Potential Benefit Of Immunotherapy Research Articles

The identification of heterogeneous reactive oxygen subtypes in esophageal squamous cell carcinoma to aid patient prognosis and immunotherapy

IntroductionEsophageal cancer is increasingly recognized as a significant global malignancy. The main pathological subtype of this cancer is esophageal squamous cell carcinoma (ESCC), which displays a higher degree of malignancy and a poorer prognosis. Reactive oxygen species (ROS) play a critical role in modulating the immune response to tumors, and understanding the regulation of ROS in ESCC could lead to novel and improved therapeutic strategies for ESCC patients. MethodsA consensus matrix derived from genes involved in the ROS pathway revealed two subtypes of ROS. These subtypes were categorized as ROS-active or ROS-suppressive based on their level of ROS activity. The heterogeneity among the different ROS subtypes was then explored from various perspectives, including gene function, immune response, genomic stability, and immunotherapy. In order to assess the prognosis and the potential benefits of immunotherapy, a ROS activity score (RAS) was developed using the identified ROS subtypes. In vitro experiments were performed to confirm the impact of core RAS genes on the proliferative activity of esophageal cancer cell lines. ResultsTwo distinctive subtypes of ROS were identified. The first subtype, referred to as ROS-active, exhibited elevated ROS activity, enhanced involvement in cancer-associated immune pathways, and increased infiltration of effector immune cells. The second subtype, named ROS-suppressive, demonstrated weaker ROS activity but displayed more pronounced dysregulation in the cell cycle and a denser extracellular matrix, indicating malignant characteristics. Genomic stability, particularly in terms of copy number variation (CNV) events, differed between the two ROS subtypes. By developing a RAS model, reliable risk assessment for overall survival (OS) in patients with ESCC was achieved, and the model demonstrated strong predictive capabilities in real-world immunotherapy cohorts. Moreover, the core gene LDLRAD1 within the RAS model was found to enhance proliferative activity in esophageal cancer cell lines. ConclusionBased on the ROS pathway, we successfully identified two distinct subtypes in ESCC: the ROS-active subtype and the ROS-suppressive subtype. These subtypes were utilized to evaluate prognosis and the sensitivity to immunotherapy.

Comparison of programmed death-ligand 1 expression in adenocarcinoma and squamous cell carcinoma of the cervix in paraffin blocks of patients with cervical cancer.

Cervical cancer (CC) is a common malignancy in women, predominantly caused by human papillomavirus. The most subtypes are adenocarcinomas (AC) and squamous cell carcinomas (SCC), which show various features and treatment responses. Programmed death-ligand 1 (PD-L1) and programmed cell death protein 1 (PD-1) as Immune checkpoint molecules, play a role in immune evasion. We investigated PD-L1 expression in AC and SCC of the cervix and explored its link to clinical characteristics. The present cross-sectional research was done between 2016 and 2022 on samples in Shahid Beheshti University of Medical Sciences-affiliated hospitals in Iran. Histological tissue samples of CCs (16 AC and 48 SCC) were assessed, and clinical information was obtained by reviewing their medical documents. PD-L1 expression was evaluated by immunohistochemistry and we used the combined positive score. SCC cases showed a higher (not significant) PD-L1 expression. The PD-L1 expression and clinical characteristics were not significantly correlated in both subgroups. Although SCC cases exhibited higher PD-L1 expression, this difference was non-significant. More investigations should highlight the role of PD-L1 in CC and the potential benefits of immunotherapy.

Delineation of fatty acid metabolism in gastric cancer: Therapeutic implications.

The prognosis of gastric cancer is extremely poor. Metabolic reprogramming involving lipids has been associated with cancer occurrence and progression. To illustrate fatty acid metabolic mechanisms in gastric cancer, detect core genes, develop a prognostic model, and provide treatment options. Raw data from The Cancer Genome Atlas and Gene Expression Omnibus databases were collected and analyzed. Differentially expressed fatty acid metabolism genes were identified and incorporated into a risk model based on least absolute shrinkage and selection operator regression analysis. Then, patients from The Cancer Genome Atlas were assigned to high- and low-risk cohorts according to the mean value of the risk score as the threshold, which was verified in the Gene Expression Omnibus database. Relationships between chemotherapeutic sensitivity and tumor microenvironment features were assessed. An integrated evaluation was performed in this study. Fatty acid metabolism-related genes were used to construct the risk model. Patients classified into the high-risk cohort were considered to be resistant to chemotherapy based on results of the "pRRophetic" R package. Patients in the high-risk cohort were associated with type I/II interferon activation, increased inflammation level, immune cell infiltration, and tumor immune dysfunction based on the exclusion algorithm, indicating the potential benefit of immunotherapy in these patients. We constructed a fatty acid-related risk score model to assess the comprehensive fatty acid features in gastric cancer and validated its vital role in prognosis, chemotherapy sensitivity, and immunotherapy.

Integrated analysis from multicentre studies identities m7G-related lncRNA-derived molecular subtypes and risk stratification systems for gastric cancer.

Gastric cancer (GC) is the fourth leading cause of cancer death worldwide. Due to the lack of effective chemotherapy methods for advanced gastric cancer and poor prognosis, the emergence of immunotherapy has brought new hope to gastric cancer. Further research is needed to improve the response rate to immunotherapy and identify the populations with potential benefits of immunotherapy. It is unclear whether m7G-related lncRNAs influence tumour immunity and the prognosis of immunotherapy. This study evaluated 29 types of immune cells and immune functions in gastric cancer patients, and m7G-related lncRNAs and their molecular subtypes were identified. In addition, we also studied the biological function characteristics of m7G-related lncRNA molecular subtypes. Finally, the patient's risk score was calculated based on m7G-related lncRNAs, and a nomogram of staging and risk groups was established to predict the prognosis. For experimental verification, RT-qPCR were preformed from the native cohort. After identifying m7G-related lncRNAs and their molecular subtypes, we found three molecular subtypes, the B subtype had the highest level of infiltration, and the B subtype may benefit more from immunotherapy. We divided GC patients into two regulator subtypes based on biological function. The two subtypes have significant immunological differences and can be used to judge ICI treatment. We established a risk score formula based on five lncRNAs, including LINC00924, LINC00944, LINC00865, LINC00702, and ZFAS1. Patients with poor prognoses were closely related to patients in the high-risk group. After comprehensive analysis of different risk groups, the efficacy of the high-risk group on bleomycin, cisplatin, docetaxel, doxorubicin and etoposide was better than that of the low-risk group, suggesting that risk subgroups based on risk scores play a guiding role in chemotherapy and that the high-risk group may benefit more from immunotherapy. RT-qPCR results showed that LINC00924, LINC00944, and LINC00865 were highly expressed in tumour tissues, while LINC00702 and ZFAS1 were expressed at low levels in tumour tissues. In conclusion, we were the first to discover that m7G-related lncRNAs play a vital role in the tumour immune microenvironment of gastric cancer, and a risk prediction model was established to identify patients with potential benefits from immunotherapy and predict the prognosis of GC patients.

Deciphering the Pyroptosis-Related Prognostic Signature and Immune Cell Infiltration Characteristics of Colon Cancer.

Background: Colon cancer (CC) remains one of the most common malignancies with a poor prognosis. Pyroptosis, referred to as cellular inflammatory necrosis, is thought to influence tumor development. However, the potential effects of pyroptosis-related regulators (PRRs) on the CC immune microenvironment remain unknown. Methods: In this study, 27 PRRs reported in the previous study were used to cluster the 1,334 CC samples into three pyroptosis-related molecular patterns. Through subtype pattern differential analysis and structure network mining using Weighted Gene Co-expression Network Analysis (WGCNA), 854 signature genes associated with the PRRs were discovered. Further LASSO-penalized Cox regression of these genes established an eight-gene assessment model for predicting prognosis. Results: The CC patients were subtyped based on three distinct pyroptosis-related molecular patterns. These pyroptosis-related patterns were correlated with different clinical outcomes and immune cell infiltration characteristics in the tumor microenvironment. The pyroptosis-related eight-signature model was established and used to assess the prognosis of CC patients with medium-to-high accuracy by employing the risk scores, which was named “PRM-scores.” Greater inflammatory cell infiltration was observed in tumors with low PRM-scores, indicating a potential benefit of immunotherapy in these patients. Conclusions: This study suggests that PRRs have a significant effect on the tumor immune microenvironment and tumor development. Evaluating the pyroptosis-related patterns and related models will promote our understanding of immune cell infiltration characteristics in the tumor microenvironment and provide a theoretical basis for future research targeting pyroptosis in cancer.

Association of LRP1B mutants with immune biomarkers in Chinese non-small cell lung cancer patients.

e21060 Background: LRP1B (low-density lipoprotein receptor-related protein 1B) is frequently mutated in non-small cell lung cancer (NSCLC). Previous studies showed LRP1B mutations were associated with prolonged survival in melanoma and NSCLC immunotherapy cohort. Higher tumor mutation burden was found in LRP1B mutated patients, suggesting potential benefit of immunotherapy. Herein, we investigate the relationship of LRP1B and immunotherapy biomarker in lager cohort of Chinese and Western NSCLC patients. Methods: Next-generation sequencing data and clinical data were collected from 1053 TCGA NSCLC patients (Western cohort). A 539-gene panel targeted sequencing assay was performed on FFPE tumor samples from 1056 Chinese pan-cancer patients (Chinese cohort). Both LRP1B mutation ratio and TMB were calculated on the two cohorts following the same criteria. TMB-H was defined as the top quartile of all TMB values. Results: In total, 208 (20%) of the 1056 Chinese patients and 385 (37%) of the 1053 Western patients had at least one mutation of LRP1B genes (LRP1B mutant group). The frequency of LRP1B mutation between Western cohort and Chinese cohort had significant difference (20% vs. 37%, p＜0.001). In both cohorts, TMB was higher in the LRP1B mutant group compared to non-LRP1B mutant group. In Chinese cohort, PD-L1 positive was not associated with LRP1B mutation. Patients with LRP1B mutation were associated with prolonged survival in Western immunotherapy cohort. Conclusions: Our study provided a landscape of LRP1B mutations in a much larger Chinese NSCLC group, which could be a valuable complement to TCGA dataset and previous study. Results of our study was consistent with previous studies. Both in Chinese and Western cohorts, the higher TMB in LRP1B mutant patients suggested potential efficacy from immunotherapy of LRP1B mutant group. This result and the potential predictive value of LRP1B in immunotherapy should be validation in a larger Chinese LRP1B mutant cohort in the further.

Clinical and genetic characterization of cancer patients with multiple germline variants.

e22523 Background: Hereditary tumors are generally monogenic diseases with autosomal dominant inheritance. However, we noticed that some individuals may harbor ≥2 germline mutations in one or multiple genes, which remains to be explored. Methods: Genetic mutations were reviewed in more than 50,000 cancer patients who underwent hybridization capture based next-generation sequencing (NGS). Germline variants were interpreted following ACMG guideline, and only pathogenic and likely pathogenic variants were included in this study. Results: Multiple germline variants were identified in 42 individuals with the detection rate of 0.075%. The median age at diagnosis was 48 years (range 31-73). Two thirds of patients were female and 26.2% of patients has cancer family history. Prostate cancer is the most common cancer type (0.6%, 2/332), followed by carcinomas of ovarian or fallopian tube (0.48%, 7/1461), breast (0.24%, 8/3302), pancreas (0.2%, 2/982) and so on. Surprisingly, 7 patients with lung cancer also harbored ≥2 germline mutations (0.02%). Most of these germline variants affected DNA damage repair pathways [75.6% homologous recombination repair (HR), 8.1% mismatch repair (MMR), 1.2% base excision repair (BER)]. Four patients had two germline variants identified on a single gene (2 ATM, 1 BRCA1, 1 BRCA2). Three variants were identified in 2 patients, and 2 variants were identified in the remaining 36 patients. Two or more germline variants in HRR pathway were identified in 64.3% of patients, among which 18.5% patients had BRCA1+ BRCA2 double variants. The efficacy of poly ADP-ribose polymerase inhibitors (PARPi) in this specific population should raise concern. Besides, double variants in HRR and MMR pathway were found in 5 patients, which suggested the potential benefit of immunotherapy and PARPi combination therapy. Conclusions: In addition to identify variants contributing to the personal and family cancer history, NGS can accidentally identify germline variants that may suggest the susceptibility of other hereditary tumors. Multiple variants on HRR or MMR genes may have important implications for the treatment strategy for these patients.

Tumour inflammation signature and expression of S100A12 and HLA class I improve survival in HPV-negative hypopharyngeal cancer

Hypopharyngeal squamous cell carcinoma (HPSCC) has a very poor prognosis. Local surgery may increase survival, but is often avoided due to significant post-op co-morbidities. Since prognostic markers are lacking, the aim was to find predictive biomarkers that identify patients whose response to oncological treatment is poor and who may benefit from primary surgery to increase survival. Pretreatment biopsies from 23 HPSCC patients, 3 human papillomavirus (HPV) positive and 20 HPV-negative, were analyzed for expression of 750 mRNAs using the Nanostring nCounter IO360 panel in relation to 3-year survival. Validation was performed through immunohistochemistry (IHC) for HLA class I and S100A12 in 74 HPV-negative HPSCC samples. Clustering identified a subset of HPV-negative HPSCC with favorable prognosis and a gene expression signature overexpressing calgranulins and immune genes, distinct from that of HPV-positive HPSCC. Enrichment analysis showed immune signaling, including the tumor inflammation signature, to be enriched in surviving patients. IHC validation confirmed high S100A12 and HLA class I expression to correlate with survival in HPV-negative HPSCC. This shows that immune activity is strongly related to survival in HPV-negative HPSCC. Enrichment of the tumor inflammation signature indicates a potential benefit of immunotherapy. Low expression of both HLA class I and S100A12 could be used to select patients for local surgery.

Abstract B11: Prognostic biomarkers in stage II-III melanoma

Abstract Introduction: Biomarkers that predict clinical response in stage II-III melanoma are critical to helping clinicians weigh the potential benefits of immunotherapy against its potential toxicities, as well as allowing for clinical trial population enrichment strategies. We previously defined and validated a 53-immune-gene panel, Melanoma Immune Profile (MIP), predictive of disease-specific survival (DSS). Combination of genomic and tissue-based immune biomarkers may help in the identification of more precise and predictive biomarkers. Methods: We performed quantitative multiplexed immunofluorescence (qmIF) on 64 primary stage II-III melanomas and 14 metastatic melanomas diagnosed at Columbia University Irving Medical Center (CUIMC) between 2000-2014 and 2014-2017, respectively. Formalin-fixed, paraffin-embedded (FFPE) slides were stained and analyzed for DAPI (nuclei), CD3 (T cells), CD8 (cytotoxic T cells, or CTLs), CD68 (macrophages), SOX10 (tumor), HLA-DR (antigen presentation and activation), and Ki67 (proliferation) according to published methods. Spatial relationships were quantified via the inhomogeneous pair correlation function (PCF). NanoString analysis of MIP was performed on extracted RNA from 78 stage II-III melanomas diagnosed between 2000-2014 with known DSS. Results: We find that high CTL and low macrophage density in the stroma correlates with DSS (p<0.001). The CTL/macrophage ratio in patients with primary stage II-III melanoma who subsequently died from melanoma is different from that in patients who did not die from melanoma (p<0.05). Interestingly, the CTL/macrophage ratio in patients with recurrence is similar to that of patients with metastatic tumors. Total immune cells and CD8+ T cells are diminished in metastatic samples compared to primary samples (p<0.01). Using PCF, we find that greater clustering among CTLs (<10-micron radius) is associated with nonrecurrence (p=0.042). HLA-DR+ macrophages and tumor cells are more dispersed than CTLs (>10-micron radius), and these cells are more repulsive of one another in recurrent patients (p=0.008). Further, we validate MIP’s prediction of nonprogression on CUIMC samples (AUC=0.695) and find that MIP correlates with DSS (AUC=0.719, p=0.003). In close evaluation of MIP, we find greater than 1-fold increase in expression of 9 immune genes (p<0.05 with Benjamini-Hochberg correction), including CD2 and CD27. Combination of low CD2 or CD27 expression with low CTL/macrophage ratio in the stroma predicts poor DSS by ROC curve (AUC=0.741, p<0.05 and AUC=0.756, p<0.05, respectively) and KM curve (p<0.01and p<0.001, respectively). Conclusion: QmIF of stage II-III melanomas shows that the stromal CTL/macrophage ratio is associated with DSS. Further, MIP identifies patients with a low risk of death from melanoma. Combination of the stromal CTL/macrophage ratio with the top genes of MIP also predicts DSS. Combining qmIF and mRNA analyses can therefore stratify stage II-III melanoma patients to receive immunotherapy. Note: This abstract was not presented at the conference. Citation Format: Emanuelle M. Rizk, Robyn D. Gartrell, Andrew Chen, Rui Chang, Douglas K. Marks, Camden L. Esancy, Bret Taback, Basil A. Horst, Charles G. Drake, Raul Rabadan, Yvonne M. Saenger. Prognostic biomarkers in stage II-III melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B11.

Perception of cure among patients with metastatic genitourinary cancer initiating immunotherapy

BackgroundDespite the advent of checkpoint inhibitors (CPIs) for advanced genitourinary (GU) cancers, existing studies suggest that durable complete responses are observed in fewer than 10% of patients. This study sought to evaluate the association between expectations of cure reported by patients with advanced GU cancers initiating immunotherapy and quality of life (QOL), anxiety and depression.Patient and methodsA single-institution, cross-sectional survey study was conducted with patients preparing to receive CPIs for treatment of metastatic renal cell carcinoma (RCC), urothelial cancer (UC) and prostate cancer (PC). Patients were assessed prior to initiation of immunotherapy for expectations of cure (divided into four quartiles), quality of life (QOL; Functional Assessment of Chronic Illness Therapy-General [FACT-G]), and symptoms of anxiety and depression (PROMIS).ResultsSixty patients were enrolled, with metastatic RCC, UC and PC comprising 63, 28 and 8% of the study population, respectively. Median age of the cohort was 65 (range, 31–91), and 68% were male; 33% received CPI in the first-line setting. Despite extensive counseling from oncologists regarding potential clinical outcomes with immunotherapy, a substantial proportion of patients (23%) harbored inaccurate expectations regarding the potential benefit of immunotherapy. Importantly, patients with accurate expectations of cure reported lower anxiety scores using the PROMIS-Anxiety inventory. No significant differences were found between expectations of cure and quality of life or depression, using the FACT-G and PROMIS-Depression inventories, respectively.ConclusionThe current study found that a considerable proportion of patients with advanced GU cancers harbor inaccurate expectations concerning the potential benefit of immunotherapy. These results suggest that more effective counselling may mitigate patient anxiety, and potentially promote treatment satisfaction and adherence.

Expectations of cure among patients with advanced genitourinary cancer treated with immunotherapy.

591 Background: Over the past 15 years, considerable progress has been made in systemic therapy options for genitourinary (GU) cancers. In diseases such as metastatic renal cell carcinoma (RCC) and urothelial cancer (UC), immunotherapeutic strategies such as programmed death-1 (PD-1) or programmed death-ligand 1 (PD-L1) inhibition have elicited durable responses, albeit in a minority of patients. We examined expectations for clinical outcome with immunotherapy among patients with advanced GU cancers. Methods: A survey study was conducted in patients with advanced GU cancers initiating PD-1/PD-L1 inhibitors from October 2017 to September 2018. Patients were screened prior to initiation of immunotherapy for their expectation of cure (divided into 4 quartiles), symptoms of anxiety and depression (PROMIS-A and PROMIS-D), and quality of life (QOL; FACT-G). For purposes of the survey, cure was equated to a durable complete response. Differences in frequency of anxiety, depression and QOL were compared amongst subsets of patients divided by expectation of cure. Results: Among 60 patients, median age was 67, 72% were male and 81% were married. Types of cancer included RCC (69%), UC (19%) and prostate cancer (12%). The majority were in the 1st or 2nd line of therapy (40% and 31%, respectively). Despite extensive counseling from GU medical oncologists, 23% of patients thought that cure was “very likely”, defined as in the range of 76-100%. Approximately 70% of patients estimated cure in the range of 0-25%, in line with clinical counseling. These patients had higher rates of anxiety (P = 0.01), depression (P = 0.002) and poorer QOL (P = 0.003) compared to patients who felt cure was very likely. Conclusions: A considerable proportion of patients with advanced GU malignancies harbor unrealistic expectations around the potential benefit of immunotherapy. Although a first instinct may be to remedy these expectations, it is important to bear in mind that these patients had better emotional well-being and QOL. We will validate these findings and assess these parameters longitudinally in an upcoming SWOG trial for patients with mRCC receiving upfront immunotherapy.

Abstract ES9-3: Triple negative breast cancer: Current and future directions in metastatic patients

Abstract Chemotherapy is the primary established systemic treatment for patients with triple-negative breast cancer (TNBC) with both early and metastatic disease. The poor prognosis of patients with TNBC have fostered a major effort to discover actionable molecular targets and other approaches to treat these patients. Massively parallel sequencing and other 'omics' technologies have revealed an unexpected level of heterogeneity of TNBCs and have led to the identification of potentially actionable molecular features in some TNBCs, such as germline BRCA1/2 mutations or 'BRCAness', as well as a subgroup with a high degree of tumor-infiltrating lymphocytes that also correlates with a lower risk of disease relapse and a higher likelihood of benefit from chemotherapy. Proof-of-principle studies with immune-checkpoint inhibitors in advanced-stage TNBC have yielded promising results, indicating the potential benefit of immunotherapy for patients with TNBC. Additional data from trials with antibody drug conjugates have yielded promising results. We discuss the most relevant molecular findings in TNBC from the past decade and the most promising therapeutic opportunities. Citation Format: Chang J. Triple negative breast cancer: Current and future directions in metastatic patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr ES9-3.

The Challenge of Managing Bladder Cancer and Upper Tract Urothelial Carcinoma: A Review with Treatment Recommendations from the Spanish Oncology Genitourinary Group (SOGUG).

Bladder cancer is the fourth most common cancer in men and the ninth most common in women in the Western world. The management of bladder carcinoma requires a multidisciplinary approach. Optimal treatment depends on several factors, including histology, stage, patient status, and possible comorbidities. Here we review recent findings on the treatment of muscle-invasive bladder carcinoma, advanced urothelial carcinoma, upper tract urothelial carcinoma, non-urothelial carcinoma, and urologic complications arising from the disease or treatment. In addition, we present the recommendations of the Spanish Oncology Genitourinary Group for the treatment of these diseases, based on a focused analysis of clinical management and the potential of current research, including recent findings on the potential benefit of immunotherapy. In recent years, whole-genome approaches have provided new predictive biomarkers and promising molecular targets that could lead to precision medicine in bladder cancer. Moreover, the involvement of other specialists in addition to urologists will ensure not only appropriate therapeutic decisions but also adequate follow-up for response evaluation and management of complications. It is crucial, however, to apply recent molecular findings and implement clinical guidelines as soon as possible in order to maximize therapeutic gains and improve patient prognosis.

Three distinct genomic subtypes of head and neck squamous cell carcinoma associated with clinical outcomes

ObjectivesHeterogeneity of head and neck squamous cell carcinomas (HNSCCs) results in unpredictable outcomes for patients with similar stages of cancer. Beyond the role of human papilloma virus (HPV), no validated molecular marker of HNSCCs has been established. Thus, clinically relevant molecular subtypes are needed to optimize HNSCC therapy. The purpose of this study was to identify subtypes of HNSCC that have distinct biological characteristics associated with clinical outcomes and to characterize genomic alterations that best reflect the biological and clinical characteristics of each subtype. Materials and methodsWe analyzed gene expression profiling data from pan-SCC tissues including cervical SCC, esophageal SCC, lung SCC, and HNSCC (n = 1346) to assess the similarities and differences among SCCs and to identify molecular subtypes of HNSCC associated with prognosis. Subtype-specific gene expression signatures were identified and used to construct predictive models. The association of the subtypes with prognosis was validated in two independent cohorts of patients. ResultsPan-SCC analysis identified three novel subtypes of HNSCC. Subtype 1 had the best prognosis and was similar to cervical SCC, whereas subtype 3 had the worst prognosis and was similar to lung SCC. Subtype 2 had a moderate prognosis. The 600-gene signature associated with the three subtypes significantly predicted prognosis in two independent validation cohorts. These three subtypes also were associated with potential benefit of immunotherapy. ConclusionWe identified three clinically relevant HNSCC molecular subtypes. Independent prospective studies to assess the clinical utility of the subtypes and associated gene signature are warranted.

Abstract 5379: Stratification of colorectal cancer patients based on various sequencing platforms and tumor mutational burden

Abstract Colorectal cancer (CRC) is the third most common type of cancer in the United States. Although chemotherapy, radiation and targeted therapies can improve survival rates, recent studies have shown the potential benefit of immunotherapies to improve outcomes for patients with advanced CRC. Targeted therapies that use monoclonal antibodies (mAbs) to EGFR have been shown to benefit some CRC patients. Until recently, KRAS has been the only predictive biomarker for anti-EGFR therapy for metastatic CRC. However, 40% to 60% of patients with wild-type KRAS do not respond to anti-EGFR therapy. Therefore, to accurately predict patients' response to treatments and improve clinical outcomes, additional prediction and treatment methods are imperative. One of the many efforts to improve prediction for CRC patient's response to the anti-EGFR therapy is the development of gene expression based RAS signature scores for identification of RAS activated tumors independent of mutations in the KRAS gene. There is also considerable effort being placed on combinations of targeted therapy and immunotherapies to improve responses for these cancers. Previously, we have stratified 55 CRC samples by applying a RAS gene signature score which measures MEK pathway functional output independent of tumor genotype. We showed that samples that have RAS activating mutations such as KRAS and BRAF have significant higher RAS scores (p<0.001). Here we investigate 120 colorectal cancer patients using exome sequencing, targeted panel sequencing, and RNA sequencing. Specifically, we acquired 40 normal-tumor pair samples and performed GATK tumor-normal pair mutation calling. Among these 120 samples, 65 of them are from patients treated with either cetuximab or panitumumab. Continued from our previous study, we stratified these samples based on calculated RAS scores, and showed how the results correlate with clinical outcome. Tumor mutational burden (TMB) can help predict the likelihood that a patient will benefit from certain immunotherapies; however, clinical applicability is limited due to cost and computing requirements of whole-exome sequencing to detect variants with high degree of accuracy. Therefore it would be helpful if TMB can be identified based on targeted sequencing. Here we investigate how TMB calculated based on different sequencing platform correlates with each other and whether targeted sequencing panel can be used instead of exome sequencing for stratifying patients. In addition, we investigated if Illumina's global screening array can be used for TMB analysis. Furthermore, to investigate the potential immune reactivity in these CRC samples, and thereby the potential benefit of immunotherapy, we performed in-silico prediction of neo-antigens and peptide binding affinity between tumor antigens derived from mutations and human HLA alleles. Citation Format: Fang Yin Lo, Claire Olson, Kerry Deutsch, Tuuli Saloranta, Inah Golez, Timothy Yeatman, Steven Anderson, Anup Madan. Stratification of colorectal cancer patients based on various sequencing platforms and tumor mutational burden [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5379.

Checkpoint Blockade in Lung Cancer and Mesothelioma.

In the last decade, immunotherapy has emerged as a new treatment modality in cancer. The most success has been achieved with the class of checkpoint inhibitors (CPIs), antibodies that unleash the antitumor immune response. After the success in melanoma, numerous clinical trials are being conducted investigating CPIs in lung cancer and mesothelioma. The programmed death protein (PD) 1-PD ligand 1/2 pathway and cytotoxic T lymphocyte-associated protein 4 are currently the most studied immunotherapeutic targets in these malignancies. In non-small cell lung cancer, anti-PD-1 antibodies have become part of the approved treatment arsenal. In small cell lung cancer and mesothelioma, the efficacy of checkpoint inhibition has not yet been proven. In this Concise Clinical Review, an overview of the landmark clinical trials investigating checkpoint blockade in lung cancer and mesothelioma is provided. Because response rates are around 20% in the majority of clinical trials, there is much room for improvement. Predictive biomarkers are therefore essential to fully develop the potential of CPIs. To increase efficacy, multiple clinical trials investigating the combination of cytotoxic T lymphocyte-associated protein 4 inhibitors and PD-1/PD ligand 1 blockade in lung cancer and mesothelioma are being conducted. Given the potential benefit of immunotherapy, implementation of current and new knowledge in trial designs and interpretation of results is essential for moving forward.

Abstract 413: Neo-epitope detection and immune infiltrate analysis of colorectal cancer samples

Abstract Colorectal cancer (CRC) is the third most common type of cancer in the United States. Targeted therapies that use monoclonal antibodies (mAbs) to EGFR have been shown to benefit some CRC patients. Until recently, KRAS has been the only predictive biomarker for anti-EGFR therapy for metastatic CRC. However, 40% to 60% of patients with wild-type KRAS do not respond to anti-EGFR therapy. Previously we have stratified 55 CRC samples by applying a RAS gene signature score which measures MEK pathway functional output independent of tumor genotype. We showed that samples that have RAS activating mutations such as KRAS and BRAF have significant higher RAS scores (p<0.001). Here, we further investigate the potential immune reactivity in these CRC samples, and thereby the potential benefit of immunotherapy, by evaluating the tumor neo-epitope burden, and the quality of immune cell infiltration based on exome-seq and RNA-seq analysis. In the 53 samples that were sequenced, 779 unique non-synonymous mutations were detected by exome-seq. These 779 mutations spanned across 263 genes. The majority of these mutations are not shared between samples (~ 5% of the mutations were shared by more than 2 samples). Several driver gene mutations were identified in this study, including KRAS, TP53, PIK3CA, APC and HER2. HLA prediction based on Exome-Seq and RNA-Seq data shows that ~86.7% of the alleles predicted to be present in 53 samples were concordant between the two RNA-seq datasets. The predicted alleles based on exome-seq and RNA-seq results have 67-69% concordance. Prediction of neo-epitopes show that HLA-binding neo-epitopes are more frequent than TCR-binding ones, and that most neo-epitopes are private and not shared between samples. A more in-depth analysis of the tumor microenvironment was performed using the RNA-seq data. The epithelial, stromal and immune content of the tumors was comparable to tumors from TCGA CRC data. Next, the immune cell compartment was further stratified into 7 different immune cell types using signatures specific to CD8 andCD4 T, T-regulatory, NK, B-cells, Macrophages and Myeloid derived suppressor cells (MDSC). The immune make up of colorectal cancer is dominated by macrophages and MDSCs. Interestingly, both granulocytic G- and monocytic M-MDSCs are present together, supporting the idea that MDSCs confer an immune suppressive microenvironment in this cancer. Significantly, high MDSC infiltrated tumors showed upregulated expression of pro-tumorigenic insulin-like growth factor pathway genes. Additionally, tumors with lower burden of MDSC showed signature of complement activation suggesting innate cell-mediated anti-tumorigenic mechanisms of tumor control in CRC. These analyses provide potential biomarkers to stratify CRC patients based on their immune reactivity and predict response to cancer immunotherapy drugs. Citation Format: Fang Yin Lo, Nitin Mandloi, Timothy Yeatman, Kiran Paul, Ashwini Patil, Steven Anderson, Ravi Gupta, Anup Madan. Neo-epitope detection and immune infiltrate analysis of colorectal cancer samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 413. doi:10.1158/1538-7445.AM2017-413

The Potential Benefit of Immunotherapy in the Treatment of Eosinophilic Esophagitis in Adult Patients

The Potential Benefit of Immunotherapy in the Treatment of Eosinophilic Esophagitis in Adult Patients

Rush immunotherapy results in allergen-specific alterations in lymphocyte function and interferon-γ production in CD4+ T cells

Background: Allergen immunotherapy results in a number of changes in clinical, inflammatory, and immunologic parameters. However, the basis for the specificity of this form of therapy is unknown, especially in the context of changes in T- and B-lymphocyte function after desensitization to specific allergens. Objective: This study was designed to determine the immunologic consequences of rush immunotherapy. Methods: We studied 10 patients who had positive skin test responses to the house dust mite Dermatophagoides pteronyssinus (Dpt) and cat dander extract. Each received rush immunotherapy to mite, but not cat dander, over a 2- to 4-week period until maintenance was achieved. Patients were evaluated before and when maintenance was achieved for skin test and nasal reactivity to mite and cat dander; antibody levels to the allergen were monitored, as were lymphocyte proliferative responses and cytokine production. Results: Rush immunotherapy to house dust mite resulted in a significant reduction in skin and nasal reactivity to mite allergen, but not to cat allergen, in 10 of 10 patients. This was accompanied by a rise in serum anti-Dpt IgE, whereas anti-cat IgE was not altered (7 of 7 patients). In seven of seven patients there was an increase in anti-Dpt IgG 4 levels. T-cell proliferative responses to mite antigen were suppressed, and numbers of CD8 T cells increased in frequency. There was a marked increase in interferon-γ production, particularly by CD4 T cells in 10 of 10 patients. The correlation between the increases in interferon-γ production and the changes in cutaneous reactivity was highly significant. Conclusion: We show that rush immunotherapy is immunologically specific in eliciting changes in T- and B-cell responses to the desensitization antigen. The specificity and potential benefit of immunotherapy may be linked to the increase in interferon-γ production by allergen-activated CD4+ T lymphocytes. (J Allergy Clin Immunol 1997;99:530-8.)