Predictive values of genomic variation, tumor mutational burden, and PD-L1 expression in advanced lung squamous cell carcinoma treated with immunotherapy

e13031 Background: In Cutaneous Squamous Cell Carcinoma (cSqCC), Notch1, Notch2, and Notch3 have been identified as tumor suppressors with a high rate of inactivating mutations early in cSqCC pathogenesis. Despite the high frequency of alterations, the biologic and therapeutic implications of Notch genomic alterations (GAs) in cSqCC are incompletely understood. Methods: 232 FFPE samples of cSqCC were evaluated by comprehensive genomic profiling (CGP) of 315 genes and analyzed for all classes of GAs, with diagnoses confirmed by central pathology review. Notch GAs with unknown functional impact were excluded. Tumor mutational burden (TMB) was calculated from 1.11 Mb of sequenced DNA and reported as mutations/Mb. Results: The cohort of 232 samples was 78% male and 22% female, aged from 17 to 88, with confirmed metastatic disease in 32% of cases. 115 (50%) samples had a Notch family member GA with a known or predicted functional impact. 96 cases had Notch1 GAs, 43 cases had Notch2 GAs, and 14 cases had Notch3 GAs with 40 cases having GAs in multiple Notch family members. These mutations were 41% missense, 34% nonsense, 15% splice site, 9% frameshift indels, and 1% non-frameshift indels alterations. Patients with Notch GAs were significantly older (median 70 years old vs median 64, p < 0.01). TMB was increased among samples with Notch GAs (median TMB of 63 mutations/mb versus 20 mutations/mb, p < 1x10-6), with similar differences for primary and metastatic samples. Cases with Notch GAs had more total GAs per case (mean 10.4 vs 7.4, p < 1.5x10-10); however, the top co-mutated genes were the same (TP53, CDKN2A, FAT1, MLL2). Both groups had a high proportion of C- > T/G- > A transitions, consistent with UV damage; however, the proportion was higher in cases with Notch GAs (median 83% vs 80%) - a difference seen in primary and metastatic samples. Conclusions: 50% of cSqCC cases had a Notch family member loss of function GA, which was associated with increased TMB in the primary and metastatic setting. With pre-clinical models and case studies showing responses to PD-1 inhibitors in cSqCC, further investigations are warranted into the associations of Notch GAs with mutational burden and response to immunotherapy.

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Clinical response and biomarker analysis of a phase II basket trial of toripalimab, a PD-1 mAb in combination with standard chemotherapy as a first-line treatment for patients with solid tumors.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e15083 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e15083-e15083

Author(s):

Chao Ren ◽

Xiao-Li Wei ◽

Nong Xu ◽

Lin Shen ◽

Guanghai Dai ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Clinical Response ◽

Solid Tumors ◽

Squamous Cell ◽

Line Treatment ◽

First Line ◽

Standard Chemotherapy ◽

Mutational Burden ◽

Tumor Mutational Burden

e15083 Background: Platinum based chemotherapy is the standard care for 1st line treatment of metastatic gastric adenocarcinoma (GC), esophageal squamous cell carcinoma (ESSC), nasopharyngeal carcinoma (NPC) and head and neck squamous cell carcinoma (HNSCC). Combinations of PD-1 blockade with chemotherapy have shown promising but mixed results in solid tumors. Predictive biomarkers for chemo-immunotherapy combination as 1st line treatment remain undefined. Methods: Patients (n = 60) included in this analysis were four complete cohorts from a multi-center, phase Ib/II trial (NCT02915432) evaluating the safety and activity of toripalimab, a humanized PD-1 antibody in combination with standard chemotherapy for the 1st line treatment of GC, EC, NPC and HNSCC (excluding NPC). Whole exome sequencing (WES), RNA sequencing and immunohistochemistry were performed on tumor biopsy samples. PD-L1 expression and tumor mutational burden (TMB) were evaluated for correlation with clinical efficacy. Results: From Oct 2016 to Feb 2019, 33 GC, 12 ESSC, 12 NPC and 3 HNSCC patients were enrolled and treated with 240mg or 360 mg toripalimab Q3W via IV infusion in combination with Oxaliplatin/Capecitabine (XELOX), Paclitaxel/Cisplatin (PP), Gemcitabine/Cisplatin (GP) and Docetaxel/Cisplatin/5-FU(TPF) respectively. By the data cutoff date of Nov 15, 2019, all patients experienced treatment related adverse event (TRAE). There was one TRAE (heart failure) leading to death. Grade 3-4 TRAEs occurred in 67% patients, mostly attributed to chemotherapy, including 27% neutropenia, 23% thrombocytopenia, 18% leukopenia and 12% anemia. As assessed by investigators according to RECIST v1.1, the ORR/DCR were 54.5%/84.8%, 66.7%/91.7%, 75.0%/83.3% and 33.3%/100% respectively for GC, EC, NPC and HSNCC cohorts. The median duration of response was 8.3, 6.8, 7.7 and 7.1 months respectively. WES showed distinctive patterns of genomic alterations among different cohorts. The clinical response was not correlated with either PD-L1 expression or tumor mutational burden. Conclusions: Toripalimab in combination with chemotherapy as first-line treatments showed promising results for metastatic GC, EC, NPC and HNSCC patients. Two randomized Phase III trials of toripalimab in combination with Paclitaxel/Cisplatin or Gemcitabine/Cisplatin versus chemotherapy alone are ongoing to further evaluate the combination as first-line treatments in metastatic EC and NPC patients. Clinical trial information: NCT02915432 .

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Combination of Tumor Mutational Burden and Specific Gene Mutations Stratifies Outcome to Immunotherapy Across Recurrent and Metastatic Head and Neck Squamous Cell Carcinoma

Frontiers in Genetics ◽

10.3389/fgene.2021.756506 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ying-Peng Peng ◽

Rong Wang ◽

Qiao-Dan Liu ◽

Xi-Wei Xu ◽

Wei Wei ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

T Cells ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Gene Mutations ◽

Neck Squamous Cell Carcinoma ◽

Related Gene ◽

Mutational Burden ◽

Tumor Mutational Burden

Purpose: To investigate the prognostic significance of tumor mutational burden (TMB) combined with specific prognosis-related gene mutations in immunotherapy for recurrent and metastatic head and neck squamous cell carcinoma (r/m HNSCC).Methods: One hundred thirty-two r/m HNSCC patients from the Morris and Allen cohorts had undergone immunotherapy. We constructed the immunotherapy-related gene prognostic index TP-PR combining TMB and PIK3CA, TP53, or ROS1 mutation. And we analyzed the differences in overall survival (OS) and immune cell infiltration between samples in different groups. The association of each signature’s single-sample gene set enrichment analysis scores with TP-PR was tested using Spearman’s correlation test.Results: The median OS of the patients with high TMB (TMB ≥10 mut/Mb) who received immunotherapy for r/m HNSCC was 2.5 times as long as that of the patients with low TMB (25 vs. 10 months). More importantly, the high TP-PR (TP-PR >0) group had better median OS (25 vs. 8 months) than the low TP-PR (TP-PR ≤0) group. CD8+ T cells and activated memory CD4+ T cells in the tissues of the patients with high TP-PR were higher than those in the patients with low TP-PR. Results showed that TP-PR stratification had a higher area under the curve (AUC) value (0.77, 95% CI 0.86–0.68) compared with TMB stratification (0.56, 95% CI 0.68–0.44). The differential gene expression in the high and low TP-PR groups mainly influenced metabolism-related signaling pathways.Conclusion: TP-PR was an effective predictor of immunotherapy outcome for r/m HNSCC, which might be better than TMB alone. Patients with high TP-PR had a better survival benefit than had the patients with low TP-PR.

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The Prognostic Value and Immune Landscapes of a m6A/m5C/m1A-Related LncRNAs Signature in Head and Neck Squamous Cell Carcinoma

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.718974 ◽

2021 ◽

Vol 9 ◽

Author(s):

Enhao Wang ◽

Yang Li ◽

Ruijie Ming ◽

Jiahui Wei ◽

Peiyu Du ◽

...

Keyword(s):

Overall Survival ◽

Squamous Cell Carcinoma ◽

High Risk ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Risk Group ◽

Prognostic Signature ◽

Mutational Burden ◽

Tumor Mutational Burden

Background: N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A) are the main RNA methylation modifications involved in the progression of cancer. However, it is still unclear whether m6A/m5C/m1A-related long non-coding RNAs (lncRNAs) affect the prognosis of head and neck squamous cell carcinoma (HNSCC).Methods: We summarized 52 m6A/m5C/m1A-related genes, downloaded 44 normal samples and 501 HNSCC tumor samples with RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) database, and then searched for m6A/m5C/m1A-related genes co-expressed lncRNAs. We adopt the least absolute shrinkage and selection operator (LASSO) Cox regression to obtain m6A/m5C/m1A-related lncRNAs to construct a prognostic signature of HNSCC.Results: This prognostic signature is based on six m6A/m5C/m1A-related lncRNAs (AL035587.1, AC009121.3, AF131215.5, FMR1-IT1, AC106820.5, PTOV1-AS2). It was found that the high-risk subgroup has worse overall survival (OS) than the low-risk subgroup. Moreover, the results showed that most immune checkpoint genes were significantly different between the two risk groups (p < 0.05). Immunity microenvironment analysis showed that the contents of NK cell resting, macrophages M2, and neutrophils in samples of low-risk group were significantly lower than those of high-risk group (p < 0.05), while the contents of B cells navie, plasma cells, and T cells regulatory (Tregs) were on the contrary (p < 0.05). In addition, patients with high tumor mutational burden (TMB) had the worse overall survival than those with low tumor mutational burden.Conclusion: Our study elucidated how m6A/m5C/m1A-related lncRNAs are related to the prognosis, immune microenvironment, and TMB of HNSCC. In the future, these m6A/m5C/m1A-related lncRNAs may become a new choice for immunotherapy of HNSCC.

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Tumor mutational burden identifies chemorefractory gastric cancer with overall survival advantage after receiving toripalimab, a PD-1 antibody.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.4021 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 4021-4021 ◽

Cited By ~ 2

Author(s):

Rui-Hua Xu ◽

Feng Wang ◽

Xiao-Li Wei ◽

Fenghua Wang ◽

Nong Xu ◽

...

Keyword(s):

Gastric Cancer ◽

Squamous Cell Carcinoma ◽

Partial Response ◽

Cell Carcinoma ◽

Squamous Cell ◽

Single Agent ◽

Objective Response ◽

Mutational Burden ◽

Single Agent Therapy ◽

Tumor Mutational Burden

4021 Background: Tumor mutational burden (TMB) is correlated with enhanced objective response rate (ORR) and progression-free survival for certain cancers receiving immunotherapy. This study aimed to investigate the safety and activity of toripalimab, a humanized PD-1 antibody, in advanced gastric cancer (AGC), and the efficacy predictive value of biomarkers including TMB and PD-L1. Methods: This study was a part of phase Ib/II trial evaluating the safety and activity of toripalimab as a single agent therapy or in combination with chemotherapy in chemo-refractory or treatment-naïve AGC, esophageal squamous cell carcinoma, nasopharyngeal carcinoma and head and neck squamous cell carcinoma. This report focused on the chemo-refractory AGC cohort receiving toripalimab (3 mg/Kg d1, Q2W) as a single agent therapy. Primary endpoint was ORR. Biomarkers including tumor PD-L1 expression, TMB, microsatellite instability (MSI) and Epstein-Barr virus (EBV) infection status were evaluated for their correlation with clinical efficacy as preplanned. Tumor PD-L1 expression was assessed with the SP142 immunohistochemistry assay, and the other biomarkers were assessed with whole exome sequencing based on tumor samples. Results: There were 58 subjects included in this cohort. The ORR was 12.1% and the disease control rate was 39.7%. Only 1 subject was MSI-H and achieved partial response. One out of 4 EBV positive subjects achieved partial response. Significant higher ORR was observed in subjects with positive PD-L1 expression (ORR 37.5%, 3/8) or TMB ≥12 Mutations/Mb (ORR 33.3%, 4/8) than those with negative PD-L1 expression (ORR 8.5%) or TMB < 12 Mutations/Mb (ORR 7.0%). The TMB-high subgroup showed significant superior OS than the TMB-low subgroup (HR = 0.48 [96% CI 0.24 to 0.96], p = 0.038), while PD-L1 expression status failed to differentiate OS. Conclusions: Toripalimab demonstrated promising anti-tumor activity in chemo-refractory AGC patients. TMB might serve as a better predictive marker for OS than PD-L1 expression for chemo-refractory AGC patients receiving PD-1 blockade immunotherapy. Clinical trial information: NCT02915432.

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On-treatment blood TMB as predictors for camrelizumab plus chemotherapy in advanced lung squamous cell carcinoma: biomarker analysis of a phase III trial

Molecular Cancer ◽

10.1186/s12943-021-01479-4 ◽

2022 ◽

Vol 21 (1) ◽

Author(s):

Tao Jiang ◽

Jianhua Chen ◽

Xingxiang Xu ◽

Ying Cheng ◽

Gongyan Chen ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Objective Response ◽

Lung Squamous Cell Carcinoma ◽

Phase Iii ◽

Chinese Patients ◽

Predictive Values ◽

Phase Iii Trial ◽

Biomarker Analysis

Abstract Background Camrelizumab plus chemotherapy significantly prolonged progression-free survival (PFS) and overall survival (OS) compared to chemotherapy alone as first-line treatment in advanced lung squamous cell carcinoma (LUSC) in the phase III trial (CameL-sq), which has become an option of standard-of-cares for Chinese patients with advanced LUSC. However, the predictive biomarkers remain unknown. Methods Tumor tissue samples at baseline, and peripheral blood samples at baseline (pretreatment) and after two cycles of treatment (on-treatment) were prospectively collected from 270 LUSC patients from the CameL-sq study. Blood tumor mutation burden (bTMB) and its dynamics were analyzed to explore their predictive values. Results Pretreatment bTMB was not associated with objective response, PFS and OS in camrelizumab or placebo plus chemotherapy groups. Low on-treatment bTMB was associated with significantly better objective response (73.8% vs 27.8%, P < 0.001), PFS (median, 9.1 vs 4.1 months; P < 0.001) and OS (median, not reached vs 8.0 months; P < 0.001) in camrelizumab plus chemotherapy group whereas it did not correlate with objective response and PFS in chemotherapy alone group. Importantly, on-treatment bTMB level could discriminate patients of initially radiological stable disease who would long-term benefit from camrelizumab plus chemotherapy (low vs high, median OS, 18.2 vs 7.8 months; P = 0.001). Combing on-treatment bTMB and its dynamics improved the ability for predicting the efficacy of camrelizumab plus chemotherapy. Conclusion On-treatment bTMB together with its dynamics could serve as a predictive biomarker for camrelizumab plus chemotherapy in patients with advanced LUSC. Trial registration ClinicalTrials.gov identifier: NCT03668496.

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