Low Tumor Mutational Burden Research Articles

Immunohistochemical analysis of the tumor microenvironment in acral lentiginous melanoma (ALM).

e21588 Background: Acral lentiginous melanoma (ALM) is a rare subtype of melanoma occurring on the palms, soles and nail beds. Molecularly, ALM is characterized by a higher frequency of chromosomal structural and copy number variants, but lower tumor mutational burden (TMB). Meanwhile, immune checkpoint inhibitors (ICI) are less efficacious in this subtype. In order to better understand these differences in outcomes to ICI, we conducted an immunohistochemical analysis of ALM to explore putative immune biomarkers. Methods: Clinically annotated samples of ALM were identified from patients treated at the USC Keck School of Medicine between 2010-2018. Immunohistochemistry stains included CD8, PD-L1, CD56, CD68, FOXP3, CTLA-4, HLA-ABC and HLA-G, and were characterized based on the intensity of staining. The percentage of tumor cells and infiltrating immune cells (IC) within the tumor microenvironment for the aforementioned antigens were recorded. Data are reported as percent of total cells ( > 1%, > 5%, > 25%, > 50%) expressing marker in the entire sample. Results: A total of 28 ALM specimens from 21 different patients were analyzed, including 19 primary and 9 metastatic tumors. The median age of all patients was 67 years (range 32-92); the majority were men (66%) and Hispanic (66%). Primary ALM tumors were located more often on the plantar foot (62%), compared to the plantar hand (29%). The median tumor thickness was 2.8 mm (range 0.25 – 6.5 mm). Among all patients, 57% had localized disease, while 19% had regional metastases and 24% had distant metastases. CD8+ TIL cells were observed in 95% (18/19) of samples, with 68.4% (13/19) showing > 50% CD8+ staining on IC. PD-L1 expression > 1% on tumor cells was noted in 37% (10/27) of samples, and 19% (5/27) on IC; PD-L1 > 5% was noted in only 18.5% (5/27) on tumor cells and on 11% (3/27) on IC. Both CD56 and CD68 were noted to have at least 1% expression on IC among nearly all (94%) of samples analyzed (7/8 and 9/9, respectively). FoxP3 expression > 1% was noted on IC in 92.3% (24/26) of samples, and > 5% in 50% (13/26). CTLA-4 expression > 1% was observed among 81.5 % (22/27) of samples, while 63% (17/27) had expression > 5%; CTLA-4 expression > 50% was noted among 100% on melanophages (7/7 samples). HLA-ABC expression was detected in 100% of samples analyzed (10/10). The percentage of samples with HLA-G expression > 1% was 60.7% (17/28), while 28.6% (8/28) demonstrated > 5% expression. Further correlations with clinical outcomes will be reported. Conclusions: Our study suggests a unique immune tumor microenvironment in ALM, characterized by low PD-L1 expression, despite infiltration by CD8+, as well as CD56 and CD68 immune cells. Furthermore, the presence of FOXP3+ Tregs and HLA-G expression, both which mediate immune response evasion, may explain the poor outcomes of ICI therapy among these patients and warrant further investigation.

A risk model constructed using 14 N6-methyladenosine-related lncRNAs as a new prognostic marker that correlates with the immunomodulatory effect and drug sensitivity in colorectal cancer.

Colorectal cancer (CRC) remains the most common gastrointestinal malignancy. Despite multimodal therapy, its mortality is high due to recurrence and metastasis. This study developed and verified a risk model consisting of 14 N6-methyladenosine (m6A) long noncoding RNAs (lncRNAs) to assess the prognosis of patients with CRC and investigated its relevance to immune regulation and drug sensitivity. The gene expression profiles and clinical data of 446 patients with CRC were retrieved from The Cancer Genome Atlas (TCGA). 14 lncRNAs were screened using the Gene Co-expression Network (corFilter =0.5, P<0.001), and univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analysis to construct the optimal risk model. The predictive performance and clinical applicability of the model were next verified. In addition, we performed Gene Ontology (GO) enrichment analysis to identify potential biological functions and detected the difference in tumor mutational burden (TMB), immune function, and sensitivity to immunotherapy and other drugs between the high- and low-risk groups to evaluate the application of the constructed risk model in depth. The model was found to be an appropriate marker for predicting the prognosis of patients with CRC, independent of other clinical features, and demonstrated good precision and broad clinical applicability. It correlated with pathways in the development of cancer and immune-related functions, and patients in the high-risk group had higher tumor immune dysfunction and escape (TIDE) scores. Furthermore, we found significant differences in the overall survival (OS) between patients in the high- and low-tumor mutation burden (TMB) groups, which may work in conjunction with the constructed model to better predict patients' prognosis. Finally, we identified 12 drugs, including A-443654 and sorafenib, with lower half maximal inhibitory concentration (IC50) values in the high-risk group. Conversely, 21 drugs, including gemcitabine and rapamycin, had lower IC50 values in the low-risk group. We constructed a risk model based on 14 m6A-related lncRNAs that could predict the prognosis of patients with CRC and provided additional therapeutic ideas for their treatment. These findings may additionally serve as a foundation for further studies on regulating CRC via m6A-related lncRNAs.

Camrelizumab Plus Apatinib and Temozolomide as First-Line Treatment in Patients With Advanced Acral Melanoma

Acral melanoma, known for low tumor mutation burden, responds poorly to immunotherapy. A standard therapy is still lacking. To investigate the activity and safety of camrelizumab (an anti-programmed cell death-1 antibody) plus apatinib (a vascular endothelial growth factor receptor 2 inhibitor) and temozolomide as first-line treatment in patients with advanced acral melanoma. In this single-arm, single-center, phase 2 nonrandomized clinical trial, patients with treatment-naive unresectable stage III or IV acral melanoma were enrolled at Peking University Cancer Hospital and Institute between June 4, 2020, and August 24, 2021. The data cutoff date was April 10, 2022. Patients received 4-week cycles of intravenous camrelizumab, 200 mg, every 2 weeks; oral apatinib 250 mg, once daily; and intravenous temozolomide, 200 mg/m2, once daily on days 1 to 5 until disease progression or unacceptable toxic effects. The primary end point was objective response rate as assessed by investigators according to the Response Evaluation Criteria In Solid Tumors (version 1.1). Secondary end points included progression-free survival, time to response, duration of response, disease control rate, overall survival, and safety. A total of 50 patients (32 men [64%]; median age, 57 years [IQR, 52-62 years]) were enrolled and received treatment. The median follow-up duration was 13.4 months (IQR, 9.6-16.2 months). The objective response rate was 64.0% (32 of 50; 95% CI, 49.2%-77.1%). The median time to response and duration of response were 2.7 months (IQR, 0.9-2.9 months) and 17.5 months (95% CI, 12.0 to not reached), respectively. The disease control rate was 88.0% (44 of 50; 95% CI, 75.7%-95.5%). The estimated median progression-free survival was 18.4 months (95% CI, 10.6 to not reached). The median overall survival was not reached. The most common grade 3 or 4 treatment-related adverse events were increased gamma-glutamyltransferase levels (15 [30%]), decreased neutrophil count (11 [22%]), increased conjugated bilirubin levels (10 [20%]), and increased aspartate aminotransferase levels (10 [20%]). No treatment-related deaths occurred. The findings of this nonrandomized clinical trial suggest that camrelizumab plus apatinib and temozolomide may be a potential first-line treatment option for patients with advanced acral melanoma, which warrants further validation in a randomized clinical trial. ClinicalTrials.gov Identifier: NCT04397770.

The clinical and genomic characteristics of KRAS G12D mutated cancers.

e15151 Background: KRAS mutations are relatively common in solid tumors. It is once considered to be “non-druggable” due to its high affinity to GTP/GDP and lack of other binding sites. Recently, irreversible inhibitors targeting specific KRAS mutations have been developed. We aimed to investigate the correlation of clinical and genomic factors with KRAS G12D mutation in pancreatic cancer (PC), colorectal cancer (CRC) and non-small-cell lung cancer (NSCLC). Methods: We retrospectively reviewed the clinical and genomic data of patients with PC (n = 300), CRC (n = 300), and NSCLC (n = 1800) who provided tumor tissues and matched peripheral blood samples (served as control to eliminate germline variants) for targeted sequencing of 450 cancer-related genes. Experiments were carried out in OrigiMed’s laboratory following the CAP/CLIA standards. Tumor mutation burden (TMB)-high was defined as TMB &gt; 10 muts/Mb. Results: The prevalence of KRAS G12D mutation in PC, CRC and NSCLC was 38.3% (115/300), 15.0% (45/300) and 2.0% (36/1800), respectively. In PC and CRC, G12D was the major type of KRAS mutations, accounting for 44.9% (115/256) and 30.8% (45/146) of all the KRAS mutations, respectively. In contrast, G12C was the most common KRAS mutation in NSCLC (35.9% [79/220]), followed by G12D (16.4% [36/220]). Patients were divided into three groups according to the KRAS mutation status: the G12D (mutated in KRAS G12D), non-G12D (mutated in KRAS, but not G12D), and wild-type (WT; no KRAS mutation) groups. Clinical features including age, sex and disease stage were not associated with the KRAS grouping in PC and CRC. However, the KRAS grouping was significantly correlated with sex in NSCLC (Female vs Male: 1.9% vs 2.1% in G12D, 4.4% vs 13.9% in non-G12D, 93.7% vs 84.1% in WT, P &lt; 0.001). In PC, KRAS G12D and BRAF mutations were mutually exclusive (P &lt; 0.01), while in CRC, KRAS G12D mutation was found to be co-occurring with PIK3CA mutation (P &lt; 0.05). For NSCLC, KRAS G12D mutation was mutually exclusive with EGFR mutation (P &lt; 0.01) and co-occurred with STK11 mutation (P &lt; 0.05). TMB was comparable between the KRAS grouping in PC and CRC. In contrast, TMB was significantly higher in the non-G12D group (median 11.7 [range 0.7-89.8] muts/Mb) compared to the G12D (median 6.9 [range 0-30.9] muts/Mb; P &lt; 0.001) and WT (median 4.6 [range 0-215.2] muts/Mb; P &lt; 0.001) groups in NSCLC. A higher proportion of TMB-high was also observed in the non-G12D group (58.5%) compared to the G12D (22.2%) and WT (22.6%) groups in NSCLC. Conclusions: Patients with KRAS G12D mutation possessed unique clinical and genomic characteristics. It was more prevalent in PC and CRC and was correlated with sex in NSCLC. KRAS G12D mutation co-occurred with STK11 mutation and showed a relatively low TMB value in NSCLC, suggesting that immunotherapy might be ineffective. While KRAS non-G12D mutated NSCLC patients may be favorable to ICI. Our results provide insights into the precision medicine of KRAS G12D-mutated cancers.

Pathway enrichment analysis in tumors with high mutation burdens and interferon-γ signature expression: A pancancer analysis.

3138 Background: Tumor mutation burden (TMB) correlates with immunotherapy response, but outcomes still vary in high TMB cancers, and many high TMB tumors lack T cell infiltration. Here, we assessed gene expression signatures of high TMB, including both inflamed and non-inflamed tumors (defined by interferon-γ [IFN-γ] gene signatures). Methods: Gene set enrichment analysis (GSEA) was assessed from RNA-sequencing data in tumors in TCGA. TMB and IFN-γ signature score were assessed by previously published methods. We performed GSEA on high vs low TMB tumors, and further stratified by high vs low IFN-γ signature expression within high TMB tumors. We validated results in Tempus RNA-sequencing data from 264 patients at Vanderbilt. Results: 4020 TCGA cases in non-small cell lung, melanoma, bladder, head and neck, kidney, and colorectal cancer were included. Major signatures upregulated in the high TMB group included cell cycle signaling, nuclear protein/mRNA export, cholesterol biosynthetics, and ubiquitin signaling. High TMB/high IFN-γ signature tumors were enriched in immune-related pathways (neutrophil and monocyte chemotaxis, T cell activation and proliferation, and interleukin-1 secretion), and non-immune pathways including cAMP metabolic process and phosphatidylinositol signaling. High TMB/low IFN-γ signature tumors had enriched pathways in nonsense mediated decay, electron transport chain/oxidative phosphorylation, and mitochondrial translational disassembly. 264 tumors from Vanderbilt were used for validation; pathways including cholesterol biosynthetics also correlated with immunotherapy response. Conclusions: High TMB tumors were enriched in pathways such as ubiquitin signaling, which could regulate immune cell function in antitumor immunity. Within high TMB cancers, tumors with higher IFN-γ signatures have enriched immune-related, and metabolic pathways, which could suggest novel therapeutic targets to make high TMB/ low IFN-γ tumors more immunogenic.

Whole genome sequencing for more accurate TMB and mutational signatures in common cancers.

e15173 Background: Due to the dramatic decrease in cost of genome sequencing, we are entering the era of whole genome sequencing (WGS) at $100. Tumor mutational burden (TMB) and mutational signatures have been introduced as potential prognostic/predictive cancer biomarkers and mostly assessed by targeted cancer gene sequencing panels. However, they are truly whole genome-wide events and thus more accurately estimated by whole genome sequencing data. Methods: We analyzed WGS data produced by Genome Insight Inc. that encompass &gt; 1,300 breast, lung, and hepatocellular carcinoma samples, collectively. Our genome-wide TMBs (wgsTMB) were systematically compared with the TMB estimates by targeted sequencing methods, such as conventional whole-exome sequencing (WES) and targeted panel sequencing from FoundationOne CDx (F1CDx). In parallel, we leveraged genome-wide somatic mutations for validating mutational signatures projected from the targeted sequencing methods. Results: Pembrolizumab is FDA approved for solid tumors with high TMB (≥ 10 mutations/Mb) assessed by F1CDx. This criterion classified that 546 of the tumors (41%) in our cohort as high F1CDx TMB (f1TMB), who may benefit from immunotherapy. However, the high f1TMB classification was inconsistent to the genome-wide TMB classification ( p &lt; 2.2e-16). For example, 132 high f1TMB tumors (24.1%; 132/546) showed lower than the median wgsTMB estimate. On the flip side, 32% of the low f1TMB tumors (251/784) demonstrate higher than median wgsTMB estimate (see table). Although there is no approved criterion in WGS that defines hypermutators, our data illustrates that WGS will be helpful for redefining the criteria for selecting patients for immune checkpoint inhibitors. The wgsTMB was also an essential factor for accurate estimation of mutational signatures from targeted sequencing. For example, in high TMB tumors, mutational signature estimated from WES showed on average 0.87 cosine similarity with signatures from WGS. However, the correlation was substantially reduced in low TMB tumors, showing only ~0.64 on average. Particularly, ~12% of breast tumors with considerable levels of homologous recombination deficiency (HRD) signatures by WGS were not captured by whole-exome sequencing based approaches. Further exploration should be performed with WGS to select proper patients for targeted therapies, including PARP inhibitors. Conclusions: Despite the current guidelines depending on targeted sequencing in precision oncology, we showed that whole-genome sequencing can deliver more accurate cancer genome profiles, such as, but not limited to, TMB and mutational signatures. Given its more comprehensive capabilities and affordable cost, we believe that WGS-based precision oncology is medically necessary. [Table: see text]

Abstract CT224: mRNA-4157, a personalized cancer vaccine, in combination with pembrolizumab, demonstrates trend for improved recurrence free survival compared to pembrolizumab alone in adjuvant melanoma patients across tumor mutational burden subgroups

Abstract Background: The open-label randomized Phase 2 mRNA-4157-P201/Keynote-942 trial met its primary endpoint of prolonged recurrence free survival (RFS) in patients with resected high-risk stage III/IV melanoma. Tumor immunogenicity provides a favorable landscape for inflammatory processes associated with clinical benefit to checkpoint inhibitors (ICI) and tumor mutational burden (TMB) has been shown to be an independent predictor of treatment outcomes in patients treated with ICI therapy. mRNA-4157 is a novel mRNA-based personalized cancer vaccine which encodes up to 34 patient-specific tumor neoantigens. Here we report analyses of baseline biopsies from the trial to explore the novel mechanism of action hypothesized to augment endogenous anti-tumor responses and generate immunity to additional tumor neoantigens. Methods: Paraffin-embedded formalin-fixed baseline tumor core biopsies underwent whole exome sequencing (WES) and whole transcriptome sequencing. According to the established WES genomic score for pembrolizumab, the TMB high threshold utilized for analysis was 175/exome (10 mutations/megabase per F1CDx). The distribution of TMB expression in baseline tumor samples across study arms and their association with the primary RFS endpoint was evaluated. The association with RFS of other markers of inflamed tumors, including those established for pembrolizumab (e.g. gene expression profile (GEP) and PD-L1 expression) was also assessed. Results: The RFS benefit of mRNA-4157 and pembrolizumab combination compared to pembrolizumab monotherapy observed in the intention-to-treat population was maintained with a similar treatment effect magnitude across both high (HR = 0.65; 95% CI: 0.3, 1.5) and low (HR = 0.59; 95% CI: 0.3,1.4) TMB subpopulations. In line with observations from historical data for pembrolizumab, improved RFS was observed in high TMB compared to low TMB patient subgroups in the pembrolizumab monotherapy arm. The trend for increased RFS benefit in the high TMB subpopulation was maintained in the mRNA-4157 and pembrolizumab study arm. Additional subgroup analyses (e.g. GEP and PD-L1) were assessed and will be discussed. Conclusions: Our results indicate that mRNA-4157 demonstrates improvements in RFS irrespective of TMB status when administered in combination with pembrolizumab compared to pembrolizumab monotherapy in patients with resected high-risk cutaneous melanoma. The novel mechanism of action of mRNA-4157 may both deepen the activity of pembrolizumab and broaden the population of patients that can benefit from immune therapy. The association between TMB and mRNA-4157 treatment effect will be further explored in upcoming planned studies. Citation Format: Ryan J. Sullivan, Matteo Carlino, Jeffrey S. Weber, Tarek Meniawy, Matthew H. Taylor, Kevin Kim, Meredith McKean, Georgiana V. Long, Mark Faries, C. Lance Cowey, Andrew Pecora, Geoffrey T. Gibney, Jason Luke, Sajeve Thomas, Vasudha Sehgal, Igor Feldman, Praveen Aanur, Michelle Brown, Robert S. Meehan, Celine Robert-Tissot, Adnan Khattak. mRNA-4157, a personalized cancer vaccine, in combination with pembrolizumab, demonstrates trend for improved recurrence free survival compared to pembrolizumab alone in adjuvant melanoma patients across tumor mutational burden subgroups [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT224.

Development of a novel copper metabolism-related risk model to predict prognosis and tumor microenvironment of patients with stomach adenocarcinoma.

Background: Stomach adenocarcinoma (STAD) is the fourth highest cause of cancer mortality worldwide. Alterations in copper metabolism are closely linked to cancer genesis and progression. We aim to identify the prognostic value of copper metabolism-related genes (CMRGs) in STAD and the characteristic of the tumor immune microenvironment (TIME) of the CMRG risk model. Methods: CMRGs were investigated in the STAD cohort from The Cancer Genome Atlas (TCGA) database. Then, the hub CMRGs were screened out with LASSO Cox regression, followed by the establishment of a risk model and validated by GSE84437 from the Expression Omnibus (GEO) database. The hub CMRGs were then utilized to create a nomogram. TMB (tumor mutation burden) and immune cell infiltration were investigated. To validate CMRGs in immunotherapy response prediction, immunophenoscore (IPS) and IMvigor210 cohort were employed. Finally, data from single-cell RNA sequencing (scRNA-seq) was utilized to depict the properties of the hub CMRGs. Results: There were 75 differentially expressed CMRGs identified, 6 of which were linked with OS. 5 hub CMRGs were selected by LASSO regression, followed by construction of the CMRG risk model. High-risk patients had a shorter life expectancy than those low-risk. The risk score independently predicted STAD survival through univariate and multivariate Cox regression analyses, with ROC calculation generating the highest results. This risk model was linked to immunocyte infiltration and showed a good prediction performance for STAD patients' survival. Furthermore, the high-risk group had lower TMB and somatic mutation counters and higher TIDE scores, but the low-risk group had greater IPS-PD-1 and IPS-CTLA4 immunotherapy prediction, indicating a higher immune checkpoint inhibitors (ICIs) response, which was corroborated by the IMvigor210 cohort. Furthermore, those with low and high risk showed differential susceptibility to anticancer drugs. Based on CMRGs, two subclusters were identified. Cluster 2 patients had superior clinical results. Finally, the copper metabolism-related TIME of STAD was concentrated in endothelium, fibroblasts, and macrophages. Conclusion: CMRG is a promising biomarker of prognosis for patients with STAD and can be used as a guide for immunotherapy.

Correlation between immunotherapy biomarker PD-L1 expression and genetic alteration in patients with non-small cell lung cancer

Programmed death-ligand 1 (PD-L1) has been widely used in immunotherapy evaluation of patients with non-small cell lung cancer (NSCLC). However, the effect is not particularly ideal, and the association between PD-L1 and genetic alterations requires more exploration. Here, we performed targeted next-generation sequencing and PD-L1 immunohistochemistry (IHC) testing for PD-L1 expression on both tumor cells (TCs) and tumor-infiltrating immune cells (ICs) in 1549 patients. Our studies showed that surgical method of resection was positively correlated with IC+, and a low tumor mutation burden (TMB) was negatively correlated with TC+. Furthermore, we found that EGFR was mutually exclusive with both ALK and STK11. In addition, the features between PD-L1 expression status and genomic alterations were characterized. These results suggest that clinical characteristics and molecular phenotypes are associated with PD-L1 expression signatures, which may provide novel insights for improving the efficiency of immune checkpoint inhibitors (ICIs) in immunotherapy.

Molecular subtypes and tumor microenvironment infiltration signatures based on cuproptosis-related genes in colon cancer.

Colon cancer is one of the common cancers, and its prognosis remains to be improved. The role of cuproptosis as a newly discovered form of cell death in the development of colon cancer has not been determined. Based on 983 colon cancer samples in the TCGA database and the GEO database, we performed a comprehensive genomic analysis to explore the molecular subtypes mediated by cuproptosis-related genes. Single-sample gene set enrichment analysis (ssGSEA) was utilized to quantify the relative abundance of each cell infiltrate in the TME. A risk score was established using least absolute shrinkage and selection operator regression (LASSO), and its predictive ability for colon cancer patients was verified to explore its guiding value for treatment. We identified two distinct cuproptosis-related molecular subtypes in colon cancer. These two distinct molecular subtypes can predict clinicopathological features, prognosis, TME activity, and immune-infiltrating cells. A risk model was developed and its predictive ability was verified. Compared with patients in the high-risk score group, patients in the low-risk score group were characterized by lower tumor microenvironment score, higher stem cell activity, lower tumor mutational burden, lower microsatellite instability, higher sensitivity to chemotherapeutics, and better immunotherapy efficacy. This study contributes to understanding the molecular characteristics of cuproptosis-related subtypes. We demonstrate a critical role for cuproptosis genes in colon cancer s in the TME. Our study contributes to the development of individualized treatment regimens for colon cancer.

Whole exome sequencing of low grade serous ovarian carcinoma identifies genomic events associated with clinical outcome

ObjectivesLow-grade serous ovarian carcinoma (LGSOC) is a distinct, rare, ovarian cancer type characterised by younger patient age and intrinsic chemoresistance. Understanding the molecular landscape is crucial for optimising targeted therapy. MethodsGenomic data from whole exome sequencing of tumour tissue was analysed in a LGSOC cohort with detailed clinical annotation. Results63 cases were analysed and three subgroups identified based on single nucleotide variants: canonical MAPK mutant (cMAPKm: 52%, KRAS/BRAF/NRAS), MAPK-associated gene mutation (MAPK-assoc: 27%) and MAPK wild-type (MAPKwt: 21%). NOTCH pathway disruption occurred across all subgroups. Tumour mutational burden (TMB), mutational signatures and recurrent copy number (CN) changes varied across the cohort with co-occurrence of chromosome 1p loss and 1q gain (CN Chr1pq) a recurrent feature. Low TMB and CN Chr1pq were associated with inferior disease-specific survival (HR 6.43; p < 0.001 and HR 3.29, p = 0.011 respectively). Stepwise genomic classification in relation to outcome resulted in four groups (TMB low; CN Chr1pq; MAPKwt/MAPKassoc; cMAPKm). 5 year disease-specific survival was 46%, 55%, 79% and 100% respectively for these groups. The two most favourable genomic subgroups were enriched for the SBS10b mutational signature, particularly the cMAPKm subgroup. ConclusionsLGSOC comprises multiple genomic subgroups with distinct clinical and molecular features. Chr1pq CN arm disruption and TMB represent promising methods to identify individuals with poorer prognosis. Further investigation of the molecular basis for these observations is required. MAPKwt cases represent around a fifth of patients. NOTCH inhibitors represent a candidate therapeutic strategy worthy of exploration across these cases.

Urothelial Bladder Cancer: Genomic Alterations in Fibroblast Growth Factor Receptor.

Genomic alterations in fibroblast growth factor receptor (FGFR) genes have been linked to a reduced response to immune checkpoint inhibitors. Some of the immune microenvironment of urothelial bladder cancer (UBC) could be distorted because of the inhibition of interferon signaling pathways. We present a landscape of FGFR genomic alterations in distorted UBC to evaluate the immunogenomic mechanisms of resistance and response. There were 4035 UBCs that underwent hybrid, capture-based comprehensive genomic profiling. Tumor mutational burden was determined in up to 1.1 Mbp of sequenced DNA and microsatellite instability was determined in 114 loci. Programmed death ligand expression in tumor cells was assessed by immunohistochemistry (Dako 22C3). The FGFR tyrosine kinases were altered in 894 (22%) UBCs. The highest frequency of alterations was inFGFRgenomic alterations withFGFR3at 17.4% followed byFGFR1at 3.7% andFGFR2at 1.1%. No FGFR4 genomic alterations were identified. The age and sex distribution were similar in all groups. Urothelial bladder cancers that featuredFGFR3genomic alterations were associated with lower driver genomic alterations/tumors. 14.7% of theFGFR3genomic alterations were FGFR3 fusions. Other findings included a significantly higher frequency ofERBB2amplification inFGFR1/2-altered UBCs compared withFGFR3-altered UBCs. Urothelial bladder cancers withFGFR3genomic alterations also had the highest frequency of the activating mTOR pathway.FGFR3-altered UBCs also featured significantly higher frequencies of biomarkers associated with a lack of response to immune checkpoint inhibitors including a lower tumor mutational burden, lower programmed death-ligand 1 expression, and higher frequencies of genomic alterations inMDM2. Also linked to IO drug resistance, CDKN2A/Bloss andMTAPloss were observed at a higher frequency in FGFR3-driven UBC. An increased frequency of genomic alterations is observed in UBC FGFR. These have been linked to immune checkpoint inhibitor resistance. Clinical trials are needed to evaluate UBC FGFR-based biomarkers prognostic of an immune checkpoint inhibitor response. Only then can we successfully incorporate novel therapeutic strategies into the evolving landscape of UBC treatment.

Integrin-based prognostic model predicts survival, immunotherapy response, and drug sensitivity in gastric cancer

BackgroundExtracellular matrix (ECM) acts as a physical barrier to tumors, resulting in the lysis or delay of drug delivery. Integrins (ITGs) are essential for tumor cell-ECM interactions. Thus, we established a novel prognostic model to predict overall survival, immunotherapy benefits, and therapeutic agents in gastric cancer (GC) based on ITGs-related ECM landscape. MethodsUsing the TCGA-STAD dataset, we studied the genetic and transcriptional changes of ITGs. We used a merged cohort for ITGs survival analysis and determined molecular pattern clusters using consensus unsupervised clustering methodology. We confirmed the distinct ECM landscape between constructed clusters by performing gene set variation and Kaplan-Meier analysis. We utilized prognostic differentially expressed genes between clusters to develop a prognostic model utilizing logistic least absolute shrinkage and selection operator cox regression analysis, followed by stepwise multivariate Cox analysis in the training dataset. The model was validated by receiver operating characteristic curves and Kaplan-Meier analysis in the testing dataset and seven validation datasets. We compared our model to 35 previously published models. To analyze immune infiltration, we used multiple algorithms, which were further confirmed by single-cell RNA-sequencing and fluorescent multiplex immunohistochemistry. We explored tumor mutation burden (TMB), microsatellite instability-high (MSI-H) grade, immunotherapy response, chemotherapy sensitivity, and clinical significance between the low-risk and high-risk groups. Finally, we assessed the risk score in five reported molecular subtypes. ResultsThe two ITGs-related clusters were identified, and their ECM landscapes were distinct. The prognostic model was constructed and had shown stable performance in internal and external validation. In addition, our model outperformed 35 previously published models. High-risk patients had a bad prognostic ECM landscape, high stromal cell inflammation, a lower TMB, a lower MSI-H grade, a worse tumor stage, a worse response to immunotherapy, and less sensitivity to chemotherapy. In five reported molecular subtypes, the worse subtypes showed a higher risk score. ConclusionsThe prognostic model could be an effective and promising tool for predicting prognosis and therapy response in GC patients.

Assessment of Tumor Mutational Burden and Outcomes in Patients With Diverse Advanced Cancers Treated With Immunotherapy

There are few studies assessing the association of tumor mutational burden (TMB) and clinical outcomes in a large cohort of patients with diverse advanced cancers. To clinically validate a TMB biomarker from a next-generation sequencing targeted gene panel assay. A prespecified cohort study using the deidentified clinicogenomic Tempus database of patients sequenced between 2018 and 2022, which contained retrospective, observational data originating from 300 cancer sites including 199 community sites and 101 academic sites. Patients with advanced solid tumors across 8 cancer types and more than 20 histologies, sequenced with Tempus xT who were treated with immune checkpoint inhibitors (ICIs) in the first-line or second-line setting were included. Data were analyzed from September 2018 to August 2022. Treatment with US Food and Drug Administration (FDA)-approved antiprogrammed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) ICI and/or in combination with a cytotoxic T-lymphocyte-associated protein-4 ICI. The primary outcome was the association of tumor mutational burden (TMB) binary category (high [≥10 mut/mb] vs low) with overall survival (OS) in patients treated with ICIs. Secondary outcomes were progression-free survival (PFS), and time to progression (TTP). In the evaluable cohort of 674 patients, the median (IQR) age was 69.4 (28.6-89.8) years, 271 patients (40.2%) were female, and 435 patients (64.5%) were White. The most common advanced cancers were non-small cell lung cancer (330 patients [49.0%]), followed by bladder cancer (148 patients [22.0%]), and head and neck squamous cell carcinoma (96 patients [14.8%]). Median (IQR) follow-up was 7.2 (3.2-14.1) months. High TMB (TMB-H) cancers (206 patients [30.6%]) were significantly associated with longer OS than low TMB (TMB-L) cancers (hazard ratio [HR], 0.72; upper confidence bound [UCB], 0.91; P = .01). In a prospective subset of 403 patients treated with ICIs after TMB testing, TMB-H cancers (135 patients [33.5%]) were significantly associated with longer OS (HR, 0.61; UCB, 0.84; P = .005), PFS (HR, 0.62; UCB, 0.82; P = .003), and TTP (HR, 0.67; UCB, 0.92; P = .02) than TMB-L cancers. An overall survival benefit was seen regardless of the type of ICI used (pembrolizumab, 339 patients; HR, 0.67; UCB, 0.94; P = .03), other ICIs (64 patients; HR, 0.37; UCB, 0.85; P = .03), and after adjusting for PD-L1 and microsatellite stability status (403 patients; HR = 0.67; UCB, 0.92; P = .02). In this cohort study of patients with advanced solid tumors treated with ICIs in diverse clinics, TMB-H cancers were significantly associated with improved clinical outcomes compared with TMB-L cancers.

A phase II open-label trial of avelumab plus axitinib in previously treated non-small-cell lung cancer or treatment-naïve, cisplatin-ineligible urothelial cancer

We hypothesized that avelumab plus axitinib could improve clinical outcomes in patients with advanced non-small-cell lung cancer (NSCLC) or urothelial carcinoma (UC). We enrolled previously treated patients with advanced or metastatic NSCLC, or untreated, cisplatin-ineligible patients with advanced or metastatic UC. Patients received avelumab 800 mg every 2 weeks (Q2W) and axitinib 5 mg orally two times daily. The primary endpoint was objective response rate (ORR). Immunohistochemistry was used to assess programmed death-ligand 1 (PD-L1) expression (SP263 assay) and the presence of CD8+ T cells (clone C8/144B). Tumor mutational burden (TMB) was assessed by whole-exome sequencing. A total of 61 patients were enrolled and treated (NSCLC, n= 41; UC, n= 20); 5 remained on treatment at data cut-off (26 February 2021). The confirmed ORR was 31.7% in the NSCLC cohort and 10.0% in the UC cohort (all partial responses). Antitumor activity was observed irrespective of PD-L1 expression. In exploratory subgroups, ORRs were higher in patients with higher (≥median) CD8+ T cells in the tumor. ORRs were higher in patients with lower TMB (<median) in the NSCLC cohort and higher TMB (≥median) in the UC cohort. Treatment-related adverse events (TRAEs) occurred in 93.4% of patients, including grade ≥3 TRAEs in 55.7%. Avelumab exposures with 800 mg Q2W dosing were similar to those observed with 10 mg/kg Q2W dosing. In previously treated patients with advanced/metastatic NSCLC, ORR appeared to be superior to anti-PD-L1 or anti-programmed cell death protein 1 monotherapy, irrespective of PD-L1 status, whereas in untreated, cisplatin-ineligible patients with advanced/metastatic UC, ORR was lower than expected, potentially limited by small patient numbers. Clinicaltrial.gov NCT03472560; https://clinicaltrials.gov/ct2/show/NCT03472560.

Development and Validation of an Immunotherapy-Related Prognostic Signature Based on Lymph Node Ratio for Gastric Cancer

Background. The long-term prognosis of gastric cancer (GC) remains poor due to postoperative recurrence and metastasis. The increasing evidence show that the lymph node ratio (LNR) serves as an independent prognostic factor in patients with GC. In this study, we aimed to develop a prognostic signature for GC based on LNR. Methods. Survival analysis was conducted by comparing low- and high-LNR groups according to the optimal cutoff value of LNR, which was identified by receiver operating characteristic (ROC) curve analysis. Then, we identified the differentially expressed genes (DEGs) related to LNR in the training cohort of GC. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression were performed to construct the risk score signature. We then evaluated the risk score signature from the viewpoints of survival, clinic-pathological characteristics, tumor microenvironment (TME), tumor mutation burden (TMB), and immunotherapeutic and chemotherapeutic efficacy. Results. High LNR was significantly correlated with poorer prognosis and was an independent predictor of recurrence in patients with GC. Then, an eleven-gene signature that could predict the prognosis of GC patients was developed based on LNR-related DEGs in the training cohort, and the results were further confirmed in external independent cohort. In addition, the high-risk group showed aggressive clinicopathological characteristics, specific TME status, low TMB, and low immunotherapeutic sensitivity. Conclusions. The present study constructed an eleven-gene prognostic signature based on LNR to predict the prognosis of patients with GC and facilitate the development of individualized treatment strategy.

Tumor Microenvironment CD8 T and Treg Cells-related Genes Signature Distinguishes Distinct Prognosis and Targeted Therapies Response in Endometrial Cancer.

Although most endometrial cancer (EC) patients have a favorable prognosis, the overall survival (OS) of metastatic and recurrent EC could hardly be improved by the current chemoradiotherapy. We aimed to reveal the tumor microenvironment immune infiltration characteristics to elucidate the underlying mechanism of EC progression and guide clinical decisions. In the Cancer Genome Atlas (TCGA) cohort, Kaplan-Meier survival curves confirmed Tregs and CD8 T cells were prognosis-protective factors in OS of EC ( P <0.05). Weighted gene coexpression network analysis identified 2 gene modules closely correlated with Tregs and CD8 T-cell infiltration. We randomly split the TCGA EC cohort into the training and testing cohorts at a ratio of 7:3. An immune-related prognosis risk index (IRPRI), including NR3C1, E2F1, OTOG, TTK, PPP1R16B, and FOXP3, was established by univariate, Least Absolute Shrinkage and Selection Operator, and multivariate Cox regression with area under the curve >0.67. Distinct clinical, immune, and mutation characteristics existed between IRPRI groups by multiomics analysis. Cell proliferation and DNA damage repair-related pathways were activated, and immune-related pathways were inactivated in the IRPRI-high group. Furthermore, patients in the IRPRI-high group had lower tumor mutation burden, programmed death-ligand 1 expression, and Tumor Immune Dysfunction and Exclusion scores, indicating a poor response to immune checkpoint inhibitors therapy ( P <0.05), which was also validated in the TCGA testing cohort and independent cohorts, GSE78200, GSE115821, and GSE168204. Also, the higher mutation frequencies of BRCA1, BRCA2, and genes enrolled in homologous recombination repair in the IRPRI-low group predicted a good response to PARP inhibitors. Finally, a nomogram integrating the IRPRI group and prognosis significant clinicopathological factors for EC OS prediction was developed and validated with good discrimination and calibration.

Development of a necroptosis-related gene signature and the immune landscape in ovarian cancer

BackgroundNecroptosis is a novel type of programmed cell death distinct from apoptosis. However, the role of necroptosis in ovarian cancer (OC) remains unclear. The present study investigated the prognostic value of necroptosis-related genes (NRGs) and the immune landscape in OC.MethodsThe gene expression profiling and clinical information were downloaded from the TCGA and GTEx databases. Differentially expressed NRGs (DE-NRGs) between OC and normal tissueswere identified. The regression analyses were conducted to screen the prognostic NRGs and construct the predictive risk model. Patients were then divided into high- and low-risk groups, and the GO and KEGG analyses were performed to explore bioinformatics functions between the two groups. Subsequently, the risk level and immune status correlations were assessed through the ESTIMATE and CIBERSORT algorithms. The tumor mutation burden (TMB) and the drug sensitivity were also analyzed based on the two-NRG signature in OC.ResultsTotally 42 DE-NRGs were identified in OC. The regression analyses screened out two NRGs (MAPK10 and STAT4) with prognostic values for overall survival. The ROC curve showed a better predictive ability in five-year OS using the risk score. Immune-related functions were significantly enriched in the high- and low-risk group. Macrophages M1, T cells CD4 memory activated, T cells CD8, and T cells regulatory infiltration immune cells were associated with the low-risk score. The lower tumor microenvironment score was demonstrated in the high-risk group. Patients with lower TMB in the low-risk group showed a better prognosis, and a lower TIDE score suggested a better immune checkpoint inhibitor response in the high-risk group. Besides, cisplatin and paclitaxel were found to be more sensitive in the low-risk group.ConclusionsMAPK10 and STAT4 can be important prognosis factors in OC, and the two-gene signature performs well in predicting survival outcomes. Our study provided novel ways of OC prognosis estimation and potential treatment strategy.

Subtypes analysis and prognostic model construction based on lysosome-related genes in colon adenocarcinoma.

Background: Lysosomes are essential for the development and recurrence of cancer. The relationship between a single lysosome-related gene and cancer has previously been studied, but the relationship between the lysosome-related genes (LRGs) and colon adenocarcinoma (COAD) remains unknown. This research examined the role of lysosome-related genes in colon adenocarcinoma. Methods: 28 lysosome-related genes associated with prognosis (PLRGs) were found by fusing the gene set that is differently expressed between tumor and non-tumor in colon adenocarcinoma with the gene set that is related to lysosomes. Using consensus unsupervised clustering of PLRGs, the colon adenocarcinoma cohort was divided into two subtypes. Prognostic and tumor microenvironment (TME) comparisons between the two subtypes were then made. The PLRGs_score was constructed using the least absolute shrinkage and selection operator regression (LASSO) method to quantify each patient's prognosis and provide advice for treatment. Lastly, Western Blot and immunohistochemistry (IHC) were used to identify MOGS expression at the protein level in colon adenocarcinoma tissues. Results: PLRGs had more somatic mutations and changes in genetic level, and the outcomes of the two subtypes differed significantly in terms of prognosis, tumor microenvironment, and enrichment pathways. Then, PLRGs_score was established based on two clusters of differential genes in the cancer genome atlas (TCGA) database, and external verification was performed using the gene expression omnibus (GEO) database. Then, we developed a highly accurate nomogram to enhance the clinical applicability of the PLRGs_score. Finally, a higher PLRGs_score was associated with a poorer overall survival (OS), a lower tumor mutation burden (TMB), a lower cancer stem cell (CSC) index, more microsatellite stability (MSS), and a higher clinical stage. MOGS was substantially elevated at the protein level in colon adenocarcinoma as additional confirmation. Conclusion: Overall, based on PLRGs, we identified two subtypes that varied significantly in terms of prognosis and tumor microenvironment. Then, in order to forecast patient prognosis and make treatment suggestions, we developed a diagnostic model with major significance for prognosis, clinical relevance, and immunotherapy. Moreover, we were the first to demonstrate that MOGS is highly expressed in colon adenocarcinoma.

Lynch syndrome-associated chordoma with high tumor mutational burden and significant response to immune checkpoint inhibitors

Chordoma is a rare malignant bone tumor arising from notochordal tissue. Conventional treatments, such as radical resection and high-dose irradiation, frequently fail to control the tumor, resulting in recurrence and re-growth. In this study, genetic analysis of the tumor in a 72-year-old male patient with refractory conventional chordoma of the skull base revealed a high tumor mutational burden (TMB) and mutations in the MSH6 and MLH1 genes, which are found in Lynch syndrome. The patient and his family had a dense cancer history, and subsequent germline genetic testing revealed Lynch syndrome. This is the first report of a chordoma that has been genetically proven to be Lynch syndrome. Chordomas usually have low TMB; however, this is an unusual case, because the TMB was high, and immune checkpoint inhibitors effectively controlled the tumor. This case provides a basis for determining the indications for immunotherapy of chordoma based on the genetic analysis. Therefore, further extensive genetic analysis in the future will help to stratify the treatment of chordoma.