Genomic and Immunophenotypic Landscape of Acquired Resistance to PD-(L)1 Blockade in Non-Small-Cell Lung Cancer

PURPOSE

Although immune checkpoint inhibitors (ICI) have extended survival in patients with non-small-cell lung cancer (NSCLC), acquired resistance (AR) to ICI frequently develops after an initial benefit. However, the mechanisms of AR to ICI in NSCLC are largely unknown.

METHODS

Comprehensive tumor genomic profiling, machine learning-based assessment of tumor-infiltrating lymphocytes, multiplexed immunofluorescence, and/or HLA-I immunohistochemistry (IHC) were performed on matched pre- and post-ICI tumor biopsies from patients with NSCLC treated with ICI at the Dana-Farber Cancer Institute who developed AR to ICI. Two additional cohorts of patients with intervening chemotherapy or targeted therapies between biopsies were included as controls.

RESULTS

We performed comprehensive genomic profiling and immunophenotypic characterization on samples from 82 patients with NSCLC and matched pre- and post-ICI biopsies and compared findings with a control cohort of patients with non-ICI intervening therapies between biopsies (chemotherapy, N = 32; targeted therapies, N = 89; both, N = 17). Putative resistance mutations were identified in 27.8% of immunotherapy-treated cases and included acquired loss-of-function mutations in STK11, B2M, APC, MTOR, KEAP1, and JAK1/2; these acquired alterations were not observed in the control groups. Immunophenotyping of matched pre- and post-ICI samples demonstrated significant decreases in intratumoral lymphocytes, CD3e+ and CD8a+ T cells, and PD-L1-PD1 engagement, as well as increased distance between tumor cells and CD8+PD-1+ T cells. There was a significant decrease in HLA class I expression in the immunotherapy cohort at the time of AR compared with the chemotherapy (P = .005) and the targeted therapy (P = .01) cohorts.

CONCLUSION

These findings highlight the genomic and immunophenotypic heterogeneity of ICI resistance in NSCLC, which will need to be considered when developing novel therapeutic strategies aimed at overcoming resistance.

A plain language summary of the PHAROS study: the combination of encorafenib and binimetinib for people with BRAF V600E-mutant metastatic non-small cell lung cancer

WHAT IS THIS SUMMARY ABOUT?

This is a summary of the results of a study called PHAROS. This study looked at combination treatment with encorafenib (BRAFTOVI®) and binimetinib (MEKTOVI®). This combination of medicines was studied in people with metastatic non-small-cell lung cancer (NSCLC). NSCLC is the most common type of lung cancer. Metastatic means that the cancer has spread to other parts of the body. All people in this study had a type of NSCLC that has a change in a gene called BRAF termed a BRAF V600E mutation. A gene is a part of the DNA that has instructions for making things that your body needs to work, and the BRAF V600E mutation contributes to the growth of the lung cancer.

WHAT WERE THE RESULTS?

In this study, 98 people with BRAF V600E-mutant metastatic NSCLC were treated with the combination of encorafenib and binimetinib (called encorafenib plus binimetinib in this summary). Before starting the study, 59 people had not received any treatment for their metastatic NSCLC, and 39 people had received previous anticancer treatment. At the time of this analysis, 44 (75%) out of 59 people who did not receive any treatment before taking encorafenib plus binimetinib had their tumors shrink or disappear. Eighteen (46%) out of 39 people who had received treatment before starting encorafenib plus binimetinib also had their tumors shrink or disappear. The most common side effects of encorafenib plus binimetinib were nausea, diarrhea, fatigue, and vomiting.

WHAT DO THE RESULTS MEAN?

These results support the use of encorafenib plus binimetinib combination treatment as a new treatment option in people with BRAF V600E-mutant metastatic NSCLC. The side effects of encorafenib plus binimetinib in this study were similar to the side effects seen with encorafenib plus binimetinib in people with a type of skin cancer called metastatic melanoma.

A cellular and spatial atlas of TP53 -associated tissue remodeling in lung adenocarcinoma

TP53 is the most frequently mutated gene across many cancers and is associated with shorter survival in lung adenocarcinoma (LUAD). To define how TP53 mutations affect the LUAD tumor microenvironment (TME), we constructed a multi-omic cellular and spatial tumor atlas of 23 treatment-naïve human lung tumors. We found that TP53 -mutant ( TP53 mut ) malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across resectable LUAD patient tumors, genetically engineered mouse models, and cell lines harboring a wide spectrum of TP53 mutations. We further identified a multicellular tumor niche composed of SPP1 + macrophages and collagen-expressing fibroblasts that coincides with hypoxic, pro-metastatic expression programs in TP53 mut tumors. Spatially correlated angiostatic and immune checkpoint interactions, including CD274 - PDCD1 and PVR - TIGIT , are also enriched in TP53 mut LUAD tumors, which may influence response to checkpoint blockade therapy. Our methodology can be further applied to investigate mutation-specific TME changes in other cancers.

A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.

Canakinumab Versus Placebo in Combination With First-Line Pembrolizumab Plus Chemotherapy for Advanced Non-Small-Cell Lung Cancer: Results From the CANOPY-1 Trial

PURPOSE

The addition of checkpoint inhibitors to first-line treatment has prolonged survival of patients with non-small-cell lung cancer (NSCLC), but prognosis remains poor, with new treatment options needed. Canakinumab, a human, monoclonal anti-interleukin (IL)-1β antibody, has potential to enhance the activity of PD-L1 inhibitors and chemotherapy (CT) by inhibiting protumor inflammation.

METHODS

CANOPY-1 was a phase III, randomized, double-blind study comparing canakinumab (200 mg subcutaneously once every 3 weeks) versus placebo, both combined with pembrolizumab (200 mg intravenously once every 3 weeks) and platinum-based doublet CT, as first-line treatment for advanced/metastatic NSCLC without EGFR or ALK mutations. The primary end points were progression-free survival (PFS) and overall survival (OS). The secondary endpoints included overall response rate, safety, and patient-reported outcomes.

RESULTS

Overall, 643 patients were randomly assigned to canakinumab (n = 320) or placebo (n = 323). With a median study follow-up of 6.5 months, the median PFS was 6.8 months with canakinumab versus 6.8 months with placebo (hazard ratio [HR], 0.85; 95% CI, 0.67 to 1.09; P = .102). With a median study follow-up of 21.2 months, the median OS was 20.8 months with canakinumab versus 20.2 months with placebo (HR, 0.87; 95% CI, 0.70 to 1.10; P = .123). No unexpected safety signals were observed for canakinumab combination. Infection rates were comparable between treatment and control arms. A higher frequency of neutropenia and ALT increase (grade ≤2) were reported in the treatment arm. Higher baseline C-reactive protein and IL-6 levels were associated with shorter PFS and OS. Patients treated with canakinumab had clinically meaningful delays in deterioration of lung cancer symptoms, including chest pain and coughing per LC13 and dyspnea per LC13 and C30.

CONCLUSION

The addition of canakinumab to first-line pembrolizumab and CT did not prolong PFS or OS in patients with NSCLC.

Ultrasensitive Detection of Circulating LINE-1 ORF1p as a Specific Multicancer Biomarker

Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. Although proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible expression in normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 mol/L) ORF1p concentrations in plasma across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multianalyte panel, provides early therapeutic response monitoring in gastroesophageal cancers, and is prognostic for overall survival in gastroesophageal and colorectal cancers. Together, these observations nominate ORF1p as a multicancer biomarker with potential utility for disease detection and monitoring.

SIGNIFICANCE

The LINE-1 ORF1p transposon protein is pervasively expressed in many cancers and is a highly specific biomarker of multiple common, lethal carcinomas and their high-risk precursors in tissue and blood. Ultrasensitive ORF1p assays from as little as 25 μL plasma are novel, rapid, cost-effective tools in cancer detection and monitoring. See related commentary by Doucet and Cristofari, p. 2502. This article is featured in Selected Articles from This Issue, p. 2489.

Artificial Intelligence-Powered Assessment of Pathologic Response to Neoadjuvant Atezolizumab in Patients With NSCLC: Results From the LCMC3 Study

INTRODUCTION

Pathologic response (PathR) by histopathologic assessment of resected specimens may be an early clinical end point associated with long-term outcomes with neoadjuvant therapy. Digital pathology may improve the efficiency and precision of PathR assessment. LCMC3 (NCT02927301) evaluated neoadjuvant atezolizumab in patients with resectable NSCLC and reported a 20% major PathR rate.

METHODS

We determined PathR in primary tumor resection specimens using guidelines-based visual techniques and developed a convolutional neural network model using the same criteria to digitally measure the percent viable tumor on whole-slide images. Concordance was evaluated between visual determination of percent viable tumor (n = 151) performed by one of the 47 local pathologists and three central pathologists.

RESULTS

For concordance among visual determination of percent viable tumor, the interclass correlation coefficient was 0.87 (95% confidence interval [CI]: 0.84-0.90). Agreement for visually assessed 10% or less viable tumor (major PathR [MPR]) in the primary tumor was 92.1% (Fleiss kappa = 0.83). Digitally assessed percent viable tumor (n = 136) correlated with visual assessment (Pearson r = 0.73; digital/visual slope = 0.28). Digitally assessed MPR predicted visually assessed MPR with outstanding discrimination (area under receiver operating characteristic curve, 0.98) and was associated with longer disease-free survival (hazard ratio [HR] = 0.30; 95% CI: 0.09-0.97, p = 0.033) and overall survival (HR = 0.14, 95% CI: 0.02-1.06, p = 0.027) versus no MPR. Digitally assessed PathR strongly correlated with visual measurements.

CONCLUSIONS

Artificial intelligence-powered digital pathology exhibits promise in assisting pathologic assessments in neoadjuvant NSCLC clinical trials. The development of artificial intelligence-powered approaches in clinical settings may aid pathologists in clinical operations, including routine PathR assessments, and subsequently support improved patient care and long-term outcomes.

Comprehensive genomic characterization of HER2-low and HER2-0 breast cancer

The molecular underpinnings of HER2-low and HER2-0 (IHC 0) breast tumors remain poorly defined. Using genomic findings from 1039 patients with HER2-negative metastatic breast cancer undergoing next-generation sequencing from 7/2013-12/2020, we compare results between HER2-low (n = 487, 47%) and HER2-0 tumors (n = 552, 53%). A significantly higher number of ERBB2 alleles (median copy count: 2.05) are observed among HER2-low tumors compared to HER2-0 (median copy count: 1.79; P = 2.36e-6), with HER2-0 tumors harboring a higher rate of ERBB2 hemideletions (31.1% vs. 14.5%). No other genomic alteration reaches significance after accounting for multiple hypothesis testing, and no significant differences in tumor mutational burden are observed between HER2-low and HER2-0 tumors (median: 7.26 mutations/megabase vs. 7.60 mutations/megabase, p = 0.24). Here, we show that the genomic landscape of HER2-low and HER2-0 tumors does not differ significantly, apart from a higher ERBB2 copy count among HER2-low tumors, and a higher rate of ERBB2 hemideletions in HER2-0 tumors.

Impact of Aneuploidy and Chromosome 9p Loss on Tumor Immune Microenvironment and Immune Checkpoint Inhibitor Efficacy in NSCLC

INTRODUCTION

Although gene-level copy number alterations have been studied as a potential biomarker of immunotherapy efficacy in NSCLC, the impact of aneuploidy burden and chromosomal arm-level events on immune checkpoint inhibitor (ICI) efficacy in NSCLC is uncertain.

METHODS

Patients who received programmed cell death protein 1 or programmed death-ligand 1 (PD-L1) inhibitor at two academic centers were included. Across all 22 chromosomes analyzed, an arm was considered altered if at least 70% of its territory was either gained or deleted. Among nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the adjusted fraction of chromosomal arm alterations (FAA), defined as the number of altered chromosome arms divided by the number of chromosome arms assessed, adjusted for tumor purity.

RESULTS

Among 2293 nonsquamous NSCLCs identified, the median FAA increased with more advanced cancer stage and decreased with higher PD-L1 tumor proportion score (TPS) levels (median FAA in TPS < 1%: 0.09, TPS 1%-49%: 0.08, TPS ≥ 50%: 0.05, p < 0.0001). There was a very weak correlation between FAA and tumor mutational burden when taken as continuous variables (R: 0.07, p = 0.0005). A total of 765 advanced nonsquamous NSCLCs with available FAA values were treated with ICIs. With decreasing FAA tertiles, there was a progressive improvement in objective response rate (ORR 15.1% in upper tertile versus 23.2% in middle tertile versus 28.4% in lowest tertile, p = 0.001), median progression-free survival (mPFS 2.5 versus 3.3 versus 4.1 mo, p < 0.0001), and median overall survival (mOS 12.5 versus 13.9 versus 16.4 mo, p = 0.006), respectively. In the arm-level enrichment analysis, chromosome 9p loss (OR = 0.22, Q = 0.0002) and chromosome 1q gain (OR = 0.43, Q = 0.002) were significantly enriched in ICI nonresponders after false discovery rate adjustment. Compared with NSCLCs without chromosome 9p loss (n = 452), those with 9p loss (n = 154) had a lower ORR (28.1% versus 7.8%, p < 0.0001), a shorter mPFS (4.1 versus 2.3 mo, p < 0.0001), and a shorter mOS (18.0 versus 9.6 mo, p < 0.0001) to immunotherapy. In addition, among NSCLCs with high PD-L1 expression (TPS ≥ 50%), chromosome 9p loss was associated with lower ORR (43% versus 6%, p < 0.0001), shorter mPFS (6.4 versus 2.6 mo, p = 0.0006), and shorter mOS (30.2 versus 14.3 mo, p = 0.0008) to immunotherapy compared with NSCLCs without 9p loss. In multivariable analysis, adjusting for key variables including FAA, chromosome 9p loss, but not 1q gain, retained a significant impact on ORR (hazard ratio [HR] = 0.25, p < 0.001), mPFS (HR = 1.49, p = 0.001), and mOS (HR = 1.47, p = 0.003). Multiplexed immunofluorescence and computational deconvolution of RNA sequencing data revealed that tumors with either high FAA levels or chromosome 9p loss had significantly fewer tumor-associated cytotoxic immune cells.

CONCLUSIONS

Nonsquamous NSCLCs with high aneuploidy and chromosome 9p loss have a distinct tumor immune microenvironment and less favorable outcomes to ICIs.

Multi-institutional analysis of aneuploidy and outcomes to chemoradiation and durvalumab in stage III non-small cell lung cancer

There is a need to identify predictive biomarkers to guide treatment strategies in stage III non-small cell lung cancer (NSCLCs). In this multi-institutional cohort of 197 patients with stage III NSCLC treated with concurrent chemoradiation (cCRT) and durvalumab consolidation, we identify that low tumor aneuploidy is independently associated with prolonged progression-free survival (HR 0.63; p=0.03) and overall survival (HR 0.50; p=0.03). Tumors with high aneuploidy had a significantly greater incidence of distant metastasis and shorter median distant-metastasis free survival (p=0.04 and p=0.048, respectively), but aneuploidy level did not associate with local-regional outcomes. Multiplexed immunofluorescence analysis in a cohort of NSCLC found increased intratumoral CD8-positive, PD-1-positive cells, double-positive PD-1 CD8 cells, and FOXP3-positive T-cell in low aneuploid tumors. Additionally, in a cohort of 101 patients treated with cCRT alone, tumor aneuploidy did not associate with disease outcomes. These data support the need for upfront treatment intensification strategies in stage III NSCLC patients with high aneuploid tumors and suggest that tumor aneuploidy is a promising predictive biomarker.

Phase II, Open-Label Study of Encorafenib Plus Binimetinib in Patients With BRAFV600-Mutant Metastatic Non-Small-Cell Lung Cancer

PURPOSE

The combination of encorafenib (BRAF inhibitor) plus binimetinib (MEK inhibitor) has demonstrated clinical efficacy with an acceptable safety profile in patients with BRAFV600E/K-mutant metastatic melanoma. We evaluated the efficacy and safety of encorafenib plus binimetinib in patients with BRAFV600E-mutant metastatic non-small-cell lung cancer (NSCLC).

METHODS

In this ongoing, open-label, single-arm, phase II study, patients with BRAFV600E-mutant metastatic NSCLC received oral encorafenib 450 mg once daily plus binimetinib 45 mg twice daily in 28-day cycles. The primary end point was confirmed objective response rate (ORR) by independent radiology review (IRR). Secondary end points included duration of response (DOR), disease control rate (DCR), progression-free survival (PFS), overall survival, time to response, and safety.

RESULTS

At data cutoff, 98 patients (59 treatment-naïve and 39 previously treated) with BRAFV600E-mutant metastatic NSCLC received encorafenib plus binimetinib. Median duration of treatment was 9.2 months with encorafenib and 8.4 months with binimetinib. ORR by IRR was 75% (95% CI, 62 to 85) in treatment-naïve and 46% (95% CI, 30 to 63) in previously treated patients; median DOR was not estimable (NE; 95% CI, 23.1 to NE) and 16.7 months (95% CI, 7.4 to NE), respectively. DCR after 24 weeks was 64% in treatment-naïve and 41% in previously treated patients. Median PFS was NE (95% CI, 15.7 to NE) in treatment-naïve and 9.3 months (95% CI, 6.2 to NE) in previously treated patients. The most frequent treatment-related adverse events (TRAEs) were nausea (50%), diarrhea (43%), and fatigue (32%). TRAEs led to dose reductions in 24 (24%) and permanent discontinuation of encorafenib plus binimetinib in 15 (15%) patients. One grade 5 TRAE of intracranial hemorrhage was reported. Interactive visualization of the data presented in this article is available at the PHAROS dashboard (https://clinical-trials.dimensions.ai/pharos/).

CONCLUSION

For patients with treatment-naïve and previously treated BRAFV600E-mutant metastatic NSCLC, encorafenib plus binimetinib showed a meaningful clinical benefit with a safety profile consistent with that observed in the approved indication in melanoma.

Impact of TMB/PD-L1 expression and pneumonitis on chemoradiation and durvalumab response in stage III NSCLC

Although concurrent chemoradiation (CRT) and durvalumab consolidation has become a standard treatment for stage III non-small cell lung cancer (NSCLC), clinicopathologic and genomic factors associated with its efficacy remain poorly characterized. Here, in a multi-institutional retrospective cohort study of 328 patients treated with CRT and durvalumab, we identify that very high PD-L1 tumor proportion score (TPS) expression ( ≥ 90%) and increased tumor mutational burden (TMB) are independently associated with prolonged disease control. Additionally, we identify the impact of pneumonitis and its timing on disease outcomes among patients who discontinue durvalumab: compared to patients who experienced early-onset pneumonitis ( < 3 months) leading to durvalumab discontinuation, patients with late-onset pneumonitis had a significantly longer PFS (12.7 months vs not reached; HR 0.24 [95% CI, 0.10 to 0.58]; P = 0.001) and overall survival (37.2 months vs not reached; HR 0.26 [95% CI, 0.09 to 0.79]; P = 0.017). These findings suggest that opportunities exist to improve outcomes in patients with lower PD-L1 and TMB levels, and those at highest risk for pneumonitis.

Clinicopathologic and Genomic Factors Impacting Efficacy of First-Line Chemoimmunotherapy in Advanced NSCLC

INTRODUCTION

Although programmed cell death protein 1 and programmed death-ligand 1 (PD-L1) blockade in combination with platinum-doublet chemotherapy has become a mainstay of first-line treatment for advanced NSCLC, factors associated with efficacy of chemoimmunotherapy (CIT) are not well characterized.

METHODS

In this multicenter retrospective analysis, clinicopathologic and genomic data were collected from patients with advanced NSCLC (lacking sensitizing genomic alterations in EGFR and ALK) and evaluated with clinical outcomes to first-line CIT.

RESULTS

Among 1285 patients treated with CIT, a worsening performance status and increasing derived neutrophil-to-lymphocyte ratio in the blood were associated with a significantly reduced objective response rate (ORR), median progression-free survival (mPFS), and median overall survival (mOS). With increasing PD-L1 tumor proportion scores of less than 1%, 1% to 49%, 50% to 89%, and greater than or equal to 90%, there was a progressive improvement in ORR (32.7% versus 37.5% versus 51.6% versus 61.7%, p < 0.001), mPFS (5.0 versus 6.1 versus 6.8 versus 13.0 mo, p < 0.001), and generally mOS (12.9 versus 14.6 versus 34.7 versus 23.1 mo, p = 0.009), respectively. Of 789 NSCLCs with comprehensive genomic data, NSCLCs with a tumor mutational burden (TMB) greater than or equal to the 90th percentile had an improved ORR (53.5% versus 36.4%, p = 0.004), mPFS (10.8 versus 5.5 mo, p < 0.001), and mOS (29.2 versus 13.1 mo, p < 0.001), compared with those with a TMB less than the 90th percentile. In all-comers with nonsquamous NSCLC, the presence of an STK11, KEAP1, or SMARCA4 mutation was associated with significantly worse ORR, mPFS, and mOS to CIT (all p < 0.05); this was also observed in the KRAS-mutant subgroup of NSCLCs with co-occurring mutations in STK11, KEAP1, or SMARCA4 (all p < 0.05). In KRAS wild-type NSCLC, KEAP1 and SMARCA4 mutations were associated with a significantly shorter mPFS and mOS to CIT (all p < 0.05), but STK11 mutation status had no significant impact on mPFS (p = 0.16) or mOS (p = 0.38).

CONCLUSIONS

In advanced NSCLC, better patient performance status, low derived neutrophil-to-lymphocyte ratio, increasing PD-L1 expression, a very high TMB, and STK11/KEAP1/SMARCA4 wild-type status are associated with improved clinical outcomes to first-line CIT.

Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker

Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring.

Prediction Model for Tumor Volume Nadir in EGFR -mutant NSCLC Patients Treated With EGFR Tyrosine Kinase Inhibitors

PURPOSE

In patients with advanced non-small cell lung cancer (NSCLC) and oncogenic driver mutations treated with effective targeted therapy, a characteristic pattern of tumor volume dynamics with an initial regression, nadir, and subsequent regrowth is observed on serial computed tomography (CT) scans. We developed and validated a linear model to predict the tumor volume nadir in EGFR -mutant advanced NSCLC patients treated with EGFR tyrosine kinase inhibitors (TKI).

MATERIALS AND METHODS

Patients with EGFR -mutant advanced NSCLC treated with EGFR-TKI as their first EGFR-directed therapy were studied for CT tumor volume kinetics during therapy, using a previously validated CT tumor measurement technique. A linear regression model was built to predict tumor volume nadir in a training cohort of 34 patients, and then was validated in an independent cohort of 84 patients.

RESULTS

The linear model for tumor nadir prediction was obtained in the training cohort of 34 patients, which utilizes the baseline tumor volume before initiating therapy (V 0 ) to predict the volume decrease (mm 3 ) when the nadir volume (V p ) was reached: V 0 -V p =0.717×V 0 -1347 ( P =2×10 -16 ; R2 =0.916). The model was tested in the validation cohort, resulting in the R2 value of 0.953, indicating that the prediction model generalizes well to another cohort of EGFR -mutant patients treated with EGFR-TKI. Clinical variables were not significant predictors of tumor volume nadir.

CONCLUSION

The linear model was built to predict the tumor volume nadir in EGFR -mutant advanced NSCLC patients treated with EGFR-TKIs, which provide an important metrics in treatment monitoring and therapeutic decisions at nadir such as additional local abrasive therapy.

Acquiring tissue for advanced lung cancer diagnosis and comprehensive biomarker testing: A National Lung Cancer Roundtable best-practice guide

Advances in biomarker-driven therapies for patients with nonsmall cell lung cancer (NSCLC) both provide opportunities to improve the treatment (and thus outcomes) for patients and pose new challenges for equitable care delivery. Over the last decade, the continuing development of new biomarker-driven therapies and evolving indications for their use have intensified the importance of interdisciplinary communication and coordination for patients with or suspected to have lung cancer. Multidisciplinary teams are challenged with completing comprehensive and timely biomarker testing and navigating the constantly evolving evidence base for a complex and time-sensitive disease. This guide provides context for the current state of comprehensive biomarker testing for NSCLC, reviews how biomarker testing integrates within the diagnostic continuum for patients, and illustrates best practices and common pitfalls that influence the success and timeliness of biomarker testing using a series of case scenarios.

Tumor Volume Nadir in Patients With ALK-Rearranged Non-Small-Cell Lung Cancer Treated With Alectinib

PURPOSE

Patients with oncogene-driven advanced non-small-cell lung cancer (NSCLC) treated with effective targeted therapy demonstrate characteristic tumor volume dynamics with initial response, nadir, and subsequent regrowth. This study investigated tumor volume nadir and time to nadir in patients with ALK-rearranged advanced NSCLC treated with alectinib.

MATERIALS AND METHODS

In patients with advanced ALK-rearranged NSCLC treated with alectinib monotherapy, tumor volume dynamics were evaluated on serial computed tomography (CT) scans using a previously validated CT tumor measurement technique. A linear regression model was built to predict tumor volume nadir. Time-to-event analyses were performed to evaluate time to nadir.

RESULTS

Among 45 patients who experienced initial volume decrease, 37 patients (25 with tumor regrowth and 12 without regrowth but >6 months follow-up) were studied for nadir volume (V_p). The linear model to predict tumor volume nadir was built using the baseline tumor volume (V₀): V₀-V_p = .696 × V₀ + 5,326 (P < 2 × 10^-16; adjusted R² = 0.86). The percent volume changes at nadir (median, -90.9%, mean, -85.3%) showed larger decrease in patients who were treated with alectinib as first-line therapy than in the ≥2nd-line group and were independent of V₀ and clinical variables. Time to nadir had a median of 11.5 months and was longer in the first-line group (P = .04).

CONCLUSION

The tumor nadir volume in patients with ALK-rearranged advanced NSCLC treated with alectinib can be predicted by the liner regression model and consists of approximately 30% of the baseline volume minus 5 cm³, providing additional insights into precision therapy monitoring and potential guides for local ablative therapy to prolong disease control.

Surgical results of the Lung Cancer Mutation Consortium 3 trial: A phase II multicenter single-arm study to investigate the efficacy and safety of atezolizumab as neoadjuvant therapy in patients with stages IB-select IIIB resectable non-small cell lung cancer

OBJECTIVE

Multimodality treatment for resectable non-small cell lung cancer has long remained at a therapeutic plateau. Immune checkpoint inhibitors are highly effective in advanced non-small cell lung cancer and promising preoperatively in small clinical trials for resectable non-small cell lung cancer. This large multicenter trial tested the safety and efficacy of neoadjuvant atezolizumab and surgery.

METHODS

Patients with stage IB to select IIIB resectable non-small cell lung cancer and Eastern Cooperative Oncology Group performance status 0/1 were eligible. Patients received atezolizumab 1200 mg intravenously every 3 weeks for 2 cycles or less followed by resection. The primary end point was major pathological response in patients without EGFR/ALK+ alterations. Pre- and post-treatment computed tomography, positron emission tomography, pulmonary function tests, and biospecimens were obtained. Adverse events were recorded by Common Terminology Criteria for Adverse Events v.4.0.

RESULTS

From April 2017 to February 2020, 181 patients were entered in the study. Baseline characteristics were mean age, 65.1 years; female, 93 of 181 (51%); nonsquamous histology, 112 of 181 (62%); and clinical stages IIB to IIIB, 147 of 181 (81%). In patients without EGFR/ALK alterations who underwent surgery, the major pathological response rate was 20% (29/143; 95% confidence interval, 14-28) and the pathological complete response rate was 6% (8/143; 95% confidence interval, 2-11). There were no grade 4/5 treatment-related adverse events preoperatively. Of 159 patients (87.8%) undergoing surgery, 145 (91%) had pathologic complete resection. There were 5 (3%) intraoperative complications, no intraoperative deaths, and 2 postoperative deaths within 90 days, 1 treatment related. Median disease-free and overall survival have not been reached.

CONCLUSIONS

Neoadjuvant atezolizumab in resectable stage IB to IIIB non-small cell lung cancer was well tolerated, yielded a 20% major pathological response rate, and allowed safe, complete surgical resection. These results strongly support the further development of immune checkpoint inhibitors as preoperative therapy in locally advanced non-small cell lung cancer.

Defining equitable genomic testing uptake in gastrointestinal oncology: Ensuring capture of demographic data

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Background: Tumor genomic testing (GT) has increased diagnostic accuracy and treatment options for patients (pts) with cancer. Dana-Farber Cancer Institute (DFCI) has made GT accessible as an institute-supported research effort for >10 yrs. We estimate 50% standard therapies and 15-35% clinical trials in Gastrointestinal Cancer Clinic (GCC) require GT to determine eligibility. Pts in GCC with certain cancers are eligible for GT as a clinical test – these include metastatic/locally advanced colorectal, gastric, pancreatic, or biliary cancers. Clinical testing requires CLIA lab certification and insurance reimbursement; research does not. Herein we ID gaps in our GT database. Methods: We reviewed data on GT uptake in GCC between 4/2015 - 6/2022. 20,096 pts were captured by the GT tracking system. Data included: testing ordered and completed (proportion, type, time to receiving tissue for testing [TR], time to testing completion [TC]). Demographic data is not captured in the tracking system; matching unique patient identifiers with electronic health record is pending. Results: Most pts received GT (57.6%); 12% were not eligible; 30.4% declined consent. Most testing was completed (67.6%), but 21.3% of tests failed (45.5% of these from insufficient tissue). Research testing (71%) comprised most tests, but clinical tests were completed faster (median 34 days research vs 20 days clinical). Ampullary (91%), anal (90%), colon (90%) had highest completion rates; pancreatic (59%), hepatocellular carcinoma (56%) had lowest (from insufficient viable tumor in submitted specimens). Conclusions: GCC has a robust recruitment program that has yielded high GT uptake. Given the frequency that GT is used for treatment and trials, building a demographically representative dataset is crucial, especially for pts with largest burden of morbidity and mortality from cancer. We ID'd data gaps in the GT tracking system, which lacks demographics and reason for not testing. Demographic data is available in the electronic health record but does not speak with the GT tracking system so this analysis is not routinely done. Ability to visualize this data is important to ensure equitable GT uptake. Future efforts will focus on improving rates of consent in genomics databases and cancer clinical trials. Genomic testing at Dana-Farber Cancer Institute Gastrointestinal Cancer Center, 4/2015 – 6/2022.[Table: see text]

Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer

Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effective for many patients with lung cancer with EGFR mutations. However, not all patients are responsive to EGFR TKIs, including even those harboring EGFR-sensitizing mutations. In this study, we quantified the cells and cellular interaction features of the tumor microenvironment (TME) using routine H&E-stained biopsy sections. These TME features were used to develop a prediction model for survival benefit from EGFR TKI therapy in patients with lung adenocarcinoma and EGFR-sensitizing mutations in the Lung Cancer Mutation Consortium 1 (LCMC1) and validated in an independent LCMC2 cohort. In the validation data set, EGFR TKI treatment prolonged survival in the predicted-to-benefit group but not in the predicted-not-to-benefit group. Among patients treated with EGFR TKIs, the predicted-to-benefit group had prolonged survival outcomes compared with the predicted not-to-benefit group. The EGFR TKI survival benefit positively correlated with tumor-tumor interaction image features and negatively correlated with tumor-stroma interaction. Moreover, the tumor-stroma interaction was associated with higher activation of the hepatocyte growth factor/MET-mediated PI3K/AKT signaling pathway and epithelial-mesenchymal transition process, supporting the hypothesis of fibroblast-involved resistance to EGFR TKI treatment.

Rare FGFR Oncogenic Alterations in Sequenced Pediatric Solid and Brain Tumors Suggest FGFR Is a Relevant Molecular Target in Childhood Cancer

PURPOSE

Multiple FGFR inhibitors are currently in clinical trials enrolling adults with different solid tumors, while very few enroll pediatric patients. We determined the types and frequency of FGFR alterations (FGFR1-4) in pediatric cancers to inform future clinical trial design.

METHODS

Tumors with FGFR alterations were identified from two large cohorts of pediatric solid tumors subjected to targeted DNA sequencing: The Dana-Farber/Boston Children's Profile Study (n = 888) and the multi-institution GAIN/iCAT2 (Genomic Assessment Improves Novel Therapy) Study (n = 571). Data from the combined patient population of 1,395 cases (64 patients were enrolled in both studies) were reviewed and cases in which an FGFR alteration was identified by OncoPanel sequencing were further assessed.

RESULTS

We identified 41 patients with tumors harboring an oncogenic FGFR alteration. Median age at diagnosis was 8 years (range, 6 months-26 years). Diagnoses included 11 rhabdomyosarcomas, nine low-grade gliomas, and 17 other tumor types. Alterations included gain-of-function sequence variants (n = 19), amplifications (n = 10), oncogenic fusions (FGFR3::TACC3 [n = 3], FGFR1::TACC1 [n = 1], FGFR1::EBF2 [n = 1], FGFR1::CLIP2 [n = 1], and FGFR2::CTNNA3 [n = 1]), pathogenic-leaning variants of uncertain significance (n = 4), and amplification in combination with a pathogenic-leaning variant of uncertain significance (n = 1). Two novel FGFR1 fusions in two different patients were identified in this cohort, one of whom showed a response to an FGFR inhibitor.

CONCLUSION

In summary, activating FGFR alterations were found in approximately 3% (41/1,395) of pediatric solid tumors, identifying a population of children with cancer who may be eligible and good candidates for trials evaluating FGFR-targeted therapy. Importantly, the genomic and clinical data from this study can help inform drug development in accordance with the Research to Accelerate Cures and Equity for Children Act.

MatchMiner: an open-source platform for cancer precision medicine

Widespread, comprehensive sequencing of patient tumors has facilitated the usage of precision medicine (PM) drugs to target specific genomic alterations. Therapeutic clinical trials are necessary to test new PM drugs to advance precision medicine, however, the abundance of patient sequencing data coupled with complex clinical trial eligibility has made it challenging to match patients to PM trials. To facilitate enrollment onto PM trials, we developed MatchMiner, an open-source platform to computationally match genomically profiled cancer patients to PM trials. Here, we describe MatchMiner’s capabilities, outline its deployment at Dana-Farber Cancer Institute (DFCI), and characterize its impact on PM trial enrollment. MatchMiner’s primary goals are to facilitate PM trial options for all patients and accelerate trial enrollment onto PM trials. MatchMiner can help clinicians find trial options for an individual patient or provide trial teams with candidate patients matching their trial’s eligibility criteria. From March 2016 through March 2021, we curated 354 PM trials containing a broad range of genomic and clinical eligibility criteria and MatchMiner facilitated 166 trial consents (MatchMiner consents, MMC) for 159 patients. To quantify MatchMiner’s impact on trial consent, we measured time from genomic sequencing report date to trial consent date for the 166 MMC compared to trial consents not facilitated by MatchMiner (non-MMC). We found MMC consented to trials 55 days (22%) earlier than non-MMC. MatchMiner has enabled our clinicians to match patients to PM trials and accelerated the trial enrollment process.

Neoadjuvant atezolizumab for resectable non-small cell lung cancer: an open-label, single-arm phase II trial

In an ongoing, open-label, single-arm phase II study ( NCT02927301 ), 181 patients with untreated, resectable, stage IB-IIIB non-small cell lung cancer received two doses of neoadjuvant atezolizumab monotherapy. The primary end point was major pathological response (MPR; ≤10% viable malignant cells) in resected tumors without EGFR or ALK alterations. Of the 143 patients in the primary end point analysis, the MPR was 20% (95% confidence interval, 14-28%). With a minimum duration of follow-up of 3 years, the 3-year survival rate of 80% was encouraging. The most common adverse events during the neoadjuvant phase were fatigue (39%, 71 of 181) and procedural pain (29%, 53 of 181), along with expected immune-related toxicities; there were no unexpected safety signals. In exploratory analyses, MPR was predicted using the pre-treatment peripheral blood immunophenotype based on 14 immune cell subsets. Immune cell subsets predictive of MPR in the peripheral blood were also identified in the tumor microenvironment and were associated with MPR. This study of neoadjuvant atezolizumab in a large cohort of patients with resectable non-small cell lung cancer was safe and met its primary end point of MPR ≥ 15%. Data from this single-arm, non-randomized trial suggest that profiles of innate immune cells in pre-treatment peripheral blood may predict pathological response after neoadjuvant atezolizumab, but additional studies are needed to determine whether these profiles can inform patient selection and new therapeutic approaches.

Safety of image guided research biopsies in patients with thoracic malignancies

OBJECTIVE

A common opportunity to collect research samples is during image-guided percutaneous core needle biopsies (CNBs) performed when clinically indicated or for assessing clinical trial eligibility. The relative safety of extra CNBs collected for research is undefined.

MATERIALS AND METHODS

Patients who underwent CNB for research purposes only [RO], as clinically indicated [CI], or as part of a clinical trial [CT] were identified. 30-day post-procedure adverse events (AEs) among the cohorts were examined and compared to the 2020 Society of Interventional Radiology QI guidelines.

RESULTS

236 patients with thoracic cancers (90 % NSCLC, 5 % SCLC, 4 % mesothelioma, and 1 % thymic) had 292 CNBs (63 RO, 229 CI + CT). AEs occurred in 13 % of both the RO and CI + CT groups. Compared to the CI + CT group, the RO group did not have a higher pneumothorax incidence (RO: 5/29 [17 %], CI + CT: 18/114 [16 %], p = 0.79); both were below the suggested QI threshold of 45 % for pneumothorax. There was a negative association between number of cores obtained and risk of AE (AE vs no AE mean cores = 3.5 vs 4.8). After adjusting for the number of cores and smoking history, RO vs CI + CT lung biopsies had a higher risk of AEs (adjusted relative risk [aRR] = 2.44, 1.08-5.55, p = 0.03 vs non-lung aRR = 0.86, 0.10-7.09, p = 0.89).

CONCLUSION

CNBs performed for research purposes do not have a significantly increased risk of AEs when compared to those performed for clinical trials and/or when clinically indicated. However, AEs were most frequent in lung biopsies. When performing research biopsies, a target other than lung may be preferred when clinically appropriate.

Abstract 3890: Sequencing of 888 pediatric solid tumors informs precision oncology trial design and data sharing initiatives in pediatric cancer

Pediatric pan-cancer genome analyses do not capture the full range of diagnoses encountered in clinical practice. To inform basket trial design and real-world precision oncology practice, we classified diagnoses and assessed the landscape of mutations, including trial-matching, in an unselected cohort of pediatric solid tumors.

Since 2013 all Dana-Farber/Boston Children’s patients have been offered participation in the Profile study. Participant tumor samples were sequenced with DFCI-OncoPanel, a targeted panel test sequencing exons of up to 447 cancer genes for single nucleotide variants, insertions and deletions and copy number alterations, and introns and exons of up to 60 genes for rearrangements. Patient diagnosis was classified according to ICD-O, version 3.2. Genomic alterations were analyzed for matching to the actionable mutation lists of precision oncology basket trials (NCI-COG Pediatric MATCH, NCI-MATCH, and the ASCO TAPUR Study v.3). Data will be shared with the Childhood Cancer Data Initiative.

There were 888 pediatric patients with sequencing enrolled in Profile between January 2013 and March 2019; 512 (58%) with solid tumors and 376 (42%) with CNS tumors. Fifty-five percent (491/888) of patients had one of ten common pediatric cancer diagnoses: neuroblastoma (n=80), low-grade glioma (n=72), Wilms tumor (n=57), medulloblastoma (n=55), pilocytic astrocytoma (n=47), rhabdomyosarcoma (n=44), osteosarcoma (n=42), ependymoma (n=39), Ewing sarcoma (n=28) and glioblastoma (n=27). The remaining 45% (397/888) had one of 85 distinct rare malignancies with less than 25 cases per diagnosis. Most (80/85) of these rare diagnoses are not represented in prior pediatric pan-cancer sequencing studies. Recurrent (&gt;5%) pathogenic alterations were, in common and rare diagnoses, TP53 mutations(m) and deletions(del) and BRAFm and rearrangements(r), in common diagnoses, MYC/MYCN amplification (amp) and EWSR1r and, in rare diagnoses, CTNNB1m, CDKN2A/Bdel and NF1m/del. We found that 31% (n=271/888) of patients had at least 1 variant matching a basket trial treatment arm. Genes with matching alterations include BRAF (10%), NF1 (4%), PI3KCA (3%), NRAS (2%), BRCA2 (2%), ALK (1%), and FGFR1 (1%).

Sequencing of pediatric malignancies is increasing. This study highlights opportunities to use the resulting genomic data to inform genome-selected clinical trial design and uncover drivers in pediatric cancers. The proportion of cases in this cohort with genomic alterations meeting eligibility for basket trials is equivalent to that seen in the pediatric MATCH screening study. Due to the low prevalence of the diagnoses in the long tail of cancer types in this study, defining the genomic landscape of ultra-rare cancers will require data sharing. Classifying pediatric cancer diagnoses using the ICD-O standard ontology system is feasible and will facilitate data sharing.

Citation Format: Suzanne J. Forrest, Hersh Gupta, Abigail Ward, Yvonne Li, Duong Doan, Alyaa Al-Ibraheemi, Sanda Alexandrescu, Pratiti Bandopadhayay, Suzanne Shusterman, Elizabeth A. Mullen, Natalie Collins, Susan N. Chi, Karen D. Wright, Priti Kumari, Tali Mazor, Keith L. Ligon, Priyanka Shivdasani, Phani Davineni, Monica Manam, Richard L. Schilsky, Suanna S. Bruinooge, Jaime M. Guidry Auvil, Ethan Cerami, Barrett J. Rollins, Matthew L. Meyerson, Neal I. Lindeman, Laura MacConaill, Bruce E. Johnson, Andrew D. Cherniack, Alanna J. Church, Katherine A. Janeway. Sequencing of 888 pediatric solid tumors informs precision oncology trial design and data sharing initiatives in pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3890.

Abstract CT112: AI-powered and manual assessment of PD-L1 are comparable in predicting response to neoadjuvant atezolizumab in patients (pts) with resectable non-squamous, non-small cell lung cancer (NSCLC)

Background: PD-L1 expression evaluated by immunohistochemistry (IHC) is a well-established predictor of anti-PD-L1/PD-1 cancer immunotherapy (CIT). The Phase II LCMC3 (NCT02927301) study evaluated pre-operative treatment (tx) with atezolizumab (anti-PD-L1) in pts with untreated early stage resectable NSCLC, achieving a 20% major pathologic response (MPR) rate (primary efficacy pts, n=143). A digital PD-L1 scoring method was developed to assess PD-L1 expression as a potential predictive marker for MPR in squamous and non-squamous tumor samples from LCMC3.

Methods: Manual scoring was used to determine PD-L1 status on pre-tx biopsy samples using the tumor proportion score (TPS) with a positive threshold of TPS≥50 (22C3). Binary results were correlated with MPR and stratified by squamous/non-squamous histology. A digital pathology workflow for automated PD-L1 scoring was developed to yield a precise continuous PD-L1 TPS. Deep convolutional neural networks trained using pathologist annotations were used to detect individual cells within the tumor and tumor microenvironment and quantify their PD-L1 expression. These cell type predictions were used to compute a digital PD-L1 TPS. LCMC3 pts with available digital and manual PD-L1 scores were then used to assess the role of PD-L1 expression in predicting MPR.

Results: PD-L1 scores were available for pre-tx biopsies from 108 pts. No significant difference in scores was seen between histological subtypes. At cutoff (Oct 15, 2021), TPS≥50 was seen in 41 (non-squamous, n=26 [39%]; squamous, n=15 [36%]) of 108 pts and was associated with MPR in non-squamous (odds ratio [OR], 28.6; P&lt;0.001; Fisher’s exact test) but not squamous histology (OR, 1.3; P=1.0). Continuous digital PD-L1 scores (range: 0-100) were highly correlated with local manual PD-L1 scores (range: 0-100) for squamous (n=42, Pearson r=0.90, P&lt;0.001) and non-squamous stained histology slides (n=66, Pearson r=0.90, P&lt;0.001). Continuous digital and manual PD-L1 TPS on pre-tx biopsies (n=108) were predictive of MPR (digital: area under the receiver operating curve (AUROC)=0.678, logistic regression [LR] P=0.01; manual: AUROC=0.675, LR P=0.003). Strikingly, when pts were stratified by histology, PD-L1 scores were predictive of MPR from pre-tx biopsies for non-squamous samples (n=66; digital: AUROC=0.821, LR P=0.002; manual: AUROC=0.819, LR P=0.001) but not for squamous samples (n=42; digital: AUROC=0.519, LR P=0.93; manual: AUROC=0.506, LR P=0.90), despite no significant difference in MPR rate between the 2 groups.

Conclusions: These findings support using digitally assessed PD-L1 IHC as a centralized and standardized scoring system and suggest that tumor histological subtype could be an important factor in the utility of PD-L1 as a predictive biomarker for neoadjuvant CIT in early stage NSCLC.

Citation Format: John Abel, Christopher Rivard, Filip Kos, Guillaume Chhor, Yi Liu, Jennifer Giltnane, Sara Hoffman, Murray Resnick, Cyrus Hedvat, Amaro Taylor-Weiner, Farah Khalil, Alan Nicholas, Gregory A. Fishbein, Lynette M. Sholl, Natasha Rekhtman, Stephanie Hennek, Ilan Wapinski, Ann Johnson, Michael Montalto, Katja Schulze, Bruce E. Johnson, David P. Carbone, Konstantin Shilo, Andrew H. Beck, Sanja Dacic, William D. Travis, Ignacio Wistuba. AI-powered and manual assessment of PD-L1 are comparable in predicting response to neoadjuvant atezolizumab in patients (pts) with resectable non-squamous, non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT112.

Abstract CT037: Canakinumab in combination with first-line (1L) pembrolizumab plus chemotherapy for advanced non-small cell lung cancer (aNSCLC): Results from the CANOPY-1 phase 3 trial

Background: Pembrolizumab improves overall survival (OS) when added to platinum-based doublet chemotherapy (PDC) in patients with aNSCLC. However, progression-free survival (PFS) and OS remain disappointing for most patients and can vary depending on programmed death-ligand 1 (PD-L1) status. This highlights the need for additional therapeutic options. Canakinumab is a monoclonal anti-interleukin-1β antibody that inhibits pro-tumor inflammation and potentially enhances anti-tumor immune responses, with the potential to synergize with programmed death 1 inhibitors plus chemotherapy.

Methods: CANOPY-1 is a randomized, double-blind phase 3 study investigating the addition of canakinumab or placebo (PBO) to 1L pembrolizumab + PDC. Patients with previously untreated stage IIIB/C or IV NSCLC, of any histology and no known EGFR or ALK alterations, were randomized 1:1 and stratified based on PD-L1 status, geographic region, and histology to canakinumab 200 mg or PBO every 3 weeks, plus pembrolizumab and histology-guided PDC for 4 cycles, followed by maintenance canakinumab or PBO, with pembrolizumab ± pemetrexed. The primary endpoints were investigator-assessed PFS (Response Evaluation Criteria In Solid Tumors 1.1) and OS. Exploratory biomarker analyses were also investigated and will be presented at the time of the congress. The cut-off dates for these analyses were May 18, 2020 (PFS) and August 9, 2021 (OS).

Results: A total of 643 patients were randomized to canakinumab (n=320) or PBO (n=323) in combination with pembrolizumab + PDC. Baseline characteristics were well balanced across treatment arms. Median PFS was 6.8 months for both treatment arms (HR 0.85, 95% CI, 0.67-1.09; one-sided P=0.102). Median OS was 20.8 and 20.2 months for the canakinumab and PBO arms, respectively (HR 0.87, 95% CI, 0.70-1.10; one-sided P=0.123). Grade 3/4 adverse events (AEs) were reported for 205 (64.1%) patients in the canakinumab arm and 191 (59.3%) patients in the PBO arm, and fatal AEs were reported for 37 (11.6%) and 47 (14.6%) patients, respectively. AEs (any grade) leading to discontinuation of any study drug were reported for 72 (22.5%) patients in the canakinumab arm and 61 (18.9%) patients in the PBO arm.

Conclusions: The addition of canakinumab to pembrolizumab plus PDC did not statistically improve PFS nor OS for 1L treatment of patients with aNSCLC. No unexpected safety findings were observed with the addition of canakinumab to pembrolizumab plus PDC.

Citation Format: Daniel S. Tan, Enriqueta Felip, Gilberto Castro, Benjamin J. Solomon, Alastair Greystoke, Byoungchul Cho, Manuel Cobo, Tae Min Kim, Sandip Ganguly, Enric Carcereny, Luis Paz-Ares, Jaafar Bennouna, Marina Garassino, Michael Schenker, Sang-We Kim, Bijoyesh Mookerje, Vanessa Q. Passos, Stephanie Deudon, Bharani Dharan, Yuanbo Song, Rafael Caparica, Bruce E. Johnson. Canakinumab in combination with first-line (1L) pembrolizumab plus chemotherapy for advanced non-small cell lung cancer (aNSCLC): Results from the CANOPY-1 phase 3 trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT037.

Oncology clinical trial disruption during the COVID-19 pandemic: a COVID-19 and cancer outcomes study

Background

COVID-19 disproportionately impacted patients with cancer as a result of direct infection, and delays in diagnosis and therapy. Oncological clinical trials are resource-intensive endeavors that could be particularly susceptible to disruption by the pandemic, but few studies have evaluated the impact of the pandemic on clinical trial conduct.

Patients and methods

This prospective, multicenter study assesses the impact of the pandemic on therapeutic clinical trials at two large academic centers in the Northeastern United States between December 2019 and June 2021. The primary objective was to assess the enrollment on, accrual to, and activation of oncology therapeutic clinical trials during the pandemic using an institution-wide cohort of (i) new patient accruals to oncological trials, (ii) a manually curated cohort of patients with cancer, and (ii) a dataset of new trial activations.

Results

The institution-wide cohort included 4756 new patients enrolled to clinical trials from December 2019 to June 2021. A major decrease in the numbers of new patient accruals (−46%) was seen early in the pandemic, followed by a progressive recovery and return to higher-than-normal levels (+2.6%). A similar pattern (from −23.6% to +30.4%) was observed among 467 newly activated trials from June 2019 to June 2021. A more pronounced decline in new accruals was seen among academically sponsored trials (versus industry sponsored trials) (P < 0.05). In the manually curated cohort, which included 2361 patients with cancer, non-white patients tended to be more likely taken off trial in the early pandemic period (adjusted odds ratio: 2.60; 95% confidence interval 1.00-6.63), and substantial pandemic-related deviations were recorded.

Conclusions

Substantial disruptions in clinical trial activities were observed early during the pandemic, with a gradual recovery during ensuing time periods, both from an enrollment and an activation standpoint. The observed decline was more prominent among academically sponsored trials, and racial disparities were seen among people taken off trial.

Associations between biomarker testing and characteristics of patients with metastatic non–small cell lung cancer (mNSCLC): An analysis of CancerLinQ Discovery (CLQD) data

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Background: Guidelines have evolved from 2011-2019; there are now 23 approved therapies targeting various predictive biomarkers in mNSCLC. 2021 NCCN Guidelines advocate for a minimum of ALK, EGFR, BRAF, METex14, NTRK1/2/3, RET, KRAS, and ROS1 testing before determining a treatment regimen. The study objective was to estimate the association between the presence of biomarker testing and smoking status, age, sex, race, ethnicity, histology, and diagnosis year in patients with mNSCLC. Methods: CLQD is a real-world data source that provides de-identified electronic health record (EHR) data from more than 60 U.S. oncology practices utilizing 10 different EHRs. This retrospective analysis included patients initially diagnosed with mNSCLC from January 1, 2011, to December 31, 2019. Standard logistic regression models were fit separately by practice to estimate practice-specific odds ratios to assess variability across practices in associations between covariates (smoking status, age, race, etc.) and the primary outcome of biomarker testing, defined as documented testing for EGFR, ALK, ROS1, BRAF, KRAS, MET, RET, ERBB2, and/or PD-L1 within -60 to +365 days of mNSCLC diagnosis. Random effects logistic regression was then used to estimate associations with random intercepts, accounting for clustering by practices. Results are reported as odds ratios (OR) with 95% confidence intervals (CI). Results: 8704 patients from 31 practices were eligible. Testing rates increased from 31.5% in 2011 to a peak of 62.3% in 2017. Patients with a smoking history were half as likely to receive testing than patients without a smoking history (OR = 0.50, 95% CI: 0.41, 0.60); patients with unknown smoking history were 0.66 times as likely (95% CI: 0.52, 0.84). Females were more likely to be tested than males (OR = 1.19, 95% CI: 1.07, 1.32). After adjusting for other covariates, Asian patients were 1.51 times more likely to be tested than patients of other races (95% CI: 1.05, 2.17); Hispanic patients were 1.33 times more likely to be tested than patients without Hispanic ethnicity (95% CI: 0.99, 1.78). The odds of receiving biomarker testing were 6x greater for patients with non-squamous mNSCLC versus squamous mNSCLC (95% CI: 5.45, 7.20). Patients > 70 years old were less likely to be tested (OR = 0.83, 95% CI: 0.75, 0.93) than younger patients. Conclusions: Our data demonstrate annual increases in testing rates, reflecting guideline changes. However, in this cohort of patients with mNSCLC, biomarker testing was more likely for non-squamous mNSCLC patients, females, Asians, Hispanics, or those who did not have a history of smoking. Patient characteristics should no longer factor into obtaining biomarker testing. Non-discriminant, broad panel-based reflex molecular testing in mNSCLC can reduce treatment choice ambiguity and enhance patient opportunities.

State legislative trends related to biomarker testing

Comprehensive biomarker testing has become the standard of care for informing the choice of the most appropriate targeted therapy for many patients with advanced cancer. Despite evidence demonstrating the need for comprehensive biomarker testing to enable the selection of appropriate targeted therapies and immunotherapy, the incorporation of biomarker testing into clinical practice lags behind recommendations in National Comprehensive Cancer Network guidelines. Coverage policy differences across insurance health plans have limited the accessibility of comprehensive biomarker testing largely to patients whose insurance covers the recommended testing or those who can pay for the testing, and this has contributed to health disparities. Furthermore, even when insurance coverage exists for recommended biomarker testing, patients may incur burdensome out-of-pocket costs depending on their insurance plan benefits, which may also create barriers to testing. Prior authorization for biomarker testing for some patients can add an administrative burden and may delay testing and thus treatment if it is not done in a timely manner. Recently, three states (Illinois, Louisiana, and California) passed laws designed to improve access to biomarker testing at the state level. However, there is variability among these laws in terms of the population affected, the stage of cancer, and whether the coverage of testing is mandated, or the legislation addresses only prior authorization. Advocacy efforts by patient advocates, health care professionals, and professional societies are imperative at the state level to further improve coverage for and access to appropriate biomarker testing.

Serological testing for SARS-CoV-2 antibodies of employees shows low transmission working in a cancer center

BACKGROUND

The COVID-19 pandemic led to emergency measures to continue patient care and research at a comprehensive cancer center while protecting both employees and patients. Determining exposure and infection rates with SARS-CoV-2 were important to adjust workplace policies over time.

METHODS

Dana-Farber Cancer Institute (DFCI) has over 7,000 employees. Participation was voluntary. After consent, participants completed questionnaire of demographics, exposures and risk factors for COVID-19 illness at each time point (baseline, 3, 6, and 12 months) along with blood draws for SARS-CoV-2 antibody testing. Primary measure was determination of titers of SARS-CoV-2 spike protein IgG over time.

RESULTS

In total, 745 employees enrolled from May 2020 to February 2021 (mean [SD] age, 40[14] years; 572[80%] women). From May to July 2020, 47 of 519 employees (9.2%, 95% confidence interval [CI] 6.7-12.0%) tested positive for SARS-CoV-2 spike protein IgG antibodies. Three months later, 40 of 428 employees had positive antibodies (8.5%, 95% CI 6.0-11.0%) with 17 newly positive. At month 6, 78.5% of participants reported having received at least one dose of vaccine and the positivity rate for those vaccinated was 98% (95% CI, 95-100%). Spike protein IgG titers for those vaccinated were 7.9 times higher than participants not vaccinated (median IgG titer = 0.28 for positive antibody but not vaccinated versus 2.2 for vaccinated) but demonstrate evidence of waning over time.

CONCLUSIONS

SARS-CoV-2 antibody positivity remained less than 10% at a single comprehensive cancer center prior to vaccination and there is evidence of waning IgG titers over time after vaccination.

Identification and Management of Pathogenic Variants in BRCA1, BRCA2, and PALB2 in a Tumor-Only Genomic Testing Program

PURPOSE

Tumor-only genomic testing can uncover somatic and germline pathogenic variants (P/LPs) in cancer predisposition genes. We describe the prevalence of P/LPs in BRCA1/2 and PALB2 (B1B2P2) across malignancies and the frequency of clinical germline testing (CGT) in patients with P/LPs in B1B2P2 identified on tumor-only testing.

EXPERIMENTAL DESIGN

Among 7,575 patients tested between 2016-2018 with the OncoPanel tumor-only sequencing assay, we characterized P/LP frequencies by tumor type, receipt of CGT prior to or within 12 months (m) after OncoPanel, and factors associated with CGT.

RESULTS

272 (3.6%) had OncoPanel-detected P/LPs in B1B2P2: 37.5% of P/LPs were in BRCA-related cancers; the remainder were in non-BRCA tumors. P/LPs were detected in {greater than or equal to}5% of breast, pancreatic, prostate, ovarian, non-melanoma skin, endometrial, small-cell lung and colorectal cancers. 37.9% of patients with P/LPs received GCT prior to OncoPanel; an additional 10.7% underwent CGT within 12m of OncoPanel. Among 132 with CGT, 88.6% had {greater than or equal to}1 clinical factor for CGT compared to 47.1% who did not undergo CGT. Patients with BRCA-tumors were more likely to have CGT compared to those without (81.4% vs. 29.0%, p&lt;0.0001). Among patients with CGT, 70.5% (93/132) of P/LPs were germline.

CONCLUSION

Tumor-only genomic testing identified P/LPs in B1B2P2 in 3.6% of patients. 52.9% of patients with tumor-detected P/LPs and without CGT did not meet personal or family history criteria for CGT. Additionally, some patients with tumor-detected P/LPs were not referred for CGT, especially those with non-BRCA tumors. Given implications for treatment selection and familial cancer risk, processes to reliably trigger CGT from tumor-genomic findings are needed.

Abstract PD6-03: Spatio-molecular dissection of the breast cancer metastatic microenvironment

Metastatic breast cancer (MBC) remains incurable due to inevitable development of therapeutic resistance. Although tumor cell intrinsic mechanisms of resistance in MBC are beginning to be elucidated by bulk sequencing studies, the roles of the tumor microenvironment and intratumor heterogeneity in therapeutic resistance remain underexplored due to both technological barriers and limited availability of samples. To comprehensively capture these characteristics we have adapted a research biopsy protocol to collect tissue for an array of single-cell and spatio-molecular assays whose performance we have optimized for MBC, including single-cell and single-nucleus RNA sequencing, Slide-Seq, Multiplexed Error-Robust FISH (MERFISH), Expansion Sequencing (ExSEQ), Co-detection by Indexing (CODEX) and Multiplexed Ion Beam Imaging (MIBI). To date, we have successfully performed single-cell or single-nucleus RNAseq in 67 MBC biopsies and generated detailed accompanying clinical annotations for each. These samples provide a representation of the clinicopathological diversity of MBC including different breast cancer subtypes (44 HR+/HER2-, 3 HR-/HER2+, 3 HR+/HER2+, 16 TNBC, 1 unknown), common anatomic sites of metastasis (37 liver, 9 axilla, 7 breast, 5 bone, 3 chest wall, 3 neck, 1 brain, 1 lung, 1 skin), metastatic presentations (53 recurrent, 14 de novo) and histologic subtypes in the breast (45 IDC, 7 ILC, 6 mixed, 3 DCIS, 1 mucinous, 5 unknown/NA). Following optimization, both single-cell and single-nucleus RNA seq perform well in these MBC biopsies recovering all expected cell types including the malignant, stromal (e.g. fibroblasts, endothelial cells), myeloid (e.g. monocytes, macrophages) and lymphoid compartments (e.g. T cells, B cells, NK cells) as well as relevant oncogenic programs (e.g. cell cycle programs in all compartments; EMT-like and ER signaling programs in the malignant compartment, immune checkpoint programs in the lymphoid compartment; and fibroblast activation and vascular homeostasis programs in the stromal compartment). In addition to differences between the two techniques, these data demonstrate substantial intratumor heterogeneity in cell type composition. For example in liver biopsies the average number of cells per sample compartment by single nucleus RNA-seq was 6745 malignant (56%, SD 4216), 4637 stromal (41%, SD 3727), 1196 lymphoid (8%, SD 1617) and 874 myeloid (6%, SD 852); in breast biopsies the average number of cells per compartment by single nucleus RNA-seq was 6421 malignant (70%, SD 3497), 1628 stromal (24%, SD 117), 333 lymphoid (4%, SD 170) and 213 myeloid (3%, SD 117). Additionally, we find both inter- and intra-tumor heterogeneity in expression patterns and programs including, for example, expression of ER, PR and HER2 within clinical receptor subtypes (log normalized counts for ER expression in tumor cells by single cell RNA-seq: HR+/HER2- 0.921 (SD 0.714); HR+/HER2+ 0.768 (SD 0.624); HR-/HER2+ 0.018 (SD 0.122); and HR-/HER2- 0.005 (SD 0.066). For a subset of 13 biopsies we are also completing the spatiomolecular characterization methods on serial sections of a single adjacent biopsy. This unique experimental setup was designed to enable efficient comparison and integration of these assays. In spite of differences between experimental techniques and readouts, cell typing can be approached by annotation transfer from matching single cell or single nucleus RNAseq data, enabling exploratory analyses including evaluation of spatial phenotypes and cell type colocalization. Overall, these single cell and spatial data afford a comprehensive atlas including cell types, cell states/programs, cell interactions and spatial organization in MBC lesions. Future analyses will include serial biopsies over time and integration of clinicopathologic data including therapeutic response and resistance.

Citation Format: Daniel L Abravanel, Johanna Klughammer, Timothy Blosser, Yury Goltsev, Sizun Jiang, Yunjao Bai, Evan Murray, Shahar Alon, Yi Cui, Daniel R Goodwin, Anubhav Sinha, Ofir Cohen, Michal Slyper, Orr Ashenberg, Danielle Dionne, Judit Jané-Valbuena, Caroline BM Porter, Asa Segerstolpe, Julia Waldman, Sébastien Vigneau, Karla Helvie, Allison Frangieh, Laura DelloStritto, Miraj Patel, Jingyi We, Kathleen Pfaff, Nicole Cullen, Ana Lako, Madison Turner, Isaac Wakiro, Sara Napolitano, Abhay Kanodia, Rebecca Ortiz, Colin MacKichan, Stephanie Inga, Judy Chen, Aaron R Thorner, Asaf Rotem, Scott Rodig, Fei Chen, Edward S Boyden, Garry P Nolan, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Bruce E Johnson, Aviv Regev, Nikhil Wagle. Spatio-molecular dissection of the breast cancer metastatic microenvironment [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-03.

Real-World Analysis of Off-Label Use of Molecularly Targeted Therapy in a Large Academic Medical Center Cohort

PURPOSE

The primary objective of this study is to quantify the use of off-label molecularly targeted therapy and describe the clinical situations in which off-label targeted therapy are used. A key secondary objective is to report the outcomes of patients treated with off-label use of targeted therapy.

PATIENTS AND METHODS

We searched the electronic health record between 2000 and 2020 at our center to characterize the volume, clinical settings, and outcomes associated with off-label use of targeted therapies in different types of solid tumors.

RESULTS

Among 46,712 patients who received targeted therapies, we identified 119 instances of off-label use of targeted therapy. Colon cancer was the most common cancer type to receive off-label targeted therapy in 18 patients (15.1%), followed by 13 with non-small-cell lung cancer (10.9%), eight with cholangiocarcinoma (6.7%), and seven with glioblastoma (5.9%). The most frequent molecular rationale for off-label therapy came from a comprehensive next-generation sequencing test (53.7%). The most frequently mutated gene that provided the rationale for targeted therapy was BRAF (20.1%), with BRAFV600E being the most common molecular alteration overall (15.1%). The median duration of off-label targeted therapy was 3.58 months, and the overall survival of treated patients was 7.59 months. There were 37 patients (31.1%) treated for longer than 6 months, 23 patients (19.3%) who survived ≥ 2 years, and 13 patients who were still on therapy as of June 2020.

CONCLUSION

In this large cohort study of patients with solid tumors, off-label use of targeted therapy was uncommon. With that said, a notable proportion of patients had treatment durations ≥ 6 months and survivals of ≥ 2 years.

Defining comprehensive biomarker-related testing and treatment practices for advanced non-small-cell lung cancer: Results of a survey of U.S. oncologists

BACKGROUND

An ASCO taskforce comprised of representatives of oncology clinicians, the American Cancer Society National Lung Cancer Roundtable (NLCRT), LUNGevity, the GO2 Foundation for Lung Cancer, and the ROS1ders sought to: characterize U.S. oncologists' biomarker ordering and treatment practices for advanced non-small-cell lung cancer (NSCLC); ascertain barriers to biomarker testing; and understand the impact of delays on treatment decisions.

METHODS

We deployed a survey to 2374 ASCO members, targeting U.S. thoracic and general oncologists.

RESULTS

We analyzed 170 eligible responses. For non-squamous NSCLC, 97% of respondents reported ordering tests for EGFR, ALK, ROS1, and BRAF. Testing for MET, RET, and NTRK was reported to be higher among academic versus community providers and higher among thoracic oncologists than generalists. Most respondents considered 1 (46%) or 2 weeks (52%) an acceptable turnaround time, yet 37% usually waited three or more weeks to receive results. Respondents who waited ≥3 weeks were more likely to defer treatment until results were reviewed (63%). Community and generalist respondents who waited ≥3 weeks were more likely to initiate non-targeted treatment while awaiting results. Respondents <5 years out of training were more likely to cite their concerns about waiting for results as a reason for not ordering biomarker testing (42%, vs. 19% with ≥6 years of experience).

CONCLUSIONS

Respondents reported high biomarker testing rates in patients with NSCLC. Treatment decisions were impacted by test turnaround time and associated with practice setting and physician specialization and experience.

Encorafenib plus binimetinib in patients with BRAFV600-mutant non-small cell lung cancer: Phase II PHAROS study design

BRAF^V600 oncogenic driver mutations occur in 1-2% of non-small cell lung cancers (NSCLCs) and have been shown to be a clinically relevant target. Preclinical/clinical evidence support the efficacy and safety of BRAF and MEK inhibitor combinations in patients with NSCLC with these mutations. We describe the design of PHAROS, an ongoing, open-label, single-arm, Phase II trial evaluating the BRAF inhibitor encorafenib plus the MEK inhibitor binimetinib in patients with metastatic BRAF^V600-mutant NSCLC, as first- or second-line treatment. The primary endpoint is objective response rate, based on independent radiologic review (per RECIST v1.1); secondary objectives evaluated additional efficacy endpoints and safety. Results from PHAROS will describe the antitumor activity/safety of encorafenib plus binimetinib in patients with metastatic BRAF^V600-mutant NSCLC.

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo-relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.

Knowledge and Practice Patterns Among Pulmonologists for Molecular Biomarker Testing in Advanced Non-small Cell Lung Cancer

BACKGROUND

Targeted therapies for advanced non-small cell lung cancer (NSCLC) with oncogenic drivers have caused a paradigm shift in care. Biomarker testing is needed to assess eligibility for these therapies. Pulmonologists often perform bronchoscopy, providing tissue for both pathologic diagnosis and biomarker analysis. We performed this survey to define the existing knowledge and practices regarding the pulmonologists' role in biomarker testing for advanced NSCLC.

RESEARCH QUESTION

What is the current knowledge and practice of pulmonologists regarding biomarker testing and targeted therapies in advanced NSCLC?

STUDY DESIGN AND METHODS

This cross-sectional study was performed using an electronic survey of a random sample of 7,238 pulmonologists. Questions focused on diagnostic steps and biomarker analyses for NSCLC.

RESULTS

A total of 453 pulmonologists responded. Respondents vary by reported lung cancer patient volume, ranging from 51% evaluating one to four new cases per month to 19% evaluating > 10 cases per month. Interventional training, academic practice setting, and higher volume of endobronchial ultrasound with transbronchial needle aspiration (EBUS-TBNA) were associated with increased knowledge of practice guidelines for the number of recommended passes during EBUS-TBNA (P < .05). Academic pulmonologists more commonly performed or referred for EBUS-TBNA than community pulmonologists (96% and 83%, respectively; P < .0005). Higher testing rates were associated with interventional training, academic setting, and the presence of an institutional policy, whereas lower testing rates were associated with general pulmonologists, practice in community settings, and lack of a guiding institutional policy (P < .05).

INTERPRETATION

Substantial differences among pulmonologists' evaluation of advanced NSCLC, variation in knowledge of available biomarkers and the importance of targeted therapies, and differences in institutional coordination likely lead to underutilization of biomarker testing. Interventional training appears to drive improved knowledge and practice for biomarker testing more than practice setting. Improvements are needed in tissue acquisition and interdisciplinary coordination to ensure universal and comprehensive testing for eligible patients.

Germline Testing Data Validate Inferences of Mutational Status for Variants Detected From Tumor-Only Sequencing

Pathogenic germline variants (PGVs) in cancer susceptibility genes are usually identified through germline testing of DNA from blood or saliva: their detection can affect treatment options and potential risk-reduction strategies for patient relatives. PGV can also be identified in tumor sequencing assays, which, when performed without patient-matched normal specimens, render determination of variants' germline or somatic origin critical.

Germline testing data from 1,600 cancer patients validate information-theoretic, gene-independent inference of germline vs. somatic status for variants detected by clinical tumor-only sequencing.

Postdiagnosis BMI Change Is Associated with Non-Small Cell Lung Cancer Survival

BACKGROUND

Body mass index (BMI) change after a lung cancer diagnosis has been associated with non-small cell lung cancer (NSCLC) survival. This study aimed to quantify the association based on a large-scale observational study.

METHODS

Included in the study were 7,547 patients with NSCLC with prospectively collected BMI data from Massachusetts General Hospital and Brigham and Women's Hospital/Dana-Farber Cancer Institute. Cox proportional hazards regression with time-dependent covariates was used to estimate effect of time-varying postdiagnosis BMI change rate (% per month) on overall survival (OS), stratified by clinical subgroups. Spline analysis was conducted to quantify the nonlinear association. A Mendelian Randomization (MR) analysis with a total of 3,495 patients further validated the association.

RESULTS

There was a J-shape association between postdiagnosis BMI change and OS among patients with NSCLC. Specifically, a moderate BMI decrease [0.5-2.0; HR = 2.45; 95% confidence interval (CI), 2.25-2.67] and large BMI decrease (≥2.0; HR = 4.65; 95% CI, 4.15-5.20) were strongly associated with worse OS, whereas moderate weight gain (0.5-2.0) reduced the risk for mortality (HR = 0.78; 95% CI, 0.68-0.89) and large weight gain (≥2.0) slightly increased the risk of mortality without reaching statistical significance (HR = 1.10; 95% CI, 0.86-1.42). MR analyses supported the potential causal roles of postdiagnosis BMI change in survival.

CONCLUSIONS

This study indicates that BMI change after diagnosis was associated with mortality risk.

IMPACT

Our findings, which reinforce the importance of postdiagnosis BMI surveillance, suggest that weight loss or large weight gain may be unwarranted.

Tumor Growth Rate After Nadir Is Associated With Survival in Patients With EGFR-Mutant Non-Small-Cell Lung Cancer Treated With Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor

PURPOSE

To investigate the association between tumor volume growth rate after the nadir and survival in patients with EGFR-mutant advanced non-small-cell lung cancer (NSCLC) treated with erlotinib.

MATERIALS AND METHODS

Seventy-one patients with EGFR-mutant advanced NSCLC treated with erlotinib were studied for computed tomography tumor volume kinetics during therapy. The tumor growth rate after nadir was obtained using a previously published analytic module for longitudinal volume tracking to study its relationship with overall survival (OS).

RESULTS

The median tumor volume for the cohort was 19,842 mm3 at baseline and 4,083 mm3 at nadir. The median time to nadir was 6.2 months. The tumor growth rate after nadir for logeV (the natural logarithm of tumor volume measured in mm3) was 0.11/mo on average for the cohort (SE: 0.014), which was very similar to the previously validated reference value of 0.12/mo to define slow and fast tumor growth. The OS of 48 patients with slow tumor growth (≤ 0.12/mo) was significantly longer compared with 23 patients with fast tumor growth (> 0.12/mo; median OS: 37.8 v 25.0 months; P = .0012). In Cox models, tumor growth rate was also associated with survival (regression coefficient: 3.9903; P = .0024; faster rate leads to increased hazards), after adjusting for time to nadir (regression coefficient: -0.0863; P = .0008; longer time to nadir leads to decreased hazards) and smoking history.

CONCLUSION

In patients with EGFR-mutant advanced NSCLC treated with erlotinib, slower tumor growth rates after nadir were associated with longer OS, providing a rationale for using tumor growth rates to guide precision therapy for lung cancer.

Tumor Growth Rate After Nadir Is Associated With Survival in Patients With EGFR-Mutant Non-Small-Cell Lung Cancer Treated With Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor

PURPOSE

To investigate the association between tumor volume growth rate after the nadir and survival in patients with EGFR-mutant advanced non-small-cell lung cancer (NSCLC) treated with erlotinib.

MATERIALS AND METHODS

Seventy-one patients with EGFR-mutant advanced NSCLC treated with erlotinib were studied for computed tomography tumor volume kinetics during therapy. The tumor growth rate after nadir was obtained using a previously published analytic module for longitudinal volume tracking to study its relationship with overall survival (OS).

RESULTS

The median tumor volume for the cohort was 19,842 mm³ at baseline and 4,083 mm³ at nadir. The median time to nadir was 6.2 months. The tumor growth rate after nadir for log_eV (the natural logarithm of tumor volume measured in mm³) was 0.11/mo on average for the cohort (SE: 0.014), which was very similar to the previously validated reference value of 0.12/mo to define slow and fast tumor growth. The OS of 48 patients with slow tumor growth (≤ 0.12/mo) was significantly longer compared with 23 patients with fast tumor growth (> 0.12/mo; median OS: 37.8 v 25.0 months; P = .0012). In Cox models, tumor growth rate was also associated with survival (regression coefficient: 3.9903; P = .0024; faster rate leads to increased hazards), after adjusting for time to nadir (regression coefficient: -0.0863; P = .0008; longer time to nadir leads to decreased hazards) and smoking history.

CONCLUSION

In patients with EGFR-mutant advanced NSCLC treated with erlotinib, slower tumor growth rates after nadir were associated with longer OS, providing a rationale for using tumor growth rates to guide precision therapy for lung cancer.

Spatially organized multicellular immune hubs in human colorectal cancer

Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd individuals. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across tumors from affected individuals and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T cell-attracting chemokines. By identifying interacting cellular programs, we reveal the logic underlying spatially organized immune-malignant cell networks.

Natural Language Processing to Ascertain Cancer Outcomes From Medical Oncologist Notes

PURPOSE

Cancer research using electronic health records and genomic data sets requires clinical outcomes data, which may be recorded only in unstructured text by treating oncologists. Natural language processing (NLP) could substantially accelerate extraction of this information.

METHODS

Patients with lung cancer who had tumor sequencing as part of a single-institution precision oncology study from 2013 to 2018 were identified. Medical oncologists' progress notes for these patients were reviewed. For each note, curators recorded whether the assessment/plan indicated any cancer, progression/worsening of disease, and/or response to therapy or improving disease. Next, a recurrent neural network was trained using unlabeled notes to extract the assessment/plan from each note. Finally, convolutional neural networks were trained on labeled assessments/plans to predict the probability that each curated outcome was present. Model performance was evaluated using the area under the receiver operating characteristic curve (AUROC) among a held-out test set of 10% of patients. Associations between curated response or progression end points and overall survival were measured using Cox models among patients receiving palliative-intent systemic therapy.

RESULTS

Medical oncologist notes (n = 7,597) were manually curated for 919 patients. In the 10% test set, NLP models replicated human curation with AUROCs of 0.94 for the any-cancer outcome, 0.86 for the progression outcome, and 0.90 for the response outcome. Progression/worsening events identified using NLP models were associated with shortened survival (hazard ratio [HR] for mortality, 2.49; 95% CI, 2.00 to 3.09); response/improvement events were associated with improved survival (HR, 0.45; 95% CI, 0.30 to 0.67).

CONCLUSION

NLP models based on neural networks can extract meaningful outcomes from oncologist notes at scale. Such models may facilitate identification of clinical and genomic features associated with response to cancer treatment.

Performance of a Machine Learning Algorithm Using Electronic Health Record Data to Identify and Estimate Survival in a Longitudinal Cohort of Patients With Lung Cancer

IMPORTANCE

Electronic health records (EHRs) provide a low-cost means of accessing detailed longitudinal clinical data for large populations. A lung cancer cohort assembled from EHR data would be a powerful platform for clinical outcome studies.

OBJECTIVE

To investigate whether a clinical cohort assembled from EHRs could be used in a lung cancer prognosis study.

DESIGN, SETTING, AND PARTICIPANTS

In this cohort study, patients with lung cancer were identified among 76 643 patients with at least 1 lung cancer diagnostic code deposited in an EHR in Mass General Brigham health care system from July 1988 to October 2018. Patients were identified via a semisupervised machine learning algorithm, for which clinical information was extracted from structured and unstructured data via natural language processing tools. Data completeness and accuracy were assessed by comparing with the Boston Lung Cancer Study and against criterion standard EHR review results. A prognostic model for non-small cell lung cancer (NSCLC) overall survival was further developed for clinical application. Data were analyzed from March 2019 through July 2020.

EXPOSURES

Clinical data deposited in EHRs for cohort construction and variables of interest for the prognostic model were collected.

MAIN OUTCOMES AND MEASURES

The primary outcomes were the performance of the lung cancer classification model and the quality of the extracted variables; the secondary outcome was the performance of the prognostic model.

RESULTS

Among 76 643 patients with at least 1 lung cancer diagnostic code, 42 069 patients were identified as having lung cancer, with a positive predictive value of 94.4%. The study cohort consisted of 35 375 patients (16 613 men [47.0%] and 18 756 women [53.0%]; 30 140 White individuals [85.2%], 1040 Black individuals [2.9%], and 857 Asian individuals [2.4%]) after excluding patients with lung cancer history and less than 14 days of follow-up after initial diagnosis. The median (interquartile range) age at diagnosis was 66.7 (58.4-74.1) years. The area under the receiver operating characteristic curves of the prognostic model for overall survival with NSCLC were 0.828 (95% CI, 0.815-0.842) for 1-year prediction, 0.825 (95% CI, 0.812-0.836) for 2-year prediction, 0.814 (95% CI, 0.800-0.826) for 3-year prediction, 0.814 (95% CI, 0.799-0.828) for 4-year prediction, and 0.812 (95% CI, 0.798-0.825) for 5-year prediction.

CONCLUSIONS AND RELEVANCE

These findings suggest the feasibility of assembling a large-scale EHR-based lung cancer cohort with detailed longitudinal clinical measurements and that EHR data may be applied in cancer progression with a set of generalizable approaches.

Abstract 370: Smoking history as an independent predictor for immune checkpoint inhibitors (ICIs) in metastatic non-small cell lung cancer (NSCLC)

Importance: Immune Checkpoint Inhibitors (ICIs) induce durable response in a subset of non-small cell lung cancer (NSCLC) patients. There is an unmet need to develop effective predictors for ICIs in metastatic NSCLC.

Objective: Define the predictive impact of smoking history (pack-years) on the clinical outcomes of ICI monotherapy and further to validate the potential clinical utility in metastatic NSCLC.

Design, setting, and participants: This study was conducted on 680 metastatic NSCLC patients treated with ICIs between April 2013 and September 2020 at the Dana-Farber Cancer Institute and Brigham and Women's Hospital. Patient TMB and programmed cell death-ligand 1 (PD-L1) tumor proportion score (TPS) were determined by clinical targeted Next Generation Sequencing (NGS) and immunohistochemistry (IHC) and detailed smoking history and clinicopathological characteristics were prospectively collected.

Main outcomes and measures: Evaluation of the association of smoking pack-years with objective response rate (ORR), progression-free survival (PFS) and overall survival (OS) in metastatic NSCLC patients treated with ICI monotherapy. Assessment of time-dependent area under the curve (AUC) for predictive models of clinical outcomes.

Results: Among 680 metastatic NSCLC patients who received ICI monotherapy: 109 (16.0%) never smokers, 397 (58.4%) former smokers [median 30 pack-years], and 174 (25.6%) current smokers [median 40 pack-years]. Multivariable analysis suggested that doubling of smoking pack-years is significantly associated with better clinical outcomes of ICIs. (ORR OR = 1.20, P &lt; 0.001; PFS HR = 0.92, P &lt; 0.001; OS HR = 0.94, P = 0.01) Predictive models incorporating smoking pack-years yielded additional information and achieved similar model performance compared to the one using TMB.

Conclusions and Relevance: This finding suggests that detailed smoking information has a significant predictive value on clinical outcomes of ICI monotherapy independent of PD-L1 TPS. Smoking pack-years could serve as a non-invasive and consistent surrogate for TMB when it is not readily available for treatment-decision in metastatic NSCLC.

Citation Format: Xinan Wang, Biagio Ricciuti, Joao V. Alessi, Tom Nguyen, Mark M. Awad, Xihong Lin, Bruce E. Johnson, David C. Christiani. Smoking history as an independent predictor for immune checkpoint inhibitors (ICIs) in metastatic non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 370.