Abstract Background: RET fusions occur in ∼1-2% of advanced NSCLC (aNSCLC). Selective RET inhibitors (SRIs) significantly improve outcomes, yet ∼10% of patients progress by 6 months and ∼30% by 12 months. Predictors of response or early progression remain poorly defined. Methods: A multicenter retrospective analysis (RET-MAP) of RET+ aNSCLC from 47 international centers evaluated clinical/genomic correlates of SRI outcomes. Multivariable Cox models estimated progression-free (PFS) and overall survival (OS) and tested interactions with first-line (1L) SRI versus chemotherapy ± immune checkpoint inhibitor (CH±ICI). In parallel, genomic/transcriptomic features were characterized in an external Caris Life Sciences (CLS) RET+ aNSCLC cohort. Results: Among 510 RET-MAP patients (median age 63; 59% female; 36% ever-smokers; 92% adenocarcinoma), 401 received an SRI (1L n=151; later lines n=250). Median PFS on SRI (any line) was 17.1 months (95% CI, 14.5-21.1), median OS 30.4 months (95% CI, 27.0-41.1). TP53 co-mutation was present in 27% (78/292 tested) and was associated with shorter PFS (8.9 vs 19.2 months; p<0.001) and OS (22.7 vs 30.9 months; p=0.002), without a significant treatment-by-TP53 interaction for 1L SRI versus CH±ICI (p=0.22). Fusion partner contributed with additional signal: KIF5B (73%, 274/373) had inferior PFS (13.4 vs 60.2 months; p<0.001) and OS (26.6 vs 73.0 months; p=0.002) compared with CCDC6 (17%, 65/373), and a significant treatment-by-fusion interaction favored SRI over CH±ICI in CCDC6 versus KIF5B (p=0.007). On multivariate analysis, shorter PFS and OS were independently associated with TP53 mutation (HR 1.74, p<0.001; HR 1.77, p=0.001), KIF5B fusion (HR 1.98, p=0.002; HR 1.64, p=0.040), ECOG ≥2 (HR 2.20, p<0.001; HR 3.06, p<0.001), and brain metastases (HR 1.59, p=0.003; HR 1.88, p<0.001); worse OS was associated with non-adenocarcinoma histology (HR 1.74, p=0.049) and smoking (HR 1.42, p=0.034). Notably, KIF5B fusions were enriched for TP53 mutations versus CCDC6 (40% vs 19.6%, p=0.011), suggesting partially overlapping biology. In the CLS cohort (N=211), TP53-mutant tumors (74/211) were enriched for RB1 mutations, had higher PD-L1 expression and tumor mutational burden, and demonstrated increased M1 macrophage/B-cell infiltration with reduced neutrophils; by fusion partner, CCDC6 showed higher PD-L1, while global transcriptomes were otherwise similar to KIF5B. Conclusions: In RET+ aNSCLC, TP53 mutation is prognostic for inferior outcomes on SRIs but not predictive of differential benefit versus CH±ICI. Fusion partner carries both prognostic and predictive relevance; CCDC6 is associated with a more indolent course and greater relative benefit from SRI. External profiling supports an inflammatory microenvironment in TP53-mutant disease, reinforcing biologically distinct—and clinically meaningful—subsets within RET-driven lung cancer. Citation Format: Daniela Miliziano, Julia K. Rotow, Meghanne Lomibao, Tolulope Adeyelu, Arianna Marinello, Helena Bote-de Cabo, Jamie Feng, Andrea De Giglio, Mariana Brandão, Florian Guisier, Michael Duruisseaux, Christina Falcon, Massimiliano Cani, Francesca Colamartini, Barliz Waissengrin, Isabelle Monnet, Anna Eisert, Emilio Bria, Amin H. Nassar, Ayesha Aijaz, Patricia Iranzo, Colin R. Lindsay, Elizabeth Fabre, Vladmir Cordeiro de Lima, Judith Raimbourg, Laura Mezquita, Nicolas Minatta, Sophie Cousin, Katarzyna Szymczak, Vincent Fallet, Clarisse Audigier-Valette, Helene Doubre, Philippe Rochigneux, Annarita Avanzo, Antonio Calles, Marco Tagliamento, Diego Cortinovis, Balazs Halmos, Nicholas Girard, Andrew Elliott, Jair Bar, Alessio Cortellini, Diana N. Ionescu, Frances A. Shepherd, Fabrice Barlesi, Karen L. Reckamp, David Planchard, Benjamin Besse, Alexander Drilon, Mihaela Aldea. Prognostic and predictive effects of TP53 co-mutations and RET fusion partners in RET-rearranged advanced NSCLC [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 2434.

Concurrent driver mutations according to oncogenic / likely oncogenic MET TKD mutations detected in cohort #2.

Abstract Purpose: In RET-rearranged non–small cell lung cancer (NSCLC), treatment options after first-generation selective RET inhibitors (SRI) are limited, and the value of SRI retreatment remains unclear. This study evaluates outcomes of SRI retreatment. Experimental Design: This multicenter retrospective study included patients with advanced RET-rearranged NSCLC who received ≥2 SRI-based therapy lines. Of 411 SRI-treated patients, 41 (10%) underwent SRI retreatment. Outcomes included objective response rate (ORR), progression-free survival (PFS), 6-month PFS, time to treatment failure, adverse events (AE). Results: Among 41 patients, 14 (34%) discontinued the initial SRI because of toxicity and 27 (66%) because of progression. After discontinuation for toxicity, all switched to an alternate SRI, achieving an ORR of 67%, median PFS of 9.9 months, and 6-month PFS of 80.3%. AEs reoccurred in nine patients (64%), with grade ≥3 AEs in 3 (21%) who switched at full dose. Among patients who discontinued because of progression, SRI monotherapy (n = 13) achieved an ORR of 23%, median PFS of 7 months, and 6-month PFS of 61.5%. Benefit was observed in patients with brain-only or oligoprogressive disease or dose reduction on first SRI. Combination therapy (n = 14; targeted agents, n = 11; chemotherapy, n = 3) achieved an ORR of 39%, median PFS of 4 months, and 6-month PFS of 27.3%. Conclusions: Same-class SRI switch after toxicity is feasible and clinically active but warrants cautious, dose-adjusted switching to mitigate toxicities. The efficacy of SRI rechallenge after progression seems limited overall. However, selected patients, such as those with brain-only or oligoprogressive disease, may derive benefit.

MET TKD mutations in NSCLC cohort of Caris Life Sciences. (A) Flowchart of the NSCLC subgroup in the Caris Life Sciences dataset. (B) Prevalence of MET TKD mutations in NSCLC cases in the Caris Life Sciences dataset (MET TKD mutations in 280 unique patients). (C) Lollipop plot of the oncogenic / likely oncogenic MET TKD mutations detected in NSCLC cases in the Caris Life Sciences dataset (35 oncogenic / likely oncogenic MET TKD mutations in 35 unique patients). (D) concurrent driver alterations (information available for 24 cases, unavailable for 11 cases) and (E) concurrent MET amplification status (information available for 33 cases, unavailable for 2 cases) of NSCLC cases harboring oncogenic / likely oncogenic MET TKD mutations in the Caris Life Sciences dataset.

Equilibration of interactions that drives ATP affinity in the presence MET R1170Q mutant. (A) Representative structure of ATP bound MET R1170Q with the regions of interest highlighted [hinge site (green), and mutation site (blue)]. (B) Mutation at position 1170 facilitates the formation of a hydrogen bonding network. (C) Interatomic distances for non solvent mediated hydrogen bonding.

Supplementary Figure S7. HER2 IHC Concordance In A Subset Of Breast Cancers With ERBB2-Activating Mutations (+) and (-) indicate the results of confirmatory FISH, if performed. ECD, Extracellular Domain; IDC, Invasive Ductal Carcinoma; ILC, Invasive Lobular Carcinoma; KD, Kinase Domain; NOS, Not Otherwise Specified

Single trajectory generalized Born and surface area solvation (MM/GBSA) calculated free energy of ATP binding into the orthosteric pocket.

List of missense mutations with unknown biologic function and their pathogenicity scores using all three in silico tools in cohort #1

Supplementary Figure S11. Pan-Tumor Landscape Of ERBB2 Activating Alterations Detected In The MSKCC Clinicogenomic Cohort a) Prevalence of ERBB2 activating alterations (known or likely functional significance) across solid tumors in the MSKCC clinicogenomic cohort. ‘Multiple’ includes patients with AMP + MUT, AMP + RE, MUT + RE, AMP + MUT + RE and patients with >1 MUT. b) Cancer type distribution of ERBB2 MUT tumors. AMP, Amplification (CN ≥ 6); MUT, Mutation (SNV, Indel); RE, Rearrangement.

Advanced tumors harboring SWI/SNF mutations are rare and aggressive. Often presenting in young patients, treatment options are limited. This phase II basket study (NCT02601950) assessed oral tazemetostat, an EZH2 inhibitor, at 800 mg twice daily (N = 129). Cohorts included malignant rhabdoid tumors (n = 32, Cohort 1), synovial sarcoma (n = 33, Cohort 2), INI1-negative tumors (n = 32, Cohort 3), renal medullary carcinoma (n = 14, Cohort 4), and poorly differentiated chordoma (n = 18, Cohort 7). Efficacy assessments used a 2-stage Green-Dahlberg design. Stage 1 futility was predefined as objective responses (complete/partial [CR/PR]) <5% (Cohorts 1, 3, 4, 7) or 16-week progression-free survival (PFS) <15% (Cohort 2). Sufficient clinical activity was declared in Stage 2 if ≥5 patients had a CR/PR (Cohorts 1,3,4,7) or ≥9 patients had a CR/PR, or stable disease (Cohort 2; primary endpoints). Responses were observed in malignant rhabdoid tumors (9%; n = 2 PR, n = 1 CR), INI1-negative tumors (9%; n = 3 PR, n = 0 CR), and poorly differentiated chordoma (6%; n = 1 PR, n = 0 CR) but not the remaining 2 cohorts (both 0%). 16-week PFS for synovial sarcoma was 15.2% (n = 5). Grade ≥3 treatment-related adverse events occurred in 10% of patients. Tazemetostat demonstrated preliminary antitumor activity in a subset of poor-prognosis cancers, underscoring the need for combination strategies when EZH2 signaling is not the sole disease driver.

BACKGROUND:Convex probe endobronchial ultrasound (EBUS) bronchoscopy-guided transbronchial needle aspiration (TBNA) is the mainstay of mediastinal and hilar lesion sampling, and EBUS-TBNA allows for the acquisition of cytologic material. However, certain clinicopathologic conditions require the acquisition of histopathologic specimens. This can be accomplished via EBUS-guided transbronchial mini-forceps biopsy (TBFB) and cryobiopsy (TBCB), but the incremental value of these -modalities in various clinicopathologic conditions has yet to be explored. OBJECTIVE:Define the incremental value of EBUS-guided TBFB and TBCB over TBNA via evaluation of diagnostic yield, tissue quality, and adequacy for ancillary assays. METHODS:All patients who underwent EBUS-TBNA supplemented by TBFB and/or TBCB across 2 large academic centers were reviewed retrospectively. Cytology and histopathology tissue specimens were scrutinized for quantity, quality, tissue diagnosis, and adequacy for immunohistochemistry, molecular assays, and flow cytometry. Comparisons were made across TBNA, TBFB, and TBCB, as well as with a control group of EBUS-TBNA-only procedures for safety and procedural duration. RESULTS:A total of 204 lesions were sampled in 156 patients. Overall diagnostic yield was similar across TBNA, TBFB, and TBCB (P = .7); however, TBFB and TBCB outperformed TBNA for the diagnosis of lymphoproliferative and inflammatory conditions (P = .03 and P < .001, respectively). Compared with TBNA and TBFB, TBCB provided higher-quality tissue for immunohistochemistry and molecular profiling assays (P = .002 and P < .001, respectively). Adequacy of TBNA for flow cytometry outperformed that of TBFB and TBCB (P < .001). Compared with TBFB, TBCB tissue specimens provided more diagnostic tissue (P < .0001) with less crush artifact (P < .0001). The rate and severity of procedure-related complications were similar across study cases and the EBUS-TBNA-only control group. CONCLUSIONS:For the sampling of mediastinal and hilar lesions, supplementation of EBUS-TBNA by TBFB or TBCB should be primarily considered when suspecting a lymphoproliferative or an inflammatory etiology or when high-quality tissue is -required for predictive immunohistochemistry and molecular assays. For accurate diagnosis and classification of lymphomas, the combination of TBNA for flow cytometry with TBCB for histopathologic interpretation appears to be optimal.

Supplementary Figure S10. HER2-Directed Therapy Response Modifying Alterations In Select Cancers (Related To Figure 4) Co-occurrence of alterations that have been reported to impact response to HER2-directed therapies (mAB, TKI, ADC) in tumors with ERBB2 amplification or ERBB2 activating mutations including TP53 MUT, PIK3CA MUT, CCNE1 AMP, RB1 MUT/DEL, PTEN MUT/DEL, ERBB3 AMP/MUT, EGFR MUT, MET AMP/Ex14 MUT, and IGF1R AMP. Patients with multiple ERBB2 alteration types (e.g., AMP + MUT) were excluded from the analysis. ADC, Antibody-Drug Conjugate; AMP, Amplification; mAB, Monoclonal Antibodies; MUT, Mutation (SNV, Indel); TKI, Tyrosine Kinase Inhibitor.

Concurrent genomic drivers in cases with oncogenic / likely oncogenic MET tyrosine kinase domain (TKD) mutations and co-occurring MET gene amplification in cohort #2.

BACKGROUND:NRG1 fusions are unique oncogenic drivers that activate the HER3/HER2/PI3K pathway. The US Food and Drug Administration granted accelerated approval to a HER2/HER3 antibody, zenocutuzumab, for treatment of NRG1 fusion-positive non-small cell lung cancer and pancreatic ductal adenocarcinoma (PDAC). The optimal detection methods and clinicopathological features of patients with NRG1 fusion-positive cancer have not been systematically studied. Here, we review NRG1 fusion-positive cancer and focus on outcomes in PDAC. METHODS:Patients with NRG1 fusion-positive disease at Memorial Sloan Kettering Cancer Center were identified using institutional databases. Clinicopathological data were extracted from medical records. NRG1 fusion-positive PDAC cases underwent review of radiology, pathology, treatment data, and assessment of progression-free and overall survival. RESULTS:Of 76 531 patients, 48 NRG1 fusion-positive cases were identified. The most common tumor types were lung (60%), PDAC (21%), and breast (10%). Approximately half (46%) of these patients received HER2- and/or HER3-directed therapy. Patients were identified by RNA (n = 34), DNA (n = 11), or both (n = 3). RNA was superior to DNA for fusion identification. Twenty-one fusion partners were detected, most commonly CD74 (40%) and ATP1B1 (10%). Lung cancers were otherwise driver negative, and PDAC cases were KRAS wild type. NRG1 fusion-positive PDAC exhibited distinct histopathological and clinical features. Median patient age was 48.5 years, median progression-free survival on first-line chemotherapy was 12.6 months (n = 7; 95% confidence interval [CI] = 2.9 to not reached), and median overall survival from diagnosis was 39.6 months (n = 9; 95% CI = 23.2 to not reached). CONCLUSIONS:NRG1 fusions are a newly described, clinically actionable target in solid tumors. We report the landscape of NRG1 fusion-positive cancers and highlight the importance of RNA testing. NRG1 fusion-positive PDAC is enriched in younger patients with KRAS wild-type disease and has unique biology.

Additional information regarding the methods used in this study

Detailed genomic characteristics for each case of NSCLC with oncogenic / likely oncogenic MET tyrosine kinase domain (TKD) mutations in cohort #1.

Clinicopathologic and genomic characteristics of 171 cases of cancers other than NSCLC harboring oncogenic / likely oncogenic MET TKD mutations in cohort #2.

Study flowchart. Cohort #1 (multi-institutional cohort): GENIE V.11.0, China Pan-cancer (OrigiMed2020, Nature 2022), The Cancer Genome Atlas (TCGA) Pan-Cancer Atlas studies, Dana-Farber Cancer Institute (DFCI) and NSCLC from Memorial Sloan Kettering Cancer Center (MSKCC); cohort #2: Foundation Medicine Pan-Cancer cohort.

Abstract ALK gene fusions drive oncogenesis in ∼5% of lung adenocarcinomas (LUADs), and ALK tyrosine kinase inhibitors (TKIs) such as lorlatinib have improved outcomes. However, acquired resistance remains a challenge, with >30% of mechanisms unknown. To uncover novel drivers of resistance, we performed multi-omic profiling of clinical samples and PDXs. Genomic analysis of 83 ALK+ LUADs revealed frequent co-occurring alterations, including CDKN2A deletion (34%), TP53 mutation (32%), and MYC amplification (13%). Transcriptomic profiling highlighted enrichment of DNA replication and repair pathways, MYC targets, epithelial-to-mesenchymal transition, and TGF-β signaling in resistant tumors. scRNAseq of matched sensitive and resistant PDXs revealed extensive heterogeneity and diverse resistance pathways, mirroring those in clinical samples. Notably, elevated DNA replication and repair activity strongly correlated with TP53 missense mutations in clinical samples. Analysis of MSK clinical cohort showed that 80% of TP53 mutations in ALK+ LUAD occur in the DNA-binding domain, predominantly missense variants with potential gain-of-function (GOF) properties. The presence of TP53 missense mutations predicted worse prognosis in ALK-fusion LUAD patients treated with TKIs.To assess the role of mutp53 in resistance, we overexpressed R175H and R273H in ALK+ H3122 and H2228 cells. Co-immunoprecipitation and mass spectrometry revealed that mutp53 associates with DNA repair, cell cycle, and chromatin remodeling proteins. Mutp53-expressing cells were refractory to lorlatinib compared to isogenic p53-deficient clones. Overexpression of mutp53 upregulated DNA replication proteins, including ORC and MCM family members, as well as DNA repair proteins such as BRCA1, ATM, CHEK1, and MSH6. Notably, mutp53-expressing cells maintained DNA replication and repair protein levels following lorlatinib-induced DNA damage, unlike p53-deficient counterparts. Immunofluorescence of the DNA damage marker pH2A demonstrated complete repair of lorlatinib-induced lesions in the presence of mutp53, revealing a novel GOF role for these mutants. Furthermore, mutp53 enhanced DNA synthesis by promoting origin firing, thereby facilitating cellular survival under targeted therapy. Similar effects were observed in EGFR-driven LUAD cells, indicating that mutp53 contributes to resistance across oncogene-driven LUADs.To target this axis, we tested the proteasome inhibitor carfilzomib which inhibited mutp53 proteins and promoted the degradation of DNA replication proteins. Carfilzomib synergized with lorlatinib in resistant ALK+ p53 mutant cells and induced robust tumor response in TP53 mutant ALK+ PDX models resistant to lorlatinib, demonstrating therapeutic potential. In summary, missense mutp53 promotes ALK TKI resistance by enhancing DNA replication and repair. Citation Format: Esther Redin, Barbara P. Mello, Yingian A. Zhan, Nicholas Socci, Samuel Tischfield, Alexander Lim, Hong Zhong, Mark Donoghue, Richard Koche, Elisa De Stanchina, Alexander Drilon, Alvaro Quintanal-Villalonga, Charles M. Rudin. Missense mutant p53 regulates DNA replication and damage response to promote resistance to targeted therapies in ALK fusion lung adenocarcinoma [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 7042.