The correlation of miRNA expression and tumor mutational burden in uterine corpus endometrial carcinoma

Background:The relationship between microRNA(miRNA)expression patterns and tumor mutation burden(TMB)in uterine corpus endometrial carcinoma(UCEC)was investigated in this study.Methods:The UCEC dataset from The Cancer Genome Atlas(TCGA)database was used to identify the miRNAs that differ in expression between high TMB and low TMB sample sets.The total sample sets were divided into a training set and a test set.TMB levels were predicted using miRNA-based signature classifiers developed by Lasso Cox regression.Test sets were used to validate the classifier.This study investigated the relationship between a miRNA-based signature classifier and three immune checkpoint molecules(programmed cell death protein 1[PD-1],programmed cell death ligand 1[PD-L1],cytotoxic T lymphocyte-associated antigen 4[CTLA-4]).For the miRNA-based signature classifier,functional enrichment analysis was performed on the miRNAs.An analysis of the relationship between PD-1,PD-L1,and CTLA-4 immune checkpoint genes was carried out using the miRNA-based signature classifier.Results:We identified 27 differentially expressed miRNAs in miRNA-base signature.For predicting the TMB level,27-miRNA-based signature classifiers had accuracies of 0.8689 in the training cohort,0.8276 in the test cohort,and 0.8524 in the total cohort.The correlation between the miRNA-based signature classifier and PD-1 was negative,while the correlation between PD-L1 and CTLA4 was positive.Based on the miRNA profiling described above,we validated the expression levels of 9 miRNAs in clinical samples by quantitative reverse transcription PCR(qRT-PCR).Four of them were highly expressed and many cancer-related and immune-associated biological processes were linked to these 27 miRNAs.Thus,the developed miRNA-based signature classifier was correlated with TMB levels that could also predict TMB levels in UCEC samples.Conclusion:In this study,we investigated the relationship between a miRNAbased signature classifier and TMB levels in Uterine Corpus Endometrial Carcinoma.Further,this is the first study to confirm their relationship in clinical samples,which may provide more evidence support for immunotherapy of endometrial cancer.

Tumour mutational burden is overestimated by target cancer gene panels

Background:Tumour mutational burden(TMB)has emerged as a predictive marker for responsiveness to immune checkpoint inhibitors(ICI)in multiple tumour types.It can be calculated from somatic mutations detected from whole exome or targeted panel sequencing data.As mutations are unevenly distributed across the cancer genome,the clinical implications from TMB calculated using different genomic regions are not clear.Methods:Pan-cancer data of 10,179 samples were collected from The Cancer Genome Atlas cohort and 6,831 cancer patients with either ICI or non-ICI treatment outcomes were derived from published papers.TMB was calculated as the count of non-synonymous mutations and normalised by the size of genomic regions.Dirichlet method,linear regression and Poisson calibration models are used to unify TMB from different gene panels.Results:We found that panels based on cancer genes usually overestimate TMB compared to whole exome,potentially leading to misclassification of patients to receive ICI.The overestimation is caused by positive selection for mutations in cancer genes and cannot be completely addressed by the removal of mutational hotspots.We compared different approaches to address this discrepancy and developed a generalised statistical model capable of interconverting TMB derived from whole exome and different panel sequencing data,enabling TMB correction for patient stratification for ICI treatment.We show that in a cohort of lung cancer patients treated with ICI,when using a TMB cutoffof 10 mut/Mb,our corrected TMB outperforms the original panel-based TMB.Conclusion:Cancer gene-based panels usually overestimate TMB,and these findings will be valuable for unifying TMB calculations across cancer gene panels in clinical practice.

Ferroptosis biomarkers predict tumor mutation burden's impact on prognosis in HER2-positive breast cancer

BACKGROUND Ferroptosis has recently been associated with multiple degenerative diseases.Ferroptosis induction in cancer cells is a feasible method for treating neoplastic diseases.However,the association of iron proliferation-related genes with prognosis in HER2+breast cancer(BC)patients is unclear.AIM To identify and evaluate fresh ferroptosis-related biomarkers for HER2+BC.METHODS First,we obtained the mRNA expression profiles and clinical information of HER2+BC patients from the TCGA and METABRIC public databases.A four gene prediction model comprising PROM2,SLC7A11,FANCD2,and FH was subsequently developed in the TCGA cohort and confirmed in the METABRIC cohort.Patients were stratified into high-risk and low-risk groups based on their median risk score,an independent predictor of overall survival(OS).Based on these findings,immune infiltration,mutations,and medication sensitivity were analyzed in various risk groupings.Additionally,we assessed patient prognosis by combining the tumor mutation burden(TMB)with risk score.Finally,we evaluated the expression of critical genes by analyzing single-cell RNA sequencing(scRNA-seq)data from malignant vs normal epithelial cells.RESULTS We found that the higher the risk score was,the worse the prognosis was(P<0.05).We also found that the immune cell infiltration,mutation,and drug sensitivity were different between the different risk groups.The highrisk subgroup was associated with lower immune scores and high TMB.Moreover,we found that the combination of the TMB and risk score could stratify patients into three groups with distinct prognoses.HRisk-HTMB patients had the worst prognosis,whereas LRisk-LTMB patients had the best prognosis(P<0.0001).Analysis of the scRNAseq data showed that PROM2,SLC7A11,and FANCD2 were significantly differentially expressed,whereas FH was not,suggesting that these genes are expressed mainly in cancer epithelial cells(P<0.01).CONCLUSION Our model helps guide the prognosis of HER2+breast cancer patients,and its combination with the TMB can aid in more accurate assessment of patient prognosis and provide new ideas for further diagnosis and treatment.

Favorable response to immunotherapy in a pancreatic neuroendocrine tumor with temozolomide-induced high tumor mutational burden

Neuroendocrine neoplasm of the pancreas is a rare tumor with limited treatment options.Among such tumors,treatment for pancreatic neuroendocrine tumor(PanNET)G3 is the most difficult.Temozolomide(TMZ)is commonly used to treat PanNET.However,TMZ may cause tumor gene alkylation,which induces drug resistance and rapid disease progression.Herein,we present a case of a female who was diagnosed with PanNET G3 and achieved a partial response to toripalimab,an anti-programmed cell death-ligand 1(anti-PD-L1)monoclonal antibody,after multiple cycles of TMZ treatment.Genomic profiling revealed that compared with the patient’s samples collected at baseline,the postTMZ-treatment samples had markedly higher levels of tumor mutational burden(TMB)associated with characteristic alkylating mutational signature representing a positive correlation with favorable response to anti-PD-1 treatment.In addition,we observed a germline truncating mutation of MUTYH(W156*)that was considered to be pathogenic and potentially conferred to genomic instability.This case suggests that anti-PD-1 therapy could be a treatment option for PanNET patients with increased TMB after TMZ-based treatment.

Mechanisms and potential applications of COPS6 in pan-cancer therapy

The COP9 signalosome subunit 6(COPS6)is abnormally overexpressed in many malignancies,yet its precise role in carcinogenesis is unknown.To gain a better understanding of COPS6's role,the authors conducted a pan-cancer analysis using various bioinformatics techniques such as differential expression patterns,prognostic value,gene mutations,immune infiltration,correlation analysis,and functional enrichment assessment.Results showed that COPS6 was highly correlated with prognosis,immune cell infiltration level,tumor mutation burden,and microsatellite instability in patients with a range of tumor types.This suggests that COPS6 may be a potential target for cancer treatment.Overall,this research provides insight into COPS6's role in cancer development and its potential therapeutic applications.

Deciphering the role of FSCN family genes in cancer:a pan-cancer bioinformatics study

Background:The Fascin(FSCN)family,comprising actin-bundling proteins,plays vital roles in cytoskeletal reorganization and cell migration.FSCN1,FSCN2,and FSCN3 are implicated in cancer progression through cell motility,invasion,and metastasis.However,their specific contributions across different cancer types remain unclear.Methods:We conducted a pan-cancer bioinformatics analysis of FSCN genes using data from The Cancer Genome Atlas.This included differential expression patterns,copy number variations(CNVs),mutations,methylation status,and correlations with tumor mutational burden,microsatellite instability,and immune checkpoint molecule expression.Differential expression was analyzed using DESeq2,while CNV and mutation analyses utilized GISTIC2.0 and MuTect2.Methylation data were assessed using the Illumina Human Methylation 450K BeadChip.Results:FSCN1 and FSCN2 showed significant differential expression in multiple cancers,often correlating with poor prognosis.FSCN3 exhibited less variability but a protective role in certain contexts.CNV analysis indicated frequent gene gains in FSCN genes,correlating with increased expression.FSCN3 had a higher mutation rate,suggesting genetic instability.Methylation analysis showed hypomethylation of FSCN1 and FSCN2 in tumors compared to normal tissues,whereas FSCN3 had minor changes.Significant associations were found between FSCN gene expression and tumor mutational burden,microsatellite instability,and immune checkpoint molecules,suggesting their involvement in tumor immunogenicity and the immune microenvironment.Conclusions:This pan-cancer analysis highlights the multifaceted roles of FSCN genes in cancer biology,emphasizing their potential as biomarkers and therapeutic targets.FSCN1 and FSCN2 are associated with poor prognosis and aggressive phenotypes,while FSCN3 shows protective roles in specific contexts.These findings offer new avenues for cancer diagnosis and treatment,particularly in personalized medicine.Future studies should validate these findings and explore the underlying mechanisms to fully harness the clinical potential of FSCN family proteins in oncology.

Mining The Cancer Genome Atlas database for tumor mutation burden and its clinical implications in gastric cancer

BACKGROUND Tumor mutational burden(TMB)is an important independent biomarker for the response to immunotherapy in multiple cancers.However,the clinical implications of TMB in gastric cancer(GC)have not been fully elucidated.AIM To explore the landscape of mutation profiles and determine the correlation between TMB and microRNA(miRNA)expression in GC.METHODS Genomic,transcriptomic,and clinical data from The Cancer Genome Atlas were used to obtain mutational profiles and investigate the statistical correlation between mutational burden and the overall survival of GC patients.The difference in immune infiltration between high-and low-TMB subgroups was evaluated by Wilcoxon rank-sum test.Furthermore,miRNAs differentially expressed between the high-and low-TMB subgroups were identified and the least absolute shrinkage and selection operator method was employed to construct a miRNA-based signature for TMB prediction.The biological functions of the predictive miRNAs were identified with DIANA-miRPath v3.0.RESULTS C>T single nucleotide mutations exhibited the highest mutation incidence,and the top three mutated genes were TTN,TP53,and MUC16 in GC.High TMB values(top 20%)were markedly correlated with better survival outcome,and multivariable regression analysis indicated that TMB remained prognostic independent of TNM stage,histological grade,age,and gender.Different TMB levels exhibited different immune infiltration patterns.Significant differences between the high-and low-TMB subgroups were observed in the infiltration of CD8+T cells,M1 macrophages,regulatory T cells,and CD4+T cells.In addition,we developed a miRNA-based signature using 23 differentially expressed miRNAs to predict TMB values of GC patients.The predictive performance of the signature was confirmed in the testing and the whole set.Receiver operating characteristic curve analysis demonstrated the optimal performance of the signature.Finally,enrichment analysis demonstrated that the set of miRNAs was significantly enriched in many key cancer and immune-related pathways.

Pan-Cancer dissection of ORAI1:prognostic implications and immune landscapecorrelation

Background:The ORAI1 gene,central to store-operated calcium entry(SOCE),is increasingly recognized for its pivotal role in cancer progression and patient prognosis across a broad spectrum of malignancies.Despite its critical involvement in calcium signaling pathways that are essential for cellular functions such as proliferation,migration,and apoptosis,the comprehensive impacts of ORAI1 within the tumor microenvironment(TME)and its modulation across various cancers have not been fully elucidated.Methods:We conducted a pan-cancer analysis leveraging data from The Cancer Genome Atlas(TCGA)and Genotype-Tissue Expression(GTEx)to assess ORAI1 expression.Differential expression analyses were performed,complemented by correlative studies with tumor mutation burden(TMB),microsatellite instability(MSI),immune infiltration,and key biological processes and pathways.Results:Our results demonstrate that ORAI1 is consistently upregulated in a range of cancer types,associated with aggressive tumor characteristics and poor patient outcomes.Significantly,ORAI1 upregulation correlates with increased tumor mutation burden(TMB)and microsatellite instability(MSI),markers of genomic instability that are predictive of response to immunotherapy,underscoring its potential utility in clinical stratification and treatment decision-making.ORAI1's influence extended to the immune landscape,showing associations with immune cell infiltration and both immunosuppressive and immunostimulatory gene sets,thereby affecting the TME and possibly the efficacy of immunotherapeutic interventions.Conclusions:The multifaceted nature of ORAI1's involvement in cancer pathophysiology positions it as a prospective biomarker and therapeutic target.Its expression dynamics and correlative significance with prognostic and immune regulatory elements underscore its potential in guiding therapeutic strategies and improving clinical outcomes.This study lays a foundation for future research,aiming to leverage ORAI1's biological significance in cancer prognosis and therapy optimization.

High tumor mutation burden indicates a poor prognosis in patients with intrahepatic cholangiocarcinoma

BACKGROUND Intrahepatic cholangiocarcinoma(ICC)is malignancies of the biliary duct system and constitutes approximately 10%-20%of all primary liver cancers.Tumor mutation burden(TMB)is a useful biomarker across many cancer types for the identification of patients who will benefit from immunotherapy.Despite the role of TMB in calculating the effectiveness and prognosis of immune checkpoint inhibitors has been confirmed in multiple human cancer types,the prognostic value of TMB in ICC patients is rare investigated.AIM To investigate the prognostic value of TMB in patients with ICC.METHODS Data of 412 patients with ICC were included in the study.TMB was calculated as the total number of somatic non-silent protein-coding mutations divided by the coding region.The Kaplan-Meier method was used to analyze overall survival(OS),and relapse free survival(RFS).The cut-off value of TMB was determined by time-dependent receiver operating characteristic(ROC)curve.Cox regression was performed for multivariable analysis of OS.The nomogram and calibration curve were analyzed to construct and evaluate the prognostic model.RESULTS In the analysis of the time-dependent ROC curve,we defined 3.1 mut/Mb as the cut-off value of TMB.The Kaplan-Meier plot revealed that patients with high TMB had poor OS(HR=1.47,P=0.002)and RFS(HR=1.42,P=0.035).Cox regression analysis also demonstrated that TMB was an independent risk predictor for ICC(HR=1.43,P=0.0240).Furthermore,independent prognostic factors of ICC included CA19-9(HR=1.78,P=0.0005),chronic viral hepatitis(HR=1.72,P=0.0468),tumor resection(HR=2.58,P<0.0001)and disease progression(metastatic disease vs.solitary liver tumor;HR=2.55,P=0.0002).The nomogram and calibration curve also indicated the effectiveness of the constructed prognostic model.CONCLUSION TMB was an independent prognostic biomarker in patients with ICC.Moreover,patients with ICC with high TMB had poor OS and RFS as compared to those with low TMB.

Computational exploration of the significance of COPS6 in cancer:Functional and clinical relevance across tumor types

BACKGROUND The COP9 signalosome subunit 6(COPS6)has been implicated in cancer progression,while its precise role in most types of cancer remains elusive.AIM To investigate the functional and clinical relevance of COPS6 across various tumor types using publicly available databases.METHODS We used R software and online analysis databases to analyze the differential expression,prognosis,mutation and related functions of COPS6 in pan-cancer.RESULTS Differential expression analysis and survival analysis demonstrated that COPS6 was highly expressed and associated with high-risk profiles in the majority of cancer types.Possible associations between COPS6 expression level and prognostic outcomes were found using data from public databases.Mutational analysis revealed that missense mutations were the predominant type of COPS6 mutation.Additionally,positive correlations were identified between COPS6 expression level and tumor mutational burden and microsatellite instability in most types of cancer.Immune infiltration analysis demonstrated a negative correlation between COPS6 expression level and CD8+T cell infiltration in certain types of cancer.The correlation between COPS6 expression level and cancerassociated fibroblast infiltration exhibited heterogeneity,in which a positive correlation was found in head and neck squamous cell carcinoma and tenosynovial giant cell tumor,and a negative correlation was identified in diffuse large B-cell lymphoma and thymoma.The correlation between COPS6 expression level and macrophage infiltration was closely related to macrophage type.Gene co-expression and enrichment analysis highlighted transcription elongation factor B polypeptide 2 and G protein pathway suppressor 1 were significantly and positively associated with COPS6 expression level.These genes were predominantly involved in processes,such as ubiquitin-mediated proteolysis and human immunodeficiency virus 1 infection.CONCLUSION In conclusion,this study systematically explored the significance of COPS6 across different tumor types,providing a solid foundation for considering COPS6 as a novel biomarker in cancer research.

ABCC8 is correlated with immune cell infiltration and overall survival in lower grade glioma

ATP binding cassette subfamily C member 8(ABCC8)encodes a protein regulating the ATP-sensitive potassium channel.Whether the level of ABCC8 mRNA in lower grade glioma(LGG)correlates with immune cell infiltration and patient outcomes has not been evaluated until now.Comparisons of ABCC8 expression between different tumors and normal tissues were evaluated by exploring publicly available datasets.The association between ABCC8 and tumor immune cell infiltration,diverse gene mutation characteristics,tumor mutation burden(TMB),and survival in LGG was also investigated in several independent datasets.Pathway enrichment analysis was conducted to search for ABCC8-associated signaling pathways.Through an online database,we found that ABCC8 expression in LGG was lower than in normal tissues.Then,the association of ABCC8 expression and immune cell infiltration in LGG was discussed.As we expected,the ABCC8 mRNA levels were negatively associated with non-T immune cell infiltration levels in all datasets.Consistently,TCGA_LGG RNA-seq data revealed that ABCC8 downregulated several non-T immune cell-associated signaling pathways in gene set enrichment analysis.Different ABCC8 expression groups showed diverse gene mutation characteristics and TMB.The high expression of ABCC8 was linked to improved survival of LGG patients.A pathway enrichment analysis of ABCC8-associated genes indicated that the GABAergic synapse signaling pathway might be involved in regulating immunity in LGG.Our findings show that ABCC8 reflects LGG tumor immunity and is an ideal prognostic biomarker for LGG.

Therapeutic guidance of tumor mutation burden on immune checkpoint inhibitors in advanced non-small cell lung cancer:a systematic review and comprehensive meta-analysis

Background:Tumor mutation burden(TMB)remains a promising but ambiguous predictive biomarker for the efficacy of immune checkpoint inhibitors(ICIs).We investigated the predictive value of TMB in patients with advanced non-small cell lung cancer(NSCLC)treated by ICI-containing therapies under strictly matched clinical settings.Methods:PubMed,Embase,Cochrane Central,ClinicalTrials.gov,and bioRxiv databases were searched till October 16,2021.All randomized controlled trials(RCTs)that compared patients with high TMB(TMB-H)and low TMB(TMB-L)and provided hazard ratio(HR)and corresponding 95%confidence interval(CI)in advanced NSCLC patients receiving ICIs were included,and mirror-based meta-analysis was performed(Part1).Bayesian network meta-analysis was conducted to investigate the efficacy of distinct first-line regimens in TMB-H and TMB-L groups(Part2).Public cohorts were used for validation and further exploration(Part3).Results:Twelve RCTs(n=5527)and 5 public cohorts(n=573)were included.In Part1,TMB-H patients generally exhibited a more significant progression-free survival(PFS)benefit from ICI-containing therapies compared to TMB-L patients(HR=0.58,95%CI:0.49-0.67,P<0.0001).In Part2,anti-PD-1 plus chemotherapy ranked best for PFS in both TMB-H and TMB-L groups.Anti-PD-L1 plus anti-CTLA-4 therapies indicated better PFS and overall survival(OS)benefit than single ICI and chemotherapy in the TMB-H group,but ranked worst in the TMB-L group.Finally,TMB was validated to be an independent predictive biomarker from programmed cell death-ligand 1(PD-L1)expression in Part3,which could further distinguish beneficiaries of ICI-containing therapies with PD-L1<50%.Conclusion:TMB-H could be a predictive biomarker independent of PD-L1 expression to identify beneficiaries of ICI-containing therapy in advanced NSCLC patients.

Successful response to camrelizumab in metastatic bladder cancer: A case report

BACKGROUND There has been no report to use camrelizumab with chemotherapy for advanced bladder cancer patients with positive programmed death-ligand 1(PD-L1)expression and high tumor mutational burden(TMB).More effective predictors of bladder cancer immunotherapy have yet to be explored,and the combination of multiple factors may be more predictive than a single factor.CASE SUMMARY We report the case of a 74-year-old male patient with recurrent metastatic bladder cancer,which demonstrated positive PD-L1 expression and high TMB.The immune checkpoint inhibitor camrelizumab was administered to the patient in combination with gemcitabine and cisplatin.The patient achieved a partial response with a progression-free survival of 11 mo.CONCLUSION This is the first report to use camrelizumab with chemotherapy for advanced bladder cancer patients with positive PD-L1 expression and high TMB.

Immunotherapy in biliary tract cancers:Current evidence and future perspectives

Bile duct tumors are comprised of tumors that originate from both intrahepatic and extrahepatic bile ducts and gallbladder tumors.These are aggressive tumors and chemotherapy is still the main treatment for advanced-stage disease and most of these cases have a poor overall survival.Strategies are aimed at treatments with better outcomes and less toxicity which makes immunotherapy an area of significant importance.Recent Food and Drug Administration approvals of immune checkpoint inhibitors(ICI)for agnostic tumors based on biomarkers such as microsatellite instability-high and tumor mutation burden-high are important steps in the treatment of patients with advanced bile duct tumors.Despite limited responses with isolated checkpoint inhibitors in later lines of systemic treatment in advanced disease,drug combination strategies have been demonstrating encouraging results to enhance ICI efficacy.

Evaluation of 30 DNA damage response and 6 mismatch repair gene mutations as biomarkers for immunotherapy outcomes across multiple solid tumor types

Objective:DNA damage response(DDR)genes have low mutation rates,which may restrict their clinical applications in predicting the outcomes of immune checkpoint inhibitor(ICI)treatment.Thus,a systemic analysis of multiple DDR genes is needed to identify potential biomarkers of ICI efficacy.Methods:A total of 39,631 patients with mutation data were selected from the cBioPortal database.A total of 155 patients with mutation data were obtained from the Fudan University Shanghai Cancer Center(FUSCC).A total of 1,660 patients from the MSK-IMPACT cohort who underwent ICI treatment were selected for survival analysis.A total of 249 patients who underwent ICI treatment from the Dana-Farber Cancer Institute(DFCI)cohort were obtained from a published dataset.The Cancer Genome Atlas(TCGA)level 3 RNA-Seq version 2 RSEM data for gastric cancer were downloaded from cBioPortal.Results:Six MMR and 30 DDR genes were included in this study.Six MMR and 20 DDR gene mutations were found to predict the therapeutic efficacy of ICI,and most of them predicted the therapeutic efficacy of ICI,in a manner dependent on TMB,except for 4 combined DDR gene mutations,which were associated with the therapeutic efficacy of ICI independently of the TMB.Single MMR/DDR genes showed low mutation rates;however,the mutation rate of all the MMR/DDR genes associated with the therapeutic efficacy of ICI was relatively high,reaching 10%–30%in several cancer types.Conclusions:Coanalysis of multiple MMR/DDR mutations aids in selecting patients who are potential candidates for immunotherapy.

Recurrent undifferentiated embryonal sarcoma of the liver in adult patient treated by pembrolizumab: A case report

BACKGROUND Undifferentiated embryonal sarcoma of the liver(UESL)is a neoplasm that rarely develops in adults.The main treatments for UESL are upfront gross total surgical resection and adjuvant multiagent chemotherapy.Here,we report a case of recurrent UESL in an adult treated with pembrolizumab and discuss a method to identify proper candidates for antibody of programmed cell death protein 1(anti-PD-1)treatment.CASE SUMMARY A 69-year-old woman was admitted for abdominal pain that developed for 1 wk.Computed tomography showed a 16 cm mass in the right lobe of the liver.Right hemihepatectomy and lymphadenectomy were performed,and histological diagnosis was UESL.Six months later,the patient suffered from painless obstructive jaundice,and positron emission tomography-computed tomography revealed multiple metastases.Then,percutaneous transhepatic cholangial drainage was applied to reduce jaundice,and radiofrequency ablation was used to control the lesion near the hepatic hilum.However,the patient suffered from a serious fever caused by the tumor.The patient received treatment with pembrolizumab,and the prescribed dosage was 2 mg/kg every 3 wk.After the seventh dose,positron emission tomography-computed tomography revealed that the multiple metastases had nearly disappeared.Radiologic exam was used to evaluate the disease state,and no new lesions were found.Next-generation sequencing and immunohistology were applied to determine the reason why the patient had such a favorable response to pembrolizumab.Tumor mutation burden,microsatellite instability,and programmed death ligand 1 expression can be combined to predict the effect of PD-1 antibodies. When every one of thesebiomarkers are detected in a tumor patient, the patient may be a proper candidatefor PD-1 antibodies.CONCLUSION Anti-PD-1 treatment for tumors needs further research to identify indications andproper biomarkers.

Identification of genomic features associated with immunotherapy response in gastrointestinal cancers

Gastrointestinal(GI) cancers prevail and account for an extremely high number of cancer deaths worldwide. The traditional treatment strategies, including surgery, chemotherapy, radiotherapy, and targeted therapy, have a limited therapeutic effect for advanced GI cancers. Recently, immunotherapy has shown promise in treating various refractory malignancies, including the GI cancers with mismatch repair deficiency(dMMR) or microsatellite instability(MSI). Thus,immunotherapy could be a promising treatment approach for GI cancers.Unfortunately, only a small proportion of GI cancer patients currently respond to immunotherapy. Therefore, it is important to discover predictive biomarkers for stratifying GI cancer patients response to immunotherapy. Certain genomic features, such as dMMR/MSI, tumor mutation burden(TMB), and tumor aneuploidy have been associated with tumor immunity and im-munotherapy response and may serve as predictive biomarkers for cancer immunotherapy. In this review, we examined the correlations between tumor immunity and three genomic features: dMMR/MSI, TMB, and tumor aneuploidy. We also explored their correlations using The Cancer Genome Atlas data and confirmed that the dMMR/MSI status, high TMB, and low tumor aneuploidy are associated with elevated tumor immunity in GI cancers. To improve the immunotherapeutic potential in GI cancers, more genetic or genomic features associated with tumor immune response need to be identified. Furthermore, it is worth exploring the combination of different immunotherapeutic methods and the combination of immunotherapy with other therapeutic approaches for cancer therapy.

Skeletal muscle metastasis with bone metaplasia from colon cancer:A case report and review of the literature

BACKGROUND Colon cancer is a common malignant disease of the gastrointestinal tract and usually occurs at the junction of the rectum and sigmoid colon.Lymphatic and hematogenous metastases occur frequently in colon cancer and the most common metastatic sites include the liver,lung,peritoneum,bone,and lymph nodes.As a manifestation of advanced tumor spread and metastasis,soft tissue metastasis,especially skeletal muscle metastasis with bone metaplasia caused by colon cancer,is rare,accounting for less than 1%of metastases.CASE SUMMARY A 43-year-old male patient developed skeletal muscle metastasis with bone metaplasia of the right proximal thigh 5 mo after colon cancer was diagnosed.The patient was admitted to the hospital because of pain caused by a local mass on his right thigh.Positron emission tomography-computed tomography showed many enlarged lymph nodes around the abdominal aorta but no signs of lung or liver metastases.Color ultrasound revealed a mass located in the skeletal muscle and the results of histological biopsy revealed a poorly differentiated adenocarcinoma suspected to be distant metastases from colon cancer.Immunohistochemistry showed small woven bone components that were considered to be ossified.CONCLUSION This case reminds us that for patients with advanced colorectal tumors,we should be alert to the possibility of unconventional metastasis.

TMB相关免疫浸润调控评分(MOTIF)预测免疫治疗响应并指导联合增效

Patients with high tumor mutational burden(TMB)levels do not consistently respond to immune checkpoint inhibitors(ICIs),possibly because a high TMB level does not necessarily result in adequate infiltration of CD8^(+)T cells.Using bulk ribonucleic acid sequencing(RNA-seq)data from 9311 tumor samples across 30 cancer types,we developed a novel tool called the modulator of TMB-associated immune infiltration(MOTIF),which comprises genes that can determine the extent of CD8^(+)T cell infiltration prompted by a certain TMB level.We confirmed that MOTIF can accurately reflect the integrity and defects of the cancer-immunity cycle.By analyzing 84 human single-cell RNA-seq datasets from 32 types of solid tumors,we revealed that MOTIF can provide insights into the diverse roles of various cell types in the modulation of CD8^(+)T cell infiltration.Using pretreatment RNA-seq data from 13 ICI-treated cohorts,we validated the use of MOTIF in predicting CD8^(+)T cell infiltration and ICI efficacy.Among the components of MOTIF,we identified EMC3 as a negative regulator of CD8^(+)T cell infiltration,which was validated via in vivo studies.Additionally,MOTIF provided guidance for the potential combinations of programmed death 1 blockade with certain immunostimulatory drugs to facilitate CD8^(+)T cell infiltration and improve ICI efficacy.

Dynamic bTMB combined with residual ctDNA improves survival prediction in locally advanced NSCLC patients with chemoradiotherapy and consolidation immunotherapy

Background:Liquid biopsy-based biomarkers,including circulating tumor DNA(ctDNA)and blood tumor muta-tional burden(bTMB),are recognized as promising predictors of prognoses and responses to immune checkpoint inhibitors(ICIs),despite insufficient sensitivity of single biomarker detection.This research aims to determine whether the combinatorial utility of longitudinal ctDNA with bTMB analysis could improve the prognostic and predictive effects.Methods:This prospective two-center cohort trial,consisting of discovery and validation datasets,enrolled unre-sectable locally advanced non-small-cell lung cancer(LA-NSCLC)patients and assigned them to chemoradiother-apy(CRT)or CRT+consolidation ICI cohorts from 2018 to 2022.Blood specimens were collected pretreatment,4 weeks post-CRT,and at progression to assess bTMB and ctDNA using 486-gene next-generation sequencing.DynamicΔbTMB was calculated as post-CRT bTMB minus baseline bTMB levels.Decision curve analyses were performed to calculate Concordance index(C-index).Results:One hundred twenty-eight patients were enrolled.In the discovery dataset(n=73),patients treated with CRT and consolidation ICI had significantly longer overall survival(OS;median not reached[NR]vs 20.2 months;P<0.001)and progression-free survival(PFS;median 25.2 vs 11.4 months;P=0.011)than those without ICI.Longitudinal analysis demonstrated a significant decrease in ctDNA abundance post-CRT(P<0.001)but a relative increase with disease progression.Post-CRT detectable residual ctDNA correlated with significantly shorter OS(median 18.3 months vs NR;P=0.001)and PFS(median 7.3 vs 25.2 months;P<0.001).For patients with residual ctDNA,consolidation ICI brought significantly greater OS(median NR vs 14.8 months;P=0.005)and PFS(median 13.8 vs 6.2 months;P=0.028)benefit,but no significant difference for patients with ctDNA clearance.DynamicΔbTMB was predictive of prognosis.Patients with residual ctDNA and increasedΔbTMB(ΔbTMB>0)had significantly worse OS(median 9.0 vs 23.0 months vs NR;P<0.001)and PFS(median 3.4 vs 7.3 vs 25.2 months;P<0.001).The combinatorial model integrating post-CRT ctDNA withΔbTMB had optimal predictive effects on OS(C-index=0.723)and PFS(C-index=0.693),outperforming individual features.In the independent validation set,we confirmed residual ctDNA predicted poorer PFS(median 50.8 vs 14.3 months;P=0.026)but identified more consolidation ICI benefit(median NR vs 8.3 months;P=0.039).The combined model exhibited a stable predictive advantage(C-index=0.742 for PFS).Conclusions:The multiparameter assay integrating qualitative residual ctDNA testing with quantitativeΔbTMB dynamics improves patient prognostic risk stratification and efficacy predictions,allowing for personalized con-solidation therapy for LA-NSCLC.