Translating transcriptome to immunophenotype in head and neck squamous cell carcinoma (HNSCC) to identify pathways promoting T-cell infiltration.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e17542-e17542
Author(s):  
Theodoros Rampias ◽  
Christos K. Kontos ◽  
Alexandros Polyzos ◽  
Aris Giotakis ◽  
Evangelos Giotakis ◽  
...  
Keyword(s):  
T Cell ◽  
Checkpoint Inhibitors ◽  
Predictive Biomarkers ◽  
Keratinocyte Differentiation ◽  
Cell Infiltration ◽  
Mrna Levels ◽  
Rna Seq ◽  
Mesenchymal Transition ◽  
Invasive Margin ◽  
T Cell Infiltration

e17542 Background: We sought to analyze the transcriptional landscape of HNSCC in an attempt to identify tumor-intrinsic oncogenic pathways that appear to mediate T-cell infiltration of tumor tissue. In this direction, we employ a methodology that integrates histopathology data of the tumor microenvironment with its corresponding transcriptome. Methods: 32 frozen HNSCCs were subjected to RNA-seq and corresponding FFPE were scored for plasma cells, tertiary lymphoid structures and CD8a+ TILs (center, invasive margin). RNA-seq data were analyzed to identify differentially expressed genes (DEGs) between tumors scored by immunohistochemistry (IHC) as CD8a high and CD8a low. Gene ontology analysis (GO) was performed based on DEGs > 1.5 fold expression change between CD8a high and CD8a low groups. Candidate genes were investigated by hierarchical clustering in TCGA RNA-seq data and further validated by IHC and quantitative RT-PCR in our cohort. Results: 32 HNSCCs were either scored as CD8a high or CD8a low based on IHC detection of CD8a+ cells in invasive margin of tumors. Comparative analysis of mRNA expression data between CD8a high and CD8a low groups in our cohort revealed that Muc1/16 overexpression and glycosylation was highly enriched in T cell infiltrated group of tumors. This finding was further validated using antibodies that detect glycosylated epitopes for both mucins. Analysis of TCGA RNA-seq data indicated that Muc1/16 overexpressing tumors share signatures of early keratinocyte differentiation and stem cell identity and co-express high levels of enzymes that promote Muc1/16 glycosylation. Interestingly, loss of CDH1 and acquisition of epithelial mesenchymal transition (EMT) markers in the cluster of Muc1/16 overexpressing tumors is strongly correlated with elevated CD8a, IDO1, CD274 and CXCL10 mRNA levels (P < 0.0001). Conclusions: Muc1/16 overexpressing tumors represent a very immunogenic HNSCC cluster. Previous studies have shown that mucins 1 and 16 in cancer cells expose glycosylated-specific epitopes that are recognized by T cells as cancer antigens. To this end, MUC1/16 expression may serve as predictive biomarkers for response to immunotherapy and MUC-targeted immunotherapy may function as an attractive partner to checkpoint inhibitors in HNSCC.

scholarly journals Risk Signature Related to Immunotherapy Reaction of Hepatocellular Carcinoma Based on the Immune-Related Genes Associated With CD8+ T Cell Infiltration

2021 ◽  
Vol 8 ◽  
Author(s):  
Yiping Zou ◽  
Zhihong Chen ◽  
Hongwei Han ◽  
Shiye Ruan ◽  
Liang Jin ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cell ◽  
Immune Checkpoint ◽  
Immune Checkpoint Inhibitors ◽  
Response Rate ◽  
Risk Group ◽  
Checkpoint Inhibitors ◽  
Cell Infiltration ◽  
T Cell Infiltration ◽  
Immune Related Genes

Background: Hepatocellular carcinoma (HCC) is the most common histological type of liver cancer, with an unsatisfactory long-term survival rate. Despite immune checkpoint inhibitors for HCC have got glories in recent clinical trials, the relatively low response rate is still a thorny problem. Therefore, there is an urgent need to screen biomarkers of HCC to predict the prognosis and efficacy of immunotherapy.Methods: Gene expression profiles of HCC were retrieved from TCGA, GEO, and ICGC databases while the immune-related genes (IRGs) were retrieved from the ImmPort database. CIBERSORT and WGCNA algorithms were combined to identify the gene module most related to CD8+ T cells in the GEO cohort. Subsequently, the genes in hub modules were subjected to univariate, LASSO, and multivariate Cox regression analyses in the TCGA cohort to develop a risk signature. Afterward, the accuracy of the risk signature was validated by the ICGC cohort, and its relationships with CD8+ T cell infiltration and PDL1 expression were explored.Results: Nine IRGs were finally incorporated into a risk signature. Patients in the high-risk group had a poorer prognosis than those in the low-risk group. Confirmed by TCGA and ICGC cohorts, the risk signature possessed a relatively high accuracy. Additionally, the risk signature was demonstrated as an independent prognostic factor and closely related to the CD8+ T cell infiltration and PDL1 expression.Conclusion: A risk signature was constructed to predict the prognosis of HCC patients and detect patients who may have a higher positive response rate to immune checkpoint inhibitors.

A phase Ib/IIa study of rucaparib (PARP inhibitor) combined with nivolumab in metastatic castrate-resistant prostate cancer.

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. TPS270-TPS270
Author(s):  
Akash Patnaik ◽  
Priyanka Duttagupta ◽  
Kiranj Chaudagar ◽  
Raanan Alter ◽  
Hanna Hieromnimon ◽  
...  
Keyword(s):  
Clinical Trial ◽  
T Cell ◽  
Predictive Biomarkers ◽  
Cell Infiltration ◽  
Parp Inhibition ◽  
Rna Seq ◽  
Phase Ib ◽  
Wide Range ◽  
Castrate Resistant ◽  
The Impact

TPS270 Background: Immune checkpoint blockade (ICB) therapies have had a major impact across a wide range of cancers. However, only subsets of patients across all malignancies benefit from ICB. In particular, metastatic castrate-resistant prostate cancers (mCRPC) have shown very limited responses to ICB. While there is ongoing work to identify predictive biomarkers to ICB responsiveness, early preclinical data from our group suggests that targeting fundamental DNA repair pathways could markedly increase the fraction of patients responsive to immunotherapeutic interventions. Based on these preclinical studies, we are conducting an investigator-initiated Phase Ib/IIa co-clinical trial of rucaparib and nivolumab singly and in combination, in mCRPC patients. Methods: Patients are randomized to one of three arms – rucaparib, nivolumab, or both drugs in combination for 4 weeks. Metastatic biopsy samples are collected at baseline and after 4 weeks on treatment, after which all arms switch to combination therapy. The primary objective is to assess feasibility of the combination, and to elucidate changes in T cell infiltration by RNA-seq analysis using established T-cell non-inflamed and inflamed gene signatures. Secondary objectives are to assess changes in immune cell infiltration via flow cytometry, multiplex IHC, transparent tissue tomography (3D mapping) and single-cell RNA-seq. We will correlate changes in the metastatic tumor microenvironment (TME) at baseline and following 4 weeks of treatment, with genomic alterations and clinical responses. We have currently enrolled 12 patients to the study, and collected pre- and 4 week on-treatment biopsies. This study utilizes novel emerging technologies for in-depth TME analysis that will unravel the impact of PARP inhibition, singly and in combination with PD-1 blockade, on specific immune subsets within the TME. The correlative analyses will also lead to the discovery of novel biomarkers of response/resistance, and suggest additional immuno-oncology combinations for specific genomic subsets of mCRPC. Clinical trial information: NCT03572478.

T cell infiltration in matched renal biopsy (bx) and nephrectomy (nx) samples in renal cell carcinoma (RCC).

2017 ◽  
Vol 35 (6_suppl) ◽  
pp. 472-472
Author(s):  
Haris Zahoor ◽  
Paul G Pavicic ◽  
Christopher Przybycin ◽  
Paul Elson ◽  
C. Marcela Diaz-Montero ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Checkpoint Inhibitors ◽  
Locally Advanced ◽  
Cleveland Clinic ◽  
Cell Infiltration ◽  
Tissue Sections ◽  
T Cell Infiltration ◽  
Potential Biomarker ◽  
Pre Treatment

472 Background: T cell infiltration in tumors has been investigated as a biomarker of response to checkpoint inhibitors. A neo-adjuvant trial of checkpoint inhibition in locally-advanced RCC is ongoing at Cleveland Clinic, where T cell infiltration in pre-treatment renal mass bx will be compared to post-treatment nx specimens. However, there are no data regarding the association of T cell infiltration in matched bx and nx samples without intervening treatment. Understanding this association will enable further study of this potential biomarker in future neo-adjuvant studies. Methods: Matched bx and nx samples (without intervening systemic therapy) were identified from patients with non-metastatic RCC. Demographic and pathological data were collected from chart review. Selected tissue sections from bx and nx samples of each patient were reviewed, and marked for tumor and intra-tumoral lymphocytes by the pathologist. Immunohistochemistry (IHC) was utilized to stain these selected tissue sections for T cell markers (CD3, CD4 and CD8). Intra-tumoral T cells were then quantified in the pre-marked tissue sections as counts per total tumor area surveyed, using Image-Pro Plus (Media Cybernetics, Inc.). Spearman correlation (ρ) was used to measure the strength of association of T cell infiltration between matched samples. Results: 30 matched pairs were investigated. The median interval between bx and nx was 2.8 (0.2-87.7) months. Clear cell was the most common histology (29/30; 97%). 15/30 (50%) had grade 3-4 tumors, 2/19 (11%) patients had sarcomatoid features, 7/25 (29%) had necrosis, and 8/28 (29%) had lymphovascular invasion. We found a positive correlation between the frequencies of CD8+ T cells between matched bx and nx samples (ρ= 0.39; p=0.03). CD3+ and CD4+T cells did not show significant correlation. (Table) Conclusions: Bx material can be used to accurately assess the degree of CD8+T cell infiltration in RCC. [Table: see text]

scholarly journals The Role of PTEN Loss in Immune Escape, Melanoma Prognosis and Therapy Response

Cancers ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 742 ◽  
Author(s):  
Rita Cabrita ◽  
Shamik Mitra ◽  
Adriana Sanna ◽  
Henrik Ekedahl ◽  
Kristina Lövgren ◽  
...  
Keyword(s):  
T Cell ◽  
Metastatic Melanoma ◽  
Immune Evasion ◽  
Immune Escape ◽  
Therapy Response ◽  
Predictive Biomarkers ◽  
Cell Infiltration ◽  
Pten Gene ◽  
T Cell Infiltration

Checkpoint blockade therapies have changed the clinical management of metastatic melanoma patients considerably, showing survival benefits. Despite the clinical success, not all patients respond to treatment or they develop resistance. Although there are several treatment predictive biomarkers, understanding therapy resistance and the mechanisms of tumor immune evasion is crucial to increase the frequency of patients benefiting from treatment. The PTEN gene is thought to promote immune evasion and is frequently mutated in cancer and melanoma. Another feature of melanoma tumors that may affect the capacity of escaping T-cell recognition is melanoma cell dedifferentiation characterized by decreased expression of the microphtalmia-associated transcription factor (MITF) gene. In this study, we have explored the role of PTEN in prognosis, therapy response, and immune escape in the context of MITF expression using immunostaining and genomic data from a large cohort of metastatic melanoma. We confirmed in our cohort that PTEN alterations promote immune evasion highlighted by decreased frequency of T-cell infiltration in such tumors, resulting in a worse patient survival. More importantly, our results suggest that dedifferentiated PTEN negative melanoma tumors have poor patient outcome, no T-cell infiltration, and transcriptional properties rendering them resistant to targeted- and immuno-therapy.

scholarly journals 868 Overall survival on tebentafusp in metastatic uveal melanoma (mUM) across the range of tumor gp100 expression levels

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A909-A909
Author(s):  
Emma Leach ◽  
Sarah Stanhope ◽  
Revashnee Naidoo ◽  
Shaad Abdullah ◽  
Laura Collins ◽  
...  
Keyword(s):  
Overall Survival ◽  
T Cell ◽  
Fusion Protein ◽  
Uveal Melanoma ◽  
Cell Infiltration ◽  
Mrna Levels ◽  
Pharmacodynamic Response ◽  
Expression Levels ◽  
Link Type ◽  
T Cell Infiltration

BackgroundTebentafusp is a TCR–anti-CD3 bispecific fusion protein that targets melanoma-expressed gp100 antigen and has shown survival benefit in a randomized phase 3 trial in 1L patients with metastatic uveal melanoma.1 2 In phase 2 and 3 trials (NCT02570308, NCT03070392) enrolling late-stage mUM patients, we explored associations between gp100 expression in the tumor and pharmacodynamic response and clinical outcomes on tebentafusp.Methods2L+ (NCT02570308) or 1L (NCT03070392) HLA-A*02:01+ mUM patients were treated weekly with 68mcg tebentafusp after intra-patient dose escalation. Archival or fresh tumor biopsies were obtained prior to dosing. Expression of baseline gp100 was determined by immunohistochemistry (IHC) and RNAseq analysis (2L+ only) in up to 118 (2L+) and 187 (1L) samples. RNAseq analysis was used to evaluate association between baseline mRNA levels of gp100 and T cell infiltration and activation after 3 doses of tebentafusp (n=35). Serum samples (n=118, 2L+ only) collected at baseline and on-treatment were analyzed for ctDNA. An H-Score quantified tumoral gp100 protein expression. gp100 H score or mRNA levels were cut at the lowest quartile to identify gp100 low patients.ResultsDistribution of gp100 protein by IHC was similar in both studies with median H-Scores of 170 (IQR 60–260) (2L+) and 155 (IQR 68–229) (1L). Over 70% of samples had ≥ 50% gp100+ tumor cells at any intensity. gp100 H-scores were similar in archival and fresh tumor biopsies.High baseline gp100 mRNA levels were associated with ~2-fold increased CD3 and CD8 cell infiltration on tebentafusp compared to little or no change in the gp100 low group. There was greater T cell activation in the gp100 mRNA high group as demonstrated by induction of IFNα (fold change in gp100 high=2.5 p=0.00005,), IFNγ signatures (FC in gp100 high=5.7 p=0.00004) and cytotoxic genes GZMB (FC high=4.6 p=0.000006,) and PRF1 (FC high=2.4 p=0.00051,) compared to little or no activation in the gp100 mRNA low group.Tumor shrinkage (TS) and overall survival (OS) > 12 months were observed in low and high gp100 H-score subgroups (table 1), and a RECIST partial response was observed at very low gp100 (H-score 11). ctDNA reduction on tebentafusp was also observed across the range of gp100 expression levels.Abstract 868 Table 1TS and OS in gp100 high and gp100 low patient groupsConclusionsHigh gp100 expression was associated with the acute pharmacodynamic response to tebentafusp including greater T cell infiltration and activation in the tumor microenvironment. However, clinical outcomes on tebentafusp—TS, OS and ctDNA reduction—were observed across the range of gp100 expression levels.Trial RegistrationNCT02570308, NCT03070392ReferencesMiddleton MR, McAlpine C, Woodcock VK, et al. Tebentafusp, a TCR/Anti-CD3 bispecific fusion protein targeting gp100, potently activated antitumor immune responses in patients with metastatic melanoma. Clin Can Res 2020;26:5869–5878.Sacco JJ, Carvajal R, Butler MO, et al. A phase (ph) II, multi-center study of the safety and efficacy of tebentafusp (tebe) (IMCgp100) in patients (pts) with metastatic uveal melanoma (mUM). Ann Oncol 2020;31:S1442-S1143.Ethics ApprovalThe institutional review board or independent ethics committee at each center approved the trial. The trial was conducted in accordance with the Declaration of Helsinki and the International Conference on Harmonization Good Clinical Practice guidelines.

scholarly journals P08.02 CCR2/CCR5 dual-antagonist ‘licenses’ the radiation-induced effector T-cell infiltration in the anti-PD-1 antibody-treated pancreatic adenocarcinoma

2021 ◽  
Vol 9 (Suppl 1) ◽  
pp. A25.1-A25
Author(s):  
J Wang ◽  
M Tun Saung ◽  
K Fujiwara ◽  
N Niu ◽  
A Narang ◽  
...  
Keyword(s):  
T Cell ◽  
Rna Sequencing ◽  
Checkpoint Inhibitors ◽  
Cell Infiltration ◽  
Ductal Adenocarcinoma ◽  
Pancreatic Tumors ◽  
Prolonged Treatment ◽  
Effector T Cell ◽  
T Cell Infiltration ◽  
T Cell Priming

BackgroundThe resistance of pancreatic ductal adenocarcinoma(PDAC) to immune checkpoint inhibitors(ICIs) is mainly attributed to the immune-quiescent nature of its tumor microenvironment(TME). Radiotherapy(RT) activates innate responses including the RAGE and TLR2/4 pathways and subsequently modifies the TME by promoting the release of chemokines that recruit inflammatory cells into the TME. In this preclinical study, we examined the PDAC vaccine or RT as a T-cell priming mechanism together with BMS-687681, a small molecule dual-antagonist of CCR2 and CCR5(CCR2/5i) as an immunosuppressive TME-targeting agent, in combination with the anti-PD-1 antibody(αPD-1) as a new treatment.Materials and MethodsThe hemi-spleen and Orthotopic mice model were used to investigate both GVAX and RT as T-cell priming agents in combination regimens that included αPD-1 and CCR2/5i. Dissected orthotopic pancreatic tumors were collected for analysis of tumor-infiltrating immune cells by flow cytometry. RNA from tumor-infiltrating immune cell pellets and whole-exome RNA sequencing was performed for further mechanism research.ResultsCCR2 and CCR5 are associated with the immunosuppressive TME of PDAC patients and their expression were induced after treatment with GVAX+nivolumab. Using a mouse model of PDAC, we demonstrated that the addition of GVAX to CCR2/5i+αPD-1 combination therapy did not significantly improve antitumor activity. However, RT followed by αPD-1 and prolonged treatment with CCR2/5i conferred significantly better antitumor efficacy compared to the other combination treatments we studied. The combination of RT, αPD-1, and CCR2/5i enhanced intratumoral effector and memory T-cell infiltration. This combination suppressed Treg, M2-like TAM, and M-MDSC infiltration, but not M1-like TAM and PMN-MDSC infiltration. Finally, RNA sequencing showed that CCR2/5i partially inhibited RT-induced TLR2/4&RAGE signaling, which would have otherwise led to the release of immunosuppressive cytokines including CCL2 and CCL5. The inhibition of TLR2/4&RAGE signaling permitted the expression of effector T-cell chemokines such as CCL17 and CCL22.ConclusionsThis study thus supports the clinical development of CCR2/5i in combination with RT and ICIs for PDAC treatment.Disclosure InformationJ. Wang: None. M. Tun Saung: None. K. Fujiwara: None. N. Niu: None. A. Narang: None. J. He: None. L. Zheng: None.

scholarly journals Poly-IC enhances the effectiveness of cancer immunotherapy by promoting T cell tumor infiltration

2020 ◽  
Vol 8 (2) ◽  
pp. e001224 ◽  
Author(s):  
Hussein Sultan ◽  
Juan Wu ◽  
Valentyna I Fesenkova ◽  
Aaron E Fan ◽  
Diane Addis ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Immune Checkpoint ◽  
Checkpoint Inhibitors ◽  
Cell Infiltration ◽  
Mouse Tumor ◽  
Type I ◽  
Antitumor Effects ◽  
Cell Therapies ◽  
T Cell Infiltration

BackgroundImmunotherapies, such as immune checkpoint inhibitors and adoptive cell therapies, have revolutionized cancer treatment and resulted in complete and durable responses in some patients. Unfortunately, most immunotherapy treated patients still fail to respond. Absence of T cell infiltration to the tumor site is one of the major obstacles limiting immunotherapy efficacy against solid tumors. Thus, the development of strategies that enhance T cell infiltration and broaden the antitumor efficacy of immunotherapies is greatly needed.MethodsWe used mouse tumor models, genetically deficient mice and vascular endothelial cells (VECs) to study the requirements for T cell infiltration into tumors.ResultsA specific formulation of poly-IC, containing poly-lysine and carboxymethylcellulose (PICLC) facilitated the traffic and infiltration of effector CD8 T cells into the tumors that reduced tumor growth. Surprisingly, intratumoral injection of PICLC was significantly less effective in inducing tumor T cell infiltration and controlling growth of tumors as compared with systemic (intravenous or intramuscular) administration. Systemically administered PICLC, but not poly-IC stimulated tumor VECs via the double-stranded RNA cytoplasmic sensor MDA5, resulting in enhanced adhesion molecule expression and the production of type I interferon (IFN-I) and T cell recruiting chemokines. Expression of IFNαβ receptor in VECs was necessary to obtain the antitumor effects by PICLC and IFN-I was found to directly stimulate the secretion of T cell recruiting chemokines by VECs indicating that this cytokine-chemokine regulatory axis is crucial for recruiting effector T cells into the tumor parenchyma. Unexpectedly, these effects of PICLC were mostly observed in tumors and not in normal tissues.ConclusionsThese findings have strong implications for the improvement of all types of T cell-based immunotherapies for solid cancers. We predict that systemic administration of PICLC will improve immune checkpoint inhibitor therapy, adoptive cell therapies and therapeutic cancer vaccines.

scholarly journals Systemic and intravesical adoptive cell therapy of tumor-reactive T cells can decrease bladder tumor growth in vivo

2020 ◽  
Vol 8 (2) ◽  
pp. e001673
Author(s):  
Brittany L Bunch ◽  
Jennifer Morse ◽  
Sarah Asby ◽  
Jamie Blauvelt ◽  
Ahmet M Aydin ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
T Cells ◽  
T Cell ◽  
Tumor Growth ◽  
Cellular Therapy ◽  
Checkpoint Inhibitors ◽  
Adoptive Cell Therapy ◽  
Tumor Cell Line ◽  
Cell Infiltration ◽  
T Cell Infiltration

BackgroundThe therapeutic armamentarium of bladder cancer has been recently enriched with the introduction of new therapies including immune checkpoint inhibitors, receptor tyrosine kinase inhibitors and antibody drug conjugates, however treatment responses and duration of responses are still less than expected. Adoptive cellular therapy (ACT) using tumor-infiltrating lymphocytes (TILs) has potential to treat bladder cancer, as previously demonstrated by successful expansion of tumor reactive T cells from human bladder tumors.MethodsA model system using OT-I T cells and an ovalbumin expressing MB49 tumor cell line (MB49OVA) was developed to study ACT in bladder cancer. Systemic ACT-treated mice were given T cells intravenously after lymphodepleting chemotherapy and followed by interleukin (IL)-2 administration. Intravesical ACT treated mice were given T cells directly into the bladder, without chemotherapy or IL-2. TILs were isolated from MB49 orthotopic tumors and expanded ex vivo in IL-2. Immune cell infiltrates were analyzed by flow cytometry. T cell infiltration was studied using a CXCR3 blocking antibody.ResultsSystemic ACT-treated mice had a decrease in tumor growth, increase in T cell infiltration and long-term immune protection compared with control-treated mice. OT-I T cells delivered intravesically were able to control tumor growth without lymphodepleting chemotherapy or IL-2 in MB49OVA orthotopic tumors. Intravesical delivery of TIL expanded from MB49 tumors was also able to decrease tumor growth in mice with MB49 orthotopic tumors. Blocking CXCR3 on OT-I T cells prior to intravesical delivery decreased T cell infiltration into the tumor and prevented the control of tumor growth.ConclusionsThis study demonstrates how TIL therapy can be used in treating different stages of bladder cancer.

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