection of the primary tumor, who responded to first-line chemotherapy, and had better progression-free survival with second-line chemotherapy, were associated with better outcomes in multivariate analysis. Not all patients seem to benefit from second-line chemotherapy. To improve therapeutic decisions, performance status and disease control with first-line chemotherapy should lead to the decision on the usefulness of second-line treatments in advanced ICC patients.