Identification of WDFY3 Neoantigens as Prognostic Markers in Longterm Survivors of Extrahepatic Cholangiocarcinoma

Background:: Neoantigens are newly formed antigens that have not been previously recognized by the immune system. They may arise from altered tumor proteins that form as a result of mutations. Although neoantigens have recently been linked to antitumor immunity in long-term survivors of cancers, such as melanoma and colorectal cancer, their prognostic and immune-modulatory role in many cancer types remains undefined. Objective: The purpose of this study is to identify prognostic markers for long-term extrahepatic cholangiocarcinoma (EHCC) survival. Methods: We investigated neoantigens in EHCC, a rare, aggressive cancer with a 5-year overall survival rate lower than 10%, using a combination of whole-exome sequencing (WES), RNA sequencing (RNA-seq), computational biophysics, and immunohistochemistry. Results: : Our analysis revealed a decreased neutrophil infiltration-related trend of high-quality neoantigen load with IC50 <500 nM (r=-0.445, P=0.043). Among 24 EHCC patients examined, we identified four long-term survivors with WDFY3 neoantigens and none with WDFY3 neoantigens in the short-term survivors. The WDFY3 neoantigens are associated with a lower infiltration of neutrophils (p=0.013), lower expression of CCL5 (p=0.025), CXCL9 (p=0.036) and TIGIT (p=0.016), and less favorable prognosis (p=0.030). In contrast, the prognosis was not significantly associated with tumor mutation burden, neoantigen load, or immune cell infiltration. Conclusion:: We suggest that the WDFY3 neoantigens may affect prognosis by regulating antitumor immunity and that the WDFY3 neoantigens may be harnessed as potential targets for immunotherapy of EHCC.

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Abstract P3-06-14: Whole exome analysis of extreme long-term survivors with metastatic breast cancer

10.1158/1538-7445.sabcs18-p3-06-14 ◽

2019 ◽

Author(s):

RE Yan ◽

C Longhurst ◽

K Lee ◽

AD Gilbert ◽

RA Alexandridis ◽

...

Keyword(s):

Breast Cancer ◽

Metastatic Breast Cancer ◽

Metastatic Breast ◽

Whole Exome ◽

Exome Analysis ◽

Long Term Survivors

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Increased neutrophil infiltration and lower prevalence of tumor mutation burden and microsatellite instability are hallmarks of RAS mutant colorectal cancers.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3563 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3563-3563

Author(s):

Emil Lou ◽

Yasmine Baca ◽

Joanne Xiu ◽

Andrew Nelson ◽

Subbaya Subramanian ◽

...

Keyword(s):

T Cells ◽

B Cells ◽

Cd8 T Cells ◽

Immune Cell ◽

Neutrophil Infiltration ◽

Cell Fraction ◽

Colorectal Cancers ◽

Tumor Mutation Burden ◽

Immune Infiltration ◽

Mutation Burden

3563 Background: The tumor microenvironment (TME) of colorectal cancers (CRC) is modulated by oncogenic drivers such as KRAS. The TME comprises a broad landscape of immune infiltration. How tumor genomics associates with the immune cell landscape is less known. We aim to characterize immune cell types in RAS wild-type (WT) and mutant (MT) CRC, and to examine the prevalence of immuno-oncologic (IO) biomarkers (e.g. tumor mutation burden (TMB), PD-L1, MSI-H/dMMR) in these tumors. We performed genomic and transcriptomic analysis to confirm associations of mutant RAS with immune infiltration of the TME conducive to metastasis vs. potential response to immunotherapies. Methods: A total of 7,801 CRC were analyzed using next-generation sequencing on DNA (NextSeq, 592 Genes and WES, NovaSEQ), RNA (NovaSeq, whole transcriptome equencing) and IHC (Caris Life Sciences, Phoenix, AZ). MSI/MMR was tested by FA, IHC and NGS. TMB-H was based on a cut-off of > 10 mutations per MB). Immune cell fraction was calculated by QuantiSeq (Finotello 2019, Genome Medicine). Significance was determined by X2 and Fisher-Exact and p adjusted for multiple comparisons (q) was <0.05. Results: Mutant KRAS was seen in 48% of mCRC tumors; NRAS in 3.7%, HRAS in 0.1%. The distribution was similar in patients < or >= than 50 yrs. In MSS tumors, there was a significantly higher neutrophil infiltration in KRAS MT (median cell fraction 6.6% vs. 5.9%) and NRAS MT (6.9%) overall and also when individual codons were studied. B cells, M2 macrophages, CD8+ T cells, dendritic cells and fibroblasts were lower in KRAS mutant tumors; B cells and M1 macrophages are lower in NRAS (q<0.05). dMMR/MSI-H was significantly more prevalent in RAS WT (9.1%) than in KRAS (2.9%) or NRAS MT (1.8%) tumors, and highest in HRAS MT tumors (60%, q<0.05).TMB-H was more prevalent in RAS WT (11%) than KRAS (5.8%) or NRAS (5.1%) MT, and highest in HRAS MT tumors (70%, all q<0.05). In MSS tumors, KRAS MT tumors showed more TMB-H than WT (3.1% vs. 2.1%, q<0.05), especially in KRAS non 12/13/61 mutations (5.5%, vs. 2.1%, q<0.05) and G12C (4.4%, p<0.05). PD-L1 expression was studied: in MSS tumors, KRAS-G12D (10.4%) and G13 MT (11.8%) showed higher mutation rates than RAS WT tumors (q<0.05). Conclusions: KRAS & NRAS mutations are associated with increased neutrophil abundance, with codon specific differences, while HRAS shows no difference. Overall CD8+ T cells and B cells are less abundant in KRAS & NRAS mutants; substantial variability was seen amongst different protein changes. RAS mutations were more prevalent overall than generally reported, but did not vary by age. These results demonstrate significant differences in the TME of RAS mutant CRC that identify variable susceptibilities to immuno-oncologic agents, and provide further detailed characterization of heterogeneity between RAS variants, at the molecular as well as immunogenic levels.

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IMMU-21. THE COMBINATION OF DELTA-24-ACT WITH AN IMMUNE CHECKPOINT INHIBITOR RESULTS IN ANTI-GLIOMA EFFECT AND IMMUNE MEMORY

Neuro-Oncology ◽

10.1093/neuonc/noaa215.451 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii109-ii109

Author(s):

Montserrat Puigdelloses ◽

Virginia Laspidea ◽

Marc Garcia-Moure ◽

Daniel De la Nava ◽

Dolores Hambardzumyan ◽

...

Keyword(s):

Immune Checkpoint Inhibitor ◽

Immune Cell ◽

Checkpoint Inhibitor ◽

Immune Memory ◽

Long Term Survivors ◽

Anti Tumour Effect ◽

Murine Glioma

Abstract Oncolytic viruses have become promising therapeutic candidates to treat gliomas. Our group has developed Delta-24-ACT, an oncolytic adenovirus armed with the positive costimulatory ligand 4-1BBL which is capable to trigger the activation of T cells and thereby increase their antitumor immune response. Here we evaluate the anti-glioma effect of Delta-24-ACT alone or in combination with an immune checkpoint inhibitor. We observed that Delta-24-ACT was able to infect and kill murine glioma (GL261-5 and CT-2A) and also human glioma cell lines (U87-MG and U251-MG), while maintaining its replication in the latter. Of importance, Delta-24-ACT infection resulted in 4-1BBL expression on the membrane of glioma cells. Moreover, this ligand was functional and was able to stimulate CD8 lymphocytes in vitro, suggesting the potential of Delta-24-ACT to trigger an effective immune response. Furthermore, in vivo Delta-24-ACT showed anti-tumour effect in two murine glioma models by significantly increasing the median survival time and leading to long-term survivors. Mechanistic studies demonstrated an increase of the T cell infiltration and the activation of different immune cell populations by flow cytometry and a decrease of proliferative cells and tumour vessels by immunohistochemistry on FFPE brain samples. Importantly, the infiltrating lymphocytes also showed signs of exhaustion increasing the amount of IL-10 and the expression of PD-1. To overcome this exhaustion we combined Delta-24-ACT with an anti-PD-1 antibody. Evaluation of this combination in vivo further increased the median survival time of treated tumor-bearing mice and resulted in 50% long-term survivors. Rechallenge studies with the same cell line showed that combination treatment effectively protected these animals of developing tumors and therefore, the acquisition of immune memory. In summary, our data demonstrated that Delta-24-ACT induces a potent anti-tumour effect in vitro and in vivo as a result of the recruitment of immune cell populations modulating the immunosuppressive tumour microenvironment of glioma.

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Association of RYR2 Mutation With Tumor Mutation Burden, Prognosis, and Antitumor Immunity in Patients With Esophageal Adenocarcinoma

Frontiers in Genetics ◽

10.3389/fgene.2021.669694 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zaoqu Liu ◽

Long Liu ◽

Dechao Jiao ◽

Chunguang Guo ◽

Libo Wang ◽

...

Keyword(s):

Esophageal Adenocarcinoma ◽

Somatic Mutation ◽

Antitumor Immunity ◽

Immune Cell ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Immune Checkpoints ◽

Tumor Mutation Burden ◽

Mutation Burden ◽

Potential Biomarker

Background: Esophageal adenocarcinoma (EAC) remains a leading cause of cancer-related deaths worldwide and demonstrates a predominant rising incidence in Western countries. Recently, immunotherapy has dramatically changed the landscape of treatment for many advanced cancers, with the benefit in EAC thus far been limited to a small fraction of patients.Methods: Using somatic mutation data of The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium, we delineated the somatic mutation landscape of EAC patients from US and England. Based on the expression data of TCGA cohort, multiple bioinformatics algorithms were utilized to perform function annotation, immune cell infiltration analysis, and immunotherapy response assessment.Results: We found that RYR2 was a common frequently mutated gene in both cohorts, and patients with RYR2 mutation suggested higher tumor mutation burden (TMB), better prognosis, and superior expression of immune checkpoints. Moreover, RYR2 mutation upregulated the signaling pathways implicated in immune response and enhanced antitumor immunity in EAC. Multiple bioinformatics algorithms for assessing immunotherapy response demonstrated that patients with RYR2 mutation might benefit more from immunotherapy. In order to provide additional reference for antitumor therapy of different RYR2 status, we identified nine latent antitumor drugs associated with RYR2 status in EAC.Conclusion: This study reveals a novel gene whose mutation could be served as a potential biomarker for prognosis, TMB, and immunotherapy of EAC patients.

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Short Survival-Related Genes Harbor EMT Processes and Dendritic Cell Infiltration in Glioblastoma

10.21203/rs.3.rs-104471/v1 ◽

2020 ◽

Author(s):

Zhenkun Yang ◽

Bo Zhang ◽

Zhenhao Zhang ◽

Jingjing Wang ◽

Yaling Hu ◽

...

Keyword(s):

Immune Cell ◽

Cell Infiltration ◽

Biological Processes ◽

Ppi Network ◽

Hub Genes ◽

Short Term ◽

Upregulated Genes ◽

Long Term Survivors ◽

Sr Genes

Abstract Background: Glioblastoma is an aggressive primary tumour with the lowest survival time among brain tumours. Tumour-infiltrating immune cells (TIICs) are involved in tumour progression and determine the prognosis, while the association of immune cell infiltration with glioblastoma is rarely unknown. This study aimed to screen survival-related (SR) genes and major biological processes through bioinformatic analysis and to identify the relationship between SR genes and TIICs.Methods:SR genes were screened by comparing the long-term (>36 months) and short-term (<12 months) survivors in the database GSE53733. Gene set enrichment analysis (GSEA) was applied to compare the differences in biological processes between long-term survivors and short-term survivors. The SR genes were identified using the limma package of R. Gene Ontology (GO) analysis was conducted through Metascape. The protein-protein interaction (PPI) network of the SR genes was established through the Search Tool for the Retrieval of Interacting Genes (STRING) website and further analysed by the Molecular Complex Detection (MCODE) algorithm. UALCAN and GlioVis were employed to analyse the expression levels and prognostic value of hub genes. The correlation of hub genes with immune cell filtration was estimated by the Tumor Immune Estimation Resource (TIMER). The gene-drug interaction network was constructed using the Comparative Toxicogenomics Database (CTD).Results: The functions of the detected genes were mainly enriched in epithelial mesenchymal transition (EMT) and oxidative phosphorylation. Of the detected genes, a total of 220 SR genes were identified, including 78 upregulated genes and 142 downregulated genes in long-term survivors. The upregulated genes were mainly related to neuron projection morphogenesis, extracellular matrix, and cation channel activity. The downregulated genes were mainly related to extracellular matrix organization and angiogenesis. The PPI network for SR genes was constructed with 65 edges and 195 nodes, and two significant modules were selected. The results indicated that COL1A2, COL6A2, COL8A1, and COL8A2 were hub SR genes. In addition, they were correlated with immune cell infiltration, especially dendritic cell infiltration.Conclusions: These results revealed that collagens accounted for the progression and prognosis of glioblastoma. In addition, DC infiltration is a risk factor for glioblastoma patients. The expression of collagen protein COL6A2 was significantly correlated with the DC infiltration level and poor prognosis. Further, potential drugs that affect the function of COL6A2 could improve the outcomes of glioblastoma.

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Association of RYR2 Mutation with Tumor Mutation Burden, Prognosis and Antitumor Immunity in Patients with Esophageal Adenocarcinoma

10.21203/rs.3.rs-143762/v1 ◽

2021 ◽

Author(s):

Zaoqu Liu ◽

Long Liu ◽

Chunguang Guo ◽

Libo Wang ◽

Zhaonan Li ◽

...

Keyword(s):

Antitumor Immunity ◽

Immune Cell ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Immune Checkpoints ◽

Tumor Mutation Burden ◽

Mutation Burden ◽

Potential Biomarker ◽

Cancer Genome Atlas ◽

Additional Reference

Abstract BackgroundEsophageal adenocarcinoma (EAC) remains a leading cause of cancer-related deaths worldwide, and demonstrates a predominant rising incidence in Western countries. Recently, immunotherapy has dramatically changed the landscape of treatment for many advanced cancers, the benefit in EAC thus far been limited to a small fraction of patients. MethodsUsing somatic mutations data of The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), we delineated somatic mutation landscape of EAC patients from US and England. Bioinformatics algorithms were utilized to perform function annotation, immune cell infiltration analysis, and immunotherapy response assessment.ResultsWe found that RYR2 was a common frequently mutated gene (FMG) in both cohorts, and patients with RYR2 mutation suggested higher tumor mutation burden (TMB), better prognosis, and superior expression of immune checkpoints. Moreover, RYR2 mutation upregulated the signaling pathways implicated in immune response and enhanced antitumor immunity in EAC. Multiple bioinformatics algorithms for assessing immunotherapy response demonstrated that patients with RYR2 mutation might benefit more from immunotherapy. In order to provide additional reference for antitumor therapy of different RYR2 status, we identified nine latent antitumor drugs associated with RYR2 status in EAC. ConclusionsThis study reveals a novel gene whose mutation could be served as a potential biomarker for prognosis, TMB, and immunotherapy of EAC patients.

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Molecular biomarkers to identify patients (pts) who may benefit from durvalumab (D; anti-PD-L1) ± tremelimumab (T; anti-CTLA-4) in recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) from HAWK and CONDOR studies.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.6548 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 6548-6548 ◽

Cited By ~ 1

Author(s):

Weimin Li ◽

Athena Matakidou ◽

Zara Ghazoui ◽

Han Si ◽

Sophie Wildsmith ◽

...

Keyword(s):

Hla Class I ◽

Predictive Biomarker ◽

Repair Gene ◽

L1 Data ◽

Damage Repair ◽

Whole Exome ◽

Mutation Burden ◽

Ffpe Tumor ◽

D 20

6548 Background: Baseline tumor and germline biomarkers in R/M HNSCC were analyzed for predictive potential in pts benefitting from D or D+T. Methods: In HAWK (NCT02207530), 112 pts (PD-L1 tumor cells [TC]≥25%) received D (10 mg/kg Q2W for ≤12 m); in CONDOR (NCT02319044), 67 pts (PD-L1 TC < 25%) received D (10 mg/kg Q2W for ≤12 m), 133 pts received D+T (D 20 mg/kg Q4W, T 1 mg/kg Q4W for ≤12 m), and 67 pts received T (10 mg/kg Q4W [7 doses] then Q12W [2 doses] for ≤12 m) VENTANA PD-L1 (SP263) Assay determined PD-L1 status. Paired FFPE archival tumor and PBMC samples (as germline control) in the HAWK and CONDOR trials were evaluated by whole exome sequencing (WES). Tumor mutation burden (TMB) was number of somatic mutations/megabase. HLA class I types were obtained via WES of PBMCs (CONDOR only). HPV and neutrophil-to-lymphocyte ratio (NLR) were tested locally in CONDOR. Wilcoxon, log-rank tests, and COX-PH models were used. Pooled D & D+T data were analyzed unless noted. Results: 153 pts had paired evaluable FFPE tumor and PBMC samples (HAWK, n = 48; CONDOR, n = 105). TMB distributions were similar between studies ( P= 0.43). TMB correlated with smoking ( P= 0.02) but not HPV ( P= 0.24), NLR ( P= 0.66), or PD-L1 status ( P= 0.43). Overall, high TMB (≥upper tertile) trended with longer OS vs low TMB in all evaluable pts (N = 153; 9.0 vs 5.6 m; HR = 0.70; 95% CI = 0.48-1.01); P= 0.06). In HAWK, there was no association of TMB with OS. In CONDOR, pts (D and D+T arms) with high TMB vs low had significantly longer OS (N = 76; 16.3 vs 5.3 m; HR = 0.53; 95% CI = 0.31-0.92). TMB and OS association was further assessed by increasing TMB cutoffs. Improved HRs trended with higher cutoffs; cutoffs ≥upper quartile significantly linked to OS.TMB was not associated with PFS or ORR. Pts with low PD-L1 and low TMB had worse OS compared to pts with high PD-L1 or high TMB. Pts with high NLR (≥median) and low TMB had significantly worse OS than pts with low NLR and high TMB (HR = 2.63, P< 0.001). Analysis of germline HLA alleles revealed significantly poorer survival for carriers of the HLA-B*15:01 allele (9.4%) (HLA-B variant status did not affect TMB and OS association in CONDOR). Germline HLA heterozygosity did not impact OS. Pts with mutations in ATM (5%), a DNA damage repair gene, also trended with prolonged OS. Conclusions: TMB is a possible predictive biomarker of IO HNSCC therapy. Combined analysis of NLR and TMB may provide additional PD-L1 data in assessing pts most likely to have long-term benefit. Clinical trial information: NCT002207530, NCT02319044 .

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Somatic copy number alteration predicts clinical benefit of lung adenocarcinoma patients treated with cytokine-induced killer plus chemotherapy

Cancer Gene Therapy ◽

10.1038/s41417-021-00422-5 ◽

2022 ◽

Author(s):

Fan Kou ◽

Lei Wu ◽

Ye Zhu ◽

Baihui Li ◽

Ziqi Huang ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Copy Number ◽

Immune Cell ◽

Checkpoint Inhibitors ◽

Progression Free Survival ◽

The Cancer Genome Atlas ◽

Whole Exome ◽

Mutation Burden ◽

Cancer Genome Atlas ◽

Nsclc Patients

AbstractSomatic copy number alterations (SCNA), which are widespread in cancer, can predict the efficacy of immune checkpoint inhibitors in non-small-cell lung cancer (NSCLC). However, the usefulness of SCNA for predicting the survival of patients treated with cytokine-induced killer (CIK) cells or chemotherapy (CT) is unknown. This study aimed to explore the correlation between SCNA and clinical outcome in NSCLC patients treated with CIK + CT or CT alone. We performed whole-exome sequencing on 45 NSCLC patients treated with CIK + CT, as well as 305 NSCLC patients treated with CT alone, from The Cancer Genome Atlas, which showed SCNA had a superiority in predicting the progression-free survival (PFS) over tumor mutation burden (TMB) and SCNA + TMB in NSCLC patients treated with CIK + CT, especially in lung adenocarcinoma, while SCNA could not predict the efficacy of CT alone. Additionally, we investigated the association between SCNA and immune cell infiltration by RNA sequencing and immunohistochemistry. The results revealed that SCNA was negatively associated with the expression of dendritic cells. Collectively, this study revealed a negative correlation between SCNA and response to CIK + CT and showed that SCNA is a predictive indicator in LUAD patients treated with CIK + CT.

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