Non-small Cell Lung Cancer Cohort Research Articles

Role of synthetic lethal mutations for the immune response: Exploratory studies of two non-small cell lung cancer cohorts and two pan-cancer cohorts.

e21137 Background: Synthetic lethality (SL) is a phenomenon in which mutations in either of two genes do not affect cell survival, but abnormalities in both genes lead to cell death. However, it is little known whether synthetic lethality affects the response of immunotherapy. Methods: Synthetic lethal gene pairs come from the SynLethDB database, which provides a webserver to calculate the confidence scores for each SL pair by integrating individual scores derived from different evidence sources. The analysis included two immunotherapy cohorts of non-small cell lung cancer (Chan, 2015 and Hellmann, 2018) and two solid tumor cohorts (Morris, 2019 and Berger, 2020) in the published literature. Synthetic lethal gene pairs were defined as genes with a score > 0.5. The patients with synthetic lethal gene pairs were divided into one subgroup (SL group), and the other patients were divided into another subgroup (non-SL group). Kaplan-Meier analysis was used to determine progression-free (PFS) and overall survival (OS). Results: Overall, four public cohorts with 12271 patients were included in the analysis. In the cohort of Chan 2015, a total of 34 patients with non-small cell lung cancer (NSCLC) received immunotherapy. Among them, 21 patients were in the SL group and 13 were in the non-SL group, with the former having a significantly longer PFS (p = 0.0345). In the other cohort of immunotherapy (Hellmann, 2018), 90 (37.5%) patients with NSCLC were in SL group. PFS for patients with SL group was significantly longer than those in non-SL group (p = 0.0261). In cohorts with pan-cancer, patients in Morris 2019 cohort (n = 1661) received immunotherapy and patients in Berger 2020 cohort (n = 10336) received other kinds of treatment. A better prognosis was observed in patients with the immunotherapy in SL group than non-SL group (p < 0.0001). In contrast, patients with other kinds of treatment had a significantly worse prognosis in SL group than non-SL group (p < 0.0001). Conclusions: Our results suggested that synthetic lethal gene pairs containing scores greater than 0.5 may be associated with higher progression-free survival in patients with various types of tumors. The specific reasons for the impact still need to be further explored.

A phase 1, open-label, first-in-human study of TAS2940 in patients with advanced solid tumors.

TPS3165 Background: Aberrant expression and signaling of the ERBB family of receptor tyrosine kinases, including epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2), has a role in the pathogenesis of solid tumors such as breast cancer (BC), non–small cell lung cancer (NSCLC), and glioblastoma (GBM). Although therapies that target HER2 are effective in early and advanced HER2-overexpressing BC, many patients develop resistance despite tumor dependence on HER2 at the time of progression. Approximately 4% of patients with NSCLC have HER2 mutations, mostly presenting as exon 20 insertions (ex20ins); however, approved HER2/EGFR tyrosine kinase inhibitors (TKIs) have limited efficacy in patients with NSCLC and HER2 ex20ins. Many patients with NSCLC or BC develop brain metastases, and EGFR alterations, including EGFRvIII mutations, are common in GBM. There is therefore a need for a brain-penetrable TKI with activity against tumors harboring HER2/EGFR alterations. TAS2940 is a potent, selective, and orally bioavailable pan-ERBB inhibitor that has shown promising preclinical efficacy against cancers with a variety of HER2/EGFR mutations and amplifications. Further, TAS2940 inhibited tumor growth and induced tumor regression in a dose-dependent manner in nude mice intracranially implanted with NCI-N87, a HER2-overexpressing human gastric cancer cell line. Methods: TAS2940-101 (NCT04982926) is an open-label, phase 1, first-in-human trial to evaluate the safety, tolerability, pharmacokinetics (PK), and preliminary antitumor activity of TAS2940 in patients with advanced solid tumors and HER2/ EGFR aberrations. Eligible patients are aged ≥18 years, have non-measurable (Part 1) or measurable (Part 1 and 2) disease per RECIST 1.1 or RANO criteria, ECOG performance status 0/1, and adequate organ function. Patients with non-stable brain metastases are excluded. Part 1 (dose escalation) will use a Bayesian optimal interval design with a starting dose of 15 mg/kg orally QD (planned dose levels: 15, 30, 60, 120, 240 and 480 mg). Once the recommended phase 2 dose is determined, Part 2 (dose expansion) will enroll patients with NSCLC (Cohort A), HER2+ BC (Cohort B), recurrent/refractory GBM (Cohort C), or other solid tumors with EGFR/ HER2 aberrations (Cohort D). The primary objectives are the maximum tolerated dose of TAS2940 in Part 1 and antitumor activity in Part 2. Secondary objectives include antitumor activity in Part 1. The safety and PK profile of TAS2940 will be assessed in both parts. Approximately 142 patients will be enrolled, comprising ~42 in Part 1 and ~100 in Part 2. As of January 24, 2023, 15 patients have been enrolled. No dose-limiting toxicities have been reported with dose escalation up to 240 mg QD. Recruitment is ongoing. Clinical trial information: NCT04982926 .

Homologous recombination deficiency (HRD) in non-small cell lung cancer: Genomic analysis using an RNA-based HRD algorithm.

3123 Background: Recent evidence has suggested that some patients with non-small cell lung cancer (NSCLC) harbor a HRD signature that represents a distinct genomic subtype that could be targeted by PARP inhibitors (PARPi). However, there is little data on HRD prevalence in NSCLC or its genomic associations. Here, we evaluated the co-occurrence of driver mutations and established immune biomarkers with an RNA-based HRD signature in a large, real-world NSCLC cohort. Methods: We analyzed data from 5119 NSCLC patients that underwent sequencing via the Tempus xT test (DNA-seq of 648 genes; RNA-seq with whole exome capture). HRD status was predicted by the Tempus HRD-RNA test, a pan-cancer logistic regression classifier that uses an RNA gene expression signature optimized to distinguish between BRCA-biallelic loss and homologous recombination repair (HRR)-WT samples (Leibowitz et al, 2022). Cohort samples were excluded from model training. All comparisons were tested via chi-squared or Fisher’s exact tests. Results: An RNA-derived signature of HRD (HRD-RNA+) was observed in 3.53% (n=181/5119) of patients. HRD-RNA+ prevalence was higher in squamous cell carcinoma (84/1331, 6.3%) relative to adenocarcinoma (68/3015, 2.3%; p < 0.001). The prevalence of select alterations by HRD-RNA status are shown in Table. Alterations in BRCA1/2 and HRR genes (inclusive of BRCA1/2) were enriched in HRD-RNA+ vs. HRD-RNA- cases (8.8% vs. 2.5%, p < 0.001; 22% vs. 15%, p = 0.008 respectively). Notably, 141 (78%) HRD-RNA+ patients had no alterations in HRR genes. Of all NCCN targetable driver mutations assessed, KRAS G12C and ALK fusions were the only targetable drivers with significantly different prevalence in HRD-RNA+ vs. HRD-RNA- patients. Across the entire cohort, NCCN driver mutations were depleted in HRD RNA+ patients (18% in HRD-RNA+ vs. 30% in HRD-RNA-, p < 0.001). Immune biomarkers (TMB, PD-L1) did not vary by HRD-RNA status. Conclusions: Compared to HRD-RNA- NSCLC, HRD-RNA+ NSCLC represents a unique, molecularly defined subset that has a decreased prevalence of NCCN-driver mutations and is not enriched for TMB-H or PD-L1 expression. Further, this signature increases the number of patients classified as HRD-RNA+ compared to HRR gene alterations alone. Functional characterization (e.g. RAD51 foci immunofluorescence assay) and clinical benefit of targeted HRD therapies such as PARPi should be explored in this HRD-RNA+ population. [Table: see text]

CD57+CD8+ T cells and response to PD-1/PD-L1 blockade in patients with NSCLC.

e21189 Background: Immune checkpoint inhibitors (ICIs) are currently widely used and have made significant advances in the treatment of patients with advanced non-small cell lung cancer (NSCLC). Despite available biomarker stratification, clinical responses vary. Thus, potential biomarkers for identifying patients who will benefit from the immunotherapy are urgently needed. Methods: We applied mass cytometry (CyTOF) to deeply analyze the association of cell subpopulations in PBMC before and after single-agent immunotherapy with clinical outcomes in advanced NSCLC. We then performed flow cytometry of peripheral blood and multiplex immunohistochemistry/immunofluorescence (mIHC/IF) of tumor samples to validate our conclusion. In addition, RNA sequencing (RNA-seq) was performed to explore the mechanism of the ICIs treatment efficacy of NSCLC. Results: In a prospective cohort (n = 20), high CD57+ CD8+ T cell proportion in PBMC detected by CyTOF was associated with good response ( p= 0.014) in advanced NSCLC patients. The result was confirmed in an independent, prospective cohort (n = 30) using flow cytometry, and the specificity and sensitivity of flow cytometry was then assessed in this cohort. CD57+CD8+ T cell proportion, as determined by flow cytometry, successfully stratified responders and non-responders to ICIs ( P< 0.001). We also confirmed this result in FFPE samples (n = 31) ( p= 0.004). In addition, transcriptomic differences between CD57+CD8+ T cells and CD57-CD8+ T cells were found performed by RNA sequencing (RNA-seq). Conclusions: Our results suggest that CD57+CD8+ T cell proportion may serve as a predictive value of response to PD-1/PD-L1 checkpoint blockade. Further validation in additional NSCLC cohorts is warranted.

A phase I trial of sequential dosing of sonidegib and pembrolizumab in advanced solid tumors (aST) and non–small-cell lung cancer (NSCLC).

9093 Background: Pembrolizumab interrupts PD-1/-L1 interaction and is efficacious in many cancers. However, resistance invariably emerges in the majority of patients. Potential mechanisms include activation of compensatory pathways. The inhibition of sonic hedgehog signaling (sHH) was previously shown to induce intra-tumoral (IT) infiltration by CD4+, CD8+ and HLA-DR class II cells. Our preclinical data showed sHH inhibitor enhanced IT penetration by monoclonal antibodies and induced PD-L1 expression. We conducted a phase I study using a novel sequential pulse dosing of sonedegib followed by pembrolizumab in aST with an expansion cohort to determine the maximum tolerated dose (MTD), tolerability and preliminary efficacy. Methods: The dose escalation utilized a 3+3 design to determine the MTD and proceeded to expansion cohort upon determination of the MTD. Patients enrolled to each dose level were observed for dose limiting toxicities (DLTs) during the 1st cycle. The expansion cohort consisted of NSCLC and head/neck squamous cell carcinoma (HNSCC) previously treated by anti-PD1/-L1. The recommended phase 2 dose (RP2D) was determined following the review of the toxicity profile of the combination from all cycles. The study treatment consisted of sonidegib oral daily from day 1 to 8 and pembrolizumab I.V. 200 mg on day 8 on an every 3-week cycle. The sonidegib dose levels explored were 400, 600 and 800 mg. Archival tumor and blood specimens were collected for correlative studies. Adverse events (AEs) were categorized and graded per CTCAE v5.0, and tumor response by RECIST v1.1. Results: The study enrolled a total of 33 patients and 29 received treatment (13 in escalation and 16 in expansion), including patients with NSCLC, HNSCC, skin cancer, gastric cancer and melanoma. The enrollment to the NSCLC cohort is complete and HNSCC continues. No DLT was encountered during dose escalation and the MTD was not reached. The highest planned dose level was selected to proceed to expansion (sonidegib 800mg days 1-8 in combination with pembrolizumab I.V. 200 mg on day 8 on an every 3-week cycle). The expansion cohort proceeded to enroll 15 patients evaluable for AEs (10 NSCLC and 5 HSNCC). Grade 3 and above treatment-related AEs across all patients were hyperglycemia, fatigue, dyspepsia, abdominal pain. The mature efficacy data will be reported at the meeting. Conclusions: The study successfully determined the RP2D of sonidegib when dosed sequentially with pembrolizumab in advanced solid tumors. The AE profile of the combination is similar to that for respective agents given individually. The efficacy data among anti-PD1/-PDL1-treated NSCLC will be reported at the meeting. Clinical trial information: NCT04007744 .

The GENIE BPC NSCLC Cohort: A Real-World Repository Integrating Standardized Clinical and Genomic Data for 1,846 Patients with Non-Small Cell Lung Cancer.

We describe the clinical and genomic landscape of the non-small cell lung cancer (NSCLC) cohort of the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC). A total of 1,846 patients with NSCLC whose tumors were sequenced from 2014 to 2018 at four institutions participating in AACR GENIE were randomly chosen for curation using the PRISSMM data model. Progression-free survival (PFS) and overall survival (OS) were estimated for patients treated with standard therapies. In this cohort, 44% of tumors harbored a targetable oncogenic alteration, with EGFR (20%), KRAS G12C (13%), and oncogenic fusions (ALK, RET, and ROS1; 5%) as the most frequent. Median OS (mOS) on first-line platinum-based therapy without immunotherapy was 17.4 months [95% confidence interval (CI), 14.9-19.5 months]. For second-line therapies, mOS was 9.2 months (95% CI, 7.5-11.3 months) for immune checkpoint inhibitors (ICI) and 6.4 months (95% CI, 5.1-8.1 months) for docetaxel ± ramucirumab. In a subset of patients treated with ICI in the second-line or later setting, median RECIST PFS (2.5 months; 95% CI, 2.2-2.8) and median real-world PFS based on imaging reports (2.2 months; 95% CI, 1.7-2.6) were similar. In exploratory analysis of the impact of tumor mutational burden (TMB) on survival on ICI treatment in the second-line or higher setting, TMB z-score harmonized across gene panels was associated with improved OS (univariable HR, 0.85; P = 0.03; n = 247 patients). The GENIE BPC cohort provides comprehensive clinicogenomic data for patients with NSCLC, which can improve understanding of real-world patient outcomes.

Diagnostic significance of CA-62 cancer antigen for early detection and differential diagnosis of non-small cell lung cancer: results of the blind clinical trials

Background. The combination of several diagnostic methods is used to predict treatment outcomes, assess overall survival, and increase the positive predictive value of detecting malignant lung and bronchial tumors.
 Aim. To evaluate the diagnostic value of the CLIA-СА-62 chemiluminescence immunoassay reagent kit for the detection of early (IaIIb) and advanced (IIIac) stages of lung cancer (LC) in a double-blind clinical study and to assess the use of the CA-62 cancer antigen as a supportive decision-making tool in LC diagnosis in patients with suspicious changes on the tomogram or as a tool for pre-screening of LC prior to computed tomography (CT) to increase diagnostic sensitivity in the detection of early (I and II) stages of LC.
 Materials and methods. A blinded clinical study was conducted on 304 clinically verified serum samples, including 141 samples from patients with non-small cell LC (NSCLC), 133 healthy volunteers, and 30 chronic obstructive pulmonary disease patients. Quantification of other well-known tumor markers used in the diagnosis of LC (CEA, CA-125, CA 15-3, CA 19-9, CYFRА 21-1, NSE, and SCC), as well as the CA-62 marker in all serum samples was performed using electrochemiluminescent immunoassay Elecsys CA-125, ELECSYS CA 19-9, ELECSYS CYFRА 21-1 and ELECSYS SCC (COBAS, Roche Diagnostics GmbH, Germany, EU), enzyme-linked immunoassay CA 15-3-ELISA-BEST, CEA-ELISA-BEST, NSE-ELISA-BEST (AO Vector-Best, Russia) and chemiluminescent immunoassay CLIA-СА-62 (JVS Diagnostics, Skolkovo, Moscow, Russia).
 Results. CA-62 glycoprotein showed the highest level of expression at stage I NSCLC (12 745 U/mL) compared to other tumor markers studied and remained very high at the later stages of cancer: stage II (11 261 U/mL) and stage III (10 220 U/mL). A comparative analysis of the ROC curves of the most promising tumor markers CEA, CYFRA 21-1, SCC, and CA-62 for the entire NSCLC cohort versus all healthy volunteers and patients with chronic obstructive pulmonary disease showed a significant difference in the area under the curve between CA-62 (AUC 0.981) and other markers: CEA (AUC 0.84) CYFRA 21-1 (AUC 0.753)SCC (AUC 0.682). When detecting early stages (I and II) of NSCLC, a comparison of the sensitivity of the studied tumor markers showed the following pattern: CA-62 (92%)CEA (37%)CYFRA 21-1 (9%) and SCC (9%)NSE (4.5%)CA-125 (3%)CA 15-3 (1.5%)CA 199 (1%). In contrast to the CEA, CA 15-3, CA-125, NSE, CA 19-9, CYFRA 21-1, and SCC tumor markers, which are expressed proportionally to tumor growth, the epithelial carcinoma marker CA-62 showed the highest diagnostic indicators in the detection of LC early stages (III): sensitivity 92.5%, specificity 96.3%, positive predictive value 91.2%, NPV 97%, with 95% accuracy of LC detection with biopsy.
 Conclusion. The study results showed that in order to increase the specificity of computed tomography in diagnosing LC in patients with suspicious lesion on the CT scan on the tomogram, the use of the carcinoma-specific marker CA-62 can improve the interpretation of the localized focus visualized and increase the accuracy of differential diagnosis at the early stages of LC to 96%, thus contributing to an increase of the overall survival among patients with lung cancer. Of the entire panel of markers, only glycoprotein CA-62 showed a strong correlation with histology (kappa 0.91) in identifying the malignant process with inconclusive results of low-dose CT (LDCT). In the future, introducing the CA-62 marker to the current system for assessing the LC risk as a pre-screening for LDCT can improve the detection of early LC by reducing false-positive results. Once introduced into existing screening programs, it can help significantly reduce the number of patients who need LDCT, decreasing the workload of LDCT and reducing radiation exposure.

A phase II open-label trial of avelumab plus axitinib in previously treated non-small-cell lung cancer or treatment-naïve, cisplatin-ineligible urothelial cancer

We hypothesized that avelumab plus axitinib could improve clinical outcomes in patients with advanced non-small-cell lung cancer (NSCLC) or urothelial carcinoma (UC). We enrolled previously treated patients with advanced or metastatic NSCLC, or untreated, cisplatin-ineligible patients with advanced or metastatic UC. Patients received avelumab 800 mg every 2 weeks (Q2W) and axitinib 5 mg orally two times daily. The primary endpoint was objective response rate (ORR). Immunohistochemistry was used to assess programmed death-ligand 1 (PD-L1) expression (SP263 assay) and the presence of CD8+ T cells (clone C8/144B). Tumor mutational burden (TMB) was assessed by whole-exome sequencing. A total of 61 patients were enrolled and treated (NSCLC, n= 41; UC, n= 20); 5 remained on treatment at data cut-off (26 February 2021). The confirmed ORR was 31.7% in the NSCLC cohort and 10.0% in the UC cohort (all partial responses). Antitumor activity was observed irrespective of PD-L1 expression. In exploratory subgroups, ORRs were higher in patients with higher (≥median) CD8+ T cells in the tumor. ORRs were higher in patients with lower TMB (<median) in the NSCLC cohort and higher TMB (≥median) in the UC cohort. Treatment-related adverse events (TRAEs) occurred in 93.4% of patients, including grade ≥3 TRAEs in 55.7%. Avelumab exposures with 800 mg Q2W dosing were similar to those observed with 10 mg/kg Q2W dosing. In previously treated patients with advanced/metastatic NSCLC, ORR appeared to be superior to anti-PD-L1 or anti-programmed cell death protein 1 monotherapy, irrespective of PD-L1 status, whereas in untreated, cisplatin-ineligible patients with advanced/metastatic UC, ORR was lower than expected, potentially limited by small patient numbers. Clinicaltrial.gov NCT03472560; https://clinicaltrials.gov/ct2/show/NCT03472560.

Abstract A003: COVALENT-102: A phase 1/1b dose finding study of BMF-219, an oral covalent menin inhibitor, in patients with metastatic non-small cell lung cancer (NSCLC), pancreatic cancer (PDAC), and colorectal cancer (CRC) with activating KRAS mutations

Abstract Background: BMF-219 is a selective covalent inhibitor of menin, a transcriptional regulator of oncogenic signaling pathways in multiple cancers, that inhibits the menin/MYC interaction and downregulates the expression of MYC and MYC target genes, including KRAS. Mechanism of Action (hypothesis): In addition to MYC disruption, inhibition of the Menin-MLL complex by BMF-219 alters JunD genomic function, a crucial factor for KRAS-driven tumorigenesis. Inhibition of the Menin-MLL complex suppresses expression of Rasgrf1, which is essential for generation of the active RAS-GTP conformation of KRAS, activation of downstream pathways, and tumorigenesis. Preclinically, BMF-219 shows sustained potent abrogation of menin-dependent oncogenic signaling. BMF-219 exerts pan-mutant KRAS anticancer activity that is independent of the specific KRAS-activating mutation. Methods: COVALENT-102 (NCT05631574) is a prospective, open-label, multicenter, dose finding study evaluating the safety, tolerability, and clinical activity of escalating doses of BMF-219 administered daily in patients with unresectable, locally advanced, or metastatic NSCLC (Cohort 1), PDAC (Cohort 2) &amp; CRC (Cohort 3) with activating KRAS mutations who have received standard therapy. All indications as a group will follow a 3+3 dose escalation design. BMF-219 will be administered orally daily as continuous therapy as 28-days treatment cycle until progression or intolerability/unacceptable toxicity. Following conclusion of the dose-escalation, each indication will enroll patients in expansion cohorts independently to obtain further safety and efficacy data. Eligible patients include those with any KRAS mutation &amp; (Cohort 1) stage IIIB/IV NSCLC with 2-4 prior lines of therapy including immune checkpoint inhibitors (ICI) &amp;/or platinum-based chemo ± bevacizumab with ECOG PS 0-2; (Cohort 2) stage III/IV PDAC with ≥ 1 prior line of therapy including either FOLFIRINOX or gemcitabine/nab-paclitaxel, ECOG PS 0-1; or (Cohort 3) stage III/IV CRC with ≥ 1 prior line of therapy including FOLFOX or FOLFIRI ± bevacizumab (prior ICI if MSI-H/dMMR), ECOG PS 0-2. Patients must have documented progression &amp; measurable disease as defined by RECIST 1.1. Patients with prior KRAS inhibitor exposure are eligible. Key exclusion criteria include symptomatic &amp;/untreated CNS metastasis, prior menin inhibitor therapy, and clinically significant cardiovascular disease. The primary objective is to determine the optimal biological dose (OBD)/recommended Phase 2 dose (RP2D) of BMF-219 monotherapy. Secondary objectives include further evaluation of safety &amp; tolerability, characterization of the pharmacodynamics and pharmacokinetics of BMF-219, and efficacy based on duration of response (DOR) &amp; disease control rate (DCR). Assessment of progression-free survival (PFS), overall survival (OS) &amp; time to response (TTR) are part of the exploratory endpoints. The first patient in the study is anticipated to be dosed in Q4 of 2022. Citation Format: Stacey A. Cohen, Christos Fountzilas, David Sommerhalder, Sandip Patel, Ai Benson, Kai He, Apar Ganti, Alex Spira, Bhagyashree (Kelshikar) Yadav, Alex Cacovean, Steve Morris, Tom Butler, David Hong. COVALENT-102: A phase 1/1b dose finding study of BMF-219, an oral covalent menin inhibitor, in patients with metastatic non-small cell lung cancer (NSCLC), pancreatic cancer (PDAC), and colorectal cancer (CRC) with activating KRAS mutations [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A003.

The diagnostic potential of a circRNA-miRNA network in non-small cell lung cancer.

Increasing studies demonstrate the significant contributions of circRNA-related competitive endogenous RNA (ceRNA) regulatory networks to tumorigenesis and cancer progression. Here, we aimed to construct a non-small cell lung cancer (NSCLC)-specific circRNA-miRNA network and evaluate its diagnostic potential in NSCLC. MiRNA deep sequencing was performed to screen differentially-expressed serum miRNAs in NSCLC. Four bioinformatics databases (TargetScan, miRanda, starBase, and RNAhybrid) were used to analyze the integrated circRNA-miRNA interaction network. The circRNA-miRNA network, including hsa-miR-4482-3p, hsa-miR-146a-3p, hsa_circ_0008167 and hsa_circ_0003317 was constructed based on their interactions and preliminary testing in NSCLC cells. The relative levels of the selected non-coding RNAs (ncRNAs) were quantified using quantitative real-time polymerase chain reaction (qRT-PCR) in the healthy, pneumonia, benign lung tumor and NSCLC cohorts. The diagnostic power of the circRNA-miRNA network was evaluated using receiver operating characteristic (ROC) analyses. The serum levels of hsa-miR-4482-3p, hsa-miR-146a-3p, hsa_circ_0008167, and hsa_circ_0003317 were dysregulated in NSCLC. The combination of the four ncRNAs showed the highest diagnostic value to discriminate between benign lung tumors and NSCLC. Additionally, the upregulated levels of hsa_circ_0008167 were correlated to more aggressive features of NSCLC, such as lymph node metastasis, distant metastasis, and higher stage. Furthermore, the combination of hsa_circ_0008167 + hsa-miR-4482-3p, and hsa_circ_0008167 + hsa-miR-4482-3p + hsa-miR-146a-3p had the greatest diagnostic power to differentiate between lymph node +/- metastases and higher/lower stages, respectively, compared to circRNAs or miRNAs alone, and traditional tumor markers. In conclusion, we identified a specific circRNA-miRNA network with higher sensitivity and specificity to diagnose NSCLC, thereby providing a new strategy for further development of ceRNA-related tumor markers in other cancers. KEY MESSAGES: Serum miR-4482-3p, miR-146a-3p, circ_0008167 and circ_0003317 are dysregulated in NSCLC. Higher levels of serum circ_0008167 are associated with more malignant NSCLC. Multiple combinations of circRNAs and miRNAs show higher value to diagnose NSCLC.

Abstract 5459: Association between stomatitis and treatment efficacy with novel TROP2-directed antibody drug conjugate (ADC), datopotamab deruxtecan, in patients with metastatic cancer

Abstract Background: Incidence of toxicity with immunotherapy has been correlated with likelihood of treatment response (Hussaini, Cancer Treat Rev 2021; Schuell, Br J Cancer 2005). However, this phenomenon has not yet been demonstrated with antibody-drug conjugates. Datopotamab deruxtecan (Dato-DXd) is a novel ADC composed of an anti-Trop2 monoclonal antibody, a stable tetrapeptide-based cleavable linker, and a topoisomerase-I inhibitor payload (Bardia, Annals of Onc 2021). Early phase studies have demonstrated significant activity in heavily pretreated patients with metastatic non-small cell lung cancer (NSCLC) and metastatic breast cancer (MBC). Stomatitis was a common treatment-emergent adverse event (TEAE) observed in clinical trials. We conducted a study to evaluate the association between incidence of stomatitis and treatment response with Dato-DXd and evaluate the impact of steroid mouthwash. We hypothesized that presence and grade of mucositis would correlate with observed treatment efficacy. Methods: We included all patients treated at one academic institution (Massachusetts General Hospital) with Dato-DXd. Stomatitis was assessed by NCI-CTCAE V5.0. Objective Response Rate (ORR) was assessed by RECIST criteria with independent radiology review. Use of mouthwash was evaluated by secondary review and categorized as primary or secondary prophylaxis. A time-to-event analysis was performed to evaluate the time to onset of stomatitis. Results: 60 patients, including 19 with MBC and 41 with NSCLC, were treated with Dato-DXd between June 2018-September 2022. The median age of patients was 64 and 41/60 patients were female. The median time to onset of mucositis was 14 days (95% CI 12-42 days). There was no significant difference in incidence of stomatitis between the MBC and NSCLC cohorts. Compared to patients who had progressive disease (PD), patients who had a partial response (PR) or stable disease (SD) were 11 times more likely to have stomatitis (OR 11.0, 95% CI 3.61-44.01, p&amp;lt;0.001). Later in the trial (January 2020 onward), 28 patients received primary steroid prophylaxis - excluding these patients, those who were found to have PR/SD were 8.8 times more likely to develop stomatitis compared to patients who had PD (OR 8.8, 95% CI 1.5-73.3, p=0.023). Conclusion: The development of stomatitis may be associated with higher likelihood of therapeutic efficacy. Given that these findings are a hypothesis-generating post-hoc exploratory analysis from a single institution, this requires validation in larger studies before drawing strong conclusions and impacting clinical decision making. Further research is also needed evaluate the relationship between TEAEs and therapeutic efficacy with other ADCs. Citation Format: Rachel O. Abelman, Laura M. Spring, Phoebe K. Ryan, Geoffrey Fell, Dejan Juric, Rebecca S. Heist, Aditya Bardia. Association between stomatitis and treatment efficacy with novel TROP2-directed antibody drug conjugate (ADC), datopotamab deruxtecan, in patients with metastatic cancer. [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 5459.

Abstract 2508: Clinical significance of PARP7 (TIPARP) gene copy number alterations in human non-small cell and head &amp; neck carcinomas

Abstract Introduction: PARP7, encoded by the TIPARP gene, is a monoART involved in cellular stress responses and with immunomodulatory functions in cancer. The PARP7 gene is amplified in a subset of squamous cell carcinomas and ongoing clinical studies are assessing its role as anti-cancer therapeutic target (NCT04053673, NCT05127590) Here, we analyzed the frequency of PARP7 copy number alterations and its association with tumor immune microenvironment (TIME) features and outcomes in non-small cell lung cancer (NSCLC) and head &amp; neck squamous-cell carcinoma (HNSCC) cohorts. Methods: The PARP7 gene copy number and amplification was analyzed using a dual probe fluorescence in situ hybridization (FISH) assay in two retrospective cohorts of NSCLC (Cohort #1, n=124) and HNSCC (Cohort #2, n=83) represented in tissue microarray format. In a subset of cases, the PARP7 copy number was also studied using whole exome DNA sequencing. The TIME was assessed on consecutive tumor sections using a multiplexed quantitative immunofluorescence panel including the markers DAPI, cytokeratin, CD4, CD8 and PD-L1 coupled to computational pathology analysis. The association between the markers, with clinicopathologic variables and survival was studied. Results: Increased PARP7 copy number (&amp;gt;2 copies/cell) was identified in 55% of NSCLCs (85% of them of squamous-cell histology) and 76% of HNSCCs. A high copy number (&amp;gt;3 copies/cell) was identified in 22% cases from both tumor type cohorts. After adjustment of the PARP7 gene copy number by the chromosome 3 centromeric probe (CEN3) signal, PARP7 amplification (&amp;gt;1.5 PARP7/CEN3 signal) was detected in 22% of NSCLC cases and 34% of HNSCC. A higher number of cases with PARP7 copy number gains were identified using FISH than with whole exome DNA sequencing. No significant associations between the PARP7 gains/losses and major clinicopathologic variables were found. However, higher PARP7 copy number was associated with reduced CD8+ or CD4+ tumor infiltrating lymphocytes (TILs) and a numerically lower tumor PD-L1 protein levels in HNSCC. Elevated PARP7 copy number was associated with shorter overall survival in both studied tumor types. Conclusion: Elevated PARP7 gene copy number identifies a subset of lung and head &amp; neck squamous-cell carcinomas with unfavorable TIME features and adverse prognosis. Detection of PARP7 gene abnormalities using FISH in tumor biopsy samples is sensitive and has potential as a predictive biomarker. Citation Format: Viviana A. Ahumada, Kristen McEachern, Kristy Kuplast-Barr, Kurt Alex Schalper. Clinical significance of PARP7 (TIPARP) gene copy number alterations in human non-small cell and head &amp; neck carcinomas [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 2508.

Abstract 6768: The potential predictive role of spatial phenotyping in non-small cell lung cancer

Abstract Background Lung cancers are the leading cause of cancer-related deaths with a 5-year-survival of only ~20%. Whilst immunotherapies have led to durable and prolonged survival, only a subset of patients remain responsive. Additional biomarkers are thus needed to better predict if patients will respond or develop resistance against immune checkpoint inhibitor (ICI) therapies. Spatial phenotyping of the tumor microenvironment (TME) is now recognized as a proxy for ICI therapy outcomes. Our study employs an end-to-end spatial biology strategy to survey non-small-cell lung cancer (NSCLC) tissues for new biomarkers that could guide immunotherapy treatments. Methods We phenotyped pre-treatment biopsies from non-small-cell lung cancer (NSCLC) patients treated with single-agent Nivolumab. We first performed 57-plex whole-slide Single Cell Spatial Phenotyping on the PhenoCycler®-Fusion platform. Next, we developed the spatial analysis of a larger NSCLC cohort using customizable PhenoCode Signature Panels (PSP) for high-throughput immune profile (CD3/CD8/CD20/CD68/PanCK + CD4 add-in) and immuno-contexture (CD8/CD68/PD-L1/FoxP3/PanCK + PD-1 add-in) imaging. The PSP panel content combines the barcode-based antibody chemistry from the PhenoCycler platform with the signal amplification of Opal chemistry from the PhenoImager platform. PSP panels were profiled across n=27 NSCLC biopsies and provided a wider breadth of tissue profiling. Results Our whole-slide single-cell spatial phenotyping analyses revealed high phenotypic diversity in the TME of patients responsive and resistant to ICI therapy. However, higher-throughput analyses of the same tissues using targeted PSP panels revealed no significant differences in quantities of immune cell lineages, including T-cells and macrophages. On the contrary, we discovered multiple quantifiable and statistically significant spatial signatures that appear to be predictive of treatment benefit, which confirms the potential biomarker value of spatial associations in patient tissues. Conclusions This study amounts to a uniquely comprehensive Single Cell Spatial Phenotyping analysis of pre-treatment NSCLC biopsies from a single-agent Nivolumab study. Our data catalogue the diversity in the immune microenvironment of NSCLC but highlighted that immune cell quantification is insufficient to stratify patient cohorts. Single-cell spatial phenotyping, on the other hand, promises to reveal new biomarkers that may aid in better stratification of patients in pre-treatment evaluations. Citation Format: Ning Ma, Aditya Pratapa, James Monkman, Ken O’Byrne, Oliver Braubach, Arutha Kulasinghe. The potential predictive role of spatial phenotyping in non-small cell lung cancer [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 6768.

Integrative analyses of bulk and single-cell RNA-seq identified cancer-associated fibroblasts-related signature as a prognostic factor for immunotherapy in NSCLC.

An emerging view regarding cancer-associated fibroblast (CAF) is that it plays a critical role in tumorigenesis and immunosuppression in the tumor microenvironment (TME), but the clinical significance and biological functions of CAFs in non-small cell lung cancer (NSCLC) are still poorly explored. Here, we aimed to identify the CAF-related signature for NSCLC through integrative analyses of bulk and single-cell genomics, transcriptomics, and proteomics profiling. Using CAF marker genes identified in weighted gene co-expression network analysis (WGCNA), we constructed and validated a CAF-based risk model that stratifies patients into two prognostic groups from four independent NSCLC cohorts. The high-score group exhibits a higher abundance of CAFs, decreased immune cell infiltration, increased epithelial-mesenchymal transition (EMT), activated transforming growth factor beta (TGFβ) signaling, and a limited survival rate compared with the low-score group. Considering the immunosuppressive feature in the high-score group, we speculated an inferior clinical response for immunotherapy in these patients, and this association was successfully verified in two NSCLC cohorts treated with immune checkpoint blockades (ICBs). Furthermore, single-cell RNA sequence datasets were used to clarify the molecular mechanisms underlying the aggressive and immunosuppressive phenotype in the high-score group. We found that one of the genes in the risk model, filamin binding LIM protein 1 (FBLIM1), is mainly expressed in fibroblasts and upregulated in CAFs compared to fibroblasts from normal tissue. FBLIM1-positive CAF subtype was correlated with increased TGFβ expression, higher mesenchymal marker level, and immunosuppressive tumor microenvironment. Finally, we demonstrated that FBLIM1might serve as a poor prognostic marker for immunotherapy in clinical samples. In conclusion, we identified a novel CAF-based classifier with prognostic value in NSCLC patients and those treated with ICBs. Single-cell transcriptome profiling uncovered FBLIM1-positive CAFs as an aggressive subtype with a high abundance of TGFβ, EMT, and an immunosuppressive phenotype in NSCLC.

Adjuvant durvalumab after concurrent chemoradiotherapy for patients with unresectable stage III NSCLC harbouring uncommon genomic alterations

Adjuvant durvalumab is the standard of care for patients with stage III unresectable non-small cell lung cancer (NSCLC), without progression after concurrent chemo-radiation (CCRT). Patients with stage III NSCLC harbouring epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase rearrangements do not seem to benefit from durvalumab. Data are lacking about patients harbouring other driver genomic alterations (dGA). We performed a multicentre (N = 4, Netherlands and Italy) retrospective study including consecutive patients with unresectable stage III NSCLC and treated with CCRT—with or without adjuvant durvalumab—between 2016 and 2022. We enrolled 271 patients; 130 of which received adjuvant durvalumab. Sixty-six patients had dGA (41 KRAS mutations, 4 EGFR common mutations and 21 uncommon dGA). In the entire population, the median PFS was 24.9 months (95% CI 17.5–32.4) and 12.6 months (95% CI 9.0–16.1) with and without durvalumab (p = 0.001). In the dGA group (excluding common EGFR), mPFS was 12.3 months (95% CI 7.8–16.8) with and 7.6 (95% CI 3.4–11.9) without durvalumab (p = 0.038). For patients with KRAS mutations, mPFS was 12.3 months (95% CI 3.6–20.9) with and 7.2 months (95% CI 1.8–12.6) without durvalumab (p = 0.12). Among patients with uncommon dGA, mPFS was 12.9 months (95% CI 8.4–17.4) with and 7.6 months (95% CI 1.4–14) without durvalumab (p = 0.23). We have shown a meaningful survival benefit of adjuvant durvalumab in patients harbouring KRAS mutations and uncommon dGA. This is the largest stage III NSCLC cohort showing the efficacy of durvalumab in patients with uncommon dGA. Further prospective studies are needed to confirm our results.

PBRM1 mutation as a predictive biomarker for immunotherapy in multiple cancers.

Background: There has been evidence that Polybromo-1 (PBRM1) mutation was closely associated with immunotherapy response in clear cell renal cell carcinoma (ccRCC). However, it remains incompletely unclear whether PBRM1 mutations correlate with ICI response in pan-cancer. Methods: The clinical data and whole exome sequencing (WES) data were collected from seven published immunotherapy studies to evaluate the association between PBRM1 mutation and ICIs efficacy in the discovery cohort. In order to provide further insight into the relationship between PBRM1 and immunity, we analyzed a relatively large sample as a validation cohort. Moreover, we also collected the clinical data and mutation information of 134 non-small cell lung cancer (NSCLC) patients from the First Affiliated Hospital of Nanjing Medical University to verify the findings. Gene set enrichment analysis (GSEA) was used to evaluate the relationship between PBRM1 and immune-related pathway. Results: Our results found that PBRM1 mutation were associated with immune response in the discovery cohort (Progression free survival [PFS]: hazard ratio (HR) = .51, 95% CI: .28-.95, p = .030; objective response rate [ORR]: 47.92% vs. 28.21%, p = .0044; disease control rate [DCR]: 72.92% vs. 47.53%, p = .0008). In the validation cohort, the patients with PBRM1 mutation had a longer overall survival (OS) (hazard ratio = .69, 95% CI: .53-.91, p = .006). In our non-small cell lung cancer cohort, PFS, objective response rate and disease control rate had obvious superiority in the patients with PBRM1 mutation than those without PBRM1 mutation (PFS: HR = .268, 95% CI: 084-.854, p = .04, ORR: 55.56% vs. 20.00%, p = .027, DCR: 100% vs. 75.20%). Using the Gene set enrichment analysis (GSEA) in TCGA cohorts, PBRM1 mutation was closely related to immune efficacy and immune microenvironment, including killer cell mediated immunity regulation, cell cytokine production, CD8+ T-cell activation and MHC protein binding process. Conclusion: There is a strong correlation between PBRM1 mutation and prognosis and immune response. Based on the findings, PBRM1 mutation may be a promising immunotherapeutic signature that could guide clinical management and personalized immunotherapy.

Molecular epidemiology and clinical characteristics of epidermal growth factor receptor mutations in NSCLC: A single-center experience from India.

The genetic profiling of non-small cell lung cancer (NSCLC) has contributed to the discovery of actionable targetable mutations, which have significantly improved outcomes in disease with poor prognosis. Molecular epidemiological data of driver mutations in Indian populations have not been extensively elaborated compared to western and eastern Asian NSCLC populations. This study assessed the prevalence and clinical outcomes of EGFR (epidermal growth factor receptor) mutations among the Indian NSCLC cohort in South India. Retrospective analysis of 2,003 NSCLC patients who had undergone EGFR mutational analysis from 2013 to 2020 was performed. Clinical analysis was performed for 141 patients from 2013 to 2017 using Kaplan-Meier and Chi-square methods. Descriptive and survival statistics were performed using IBM SPSS Statistics for Windows, Version 23.0. Armonk, NY: IBM Corp. EGFR-sensitizing mutations were detected in 41.6% (834/2003) in the study cohort with compound mutations detected in 7.55% (63/834) of EGFR-positive cases. A significant relationship with regard to female gender and EGFR mutation status (P <.001) was observed. Exon 18 G719X (8.7%) mutations and exon 20 T790M point mutation (3.1%) were the most frequently isolated uncommon EGFR mutations. In the clinical cohort, EGFR mutations were detected at a significantly higher prevalence in females (P =0.002) and never-smokers (P < 0.001). EGFR mutation demonstrated a significant relationship with regard to brain metastasis (P = 0.011). EGFR mutated individuals had significantly longer median overall survival compared to EGFR wild type (26 months vs. 12 months, P = 0.044). We reports the highest number of EGFR mutation analysis performed from India and mutational analysis indicated a loco-regional variation in India with regard to EGFR mutation frequency and its subtypes.

Non‑small cell lung cancer carrying PBRM1 mutation suggests an immunologically cold phenotype leading to immunotherapy failure even with high TMB

High tumor mutation load (TMB-H, or TMB ≥ 10) has been approved by the U.S. FDA as a biomarker for pembrolizumab treatment of solid tumors, including non‑small cell lung cancer (NSCLC). Patients with cancer who have immunotherapy-resistant gene mutations cannot achieve clinical benefits even in TMB-H. In this study, we aimed to identify gene mutations associated with immunotherapy resistance and further informed mechanisms in NSCLC. A combined cohort of 350 immune checkpoint blockade-treated patients from Memorial Sloan Kettering Cancer Center (MSKCC) was used to identify genes whose mutations could negatively influence immunotherapy efficacy. An external NSCLC cohort for which profession-free survival (PFS) data were available was used for independent validation. CIBERSORT algorithms were used to characterize tumor immune infiltrating patterns. Immunogenomic features were analysed in the TCGA NSCLC cohort. We observed that PBRM1 mutations independently and negatively influence immunotherapy efficacy. Survival analysis showed that the overall survival (OS) and PFS of patients with PBRM1 mutations (MT) were significantly shorter than the wild type (WT). Moreover, compared with PBRM1-WT/TMB-H group, OS was worse in the PBRM1-MT/TMB-H group. Notably, in patients with TMB-H/PBRM1-MT, it was equal to that in the low-TMB group. The CIBERSORT algorithm further confirmed that the immune infiltration abundance of CD8+ T cells and activated CD4+ memory T was significantly lower in the MT group. Immunogenomic differences were observed in terms of immune signatures, T-cell receptor repertoire, and immune-related genes between WT and MT groups. Nevertheless, we noticed an inverse relationship, given that MT tumors had a higher TMB than the WT group in MSKCC and TCGA cohort. In conclusion, our study revealed that NSCLC with PBRM1 mutation might be an immunologically cold phenotype and exhibited immunotherapy resistance. NSCLC with PBRM1 mutation might be misclassified as immunoresponsive based on TMB.

Characterization of driver mutations in Chinese non-small cell lung cancer patients using a novel targeted sequencing panel.

The identification of driver mutations has greatly promoted the precise diagnosis and treatment of non-small cell lung cancer (NSCLC), but there is lack of targeted sequencing panels specifically designed and applied to Chinese NSCLC patients. This study aimed to design and validate of a novel sequencing panel for comprehensive characterization of driver mutations in Chinese NSCLC patients, facilitating further exploration of downstream pathway alterations and therapeutic utility. A novel target sequencing panel including 21 driver genes was designed and examined in a cohort of 260 Chinese NSCLC patients who underwent surgery in Peking Union Medical College Hospital (PUMCH). Genetic alterations were identified and further analyzed for driver mutations, downstream pathways and therapeutic utilities. The most frequently identified driver mutations in PUMCH NSCLC cohort were on genes TP53 (28%), EGFR (27%) and PIK3CA (19%) for lung adenocarcinoma (LUAD), and TP53 (41%), PIK3CA (14%) and CDKN2A (13%) for lung squamous cell carcinoma (LUSC), respectively. Downstream pathway analysis revealed common pathways like G1_AND_S1_PHASES pathway were shared not only between LUAD and LUSC patients, but also among three different NSCLC cohorts, while other pathways were subtype-specific, like the unique enrichment of SHC1_EVENT_IN_EGFR_SIGNALING pathway in LUAD patients, and P38_ALPHA_BETA_DOWNSTREAM pathway in LUSC patients, respectively. About 60% of both LUAD and LUSC patients harbored driver mutations as sensitive biomarkers for different targeted therapies, covering not only frequent mutations like EGFR L858R mutation, but also rare mutations like BRAF D594N mutation. Our study provides a novel target sequencing panel suitable for Chinese NSCLC patients, which can effectively identify driver mutations, analyze downstream pathway alterations and predict therapeutic utility. Overall it is promising to further optimize and apply this panel in clinic with convenience and effectiveness.

Neighborhood disadvantage is associated with KRAS-mutated non-small cell lung cancer risk

PurposeIt remains unclear why individuals living in disadvantaged neighborhoods have shorter non-small cell lung cancer (NSCLC) survival. It is possible that living in these deprived areas is linked with increased risk of developing aggressive NSCLC biology. Here, we explored the association of somatic KRAS mutations, which are associated with shorter survival in NSCLC patients, and 11 definitions of neighborhood disadvantage spanning socioeconomic and structural environmental elements.MethodsWe analyzed data from 429 NSCLC patients treated at a Comprehensive Cancer Center from 2015 to 2018. Data were abstracted from medical records and each patient’s home address was used to assign publicly available indices of neighborhood disadvantage. Prevalence Ratios (PRs) for the presence of somatic KRAS mutations were estimated using modified Poisson regression models adjusted for age, sex, smoking status, race/ethnicity, educational attainment, cancer stage, and histology.ResultsIn the NSCLC cohort, 29% had KRAS mutation-positive tumors. We found that five deprivation indices of socioeconomic disadvantage were associated with KRAS mutation. A one decile increase in several of these socioeconomic disadvantage indices was associated with a 1.06 to 1.14 increased risk of KRAS mutation. Measures of built structural environment were not associated with KRAS mutation status.ConclusionSocioeconomic disadvantage at the neighborhood level is associated with higher risk of KRAS mutation while disadvantage related to built environmental structural measures was inversely associated. Our results indicate not only that neighborhood disadvantage may contribute to aggressive NSCLC biology, but the pathways linking biology to disadvantage are likely operating through socioeconomic-related stress.