Co-Mutation of FAT3 and LRP1B in Lung Adenocarcinoma Defines a Unique Subset Correlated With the Efficacy of Immunotherapy

Immunotherapy based on immune checkpoint inhibitors (ICIs) have demonstrated remarkable survival benefits and gained regulatory approval in non-small cell lung cancer (NSCLC) patients without an actionable driver mutation, but currently there is no well-established standard for how to screen the most suitable population for ICIs treatment. Here, we conducted a comprehensive analysis of the somatic mutation landscape of lung adenocarcinoma (LUAD) samples. After the stepwise screening of high-frequency mutated genes, two genes with prominent significance, FAT3 and LRP1B, were finally screened out. Through further analysis, we discovered that the co-mutation of FAT3 and LRP1B was associated with an earlier age of onset and occurred more frequently in Black/African American. Furthermore, co-mutation defines a unique subgroup of lung adenocarcinoma that can increase tumor mutational burden (TMB), boost cytotoxicity and tumor immunogenicity, and facilitate lymphocyte infiltration. The results of gene set enrichment analysis (GSEA) indicated that co-mutation can influence tumorigenesis through a variety of mechanisms. More strikingly, the subset of LUAD with co-mutation of FAT3 and LRP1B exhibited significantly prolonged immunotherapy progression free survival (PFS). In summary, co-mutation of FAT3 and LRP1B is a promising useful biomarker for predicting the efficacy of immunotherapy, which can improve the clinical efficiency of practicing precision medicine in lung adenocarcinoma patients.

Regorafenib in metastatic colorectal cancer: more data for clinical decisions

Regorafenib is a multiple kinase inhibitor. It influences/blocks angiogenesis (VEGFR1-3, TIE2), proliferation (KIT, RET, RAF-1, BRAF), metastatic activity (VEGFR2-3, PDGFR), tumor immunogenicity (CSF1R), tumor microenvironment (PDGFR-, PDGFR-, FGFR1-2). Regorafenib has several indications including metastatic colorectal cancer. Efficacy and safety of regorafenib data from clinical trials (CORRECT, CONCUR, CONSIGN) and observational trials from real world (REBECCA, CORRELATE, RECORA, PMS, REGOTAS) are summarized and presented in this issue. State of the matter of molecular-biologic predictors (KRAS, PIK3CA ANG-2, VEGF-A, LDH, CCL5/CCR5, CA 19-9) and radiological predictors (RadioCORRECT and other trials) is highlighted. Regimens with dose modification and its influence on effectiveness and tolerability of regorafenib are described according to the data from ReDOS, RESET, REARRANGE trials. The results from retrospective trials comparing regorafenib and another approved for refractory metastatic colorectal cancer drug trifluridine/tipiracil are presented.

Homeoprotein SIX1 compromises antitumor immunity through TGF-β-mediated regulation of collagens

The tumor microenvironment (TME), including infiltrated immune cells, is known to play an important role in tumor growth; however, the mechanisms underlying tumor immunogenicity have not been fully elucidated. Here, we discovered an unexpected role for the transcription factor SIX1 in regulating the tumor immune microenvironment. Based on analyses of patient datasets, we found that SIX1 was upregulated in human tumor tissues and that its expression levels were negatively correlated with immune cell infiltration in the TME and the overall survival rates of cancer patients. Deletion of Six1 in cancer cells significantly reduced tumor growth in an immune-dependent manner with enhanced antitumor immunity in the TME. Mechanistically, SIX1 was required for the expression of multiple collagen genes via the TGFBR2-dependent Smad2/3 activation pathway, and collagen deposition in the TME hampered immune cell infiltration and activation. Thus, our study uncovers a crucial role for SIX1 in modulating tumor immunogenicity and provides proof-of-concept evidence for targeting SIX1 in cancer immunotherapy.

927 Wilms tumor reveals DNA repair gene hyper-expression is linked to lack of immune infiltration

BackgroundA T cell-rich tumor microenvironment has been associated with improved clinical outcome and response to immune checkpoint blockade therapies in several adult cancers. Understanding the mechanisms for lack of immune cell infiltration is critical for expanding immunotherapy efficacy in the clinic. To gain new insights into the mechanisms of poor tumor immunogenicity, we turned to pediatric cancers, which are generally unresponsive to checkpoint blockade.MethodsRNAseq and clinical data were obtained for Wilms tumor, rhabdoid tumor, osteosarcoma, and neuroblastoma from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, and adult cancers from TCGA. Using an 18-gene tumor inflammation signature (TIS) representing activated CD8+ T cells, we identified genes significantly anti-correlated with the signature. Immunofluorescence was performed on metastatic melanoma samples for CD8, MSH2, and the tumor cell marker SOX10, and analyzed for relationship to anti-PD-1 efficacy.ResultsAmong the four pediatric cancers, we observed the lowest TIS scores in Wilms tumor. Wilms tumors demonstrated significantly lower T cell inflammation signatures than matched normal kidney samples, other pediatric tumor samples, and adult kidney tumor samples. Pathway analysis identified multiple types of DNA repair were upregulated in Wilms tumor and a score generated from the top 50 DNA repair genes strongly anti-correlated with TIS. This striking negative association was also observed in most adult tumor types. The anti-correlation was found to be independent of tumor mutation burden, suggesting that high expression of DNA repair pathway machinery may restrict tumor immunogenicity by mechanisms beyond prevention neoantigen accumulation. MSH2 was one of the top DNA repair genes identified from the Wilms tumor analysis and was confirmed to have a strong anti-correlation with TIS in melanoma samples from TCGA. Immunofluorescence from an independent cohort of metastatic melanoma patients revealed a significant negative correlation between CD8+ T cell numbers and MSH2+ SOX10+ tumor cell numbers. Additionally, non-responders to anti-PD-1 immunotherapy had significantly higher numbers of MSH2+ SOX10+ tumor cells than responders.ConclusionsIncreased tumor expression of DNA repair genes is associated with a less robust immune response in Wilms tumor, and this was also observed in the majority of TCGA tumor types. Surprisingly, the negative relationship between DNA repair score and TIS remained strong across TCGA when correcting for mutation count, indicating a potential role for DNA repair genes outside of preventing the accumulation of mutations. Strategies targeting DNA repair pathways could be considered as new therapeutic interventions to transform non-T cell-inflamed tumors into immune-responsive tumors.Ethics ApprovalThe study obtained ethics approval under IRB protocol 15-0837.

907 Modulation of tumor immunogenicity by DNA methylation of immune synapse genes in cancers

BackgroundCancer immunotherapy represents a major paradigm shift in cancer care. Despite such breakthrough, majority of cancer patients remains refractory to existing immunotherapeutic modalities highlighting the inherent capacity of tumors to escape immunosurveillance mechanisms. Frequently, cancer cells utilize the epigenetic machinery to silence tumor suppressors or activate oncogenes for survival and proliferation. Likewise, tumor cells might employ the epigenetic reprogramming of immune-related pathways to evade the immune system. Methylation is one of the major epigenetic mechanisms modulating gene transcription. Thus, we investigated the methylation profile of both co-stimulatory and immune checkpoint genes in cancer.MethodsData from The Cancer Genome Atlas (TCGA) were used for methylation profiling and RNA-sequencing analysis. Twenty-six epithelial cancer cell lines with more than 3 mock and three 5-azacitidine–treated samples were selected for analysis from the GSE57342 dataset. t-distributed stochastic neighbor embedding (t-SNE) was calculated using 247 probes for the selected 20 genes across all TCGA samples. t-SNE analysis was performed on 8,186 solid tumors and 745 normal adjacent tissues for methylation levels for all probes. For principal component analysis, first and second principal components were used to represent the overall methylation status for 8,931 tumor and normal samples in the TCGA database. Survival analyses were retrieved from a prior publication.1ResultsWe found that methylation profile of immune synapse genes is distinct in tumor versus normal adjacent tissue. Interestingly, our results demonstrate hypermethylation of co-stimulatory genes such as CD40 and hypo-methylation of immune checkpoint genes such as HHLA2 and PDL1 across multiple tumor types in comparison with the normal adjacent tissue. In addition, an inverse correlation between methylation and gene expression was manifest among tumor and normal adjacent tissue, confirming the epigenetic mechanism of gene suppression by gene methylation. Furthermore, we observed a reversal of hypermethylation of the co-stimulatory genes including CD40 by the demethylating agent 5-azacytidine in the data set of 26 epithelial cancer cell lines. Finally, we found that that hypomethylation of co-stimulatory genes within the immune synapse correlates with functional T cell recruitment to the tumor microenvironment and is followed by a favorable clinical outcome in melanoma patients.ConclusionsOur finding unveils methylation of immune synapse genes as a crucial driver of the immune evasive phenotype of cancer cells. Notably, identification of actionable targets to restore tumor immunogenicity is an attractive strategy in combination with immune checkpoint blockade.AcknowledgementsThis work was supported by NIH grant K08 CA194273, the Immunology Innovation Fund, an NCI Cancer Center Support grant, (P30-CA076292), the Miriam and Sheldon G. Adelson Foundation, and the Moffitt Foundation.ReferenceLiu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V, Cancer Genome Atlas Research N, Hu H. An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics. Cell 2018;173(2):400–16 e11.

Electrochemotherapy as a Trigger to Overcome Primary Resistance to Anti-PD-1 Treatment: A Case Report of Melanoma of the Scalp

BackgroundImmunotherapy with immune checkpoint inhibitors is one of the main therapies for advanced melanoma. Nevertheless, albeit remarkable, immunotherapy results are still unsatisfactory as more than half of patients progress, and resistance to treatment still has a dramatic impact on clinical outcomes. Local treatments such as radiotherapy or electrochemotherapy (ECT), in addition to local control with palliative intent, have been shown to release tumoral neoantigens that can stimulate a robust systemic antitumor immune response.Case PresentationWe report the case of a patient with multiple nodular melanoma lesions of the scalp initially treated with local ECT. Soon after the procedure, multiple new lesions appeared close to the treated ones, therefore the patient started a systemic treatment with the anti-PD-1 nivolumab. The lesions of the scalp did not respond to immunotherapy, presenting a loco-regional spreading. To control the bleeding and painful lesions, we performed a second ECT, while continuing systemic immunotherapy. The treated lesions responded to the second procedure, while the other lesions continued progressing in number and dimension. Unexpectedly, after 2 months from the second ECT, the patient presented a progressive shrinkage of both treated and untreated lesions until complete remission. Concomitantly, he developed immune-related adverse events including grade 4 thyroid toxicity, grade 2 vitiligo-like depigmentation and grade 2 pemphigoid. At present, after 18 months from the first ECT and 14 months from the starting of anti-PD-1 immunotherapy, the patient is in good clinical condition and complete remission of disease still persists.ConclusionThis case highlights the potential role of ECT in increasing tumor immunogenicity and consequently in inducing a powerful immune response overcoming primary resistance to checkpoint inhibitor immunotherapy.