Abstract Background: The pan-cancer genomic landscape of brain metastases (BM) has not been well-characterized. Herein, we evaluate genomically profiled BM tumor samples and additional sequenced tumor samples from other sites to further understand disease evolution. Methods: We analyzed BM specimens from 1007 patients who underwent craniotomy between 2014 and 2024. Targeted sequencing was performed with MSK-IMPACT, a next-generation sequencing assay which detects genomic alterations in up to 505 genes. The FACETS algorithm was used to estimate tumor purity, fraction of genome altered (FGA) and whole-genome duplication (WGD) status. We analyzed matched sample pairs from patients who had additional sequenced tumor samples resulting in 227 primary-BM (P-BM) pairs, 189 extracranial metastasis-BM (ECM-BM) pairs and 60 BM-BM pairs. One pair per patient was selected for each category based on maximum purity. For paired comparisons, the Wilcoxon signed-rank test was used to compare continuous features and McNemar’s test was used to compare WGD, with Benjamini-Hochberg p-value adjustment. The Jaccard index was computed to assess mutational concordance between pairs. Private mutation analysis was limited to genes with driver mutations in >5 pairs in each P-BM/ECM-BM group. Results: Median intracranial progression-free survival (iPFS) and overall survival (OS) from craniotomy were 11.3 and 25 months, respectively. The most frequent histologies in the cohort were non-small cell lung cancer (NSCLC; n = 360), breast (n = 181), and melanoma (n = 128). The genes with the highest proportion of oncogenic alterations were TP53 (62.0%), CDKN2A (25.0%), TERT (23.4%), KRAS (19.7%), and ERBB2 (12.3%). At least one structural variant or mutation was shared by 88.1% of P-BM pairs, 90.0% of ECM-BM pairs and 98.3% of BM-BM pairs. The mean number of shared driver mutations was 2.48 for P-BM pairs, 2.43 for ECM-BM pairs and 4.02 for BM-BM pairs. In a pan-cancer paired analysis, FGA, WGD and tumor purity were higher in BM in P-BM pairs (q < 0.01 for all) and in ECM-BM pairs (q < 0.01 for all). FGA and purity were higher in BM for P-BM pairs in upper gastrointestinal (GI) and NSCLC (q < 0.01), and in ECM-BM pairs for NSCLC (q < 0.01). By histology, in P-BM pairs, lower GI (n = 22) had the highest mean Jaccard index (J = 0.71) and prostate cancer (n = 10) had the lowest (J = 0.33), while in ECM-BM pairs melanoma (n = 23) had the highest (J = 0.77) and sarcoma (n = 9) had the lowest (J = 0.36). TP53 was the most commonly mutated gene in both P-BM (n pairs = 147, shared proportion = 0.816) and ECM-BM pairs (n pairs = 111, shared proportion = 0.869). Mutations in NFE2L2 and KMT2B were most commonly private to the BM in P-BM pairs (4/6 and 5/8 pairs with driver mutations private to BM, respectively), while NF1 mutations were most often BM-private in ECM-BM pairs (4/7). Conclusion: There is a high degree of concordance in alterations between P-BM and ECM-BM pairs. Alterations more commonly private to BM warrant further investigation. Citation Format: Ramzi Homsi, Henry Walch, Roshal Patel, Anna Skakodub, Emily Miao, James Lee, Chengcheng Gui, Mitchell Parker, Zachariya Yazdani, Michel A. Padilla Mazzeo, Claire Cooper, Kyle Sporn, Brandon Imber, Yao Yu, Jessica Wilcox, Nelson Moss, Ahmet Turan Ilica, Rabih Bou-Nassif, Joseph Stember, Christopher Jackson, Connor Kinslow, Gustav Cederquist, Caleb Lareau, Helena A. Yu, Soo Ryum Yang, Pedram Razavi, Joseph Chan, Kenny Kwok Hei Yu, Walid Khaled Chatila, Nikolaus Schultz, Luke R. Pike. Genomic landscape of 1007 pan-cancer brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2116.

2032 Background: Leptomeningeal disease (LMD) remains a frequent and devastating pattern of failure following surgical resection of brain metastases (BM), occurring in up to one-third of patients despite optimal local therapy. Although mechanical disruption of BM tissues may increase the risk of subsequent LMD, the underlying biologic determinants of postoperative LMD remain undefined. This study aims to identify genomic alterations in resected BM and their association with LMD development using the largest craniotomy cohort to date with paired next-generation sequencing and longitudinal CNS outcomes data. Methods: We retrospectively identified patients who underwent surgical resection and MSK-IMPACT next-generation sequencing of one or more BM. LMD was diagnosed using brain and spine MRI and CSF cytology and classified as either classical LMD (cLMD; diffuse coating of meningeal spaces and/or positive CSF cytology), nodular LMD (nLMD; discrete nodular deposits with negative CSF cytology), or both. Fine–Gray subdistribution hazard (sHR) estimated the cumulative incidence of LMD, treating death as a competing risk. Results: Among 1,006 patients, NSCLC (360, 36%), breast (181, 18%), and melanoma (128, 13%) predominated; most patients had single (530, 53%), supratentorial (796, 79%), and large (>2cm, 886, 88%) BM, and underwent postoperative cavity radiotherapy (890, 88%). Median follow-up and OS were 24.8 and 21.5 months, respectively. The cumulative incidence of LMD was 31% (cLMD 18%, nLMD 19%) at 2 years, with the highest rates seen in breast cancer patients (45% LMD; cLMD 28%, nLMD 23%). Median time to cLMD and nLMD were 7.7 and 6.4 months, respectively. Median OS after cLMD and nLMD diagnosis were 5.7 and 12 months, respectively. The most frequently altered genes in resected BM were TP53 (62%), CDKN2A (25%), TERT (23%), KRAS (20%), ERBB2 (12%), PIK3CA (12%), PTEN (12%), and RB1 (11%). In a pan-cancer analysis, alterations in CDH1 (sHR 3.0, q=0.03), EGFR (HR 2.5, q<0.001), GATA3 (sHR 2.2, q=0.03), or RB1 (sHR 1.7; q=0.04) were associated with an increased risk of cLMD; alterations in PTEN were associated with an increased risk of nLMD (sHR 1.8, q=0.02). Within breast and lung cohorts, alterations in RB1 or EGFR, respectively, were associated with an increased risk of cLMD. BM from patients who developed LMD exhibited greater genomic instability, with a higher fraction of the genome altered compared to those who did not (0.47 vs 0.40, p<0.001). Conclusions: LMD is a common and deadly form of progression following BM resection. Distinct genomic features, present in the resected BM specimen, may identify patients at increased risk of LMD. These findings support the development of a clinicogenomic model to select BM patients for intensified surveillance and postoperative care.

Background Brain metastasis (BM) in colorectal cancer (CRC) is a rare event that undermines longevity and neurocognitive function. However, the molecular basis of BM in CRC is poorly understood. We analyzed next-generation sequencing (NGS) from patients with CRC to identify genomic features associated with BM and intracranial progression (IP).Methods Patients with CRC who had NGS between 2014 and 2024 were included. Sequenced tumor specimens were classified by the anatomic site of biopsy as primary tumors (PT), extracranial metastases (EM), or BM. Sequenced PT specimens were compared to identify genomic differences between patients who did and did not develop BM. Among patients with BM, sequenced tumor specimens were compared to identify genomic differences by anatomic site. Sequenced BM samples were compared to identify genomic differences between patients who did and did not experience IP after BM-directed local therapy.Results This analysis included 5526 patients with NGS of CRC, including 269 patients with BM. PT of patients who developed BM more frequently contained alterations in the KRAS, BRAF, and SMAD4, compared with PT of patients without BM. Among patients with BM, resected BM specimens had greater tumor mutation burden, fraction of genome altered, and frequency of TP53, SMAD4, and MYC alterations, compared with extracranial tumor specimens. Patients with BM carrying SMAD4 or PI3K pathway alterations showed a trend toward earlier IP after BM-directed therapy.Conclusions This study identifies novel genomic associations with intracranial metastasis and progression in CRC, suggesting a potential basis for personalized clinical management.

Supplementary Table S3. Baseline Radiological Characteristics Stratified by Molecular Grade.

AbstractPurpose: Isocitrate dehydrogenase–mutant (IDH-mt) gliomas are incurable primary brain tumors characterized by a slow-growing phase over several years followed by a rapid-growing malignant phase. We hypothesized that tumor volume growth rate (TVGR) on MRI may act as an earlier measure of clinical benefit during the active surveillance period. Experimental Design: We integrated three-dimensional volumetric measurements with clinical, radiologic, and molecular data in a retrospective cohort of IDH-mt gliomas that were observed after surgical resection in order to understand tumor growth kinetics and the impact of molecular genetics. Results: Using log-linear mixed modeling, the entire cohort (n = 128) had a continuous %TVGR per 6 months of 10.46% [95% confidence interval (CI), 9.11%–11.83%] and a doubling time of 3.5 years (95% CI, 3.10–3.98). High molecular grade IDH-mt gliomas, defined by the presence of homozygous deletion of CDKN2A/B, had %TVGR per 6 months of 19.17% (95% CI, 15.57%–22.89%) which was significantly different from low molecular grade IDH-mt gliomas with a growth rate per 6 months of 9.54% (95% CI, 7.32%–11.80%; P < 0.0001). Using joint modeling to comodel the longitudinal course of TVGR and overall survival, we found each one natural logarithm tumor volume increase resulted in more than a 3-fold increase in risk of death (HR = 3.83; 95% CI, 2.32–6.30; P < 0.0001). Conclusions: TVGR may be used as an earlier measure of clinical benefit and correlates well with the WHO 2021 molecular classification of gliomas and survival. Incorporation of TVGR as a surrogate endpoint into future prospective studies of IDH-mt gliomas may accelerate drug development.

Abstract Introduction: Melanoma has a high propensity for brain metastasis (BM). Although advancements in brain-penetrant treatments have resulted in improved central nervous system (CNS) disease control, BMs remain a significant cause of morbidity and mortality. The molecular features of melanoma BM are poorly defined, and there is an unmet need to identify biomarkers associated with CNS-specific outcomes. Methods: We retrospectively identified 109 patients with melanoma BM who underwent craniotomy at Memorial Sloan Kettering Cancer Center (MSK) between 01/2014 and 04/2023. BM specimens were sequenced using MSK-IMPACT, an FDA-approved next-generation sequencing assay covering 341-505 genes with 700X coverage. Clinical characteristics and CNS-specific outcomes were available from 107 patients; CNS-specific radiographic endpoints were verified through direct inspection of contrast-enhanced MRI imaging by a board-certified neuroradiologist. Clinical data included baseline characteristics, prior systemic or radiotherapy (RT), and CNS-directed follow up including recording local progression of disease (POD), regional POD, and development of leptomeningeal disease (LMD). Results: Majority (68%,73/107) patients were male with a median age at the time of primary diagnosis of 56 (range 3-88). Forty-eight patients (45%) had advanced disease (stages III and IV) at the time of initial diagnosis. At the time of BM development, half of the patients had 2-5 intracranial tumors present (50%) with a median diameter of largest BM of 33.4mm (range .9mm-64mm). The median KPS was 80 at the time of BM diagnosis, and 79% had neurologic symptoms prior to resection. 81 patients (76%) were treatment naïve at the time of resection and 56 patients (53%) developed CNS recurrence with the majority of those having local POD (29%,16/56) followed closely by regional POD of 1 lesion (25%,14/56). The most frequent genomic alterations in the cohort were TERT (87%), CDKN2A (50%), BRAF (43%), NRAS (28%), and PTEN (25%). The median fraction genome altered was 0.3047 and the median tumor mutational burden was 13.2 muts/Mb. We compared the genomic profiles of BM tumors of patients that had no progression, local POD, regional POD, and LMD. Compared to patients with no progression, patients with local POD were more likely to have RB1 alterations (18.1% vs 2.1%, p = 0.04, q = 0.83) and patients with LMD were less likely to have TERT alterations (62.5% vs 93.8%, p = 0.03, q = 0.75). Conclusions: Our analysis between genomic markers and clinical outcomes in melanoma BM reveals genomic features which may improve prediction and treatment strategies. Citation Format: Michel Padilla Mazzeo, Henry S. Walch, Rahul Kumar, Jordan Eichholz, Claire Cooper, Nishta Nandakumar, Junchao Shen, Ishaani Khatri, Luke Del Balzo, Anna Skakodub, Emily Miao, Daniel W. Kelly, Kenny Kwok Hei Yu, Jessica Wilcox, Brandon S. Imber, Yao Yu, Yoshiya Yamada, Harish Vasudevan, Ahmet Ilica, Nikolaus Schultz, Luke R. Pike. Clinical and genomic characterization of melanoma brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3785.

Supplementary Table S2. Baseline Radiological Characteristics Overall and Stratified by 1p19q Status.

Supplementary Figure S2. Tumor volume growth rates and respective genomics.

Supplementary Table S4. Clinical Characteristics and Tumor Volume Growth During Active Surveillance.

PURPOSE Small cell lung cancer (SCLC) often metastasizes to the brain and has poor prognosis. SCLC subtypes distinguished by expressing transcriptional factors ASCL1 or NEUROD1 have been identified. This study investigates the impact of transcription factor-defined SCLC subtype on incidence and outcomes of brain metastases (BMs). METHODS Patients with SCLC with ASCL1 (A) and NEUROD1 (N) immunohistochemical expression status were identified and classified: (1) A+/N-, (2) A+/N+, (3) A-/N+, and (4) A-/N-. Cumulative incidence competing risk analyses were used to assess incidence of CNS progression. Cox proportional hazards models were used for multivariable analyses of overall survival (OS) and CNS progression-free survival (CNS-PFS). RESULTS Of 164 patients, most were either A+/N- or A+/N+ (n = 62, n = 63, respectively). BMs were present at diagnosis in 24 patients (15%). Among them, the 12-month cumulative incidence of subsequent CNS progression was numerically highest for A+/N- (50% [95% CI, 10.5 to 74.7]; P = .47). Among those BM-free at diagnosis, the 12-month cumulative incidence of CNS progression was numerically the highest for A+/N- (16% [95% CI, 7.5 to 27.9]) and A-/N+ (9.1% [95% CI, 0.0 to 34.8]; P = .20). Both subtypes, A+/N- and A-/N+, had worse OS compared with A+/N+ (A+/N-: hazard ratio [HR], 1.62 [95% CI, 1.01 to 2.51]; P < .05; A-/N+: HR, 3.02 [95% CI, 1.35 to 6.76]; P = .007). Excellent response rates (28, 65% CR/PR) across subtypes were seen in patients who had CNS-directed radiotherapy versus systemic therapy alone (9, 36% CR/PR). CONCLUSION To our knowledge, this report is the first to investigate CNS-specific outcomes based on transcription factor subtypes in patients with SCLC. BM-free patients at diagnosis with A+/N- or A-/N+ subtypes had worse outcomes compared with those with transcriptional factor coexpression. Further investigation into the mechanisms and implications of SCLC subtyping on CNS-specific outcomes is warranted to ultimately guide personalized care.

Supplementary Figure S3. Next-Intervention-Free Survival and overall survival.

Abstract BACKGROUND Brain metastases (BM) from colorectal cancer (CRC) are associated with dismal prognosis, but little is understood regarding their molecular characteristics. We identified genomic features that predispose to brain tropism, differentiate BM from extracranial disease, and predict early intracranial progression (IP) after BM-directed therapy. METHODS We analyzed next-generation sequencing (NGS) of tumor biopsies from three subgroups of CRC patients: patients with BM (BM+, n=379), patients with extracranial metastases (EM) but without BM (BM-/EM+, n=3968), and patients without metastatic disease (BM-/EM-, n=1061). NGS was performed with MSK-IMPACT, a targeted panel of >300 genes. First, we compared genomic alterations in primary tumors (PT) among the BM+, BM-/EM+, and BM-/EM- subgroups. Second, we focused on patients in the BM+ subgroup who received stereotactic radiosurgery (SRS) for limited BM, comparing tumor genomic alterations from different anatomic sites: BM (n=32), EM (n=62), and PT (n=68). Third, we focused on the 32 resected BM, identifying genomic alterations that predicted early IP, defined as new BM, leptomeningeal disease, or enlargement of existing BM, within 6 months of postoperative SRS. RESULTS PT of BM+ patients demonstrated lower rates of microsatellite instability, increased frequency of BRAF alterations, and fewer APC alterations compared with PT of BM-/EM+ and BM-/EM- patients. Among BM+ patients, SMAD4, MYC, and CDK8 alterations were enriched among resected BM specimens, compared with EM and PT specimens. Resected BM of patients with early IP demonstrated increased frequency of SMAD4 alterations, particularly biallelic SMAD4 loss, and decreased frequency of MYC alterations, compared with resected BM of patients without early IP. CONCLUSION Alterations in key driver genes are associated with initial development and progression of CRC BM. BRAF alterations are enriched in PT of patients who develop BM. SMAD4 alterations are enriched in BM compared to extracranial disease and furthermore predict early IP after BM-targeted therapy.

Supplementary Figure S1. Somatic genomic alterations in the cohort of IDH-mutant gliomas.

Abstract BACKGROUND Small cell lung cancer (SCLC) is characterized by a high propensity for brain metastases (BM) and is associated with a poor prognosis. Subtypes characterized by high versus low neuroendocrine states (expressing ASCL1 or NEUROD1) have been identified. This study aims to evaluate the influence of transcription factor-defined SCLC subtypes on the incidence and outcomes of BM. METHODS We identified 164 patients with SCLC based on their ASCL1 and NEUROD1 expression status by immunohistochemistry. Four transcriptional subtypes were defined: ASCL1+/NEUROD1- (A+/N-), ASCL1+/NEUROD1+ (A+/N+), ASCL1-/NEUROD1+ (A-/N+), and ASCL1-/NEUROD1- (A-/N-). Cumulative incidence competing risk analyses examined the incidence of central nervous system (CNS) progression. Cox proportional hazards models were utilized to assess both overall survival (OS) and CNS progression-free survival (CNS-PFS). RESULTS Out of 164 patients, the majority fell into either A+/N- or A+/N+ subtypes (n = 62, n = 63, respectively). BM were detected at the time of diagnosis in 12% (20/164) of patients, while 18% (29/164) developed BM later. In two distinct cohorts of patients (initially free from BM and with de novo BM at diagnosis), the 12-month cumulative incidence of CNS progression was numerically highest for the A+/N- subtype (HR = 11.8, 95%CI: 4.7-22.4, and HR = 44, 95%CI: 10.5-74.7, respectively). OS in both A+/N- and A-/N+ subtypes was worse compared to the A+/N+ subtype (HR = 1.62, 95%CI: 1.03-2.56, and HR = 1.63, 95%CI: 1.06-2.60, respectively). Similarly, CNS-PFS was poorer in same A+/N- and A-/N+ subtypes (HR = 3.10, 95%CI: 1.39-6.93, and HR = 3.38. 95% CI: 1.49-7.67) when compared to A+/N+. CONCLUSIONS This study is the first to explore CNS-specific outcomes based on transcription factor SCLC subtypes. Among patients without BM at SCLC diagnosis, those exclusively expressing ASCL1 or NEUROD1 demonstrated poorer outcomes than those with co-expression. Further investigation is warranted to elucidate the implications of SCLC subtyping, ultimately facilitating tailored disease management.

Background Resolving the differential diagnosis between brain metastases (BM), glioblastomas (GBM), and central nervous system lymphomas (CNSL) is an important dilemma for the clinical management of the main three intra-axial brain tumor types. Currently, treatment decisions require invasive diagnostic surgical biopsies that carry risks and morbidity. This study aimed to utilize methylomes from cerebrospinal fluid (CSF), a biofluid proximal to brain tumors, for reliable non-invasive classification that addresses limitations associated with low target abundance in existing approaches. Methods Binomial GLMnet classifiers of tumor type were built, in fifty iterations of 80% discovery sets, using CSF methylomes obtained from 57 BM, GBM, CNSL, and non-neoplastic control patients. Publicly-available tissue methylation profiles (N = 197) on these entities and normal brain parenchyma were used for validation and model optimization. Results Models reliably distinguished between BM (area under receiver operating characteristic curve [AUROC] = 0.93, 95% confidence interval [CI]: 0.71-1.0), GBM (AUROC = 0.83, 95% CI: 0.63-1.0), and CNSL (AUROC = 0.91, 95% CI: 0.66-1.0) in independent 20% validation sets. For validation, CSF-based methylome signatures reliably distinguished between tumor types within external tissue samples and tumors from non-neoplastic controls in CSF and tissue. CSF methylome signals were observed to align closely with tissue signatures for each entity. An additional set of optimized CSF-based models, built using tumor-specific features present in tissue data, showed enhanced classification accuracy. Conclusions CSF methylomes are reliable for liquid biopsy-based classification of the major three malignant brain tumor types. We discuss how liquid biopsies may impact brain cancer management in the future by avoiding surgical risks, classifying unbiopsiable tumors, and guiding surgical planning when resection is indicated.

Up to 50% of patients with non-small cell lung cancer (NSCLC) develop brain metastasis (BM), yet the study of BM genomics has been limited by tissue access, incomplete clinical data, and a lack of comparison with paired extracranial specimens. Here we report a cohort of 233 patients with resected and sequenced (MSK-IMPACT) NSCLC BM and comprehensive clinical data. With matched samples (47 primary tumor, 42 extracranial metastatic), we show CDKN2A/B deletions and cell cycle pathway alterations to be enriched in the BM samples. Meaningful clinico-genomic correlations are noted, namely EGFR alterations in leptomeningeal disease (LMD) and MYC amplifications in multifocal regional brain progression. Patients who developed early LMD frequently have had uncommon, multiple, and persistently detectable EGFR driver mutations. The distinct mutational patterns identified in BM specimens compared to other tissue sites suggest specific biologic underpinnings of intracranial progression.

Abstract BACKGROUND The prognosis for patients with brain metastasis (BM) is devastating, while the underlying biology of BM development remains poorly understood. Identification of genomic biomarkers can offer promising opportunities for prediction of BM development and guidance in personalized treatment. In this study we evaluate the genomic alterations present in a large cohort of resected BM. METHODS Upon retrospective review, we identified 868 patients with diagnosis of solid primary cancers who had undergone a standard of care craniotomy at Memorial Sloan Kettering Cancer Center (MSKCC). BM samples were profiled by MSK-IMPACT, a next-generation sequencing (NGS) assay designed to detect a wide range of genetic alterations in 341-505 cancer genes. Genomic alterations were filtered for driver variants using OncoKB. Disease sites included cancers of head and neck, breast, lung, lower and upper gastrointestinal tract, kidney, ovary, uterus, prostate, skin, soft tissues, and others. RESULTS More than half (57%; 493/868) of patients were female and the median age was 63 (range 22-93). Foreseeably, the most common histology was non-small cell lung cancer (NSCLC; 38%), followed by invasive carcinoma of the breast and melanoma (16% and 13%, respectively). The most frequently encountered alterations were inTP53 (60%), CDKN2A (25%), TERT (23%), KRAS (18%), and PTEN (12%) across all BM samples. The median fraction of genome altered was 0.41 [range: 0-0.99] and the median tumor mutational burden was 6.6 muts/Mb [range: 0-395]. Additionally, TP53 was the most frequently altered gene after stratifying by primary histology in most cancer types, except for melanoma, renal, and thyroid, which were enriched for alterations in TERT, CDKN2A, and TERT, respectively. CONCLUSION The landscape of genomic alterations present in BM is distinct and varies by primary histologic diagnosis. Ongoing analyses of matched primary-BM pairs and clinicogenomic correlation will identify factors predisposing patients to BM development and progression.

Intro: Half of all patients with NSCLC develop BM during their clinical course. While modern NSCLC-directed agents yield excellent systemic response, most patients require focal BM treatment. Prior reports of BM genomics have been limited by low numbers and a lack of matched specimens. Here, we report the largest cohort to date of molecularly-profiled NSCLC BM samples with comprehensive clinical follow-up. Methods: Clinical data and outcomes for 244 patients with NSCLC and resected BM were identified. Samples were assessed using MSK-IMPACT, a custom tumor-normal next generation sequencing assay. 51 (20.9%) patients had matched primary site tissue, and 44 (18%) patients had matched tissue from another metastatic site or CSF. Genomic alterations were filtered for driver variants using OncoKB. Publicly available genomic data for NSCLC primary samples was used for comparison against the primary samples from our BM cohort. Results: The most frequently altered genes in BM tumors were TP53 (72%), CDKN2A (34%), KRAS (31%), KEAP1 (26%), and EGFR (21%). CDKN2A was more frequently altered in BM samples compared to NSCLC primary lesions (34% vs 14%, p = 0.003). Additionally, cell cycle pathway alterations were enriched in BM (56% vs 31%, p = 0.002). BM samples also had a significantly higher fraction of genome altered (FGA) relative to primary samples (p < 0.0001). We then compared primary samples from BM patients against primary samples from metastatic NSCLC patients without BM and primary samples from non-metastatic NSCLC patients. We found an enrichment of alterations in TP53 (68.6% vs 27.7%, p < 0.0001), NKX2-1 (11.4% vs 1.7%, p = 0.006), SMARCA4 (11.4% vs 2.1%, p = 0.01), RB1 (11.4% vs 1.7%, p = 0.006), and FOXA1 (11.4% vs 0.9%, p = 0.001) in the primary samples from BM patients compared to non-metastatic patients. Next, we grouped patients based on CNS progression patterns and found that EGFR alterations were enriched in patients with leptomeningeal progression when compared to patients without progression (42% vs 18%, p = 0.03). Conclusions: In our cohort of molecularly-profiled NSCLC BM, we found an enrichment of cell cycle pathway alterations and a higher FGA in BMs compared to their primary tumor controls. Additionally, several genes were enriched in the primary tissue of patients that developed BM compared to primary tissue from non-metastatic patients. EGFR alterations were enriched in patients who develop leptomeningeal disease (LMD). Our work herein characterizes the genomic profiles of NSCLC patients with BM and identifies specific genes enriched in the primary tissue of BM patients compared to primary tissue from both non-BM metastatic patients and non-metastatic patients. Finally, our finding that EGFR alterations were enriched in patients with LMD suggests specific biologic underpinnings driving patterns of CNS progression. Citation Format: Henry Walch, Anna Skakodub, Kathryn R. Tringale, Harish N. Vasudevan, Jordan Eichholz, Daniel W. Kelly, Emily Lebow, Nelson S. Moss, Kenny Kwok Hei Yu, Bob T. Li, Boris Mueller, Atif Khan, Yao Yu, Simon Powell, Jorge S. Reis-Filho, Brandon S. Imber, Pedram Razavi, Daniel R. Gomez, Nikolaus Schultz, Luke R. Pike. Genomic characterization of non-small cell lung cancer (NSCLC) brain metastasis (BM) patients identifies novel alterations associated with tropisms and disease progression [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 6063.

Purpose Circulating tumor cells (CTC) in cerebrospinal fluid (CSF) are a quantitative diagnostic tool for leptomeningeal metastases (LM) from solid tumors, but their prognostic significance is unclear. Our objective was to evaluate CSF-CTC quantification in predicting outcomes in LM. Methods This is a single institution retrospective study of patients with solid tumors who underwent CSF-CTC quantification using the CellSearch® platform between 04/2016-06/2019. Information on neuroaxis imaging, CSF results, and survival was collected. LM was diagnosed by MRI and/or CSF cytology. Survival analyses were performed using multivariable Cox proportional hazards modeling, and CSF-CTC splits associated with survival were identified through recursive partitioning analysis. Results Out of 290 patients with CNS metastases, we identified a cohort of 101 patients with newly diagnosed LM. In this group, CSF-CTC count (median 200 CTCs/3ml) predicted survival continuously (HR = 1.005, 95% CI: 1.002-1.009, p = 0.0027), and the risk of mortality doubled (HR = 2.84, 95% CI: 1.45-5.56, p = 0.0023) at the optimal cutoff of ≥ 61 CSF-CTCs/3ml. Neuroimaging findings of LM (assessed by 3 independent neuroradiologists) were associated with a higher CSF-CTC count (median CSF-CTCs range 1.5-4 for patients without radiographic LM vs 200 for patients with radiographic LM, p<0.001), but did not predict survival. Conclusion Our data shows that CSF-CTCs quantification predicts survival in newly diagnosed LM, and outperforms neuroimaging. CSF-CTC analysis can be used as a prognostic tool in patients with LM and provides quantitative assessment of disease burden in the CNS compartment.