Abstract 2108: Comparative analysis of fusion gene detection rates in tissue versus blood samples from Chinese diverse solid tumors

BackgroundPoly (ADP-ribose) polymerases-1 (PARP1) alterations are associated with PARP1 inhibitor resistance, regulating the function of Treg cells and PDL1 expression in tumor cells, and high PARP1 expression is significantly associated with aggressive behavior and chemotherapeutic resistance in several tumors. However, a comprehensive analysis of the predictive values of PARP1 alteration for immune checkpoint inhibitor (ICI) effectiveness in tumors remains unclear, and the associations between its expression and immunotherapy signatures also needs to be explored further.MethodsWe performed some analyses with the cBioPortal online database (https://www.cbioportal.org), TIMER2.0 (Tumor Immune Estimation Resource 2.0, http://timer.comp-genomics.org/) and TCGA database (https://xenabrowser.net or https://portal.gdc.cancer.gov/). Survival analysis was conducted using Kaplan–Meier method, and the associations between PARP1 transcription levels and immune checkpoint gene expression, the number of neoantigens, tumor mutation burden (TMB) levels, and microsatellite instability (MSI) event are analyzed by spearman correlation analysis and visualization of those mentioned above is performed using R, version 3.6.3 (http://www.r-project.org/).ResultsWe found that PARP1 was altered in 1338 (2.9%) out of 45604 patients with diverse tumors, which was associated with markedly higher TMB levels in a variety of tumors (P < 0.01). Impressively, patients with PARP1 alterations in advanced tumors showed better overall survival (OS) in the ICI-treated cohort (P = 0.016). PARP1 altered group was substantially correlated with higher immune infiltrates across most tumors, including CD8+ T cells in colorectal adenocarcinoma (P = 0.0061), endometrial carcinoma (P = 0.0033), stomach cancer (P = 0.033), and cervical cancer (P = 0.026), respectively. The PARP1 altered group showed high expression in transcription (P < 0.001), and higher expression of LAG3, PDCD1, CTLA-4, and TIGIT (P < 0.05). Higher PARP1 expression was present in 27 tumor compared the corresponding normal tissues using the GTEx and TCGA databases and it had a worse OS in several tumors (P < 0.05). Further, high PARP1 expression was significantly associated with six immune cells (B cells, CD4+ T cells, CD8+ T cells, macrophages, neutrophils, and dendritic cells) in most tumors, including colon adenocarcinoma (COAD), head and neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), and liver hepatocellular carcinoma (LIHC) (P < 0.05). In particular, CD8+T cell infiltration, was also positively correlated with high PARP1 expression in bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), kidney renal papillary cell carcinoma (KIRP), brain lower grade glioma (LGG), LIHC, pancreatic adenocarcinoma (PAAD), pheochromocytoma and paraganglioma (PCPG), prostate adenocarcinoma (PRAD), rectum adenocarcinoma (READ), testicular germ cell tumors (TGCT), thymoma (THYM), uterine corpus endometrial carcinoma (UCEC), uveal melanoma (UVM) (P < 0.05, no data shown), and PARP1 expression was significantly positively correlated with the transcription levels of some of the 47 immune checkpoint genes, such as CD274, CTLA4, and PDCD1 in several tumors, including PAAD, LIHC, KIRC, HNSC, and BLCA (P < 0.05). A significant positive association between PARP1 expression and the number of immune neoantigen was found within COAD, KIRC, lung adenocarcinoma (LUAD), PAAD and THYM (P < 0.05), and there were also significantly positive correlations between PARP1 expression and TMB in many tumors like adrenocortical carcinoma (ACC), COAD, kidney chromophobe (KICH), LGG, LUAD, READ, skin cutaneous melanoma (SKCM) and stomach adenocarcinoma (STAD) (P < 0.05). In addition, high PARP1 expression was positively associated with microsatellite instability event in COAD, KIRP, BRCA, glioblastoma multiforme (GBM), lung squamous cell carcinoma (LUSC), LGG, READ, UCEC, SKCM and LUAD (P < 0.05).ConclusionsOur results highlight the significance of PARP1 alterations as pan-cancer predictive biomarkers for ICI treatment, and its expression levels seem to be correlated with the status of immunotherapy-associated signatures, thus may be a promising biomarker for predicting ICI response in several tumors.

ObjectiveAdenosine deaminase (ADA) plays an important role in immune response, which includes two isoenzymes: ADA1 and ADA2. This study aims to explore the roles of ADA1 and ADA2 in cancers.MethodsHuman Protein Atlas (HPA) and Gene Expression Profiling Interactive Analysis (GEPIA2) databases were used to analyze the mRNA expression of ADA1 and ADA2 in human normal cells and tumor tissues. The enzyme assay was used to detect the ADA1 and ADA2 activities in serum from cancer patients. The Kaplan–Meier (KM) plotter was used to analyze the prognostic value of ADA1 and ADA2. TIMER2.0 was used to explore how ADA1 and ADA2 correlate with immune infiltration and immune checkpoints. cBioPortal database was used to investigate the mutations of ADA1 and ADA2. LinkedOmics was used to screen the ADA1 and ADA2 expression-related genes.ResultsADA1 was significantly increased in several tumor tissues, including cholangiocarcinoma (CHOL), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), head and neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), ovarian serous cystadenocarcinoma (OV), pancreatic adenocarcinoma (PAAD), thymoma (THYM), and uterine carcinosarcoma (UCS). ADA2 expression was significantly increased in esophageal carcinoma (ESCA), glioblastoma multiforme (GBM), acute myeloid leukemia (LAML), OV, PAAD, skin cutaneous melanoma (SKCM), and stomach adenocarcinoma (STAD). There were no significant changes in serum ADA1 activities in most cancers, while serum ADA2 activities were increased in most cancers. For prognosis, high ADA1 expression was associated with the poor survival in several cancers, including esophageal squamous cell carcinoma (ESCC), HNSC, KIRC, kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), and uterine corpus endometrial carcinoma (UCEC). However, high ADA2 expression showed a favorable prognosis in breast invasive carcinoma (BRCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), HNSC, KIRC, KIRP, LUAD, OV, PAAD, sarcoma, and THYM. ADA1 showed a moderate positive correlation with multiple infiltrating immune cells in most cancers. ADA2 was positively correlated with B cells, CD8 T cells, monocytes/macrophages, and dendritic cells (DCs) and was strongly negatively correlated with myeloid-derived suppressor cells. Function analysis showed that ADA1 expression-related genes were mainly enriched in cell division biological progression. However, ADA2-related genes were mainly associated with immune response.ConclusionAs isoenzymes, ADA1 and ADA2 showed opposite prognostic values and different correlative patterns with immune infiltrating. These data demonstrated the distinct roles of ADA1 and ADA2 in cancer. ADA2 might act as a protective factor in cancer.

e14593 Background: IBI363 is a first-in-class PD-1/IL-2α-bias bispecific antibody fusion protein which could block PD-1 checkpoint and rejuvenate exhausted tumor-specific T cells by cis-activating α-bias IL-2. It was well tolerated and showed encouraging efficacy in patients (pts) with advanced melanoma, non-small cell lung cancer and colorectal cancer. Herein, we report a phase I study of IBI363 in patients (pts) with other solid tumors. Methods: Eligible pts with advanced biliary tract cancer (BTC), head and neck squamous cell carcinoma (HNSCC), cervical cancer (CC) and ovarian cancer (OC) who failed or intolerant to standard therapy were enrolled. IBI363 was intravenously administered at different dose levels ranging from 600 to 1500 μg/kg QW/Q2W/Q3W. Primary objective of the study was safety. Secondary objective was efficacy assessed by investigator per RECIST v1.1 including objective response rate (ORR) and disease control rate (DCR). Results: As of January 26, 2024, 24 pts were enrolled including 13 pts with BTC, 3 pts with HNSCC, 4 pts with CC and 4 pts with OC. In BTC, 6 (46.2%) pts received IBI363 treatment for more than 3 months and the maximum treatment duration was 7 months. In HNSCC, CC and OC, the maximum treatment duration was 4.6, 6.2 and 6.5 months respectively. Pts with at least 1 tumor assessment were included in efficacy evaluable set (n = 18). The overall ORR was 22.2% and DCR was 77.8%. In 11 evaluable pts with BTC, best overall response (BOR) was confirmed partial response (cPR) in 1 pt (600 μg/kg Q2W, immunotherapy (IO)-failed), stable disease (SD) in 9 pts (including 6 pts with tumor regression) and progressive disease (PD) in 1 pt. ORR was 9.1% and DCR was 90.9%. In 2 evaluable pts with HNSCC, 1 pt had cPR (600 μg/kg Q2W, IO-naïve, PD-L1 expression negative) and 1 pt had PD. In 3 evaluable pts with CC, 1 pt had cPR (1000 μg/kg Q2W, IO-failed), 1 pt had SD and 1 pt had PD. In 2 evaluable pts with OC, 1 pt had cPR (1000 μg/kg Q2W, platinum-resistant) and 1 pt had PD. All cPR pts had previous 1-2 lines of treatments and had tumor regression ranging from 45% to 87%. Durable tumor responses were observed with cPR remained at week 30 in BTC and remained at week 24 in HNSCC, CC and OC. In 4 pts with cPR, 3 pts still on treatment and 1 pt with HNSCC received curative resection. No new safety signals of IBI363 were observed. More updated data on safety and efficacy will be presented at the meeting. Conclusions: IBI363 showed promising and durable efficacy in pts with various solid tumors including refractory tumors such as BTC and IO or platinum-resistant tumors such as CC and OC. Further clinical investigations on these tumors using IBI363 alone or in combination with other treatments are ongoing. Clinical trial information: NCT05460767 .

3126 Background: FoundationOne CDx (F1CDx) is a US FDA-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. Tumor profiling with F1CDx detects genomic findings with evidence of additional clinical significance. This study analyzes the breadth and impact of clinical decision insights from F1CDx clinical reports across solid tumors. Methods: F1CDx consecutive reports (n = 109,695) were retrospectively analyzed for the type and frequency of clinically significant predictive, prognostic, and diagnostic genomic alterations and signatures in common cancer types and across solid tumors. Predictive markers were defined as therapeutically relevant markers in drug labels or NCCN guidelines or targets of ESCAT evidence Tier I/II (Mateo et al., 2018; PMID: 30137196). Prognostic and diagnostic markers were determined in accordance with NCCN, ESMO, or WHO guidelines. We also describe the frequency and targets of interventional clinical trials with targeted therapies or immune checkpoint inhibitors that were matched to tumor profiles based on clinical or strong preclinical evidence. Results: Predictive genomic findings of clinical significance were identified in more than half of non-small cell lung cancer (NSCLC), colorectal cancer (CRC), breast cancer (BC), and melanoma (MEL) tissue samples; over a third of ovarian cancer (OC), urothelial carcinoma (UC), and head and neck squamous cell carcinoma (HNSCC); approximately a fourth of prostate cancer (PC), gastro-esophageal adenocarcinoma (GEA), cholangiocarcinoma (CA), and glioma (GL) samples; and one in 18 pancreatic adenocarcinoma (PA) samples (Table). Prognostic markers were reported for patients with NSCLC (18%), CRC (10%), BC (16%), PC (25%), CA (8.1%), MEL (24%), GL (74%), or HNSCC (7.1%). Diagnostic markers were frequently detected for patients with GL and noted for patients with BC, GEA, or MEL (Table). Interventional clinical trials were evidence-matched to most F1CDx tumor profiles (89%, range 82% in PC to 99% in PA), with the targets of approved therapies accounting for a small subset of targets in clinical development. Conclusions: F1CDx reports support clinical decision making by interpreting predictive, prognostic, and diagnostic markers according to professional guidelines as well as investigational markers for the enrollment in clinical trials. [Table: see text]

Background: Epidermal growth factor receptor (EGFR) is a therapeutic target in non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC). Patients with NSCLC with activating mutations in EGFR typically have significant tumor regressions with gefitinib. However approximately 30% of patients treated with gefitinib develop stable disease even without EGFR mutations. EGFR mutations are rare in HNSCC. As EGFR can be activated by one of its ligands (amphiregulin, EGF, TGFα), we examined the relationship of EGFR ligands and the efficacy of gefitinib and cetuximab using EGFR wild type NSCLC, HNSCC cell lines and in tissue samples from NSCLC pts treated with gefitinib or erlotinib. Methods: Amphiregulin (AR), EGF and TGFα in cell culture media were analyzed with ELISA assays in 18 cell lines, 14 NSCLC (4 EGFR mutant; 10 EGFR wild type) and 4 HNSCC cell lines. The in vitro sensitivity was analyzed using MTS assay. EGFR, HER3, Akt, ERK1/2, Cyclin D1 and phosphorylation of these were analyzed with Western blotting. Cell cycle was analyzed by flow cytometry. Tissue samples from 29 pt with EGFR wild type NSCLC were studied using IHC. These are treated with gefitinib or erlotinib. AR expression was scored (0-400) by multiplying extent (0-100%) and intensity (0-4) of staining. Results: TGFα (range, 0 to 4.8pg/ml) and EGF (0 to 2.2pg/ml) was detected at negligible level in all cell lines except Calu3 (TGF; 116.6pg/ml). The presence of AR varied significantly among the cell lines (range, 4.6 to 1625.8pg/ml). All 4 EGFR mutant cell lines had negligible levels of AR (&amp;lt;50.3pg/ml). Seven cell lines of the 14 cell lines with wild-type EGFR had &amp;gt; 250 pg/ml (718.4 to 1625.8pg/ml) of AR and all were sensitive to gefitinib with an IC50 of &amp;lt; 1 μM (range, 0.10 to 0.33). In addition, they were also sensitive to cetuximab (mean growth inhibition following10ug/ml cetuximab 56.8%, range, 33.1 to 87.1 %). In contrast cell lines producing &amp;lt; 250 pg/ml of AR were resistant to both gefitinib (IC &amp;gt; 1 μM) and cetuximab (mean growth inhibition following 10ug/ml cetuximab 1.0%, range -4.4 to 15.3%). The AR producing cell lines underwent G1/S arrest following either gefitinib or cetuximab. AR producing cell lines exhibited dose dependent decrease in p-EGFR, p-ERK 1/2 and cyclin D1 following gefitinib or cetuximab. AR non-producing cell lines had no effect on these proteins following treatment. IHC of tissue samples showed 9/10 samples from pts, developed stable disease.following gefitinib, had high AR expression (cut off score 100), while only 3/19 samples had high AR expression from pts with progressive disease (p&amp;lt;0.001). Conclusion: Our findings suggest that in EGFR wild type NSCLC and HNSCC cell lines the presence of an AR autocrine loop is a major determinant of in vitro sensitivity to gefitinib and cetuximab. AR expression may be a suitable biomarker to select EGFR wild type NSCLC patients likely to benefit from gefitinib or erlotinib.

Previous studies have revealed the relationship between toll-like receptor 4 (TLR4) polymorphisms and cancer susceptibility. However, the relationship between TLR4 and prognosis and immune cell infiltration in pan-cancer patients is still unclear. Through the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases, the distinct expression of the TLR4 gene in 24 tumors and normal tissues was analyzed. Univariate Cox proportional hazards regression analysis was used to identify the cancer types whose TLR4 gene expression was related to prognosis. The relationship between TLR4 and tumor cell immune invasion was studied. Spearman’s rank correlation coefficient was used to analyze the relationship among TLR4 and immune neoantigens, tumor mutation burden (TMB), microsatellite instability (MSI), DNA repair genes, and DNA methylation. Gene Set Enrichment Analysis (GSEA) was used to identify the tumor-related pathways that the TLR4 gene was highly expressed in; the expression of the TLR4 gene was verified with the Human Protein Atlas (HPA) database. Low expression of TLR4 was associated with an inferior prognosis in kidney renal clear cell carcinoma (KIRC), skin cutaneous melanoma (SKCM), and uterine corpus endometrial carcinoma (UCEC), while high expression was related to a poor prognosis in head and neck squamous cell carcinoma (HNSC), prostate adenocarcinoma (PRAD), stomach adenocarcinoma (STAD), and testicular germ cell tumor (TGCT). The expression of TLR4 was negatively correlated with the expression of B cells in STAD. The expression of TLR4 was positively correlated with the infiltration of B cells, CD4 and CD8 T cells, neutrophils, macrophages, and dendritic cells in STAD, KIRC, UCEC, TGCT, and SKCM. The expression of the TLR4 gene in KIRC, SKCM, STAD, TGCT, and UCEC was highly correlated with inducible T-cell costimulator (ICOS), cytotoxic T lymphocyte-associated molecule 4 (CTLA4), and CD28 immune checkpoints. Spearman’s rank correlation coefficient showed that the expression of TLR4 gene was significantly correlated with TMB in STAD and UCEC and was prominently correlated with MSI in TGCT, STAD, and SKCM. The expression of the TLR4 gene was highly correlated with MLH1, MSH2, and MSH6 in KIRC, SKCM, and STAD. The expression of the TLR4 gene was remarkably correlated with the methyltransferases DNA methyltransferase 2 (DNMT2) and DNA methyltransferase 3-beta (DNMT3B) in SKCM and STAD. Enrichment analysis showed that TLR4 was highly expressed in the chemokine signaling pathway and the cell adhesion molecule and cytokine receptor interaction pathway. In summary, the expression of TLR4 is linked to the prognosis of KIRC, SKCM, STAD, TGCT, and UCEC patients and the level of immune infiltration of CD4, CD8 T cells, macrophages, neutrophils, and dendritic cells.

Pan-cancer analysis of ubiquitin-specific protease 7 and its expression changes in the carcinogenesis of scar ulcer

Background Bone morphogenetic protein 2 (BMP2) is essential for bone development and repair in vertebrates. Its role in tumorigenesis and progression remains incompletely characterized. Method Using the Cancer Genome Atlas (TCGA) and bioinformatic tools, we analyzed BMP2 expression, prognostic relevance, genetic alterations, immune infiltration, and signaling pathways across 33 tumor types. Results BMP2 exhibited elevated expression in tumor tissues of cholangiocarcinoma (CHOL), glioblastoma (GBM), head and neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), and liver hepatocellular carcinoma (LIHC) patients, but reduced expression in 10 other cancers. High BMP2 expression correlated with reduced overall survival (OS) in esophageal carcinoma (ESCA), LIHC, lung squamous cell carcinoma (LUSC), pancreatic adenocarcinoma (PAAD), and thyroid carcinoma (THCA) patients, and shorter disease-free survival (DFS) in uveal melanoma (UVM) patients. BMP2 mutations and amplifications were frequent in diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), and uterine corpus endometrial carcinoma (UCEC). BMP2 expression positively correlated with cancer-associated fibroblast (CAF) infiltration and interacts physically with ACVR2A, BMP4, BMPR1A/B, BMPR2, CALR, and HSPA5. Pathway analysis implicated transforming growth factor-beta (TGF-β) signaling pathway. Conclusions BMP2 expressions and alterations have tissue-specific prognostic implications. BMP2 may serve as a biomarker and therapeutic target in specific tumors via TGF-β signaling modulation.

Immunotherapy, specifically anti-PD1, has improved patient survival in a range of tumor types including head and neck squamous cell carcinoma (HNSCC) and non-small cell lung cancer (NSCLC). Despite the success of anti-PD1 therapy, only 20% of patients produce a durable response to this treatment. Thus, a need exists to develop additional therapeutic strategies to treat these patients, which includes evaluation of other tumor-infiltrating immune cells that could further augment the CD8+ and CD4+ T-cell response. Tumor-infiltrating B cells (TIL-B) represent a possible target for immunotherapy due to their predominance in the tumor microenvironment (TME) and crucial role in the immune response. However, TIL-B function in cancer and in the context of immunotherapy has been understudied. In fact, conclusions on an anti- or protumor role for TIL-Bs in the TME is dependent on the study. However, in HNSCC and NSCLC patients, current evidence suggests an antitumor role for TIL-Bs. Specifically, detection of TIL-Bs within tertiary lymphoid structures (TLS) correlates with better prognosis. While TIL-Bs have been identified in HNSCC and NSCLC patients, their complete phenotypic signature and function in the TME has been understudied with no focus on their role as antigen presenting cells (APCs) and their influence on CD8+ and CD4+ tumor infiltrating lymphocytes (TILs). We hypothesize that TIL-Bs help generate potent, long-term immune responses against cancer by presenting tumor antigens to CD4 TILs within TLS.Using unmanipulated, primary human B cells from fresh tumor, we quantified and further characterized TIL-Bs in HNSCC and NSCLC utilizing single-cell RNAseq and multiparameter flow cytometry. We observed increased numbers of activated TIL-Bs in these primary tumors compared to other immune subsets, specifically CD27+ TIL-Bs. We further assessed the TIL-Bs by correlating phenotype of the TIL-B with its location in the TME, predominantly separating out differences between TIL-Bs within TLS and outside TLS. In addition, we generated a specific antigen presentation assay in vitro, and we observed three types of CD4+ TIL responses when TIL-Bs presented autologous tumor antigens. There were activated responder CD4+ TILs that proliferated when combined with TIL-Bs alone, which indicates stimulation with endogenous tumor antigens. There were antigen-associated responders that required exogenous autologous tumor lysate to elicit a CD4+ TIL response, and there were patient CD4 TILs that did not respond to antigen presentation by TIL-Bs. Within the activated and antigen-associated responders, the TIL-B phenotype influenced the CD4+ TIL phenotype; if the TIL-Bs were activated (CD27+), the CD4+ TILs were T helper (antitumor) CD4+ T-cells and if the TIL-Bs were non-activated (CD27-), the CD4+ TILs were T regulatory cells (protumor). These data suggest that TIL-Bs influence the phenotype and function of CD4+ TILs in patient tumors. In conclusion, activated TIL-Bs are increased in human primary tumors, they can present antigen to CD4+ TILs and influence their overall phenotype. Determining the complete activation signature of TIL-Bs in HNSCC and NSCLC patients will determine the extent of their antitumor function in these cancers. Comparison of TIL-Bs in HNSCC and NSCLC is important as there are not many unified studies on TIL-B function across tumor types. Further, because HNSCC has two etiologies (viral vs. carcinogen induced), we are able to better study the differential function of activated and nonactivated TIL-Bs in solid tumors. Ultimately, results from this study will help predict how to target TIL-B functions in future TIL-B-specific immunotherapies or in combination with current immunotherapies for HNSCC and NSCLC patients like blockade of the inhibitory receptor, PD-1. Citation Format: Tullia C. Bruno, Ayana T. Ruffin, Anthony R. Cillo, Robert L. Ferris, Dario A.A. Vignali. Activated B cells in human primary tumors present antigen and increase antitumor function of CD4 T-cells in tertiary lymphoid structures [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A053.

According to the previous reports, the collagen triple helix repeat containing 1 (CTHRC1) causes tumorigenesis by modulating the tumor microenvironment, however, the evidence is limited to a few human cancer subtypes. In the current study, we analyzed and validated the CTHRC1 expression variations in 24 different human cancer tissues paired with normal tissues using publically available databases. We observed that CTHRC1 was overexpressed in all the 24 major subtypes of human cancers and its overexpression was significantly associated with the reduced overall survival (OS) duration of head and neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), Lung adenocarcinoma (LUAD), stomach adenocarcinoma (STAD), and Uterine corpus endometrial carcinoma (UCEC). This implies that CTHRC1 plays a significant role in the development and progression of these cancers. We further noticed that CTHRC1 was also overexpressed in HNSC, KIRC, LIHC, LUAD, STAD, and UCEC patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of CTHRC1 associated genes in seven diverse pathways. We also explored few interesting correlations between CTHRC1 expression and promoter methylation, genetic alterations, CNVs, CD8+ T immune cells infiltration, and tumor purity. In conclusion, CTHRC1 can serve as a shared diagnostic and prognostic biomarker in HNSC, KIRC, LIHC, LUAD, STAD, and UCEC patients of different clinicopathological features.

e22509 Background: Genomic instability is a typical characteristic of the majority of cancers. Early non-invasive detection of cancer is the most effective way of improving the success of treatment and prognosis at present. Traditional tumor screening methods have limitations in terms of selection methods, sensitivity, specificity, cost, and comfortability. Furthermore, although traditional tumor screening is useful for common cancers, there is no available screening test for rare cancers. Here we developed a novel method for cancer detection with Low-Pass Whole Genome Sequencing (WGS) of cell-free DNA (cfDNA). Methods: The cfDNA samples from 52 healthy donors were first used to establish a blacklist of bins. Then the baseline was established to calculate the chromosomal instability score (CINscore). We optimized the parameters of our model using the following discovery datasets: healthy controls (n = 50), breast invasive carcinoma (BRCA) (n = 44), ovarian serous cystadenocarcinoma (OV) (n = 25), colon adenocarcinoma/rectum adenocarcinoma esophageal carcinoma (COREAD) (n = 52), hepatocellular carcinoma (HCC) (n = 43), Gastric adenocarcinoma (GAC) (n = 31); pancreatic adenocarcinoma (PAC) (n = 38), non-small cell lung cancer (NSCLC) (n = 45). Results: We further evaluated the performance of our method using the confirmation datasets of healthy controls (n = 30), BRCA (n = 20), prostate adenocarcinoma (PRAD) (n = 6), OV (n = 7), head and Neck squamous cell carcinoma (HNSC) (n = 10), Uterine Corpus Endometrial Carcinoma (UCEC) (n = 6), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) (n = 5), COREAD (n = 75), HCC (n = 50), GAC (n = 31), cholangiocarcinoma (CHOL) (n = 8), PAC (n = 10), NSCLC (n = 98), esophageal carcinoma (ESCA) (n = 10), and nasopharyngeal carcinoma (NAC) (n = 4). Overall, the area under the curve (AUC) for pan-cancer is 88.7%, and for BRCA, COREAD, HCC, NSCLC, and GAC are 91.7%, 90.0%, 94.5%, 83.4%, and 88.6%, respectively. Moreover, our approach achieved good performance on the the early stage samples of pan-cancer (AUC = 84.3%) as well as COREAD (AUC = 89.3%) and NSCLC (AUC = 79.0%). Conclusions: Collectively, we show that the CINscore inferred from low-pass WGS could be applied in early non-invasive detection of different cancers with high accuracy. Our approach may aid the improvement of the cancer diagnosis.

BackgroundWhile clinical responses of unmodified TIL therapies have been observed in metastatic melanoma, the effectiveness and durability of response to TIL therapy may be limited by the immunosuppressive tumor microenvironment...

We conducted a phase I study to evaluate the activity and tolerability of concurrent docetaxel and cisplatinum radiosensitization with hyperfractionated irradiation, in patients with advanced non-small cell lung cancer (NSCLC) and squamous cell carcinoma of the head and neck (SCCHN). Nine patients (5 stage III(A) and 4 III(B)) with NSCLC, and 15 with SCCHN (10 stage III and 5 IV) were treated with a b.i.d. hyperfractionated (HF) radiotherapy schedule. The normalized total dose for alpha/beta ratio = 10 Gy was 69.6 Gy for NSCLC and 80.5 Gy for SCCHN patients. The standard dose of cisplatin (10 mg/m(2)) was given combined to docetaxel on a weekly basis. The docetaxel starting dose level was 10 mg/m(2)/week and was escalated by 3 mg/m(2) increments in cohorts of 8 patients (5 SCCHN and 3 NSCLC). DLT (grade 3 malaise) was observed in 4 out of 8 patients treated at the 16 mg/m(2)/week docetaxel dose level. The 13 mg/m(2)/week docetaxel dose level was defined as the MTD causing grade 3 mucositis in 4 out of 8 patients. In total 4 (17%) patients developed grade 3 neutropenia. G-CSF support was given in 1/8, 4/8, and 5/8 patients treated at the 10, 13 and 16 mg/m(2) docetaxel dose levels respectively. Fatigue was the most common adverse event (5/24: 21%) and was responsible for more than 1 week treatment delay in 4 out of 8 patients treated at the 16 mg/m(2)/week docetaxel dose level. Nine (3 NSCLC and 6 SCCHN patients: 37.5%) had treatment delay of 1 week, while 7 (3 NSCLC and 4 SCCHN: 29%) had delays of 2 weeks for combined chemoradiation sequelae. Acute hypersensitivity reactions occurred in 3 (12.5%) patients, and grade 3 mucositis in 2/8, 5/8 and 6/8 patients, treated at 10, 13 and 16 mg/m(2)/week docetaxel dose levels respectively. The overall response rate was 79% (CI = 63-96%) with 33% and 53% CRs for NSCLC and SCCHN patients respectively. There were 3 deaths among 9 NSCLC and 4 among 15 SCCHN patients. Local and/or distant disease recurrences were shown in 4 NSCLC and in 6 SCCHN patients; 5 NSCLC and 9 SCCHN patients are alive with no evidence of tumor progression at 8.5 months mean follow-up time. Radiosensitization with docetaxel and cisplatin given concurrently with HF (b.i.d.) radiotherapy on a weekly basis is a promising approach and the recommended dose for further phase II studies is 10 mg/m(2)/week for both drugs. The antitumor activity shown was significant in both types of tumors. The incorporation of docetaxel in chemoradiotherapy regimens for future treatment of squamous cell carcinoma of the lung and head and neck, merits evaluation in phase II and III trials.

e20521 Background: While tissue-based next generation sequencing (NGS) ushered in a new era of precision medicine, profiling of circulating tumor DNA (ctDNA) has also emerged as a minimally invasive alternative to inform clinical decisions. In non-small cell lung cancer (NSCLC), data describing comparison between mutational profiles of paired tissue and blood samples remained scarce. Methods: Matched formalin-fixed paraffin-embedded tissue and peripheral blood samples (≤14 days apart) were collected from treatment naïve advanced NSCLC patients. Genomic profiling was performed using whole exome sequencing (WES) for tissues and a 150-gene panel for ctDNA, with a mean sequencing depth of 239× and 3417× respectively. Tumor- and blood-based tumor mutational burdens (tTMB and bTMB) were defined as the sum of missense, stop-loss, in-frame and frameshift mutations in protein coding regions and the number of somatic single nucleotide variations and indels in targeted coding regions respectively. Maximum somatic allele frequency (MSAF) was also determined for each case as a measure of ctDNA quantity. Results: Matched tissue and blood samples from 48 patients were included for sequencing. A total of 410 mutations were identified, where 84 (20.5%) were covered in both sample types. Sixty-three (15.4%) alterations were only detected in tissues while 263 (64.1%) were exclusively seen in ctDNA. The most frequently altered genes were SMARCA2 (62.5%), TP53 (54.2%), and AR (47.9%) in ctDNA and were TP53 (37.5%) and EGFR (22.9%) in tissues. Aberrations in all genes, except for FAT1 and KRAS, occurred at a higher frequency in ctDNA. The median tTMB and bTMB were 75 and 7, respectively. bTMB displayed a moderate linear relationship with tTMB as indicated by a Spearman correlation of 0.62 (P &lt; 0.01). Patients with bTMB ≥ 7 had significantly higher MSAF (Mann-Whitney P &lt; 0.001), suggesting a positive correlation between bTMB and ctDNA fraction in blood. Conclusions: Mutational profiles as well as TMB levels were in general consistent between blood and tissue samples, further corroborating a role for ctDNA testing as a complementary approach to tissue testing in advanced NSCLC.

Background: Programmed cell death 1 (PD-1) is a receptor upregulated on activated lymphocytes that mediates a dominant-negative checkpoint signal limiting antigen receptor-driven cellular activation. PD-1 immune checkpoint inhibitors have shown durable clinical responses in patients with non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC). Budigalimab (formerly ABBV-181) is a blocking humanized recombinant anti-PD-1 monoclonal antibody, currently under evaluation in multiple studies such as phase 1 clinical trial (NCT03000257) in patients with solid tumors including HNSCC and NSCLC. Multiple clinical biomarker assessments have been incorporated into this study to accommodate pharmacodynamic (PD) and predictive analyses. Methods: Patients with previously treated, advanced HNSCC (n=41) or NSCLC (n=40) that were PD-1 inhibitor naïve received budigalimab IV at 250 mg every two weeks or 500 mg every four weeks to progression, with responses assessed every 8 weeks. Archival tumor FFPE specimens from patients with HNSCC (n=37) and NSCLC (N=33) were evaluated for CD8 infiltration and tumor PD-L1 expression by Dako 28-8 IHC assay, with remaining samples processed for RNA sequencing and whole-exome sequencing. Serum (for soluble biomarkers) and whole blood (for flow cytometric analysis of T cell biomarkers) were taken at baseline and selected on-treatment time points. Univariate analysis of biomarkers associated with the best overall response (BOR) and progression-free survival was conducted. Results: As of July 2019, responses per response evaluation criteria in solid tumors (RECIST) v1.1 or iRECIST were observed at the expected rates for a PD-1 inhibitor (BOR of partial or complete response of 15% in HNSCC and 19% in NSCLC), with responses in PD-L1+ and PD-L1- tumors in both groups. Budigalimab dosing was associated with rapid complete PD-1 receptor saturation, transient decreases in circulating lymphocytes, upregulation of proliferation (Ki67) biomarkers in T cells, and upregulation of multiple soluble biomarkers, including IFNγ-induced chemokines. Differential neoantigen burden and lymphocyte-associated gene expression in tumors were observed in responders versus non-responders. Preliminary univariate analysis of biomarkers found that baseline tumor size, serum IL-6, and T cell counts were significantly associated with outcomes. Conclusions: Our biomarker analysis of budigalimab-treated HNSCC and NSCLC patients has identified early PD biomarkers consistent with PD-1 inhibitor activity as well as pre-treatment tumor and peripheral biomarkers associated with observed clinical responses. These findings confirm that budigalimab is a biologically active PD-1 inhibitor. Citation Format: Stacie Lambert, Chun Zhang, Stefan Englert, Claire Guo, Tolga Turan, Catherine Tribouley, David Masica, Robert T. McLaughlin, Gregory S. Vosganian, Daniel E. Afar. Pharmacodynamic and predictive biomarkers of clinical responses to PD-1 inhibitor budigalimab from the first-in-human clinical trial [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4464.