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  • 1
    In: Journal for ImmunoTherapy of Cancer, BMJ, Vol. 10, No. 8 ( 2022-08), p. e004757-
    Abstract: Most patients with advanced non-small-cell lung cancer (NSCLC) fail to derive significant benefit from programmed cell death protein-1 (PD-1) axis blockade, and new biomarkers of response are needed. In this study, we aimed to discover and validate spatially resolved protein markers associated with sensitivity to PD-1 axis inhibition in NSCLC. Methods We initially assessed a discovery cohort of 56 patients with NSCLC treated with PD-1 axis inhibitors at Yale Cancer Center. Using the GeoMx Digital Spatial Profiling (DSP) system, 71 proteins were measured in spatial context on each spot in a tissue microarray. We used the AQUA method of quantitative immunofluorescence (QIF) to orthogonally validate candidate biomarkers. For external independent validation, we assessed whole tissue sections derived from 128 patients with NSCLC treated with single-agent PD-1 axis inhibitors at the 12 de Octubre Hospital (Madrid) using DSP. We further analyzed two immunotherapy untreated cohorts to address prognostic significance (n=252 from Yale Cancer Center; n=124 from University Clinic of Navarra) using QIF and DSP, respectively. Results Using continuous log-scaled data, we identified CD44 expression in the tumor compartment (pan-cytokeratin (CK)+) as a novel predictor of prolonged progression-free survival (PFS) (multivariate HR=0.68, p=0.043) in the discovery set. We validated by QIF that tumor CD44 levels assessed as continuous QIF scores were associated with longer PFS (multivariate HR=0.31, p=0.022) and overall survival (multivariate HR=0.29, p=0.038). Using DSP in an independent immunotherapy treated cohort, we validated that CD44 levels in the tumor compartment, but not in the immune compartment (panCK–/CD45+), were associated with clinical benefit (OR=1.22, p=0.018) and extended PFS under PD-1 axis inhibition using the highest tertile cutpoint (multivariate HR=0.62, p=0.03). The effect of tumor cell CD44 in predicting PFS remained significant after correcting for programmed death-ligand 1 (PD-L1) Tumor Proportion Score (TPS) in both cohorts. High tumor cell CD44 was not prognostic in the absence of immunotherapy. Using DSP data, intratumoral regions with elevated tumor cell CD44 expression showed prominent (fold change 〉 1.5, adjusted p 〈 0.05) upregulation of PD-L1, TIM-3, ICOS, and CD40 in two independent cohorts. Conclusions This work highlights CD44 as a novel indicative biomarker of sensitivity to PD-1 axis blockade that might help to improve immunotherapy strategies for NSCLC.
    Type of Medium: Online Resource
    ISSN: 2051-1426
    Language: English
    Publisher: BMJ
    Publication Date: 2022
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 15 ( 2023-08-01), p. 2513-2526
    Abstract: Immunotherapy resistance in non–small cell lung cancer (NSCLC) may be mediated by an immunosuppressive microenvironment, which can be shaped by the mutational landscape of the tumor. Here, we observed genetic alterations in the PTEN/PI3K/AKT/mTOR pathway and/or loss of PTEN expression in & gt;25% of patients with NSCLC, with higher frequency in lung squamous carcinomas (LUSC). Patients with PTEN-low tumors had higher levels of PD-L1 and PD-L2 and showed worse progression-free survival when treated with immunotherapy. Development of a Pten-null LUSC mouse model revealed that tumors with PTEN loss were refractory to antiprogrammed cell death protein 1 (anti–PD-1), highly metastatic and fibrotic, and secreted TGFβ/CXCL10 to promote conversion of CD4+ lymphocytes into regulatory T cells (Treg). Human and mouse PTEN-low tumors were enriched in Tregs and expressed higher levels of immunosuppressive genes. Importantly, treatment of mice bearing Pten-null tumors with TLR agonists and anti-TGFβ antibody aimed to alter this immunosuppressive microenvironment and led to tumor rejection and immunologic memory in 100% of mice. These results demonstrate that lack of PTEN causes immunotherapy resistance in LUSCs by establishing an immunosuppressive tumor microenvironment that can be reversed therapeutically. Significance: PTEN loss leads to the development of an immunosuppressive microenvironment in lung cancer that confers resistance to anti–PD-1 therapy, which can be overcome by targeting PTEN loss–mediated immunosuppression.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 3
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. 8594-8594
    Abstract: 8594 Background: Transcriptomic subtyping holds promise for personalized therapy in SCLC, but intratumoral transcriptomic heterogeneity and its clinical significance remain poorly defined. In this study, we aimed to assess transcription factor defined subtypes within multiple regions of intact tissues and identify gen sets associated with long-term chemo-immunotherapy benefit. Methods: We assessed baseline FFPE tumors from 32 ES-SCLC patients enrolled in the IMfirst clinical trial (EudraCT: 2019-002784-10). We used GeoMx DSP to perform transcriptomic analysis from multiple intratumoral regions of interest (ROIs). We used an assay with +1800 genes (GeoMx CTA) plus custom-designed mRNA probes targeting subtype-defining transcription factors not included in the CTA assay (POU2F3, NEUROD1, and YAP1). Custom probes were quantitatively validated using FFPE cell lines. Results: We profiled 175 ROIs from 32 tumors. Cluster analysis based on the expression of ASCL1, NEUROD1, POU2F3, and YAP1 showed that all samples clustered within 4 groups: SCLC-A (76 ROIs [43%]), SCLC-N (31 ROIs [18%] ), SCLC-P (18 ROIs [10%]), and SCLC-Y (50 ROIs [29%] ). ASCL1 was the most abundantly expressed transcription factor, prevailed in the SCLC-A subtype, and showed inverse correlation with POU2F3 (r=-0.55, p 〈 0.0001) and YAP1(r=-0.70, p 〈 0.0001). YAP1 was expressed at low levels and was more broadly distributed across all 4 subtypes. Differential expression and gene set enrichment analysis (GSEA) using linear mixed models revealed that SCLC-A subtype was enriched in cell cycle and DNA damage repair genes, and showed repression of multiple gene sets associated with anti-tumor immune response. In contrast, SCLC-Y subtype showed the opposite pattern. The SCLC-P subtype was also enriched in genes related to cancer antigens and T-cell checkpoints. Most patients (n=18, 56%) had tumors with coexistence of more than one subtype, not evident through morphological inspection. Combined SCLC-A and SCLC-Y subtypes was the most common mixed phenotype (n=8, 25%). Four patients (13%) had tumors with co-existence of three subtypes. Transcriptional subtypes, subtype-defining transcription factors as single genes, or the presence of subtype heterogeneity, were not associated with outcomes. Gene sets involved in mitochondrial metabolism and MHC class I antigen presentation were the highest enriched pathways in tumors from patients with sustained benefit (time to progression ³ 12 months). Conclusions: This study reveals substantial intratumoral transcriptomic subtype heterogeneity in human SCLC. In this limited sample set, we did not observe outcome association for transcriptional subtypes. Our findings related to long-term chemo-immunotherapy benefit require validation in independent cohorts.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 2028-2028
    Abstract: Introduction: Most patients with advanced NSCLC fail to develop durable responses from PD-1 axis blockade, and more robust predictive biomarkers are needed. In this study, we aimed to discover and validate spatially resolved protein markers associated with sensitivity to PD-1 axis inhibition across multiple NSCLC cohorts. Methods: We first used the GeoMx Digital Spatial Profiling (DSP) system in a discovery cohort of 56 NSCLC patients treated with PD-1 axis inhibitors at Yale (USA). Pre-treatment tumors were represented in a tissue microarray (YTMA471) and analyzed using a 71-plex primary antibody panel. Proteins were measured from three molecularly defined tissue compartments: tumor (CK+), leukocytes (CD45+/CD68-), and macrophages (CD68+). We used quantitative immunofluorescence (QIF) to orthogonally validate candidate biomarkers. For external validation of identified predictors, we assessed pre-treatment whole tissue sections from a cohort of 128 NSCLC patients treated with single-agent PD-1 axis inhibitors at the Hospital 12 de Octubre (Madrid, Spain) using DSP (39-plex protein panel, measured from CK+ and CD45+ compartments). In addition, we analyzed two immunotherapy untreated cohorts to address prognostic significance: YTMA423 (Yale, USA; n = 252) and CIMA-CUN (UNAV, Spain; n = 124), using QIF and DSP respectively. Results: Using continuous log-scaled data, we found 5 markers independently associated with progression-free survival (PFS) in the tumor compartment (including PD-L1, p = 0.002). Among the novel candidate predictors, tumor cell CD44, a marker of pluripotency and stemness, was associated with longer PFS (multivariate HR = 0.63, p= 0.002). Using QIF, we orthogonally validated that CD44 expression in the tumor compartment was associated with longer PFS (p & lt;0.001) and overall survival (OS) (p = 0.03). In the external validation cohort, CD44 expressed in the tumor compartment, but not in the immune compartment, was predictive of clinical benefit (OR 1.22, p = 0.018), and was significantly associated with longer PFS (first tertile cutpoint: HR 0.62, p = 0.03). In contrast, high CD44 expression was not associated with survival in the two untreated cohorts. Using DSP data from two cohorts, regions of interest with elevated expression of CD44 in tumor cells consistently showed prominent (Fold Change & gt;1.5, p & lt;0.05) upregulation of TIM-3, and PD-L1 and multiple co-stimulatory molecules (including CD40, ICOS, CD27). Conclusion: This work highlights CD44 as a novel indicative biomarker of sensitivity to PD-1 axis blockade in NSCLC. NSCLCs with high CD44 expression in epithelial cells may be associated with an immune contexture primed for higher response to immune checkpoint blockade. Further studies are needed to understand the interplay between CD44+ cancer stem cell phenotype and mechanisms of immune evasion. Citation Format: Myrto Moutafi, Magdalena Molero, Sandra Martinez-Morilla, Javier Baena, Ioannis Vathiotis, Niki Gavrielatou, Laura Castro, Gorka Ruiz de Garibay, Vera Adradas, Daniel Orive, Karmele Valencia, Alfonso Galvo, Luis M. Montuenga, Santiago Ponce, Kurt Schalper, Luis Paz-Ares, David L. Rimm, Jon Zugazagoitia. Spatially resolved proteomic profiling identifies tumor cell CD44 as a novel indicative biomarker of sensitivity to PD-1 axis blockade in advanced 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 2028.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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