Abstract 3260: Enhanced lineage plasticity in RTK-independent TKI-resistant EGFR-mutant NSCLC

Background: Resistance to targeted tyrosine kinase inhibitors (TKI) inevitably develops in metastatic EGFR-mutant non-small cell lung cancer (NSCLC). Resistance mechanisms are diverse, and mechanisms beyond receptor tyrosine kinase (RTK) pathway mutations are poorly understood. We hypothesized that the use of osimertinib as first-line therapy is increasing the prevalence of RTK-independent resistance mechanisms, and that RTK-independent resistant tumors undergo enhanced tumor cell lineage plasticity as an escape mechanism to EGFR TKI therapy.

Methods: We identified patients who developed osimertinib resistance (OR) after first line (1L, n=54) and second line (2L, n=42) treatments and determined the resistance mechanisms based on clinical sequencing and histopathology. We also performed single-cell RNA-seq of 24 samples from 13 patients with EGFRm NSCLC at TKI treatment-naïve (TN, n=2), residual disease (RD, n=4), and progression disease (PD, n=7) stages.

Results: Compared to 2L OR tumors, 1L OR tumors had increased RTK-independent mechanisms of resistance (76% vs. 46%, p=0.002), including 8% with small cell transformation (n=4), 2% with squamous transformation (n=1) and 66% with unknown mechanisms (n=34). To understand inter- and intra-tumor heterogeneity, we analyzed transcriptomic profiles of 76,266 single cells. Lung developmental lineages were assigned to 10,250 EpCAM+ cells, including 4,735 cells classified as malignant cells by inferCNV and RTK signaling analysis. In the two EGFRm TN tumors, the malignant cells demonstrated bronchoalveolar lineage and moderate EGFR expression. In the TKI resistant cases (PD, n=7), both RTK-dependent and RTK-independent resistance were observed. The RTK-dependent tumors (EGFR T790M n=1; ERBB2 amplification n=1) demonstrated preserved bronchoalveolar lineage identity. In the RTK-independent resistant tumors (n=5), one had complete lineage switch from epithelial to small cell neuroendocrine and very low expression level of EGFR. The remaining 4 PD tumors displayed varying expression of epithelial-to-mesenchymal transformation (EMT) features. One tumor had sarcomatoid histology and a high proportion of cells having positive VIM expression (84%) and 92% of cells having complete loss of NAPSA expression; 3 tumors had partial EMT demonstrated by heterogeneous proportion of cells having VIM expression (18-56%) and loss of NAPSA (26-67%). Interestingly, some of the cells with EMT and partial-EMT had moderate levels of EGFR expression, similar to the levels in the TN tumors.

Conclusion: With osimertinib use at 1L, the incidence of RTK-independent resistance has increased to become the dominant mechanism, whereas RTK-dependent resistance has decreased. Increased lineage plasticity (small cell neuroendocrine, squamous and EMT) potentially serves as an RTK-independent TKI-resistance mechanism in EGFRm NSCLC.

Citation Format: Xiuning Le, Ruiping Wang, Natalie Vokes, Yasir Elamin, Neda Kalhor, Daniel McGrail, Yuanxin Xi, Santiago Treviño III, Lingzhi Hong, Robyn Du, George Blumenschein, Carl Gay, Marcelo Negrao, Mehmet Altan, Hai Tran, Limei Hu, Jing Wang, Simon Heeke, Monique Nilsson, Jacqulyne Robichaux, Minghao Dang, Guangchun Han, Lauren Byers, Anne Tsao, Boris Sepesi, Chantale Bernatchez, Jianjun Zhang, Linghua Wang, John Heymach. Enhanced lineage plasticity in RTK-independent TKI-resistant EGFR-mutant 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 3260.

174 Combined IL-2, agonistic CD3 and 4–1BB stimulation preserve clonotype hierarchy in propagated non-small cell lung cancer tumor-infiltrating lymphocytes

Background

While immune checkpoint blockade is regarded as standard of care for treatment of non-small cell lung cancer (NSCLC), up to 50% of patients with metastatic NSCLC do not achieve an optimal response.1–3 Previous work by our group and others in adoptive cell therapy (ACT) of metastatic melanoma (MM) has shown that infusion of a CD8+-rich TIL product significantly improved clinical outcomes, yet traditional IL-2 expansion methods have resulted in a predominantly CD4+ NSCLC TIL expansion product.7–12 This preclinical study explores the feasibility of producing a tumor-specific, CD8+-enriched NSCLC TIL product for ACT with an improved culture method.

Methods

TIL from resected NSCLC tumors were cultured using 1) the traditional method using IL-2 alone in 24-well plates (TIL 1.0) or 2) IL-2 in combination with agonistic antibodies against CD3 and 4-1BB (Urelumab) in a G-Rex flask (TIL 3.0). Expanded TIL were phenotyped using flow cytometry for CD4 and CD8 subset assessment and the CDR3-beta variable region of the T-cell receptor (TCR) involved in antigen binding was sequenced to assess the T-cell repertoire.

Results

In a shorter manufacturing time (median of 14 days vs 27.5 days), TIL 3.0 expanded on average 5.3-times more NSCLC TIL (95% CI= 4.3–6.2, p<0.0001) and achieved a higher expansion success rate than the traditional TIL 1.0 method (100% vs 62.5%, respectively, p<0.0001). Additionally, TIL 3.0 greatly enriched for CD3+CD8+ TIL (81.8% vs 36.9%, p=0.001) and expanded a larger breadth of clonotypes (p=0.039) which shared greater homology with the total clonotypes found in the repertoire of the resected tumor (p=0.0007), and contained a greater fraction of the clones found at high frequency in the tumor (p<0.00001). TIL 3.0 also retained a higher proportion of putative tumor-specific TCR when compared to TIL 1.0 (p=0.0039), defined based on exclusion of known viral-specific TCR and other TCR found in the paired uninvolved lung tissue.

Conclusions

This study reports the feasibility of using the TIL 3.0 methodology to robustly expand a CD8+ T-cell repertoire which maintains the respective clonal hierarchy in NSCLC tumors and enriches for putative tumor-specific TIL clones. The robustness and speed of the new process may facilitate testing and implementing effective TIL ACT in NSCLC.

References

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Melioli G, Ratto G, Guastella M, Meta M, Biassoni R, Semino C, et al. Isolation and in vitro expansion of lymphocytes infiltrating non-small cell lung carcinoma: functional and molecular characterisation for their use in adoptive immunotherapy. Eur J Cancer 1994;30A(1):97–102.

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Besser MJ, Shapira-Frommer R, Treves AJ, Zippel D, Itzhaki O, Hershkovitz L, et al. Clinical responses in a phase II study using adoptive transfer of short-term cultured tumor infiltration lymphocytes in metastatic melanoma patients. Clin Cancer Res 2010;16(9):2646–55.

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Radvanyi LG, Bernatchez C, Zhang M, Fox PS, Miller P, Chacon J, et al. Specific Lymphocyte Subsets Predict Response to Adoptive Cell Therapy Using Expanded Autologous Tumor-Infiltrating Lymphocytes in Metastatic Melanoma Patients. Clinical Cancer Research 2012;18(24):6758–70.

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Ethics Approval

This study was performed on NSCLC tumor tissue resected from 16 patients enrolled, following informed consent, in the ImmunogenomiC prOfiling of early-stage NSCLC (ICON) project. This study was approved by the University of Texas MD Anderson Cancer Center‘s Institutional Review Board (protocol number PA15-1112_MODCR001).

46 Proximity between cytotoxic antigen-experienced T cells and tumor cells is associated with improved clinical outcomes in early-stage NSCLC

Background

While the development of immunotherapies has improved the treatment of non-small cell lung cancer (NSCLC), most patients still fail to respond. Immune cell densities have been utilized to predict clinical responses but have largely failed to do so. However, the spatial distribution and interaction of these cells at the tissue level have been less studied. Here, we performed spatial analysis of the cells within the tumor immune microenvironment in order to evaluate their relationship with clinical outcomes in early-stage NSCLC.

Methods

Multiplex immunofluorescence was performed on 123 early-stage NSCLC patients from the ICON (Immunogenomic profiling of non-small cell lung cancer) cohort including Cytokeratin (CK), CD3, CD8, CD45RO, FoxP3, CD68, CD20, CD57, Granzyme B (GzmB), PD-1, and PD-L1. Area under the curve (AUC) was calculated using Ripley’s L function, which evaluates the degree of spatial proximity of two cell populations, with a high AUC indicating clustering and low AUC indicating scattering. Findings were integrated with clinical parameters.

Results

Adenocarcinomas demonstrated CD3+PD1+ T cells were closer to CK+ tumor cells (n=60, p=0.035), and B cells were closer to cytotoxic T cells (n=43, p=0.03) than in squamous cell carcinoma. Higher AUC was observed between CD3+PD1+ T cells (n=56, p=0.035), with cytotoxic antigen-experienced T cells (CD45RO+GzmB+) closer to tumor cells (n=35, p=0.017) in stage I and II compared to stage III tumors. Untreated patient tumors exhibited higher proximity between CD20+ B cells and CD57+ NK cells (n=59, p=0.012), CD3+ T cells and PD-L1+ tumor cells (n=56, p=0.027), and CD68+ macrophages and PD-L1+ tumor cells (n=52, p=0.016) than neoadjuvant chemotherapy-treated patients. Patients with no recurrence presented higher AUC in antigen-experienced CD45RO+GzmB+ T cells and tumor cells (n=36, p=0.006), while those with improved survival demonstrated greater proximity between CD68+ macrophages and PD-L1+ tumors (n=52, p=0.016), CD20+ B cells and GzmB+ cells (n=49, p=0.03), and antigen-experienced CD45RO+GzmB+ T cells and tumor cells (n=36, p=0.047). Lastly, patients with improved survival also displayed greater proximity between CD3+CD8+ cytotoxic T cells and PD-L1- epithelial cells (n=76, p=0.04) in tumors versus matched adjacent lungs.

Conclusions

Overall, our findings shed light on some of the potential cell interactions at play in the tumor microenvironment of early-stage NSCLC patients and suggest cell distributions could be utilized to predict clinical outcomes in early-stage NSCLC patients.

962 Integrative immunomics highlight the immunomodulatory impact of neoadjuvant chemotherapy and immune-based treatments in resected non-small-cell lung cancer

Background

How neoadjuvant chemo-immunotherapy modulates tumor immune composition and response is not completely understood. We interrogate immunomodulation of neoadjuvant platinum-based chemotherapy (C), nivolumab (N), and N-plus-C (NC) and their connections to therapeutic efficacy in resected non-small cell lung cancer (NSCLC) by integrating immunomic data from the ImmunogenomiC PrOfiling of NSCLC (ICON) study and NEOSTAR trial cohorts.

Methods

In NEOSTAR (NCT03158129), patients with stage I-IIIA (single N2) resectable NSCLC (AJCC7th) received N (3 mg/kg IV, D1,15,29); patients with stage IB(≥4cm)-IIIA (single N2) resectable NSCLC received NC (N 360 mg IV plus C, D1,22,43 for 3 cycles, every 3 weeks) before surgery; major pathologic response (MPR) was the primary endpoint. In ICON, patients with stage IB(≥4cm)-IIIA resectable NSCLC received C before surgery. Surgically resected tumor samples underwent immune profiling via flow cytometry (n=16,13,9 for C,N,NC), immunohistochemistry (IHC;n=0,18,14), and multiplexed immunofluorescence (mIF;n=28,16,10). Treatment-associated immunomodulation and associations with therapeutic efficacy were analyzed using: 1) a shared nearest neighbors-based network we developed linking measurements across datasets; 2) MetaCyto, a specialized cytometry analysis method for identifying cell subsets by clustering.

Results

We holistically explored the immunomic data by integration across cohorts. Through hierarchical regression of the integrated data, we determined the overall effect of a given treatment controlling for the presence or absence of the other treatment.

We examined C’s effects across all cohorts controlling for N. Across all patients, regardless of MPR, C is associated with immunosuppression, increasing PD1+ T cell (CD45+CD3+) populations: regulatory (CD4+CD25+FOXP3+), helper (CD4+), and effector (CD8+) (effect size(ES):1.48,1.61,1.26;q<0.05). C also decreases proliferative (Ki67+) populations: helper and effector T cells as well as NK (CD45+CD3-CD56+) cells (ES:-1.27,-1.43;-1.36;q<0.05). In patients without MPR (i.e., non-responding patients), immunosuppression appears heightened by increased Ki67+ regulatory T cells (ES:1.86;q<0.05).

Conversely, we examined N’s effects across all cohorts controlling for C. Across all patients, regardless of MPR, N is associated with immune activation, increasing ICOS+ T cell populations: regulatory, helper, and effector (ES:1.29,1.29,1.47;q<0.05). Comparing N and NC reveals that adding C may drive exhaustion by increasing TIM3+ regulatory, helper and effector T cells (ES:1.16,1.17,1.23;q<0.05), an effect more pronounced in non-responding patients (ES:1.31,1.33,1.35;q<0.05).

Conclusions

We report the first integrated examination of the immunomodulatory effect of neoadjuvant C and N. C is associated with immunosuppression while N with immune activation; together, N appears to lessen C’s suppressive effects. Incorporation of transcriptomics into this integrated network of flow cytometry, mIF, and IHC immune profiling data is ongoing to augment translational insights for neoadjuvant chemo/immunotherapies.

Abstract B168: Monitoring acquired resistance to EGFR-TKIs and clonal evolution in metastatic NSCLC patients using liquid biopsies

Epidermal Growth Factor Receptor (EGFR) activating mutations predict sensitivity to first- and second-generation anti-EGFR tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancer (NSCLC). However, NSCLC invariably develops acquired resistance (AR) to these agents, leading to disease progression. EGFR-T790M secondary mutation is the most frequent AR mechanism in this setting. Patients with EGFR-T790M positive tumors demonstrate impressive response rate to osimertinib, a third-generation EGFR-TKI, but disease progression also occurs. Intratumor heterogeneity and selection of genetic alterations that confer resistance to target therapy have been recognized as crucial in the development of AR to EGFR-TKIs. In the present study, we used liquid biopsies to monitor the appearance and dynamics of genetic alterations known to be associated with EGFR-TKIs AR in circulating tumor DNA (ctDNA) of patients with metastatic NSCLC treated with EGFR-TKIs. A total of 21 patients were recruited for this study, of whom 17 were initially treated with erlotinib, 2 with gefitinib, and 2 with afatinib. Disease progression was observed in 9 patients using erlotinib, 2 patient using gefitinib, and 1 patient using afatinib. The detection of EGFR mutations in these patients was carried out in serial liquid biopsies using droplet digital PCR (ddPCR) at a sensitivity between 0.1-0.5%. Of the 12 patients with disease progression, 7 (58.3%) were positive for the EGFR-T790M mutation in tissue biopsy and for 4 (57.1%) of these patients the EGFR-T790M was also detected by liquid biopsy at disease progression. Of the 7 EGFR-T790M positive patients, 5 received osimertinib, including 2 patients with EGFR-T790M positive liquid biopsy. Patients with EGFR-T790M positive liquid biopsies were followed closely using serial liquid biopsies to monitor the levels of the original EGFR mutation and of the EGFR-T790M resistance mutation. In general, plasma levels of the activating EGFR mutation and of the EGFR-T790M mutation accurately paralleled the clinical and radiologic evolution of the disease. Patients showing sequential increase in both EGFR mutations showed marked disease progression while those with stable levels presented indolent disease. EGFR-T790M plasma levels became undetectable within 1-2 weeks after the start of osimertinib, anticipating radiologic response to the drug. Of note, increases in T790M levels during treatment anticipated AR to osimertinib in one of our patients. This was accompanied by the emergence of a second EGFR resistance mutation (C797S) and a selective amplification of the EGFR-exon19del allele. In conclusion, liquid biopsies for EGFR genotyping can be used as a complementary strategy to tissue biopsies and should be considered the initial approach to identify both EGFR-TKI sensitizing and resistance mutations due to its minimally invasive nature. Also, plasma levels of EGFR mutations accurately paralleled the clinical and radiologic evolution of disease for these patients, allowing early detection of AR to TKIs. Finally, liquid biopsies can also be used to study novel mechanisms of AR to EGFR-TKIs.

Citation Format: Franciele Knebel, Fabiana Bettoni, Andrea Shimada, Manoel Cruz, João Victor Alessi, Marcelo Negrao, David Muniz, Luiz Fernando Reis, Artur Katz, Olavo Feher, Daniel Saragiotto, Anamaria Camargo. Monitoring acquired resistance to EGFR-TKIs and clonal evolution in metastatic NSCLC patients using liquid biopsies [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B168.

Word-fragment cuing: The lexical search hypothesis

In four experiments we evaluated aspects of the hypothesis that word-fragment completion depends on the results of lexical but not semantic search. Experiment 1 showed that the number of meaningful associates linked to a studied word does not affect its recovery when the test cue consists of letters and spaces for missing letters. Experiments 2 and 3 showed retroactive interference effects in fragment completion when words in a second list were lexically related to words in a first list but not when the words in the second list were meaningfully related. Experiment 4 indicated that for studied words, instructions to search at the word level facilitated completion performance and that instructions to generate letters to fill missing spaces had no effect. Other findings indicated that completion was affected by the number of words lexically related to the fragment and by the number of letters missing from the fragment. In general, experimental manipulations that focused on lexical characteristics were effective, and those that focused on semantic characteristics were ineffective. The findings support the conclusion that word fragments engender a lexical search process that does not depend on retrieving encoded meaning.