Immune Checkpoint Biomarkers Research Articles

Integrative analysis of the immunological significances of guanylate binding protein family genes in microsatellite stability colorectal cancer

BackgroundMicrosatellite stability (MSS) colorectal cancer (CRC) has poor sensitivity to immunotherapy and its underlying mechanisms are still unclear. Guanylate binding proteins (GBPs) are a family of GTPase involving innate immune responses by providing defense against invading microbes and pathogens. However, the immunological significances of GBPs in MSS CRC remain unknown. MethodsWe utilized bioinformatic tools to comprehensively analysis the expression pattern, clinical relevance, prognostic value, biological function, and immunoregulation effect of distinct GBP members in MSS CRC. ResultsThe expression of all seven GBPs in MSS samples are remarkably decreased compared to microsatellite instability-high (MSI-H) samples. Among them, GBP1/2/4/5 are obviously correlated with distant metastasis status. High expression of GBP1/4/5/6 was remarkably related to favorable overall survival (OS) and progression-free survival (PFS) in CRC patients with MSS tumor. Subsequent enrichment analysis revealed that Interferon-gamma (IFN-γ) and NOD-like receptor signaling are the most relevant functions. Besides, the expression patterns of GBPs are remarkably associated with several tumor infiltrated immune cells (e.g. regulatory T cells, CD4+ T cells, and macrophages) and diverse immunoregulatory molecules (e.g. immune checkpoint biomarkers (ICBs) and major histocompatibility complex (MHC) molecules). Moreover, high GBP1/2/4/5 expression predicted better immunotherapy responsiveness in immunotherapy cohorts. ConclusionThese findings might provide novel insights for the identification of therapeutic targets and potential prognostic biomarkers of GBP family in CRC with MSS samples.

"Inhibitory immune checkpoints predict 7-day, in-hospital and 1-year mortality of internal medicine patients admitted with bacterial sepsis".

Sepsis is a life-threatening syndrome with complex pathophysiology and great clinical heterogeneity which complicates the delivery of personalized therapies. Our goals were to demonstrate that some biomarkers identified as regulatory immune checkpoints in preclinical studies could 1)improve sepsis prognostication based on clinical variables and 2)guide the stratification of septic patients in subgroups with shared characteristics of immune response or survival outcomes. We assayed the soluble counterparts of 12 biomarkers of immune response in 113 internal medicine patients with bacterial sepsis. IL-1 receptor-associated kinase M (IRAK-M) exhibited the highest hazard ratios (HRs) for increased 7-day (1.94 [1.17-3.20]) and 30-day mortality (1.61 [1.14-2.28]). HRs of IRAK-M and Galectin-1 for predicting 1-year mortality were 1.52 (1.20-1.92) and 1.64 (1.13-2.36), respectively. A prognostic model including IRAK-M, Galectin-1, and clinical variables (Charlson Comorbidty Index, multiple source of sepsis, and SOFA score) had high discrimination for death at 7 days and 30 days (area under the curve 0.90 [0.82-0.99]) and 0.86 [0.79-0.94], respectively). Patients with elevated serum levels of IRAK-M and Galectin-1 had clinical traits of immune suppression and low survival rates. None of the 12 biomarkers were independent predictors of 2-year mortality. Two inhibitory immune checkpoint biomarkers (IRAK-M and Galectin-1) helped identify 3 distinct sepsis phenotypes with distinct prognoses. These biomarkers shed light on the interplay between immune dysfunction and prognosis in patients with bacterial sepsis and may prove to be useful prognostic markers, therapeutic targets, and biochemical markers for targeted enrollment in targeted therapeutic trials.

Comprehensive analysis of the prognostic value and immunological role of IDO1 gene in pan-cancer

ObjectiveIt has been demonstrated that IDO1, a target of immune checkpoint inhibition, functions as an oncogene in the majority of human malignancies. IDO1’s function in human pan-cancers hasn’t been thoroughly studied, though.Materials and methodsThe Kaplan–Meier (K-M) and COX analyses were applied to the survival analysis. Furthermore, we used Spearman’s correlation analysis to examine the associations between IDO1 and microsatellite instability (MSI), DNA methyltransferases (DNMTs), tumor mutational burden (TMB), the associated genes of mismatch repair (MMR), and immune checkpoint biomarkers. Moreover, immunohistochemical analysis and qRT-PCR were used to evaluate IDO1’s expression in pan-cancer cells.ResultsThe findings of this study reveal that IDO1 has abnormal expression in a number of malignancies and is related to the prognosis for UVM, LGG, KIRP, GBM, LAML, OV, READ, MESO, SARC, SKCM, and HNSC. Furthermore, the aberrant IDO1 expression was connected to the TMB, MSI, MMR, drug sensitivity, immune cells infiltrating, and tumor immune microenvironment across a variety of cancer types. The PCR results showed that in contrast to normal cells, IDO1 was found to be significantly highly expressed in breast cancer cells and hepatocellular carcinoma cells, and significantly lowly expressed in gastric cancer cells.ConclusionThe clinical treatment of IDO1 is now better supported by a theoretical basis and guidelines provided by our study.

Development of a CD8+ T cell associated signature for predicting the prognosis and immunological characteristics of gastric cancer by integrating single-cell and bulk RNA-sequencing

The universally poor clinical outcome makes gastric cancer (GC) still a significant public health threat, the main goal of our research is to develop a prognostic signature that can forecast the outcomes and immunological characteristics of GC via integrating single-cell and bulk RNA-sequencing. The CD8+ T cell feature genes were screened out by exploring single-cell RNA-sequencing (scRNA-seq) profiles retrieved from the TISCH2 database. Then, Cox and LASSO regressions were exploited for constructing a prognostic model in TCGA cohort based on these CD8+ T cell feature genes. Survival analysis was conducted to investigate the predictive capability of the signature for the clinical outcome of GC patients in TCGA and GEO cohorts. Additionally, we further examined the correlations between the risk signature and tumor immunotherapeutic response from the perspectives of immune infiltration, tumor mutation burden (TMB), immune checkpoint biomarker (ICB) expression, tumor microenvironment (TME), microsatellite instability (MSI), TIDE, and TCIA scores. In total, 703 CD8+ T cell feature genes were identified, eight of which were selected for constructing a prognostic signature. GC patients who possess high-risk score had significantly poorer survival outcomes than those who possess low-risk score in TCGA and GEO cohorts. Immune infiltration analysis proved that the risk score was negatively connected with the infiltration abundance of CD8+ T cells. Then, our findings demonstrated that GC patients in the high-risk subgroup possess a higher proportion of MSI-L/MSS, lower immune checkpoint biomarker expression, lower TMB, higher TIDE scores and lower TCIA scores compared to those in the low-risk subgroup. What’s more, immunotherapy cohort analysis confirmed that patients who possess high-risk score are not sensitive to anti-cancer immunotherapy. Our study developed a reliable prognostic signature for GC that was significantly correlated with the immune landscape and immunotherapeutic responsiveness. The risk signature may guide clinicians to adopt more accurate and personalized treatment strategies for GC patients.

Changes in circulating immune biomarkers following nivolumab with or without ipilimumab for metastatic anal cancer (NCI9673).

3 Background: Approximately 25% of patients (pts) with squamous cell carcinoma of the anal canal (SCCA) develop metastatic disease. The ETCTN-led NCI9673 phase II trial evaluated PFS of the anti-PD-1 antibody nivolumab (N) with or without the anti-CTLA-4 antibody ipilimumab (I) in metastatic SCCA. We analyzed serial blood samples from NCI9673 for immune biomarker profiling following N or N+I. Methods: PBMCs from 47 pts (24 N, 23 N+I) were collected at pretreatment (N=47), week 9 (N=26), and at progression (N=15). Immune cell populations - effector CD4 T cells, CD8 T cells, natural killer (NK) cells, and regulatory T cells - were analyzed by flow cytometry for immune inhibitory (PD-1, CTLA-4, TIM-3, LAG-3, TIGIT) and immune stimulatory (OX40, ICOS) expression. Mean expression (as percentage of cells with any expression) for each biomarker at a matched time point was compared between the N and N+I arms by a corrected student’s t test, with an alpha= .10 for significance. Changes in mean expression for each biomarker were compared by one-way ANOVA. Results: Mean TIGIT expression at baseline was highest on CD4 and CD8 T-cells relative to other immune checkpoint biomarkers (p< .0001 for all subsets; see Table). N+I was associated with higher TIGIT expression on CD4 cells at progression than for N alone (21.3% vs. 10.9%, p=.08). Among NK cells, TIGIT expression decreased at progression relative to baseline for N (14.1% vs. 5.9%, p=.06). Relative to non-responders, responders to N had OX40 expression that increased on CD4 T cells but decreased on NK cells at week 9 relative to baseline. Conclusions: In previously metastatic SCCA pts, TIGIT expression was greater on CD4 and CD8 T cells and was modulated on differing immune cell populations according to treatment arm. These data not only implicate T and NK cells in mediating treatment effect following single agent and/or combination immunotherapy, but also support the exploration of TIGIT as a potential novel target for treatment of metastatic SCCA.[Table: see text]

Prognostic value and immunological role of PD-L1 gene in pan-cancer

ObjectivePD-L1, a target of immune checkpoint blockade, has been proven to take the role of an oncogene in most human tumors. However, the role of PD-L1 in human pan-cancers has not yet been fully investigated.Materials and methodsPan-cancer analysis was conducted to analyze expression, genetic alterations, prognosis analysis, and immunological characteristics of PD-L1. Estimating the correlation between PD-L1 expression and survival involved using pooled odds ratios and hazard ratios with 95% CI. The Kaplan–Meier (K-M) technique, COX analysis, and receiver operating characteristic (ROC) curves were applied to the survival analysis. Additionally, we investigated the relationships between PD-L1 and microsatellite instability (MSI), tumor mutational burden (TMB), DNA methyltransferases (DNMTs), the associated genes of mismatch repair (MMR), and immune checkpoint biomarkers using Spearman's correlation analysis. Also, immunohistochemical analysis and qRT-PCR were employed in evaluating PD-L1’s protein and mRNA expression in pan-caner.ResultsPD-L1 showed abnormal mRNA and protein expression in a variety of cancers and predicted prognosis in cancer patients. Furthermore, across a variety of cancer types, the aberrant PD-L1 expression was connected to the MSI, MMR, TMB, drug sensitivity, and tumor immune microenvironment (TIME). Moreover, PD-L1 was significantly correlated with infiltrating levels of immune cells (T cell CD8 + , neutrophil, and so on).ConclusionOur study provides a better theoretical basis and guidance for the clinical treatment of PD-L1.

Exploring the immune microenvironment in small bowel adenocarcinoma using digital image analysis.

Small bowel adenocarcinoma (SBA) is a rare malignancy of the small intestine associated with late stage diagnosis and poor survival outcome. High expression of immune cells and immune checkpoint biomarkers especially programmed cell death ligand-1 (PD-L1) have been shown to significantly impact disease progression. We have analysed the expression of a subset of immune cell and immune checkpoint biomarkers in a cohort of SBA patients and assessed their impact on progression-free survival (PFS) and overall survival (OS). 25 patient samples in the form of formalin fixed, paraffin embedded (FFPE) tissue were obtained in tissue microarray (TMAs) format. Automated immunohistochemistry (IHC) staining was performed using validated antibodies for CD3, CD4, CD8, CD68, PD-L1, ICOS, IDO1 and LAG3. Slides were scanned digitally and assessed in QuPath, an open source image analysis software, for biomarker density and percentage positivity. Survival analyses were carried out using the Kaplan Meier method. Varying expressions of biomarkers were recorded. High expressions of CD3, CD4 and IDO1 were significant for PFS (p = 0.043, 0.020 and 0.018 respectively). High expression of ICOS was significant for both PFS (p = 0.040) and OS (p = 0.041), while high PD-L1 expression in tumour cells was significant for OS (p = 0.033). High correlation was observed between PD-L1 and IDO1 expressions (Pearson correlation co-efficient = 1) and subsequently high IDO1 expression in tumour cells was found to be significant for PFS (p = 0.006) and OS (p = 0.034). High levels of immune cells and immune checkpoint proteins have a significant impact on patient survival in SBA. These data could provide an insight into the immunotherapeutic management of patients with SBA.

Role of Programmed Cell Death-1 and Programmed Cell Death Ligand-1 immune checkpoint biomarkers among chronic Hepatitis C virus patients under Hemodialysis

Background: Hepatitis C virus (HCV) infection is one of the most common infections associated with chronic kidney disease (CKD) patients undergoing hemodialysis (HD) in Iraq. Aim of the study: To determine the prognostic factor value of Programmed Cell Death-1 (PD-1) and Programmed Cell Death Ligand-1 (PD-L1) immune checkpoint biomarkers among CKD patients with HCV infection under HD. Methodology: ELISA technique was used for the measurement of the above-mentioned biomarkers in the serum of 90 Iraqi patients. The participants were divided into three groups; Group I included 30 patients infected with HCV without antiviral treatment, group II included 30 patients infected with HCV with recent/previous antiviral treatment, and Group III included 30 patients without viral infection (control group). Results: Serum levels of the measured biomarkers were elevated among all the participants, and highly statistically significant differences were found between patients with no treatment. The area under the curve (AUC) of PD-1 was 99% and for PD-L1 was 96%. Conclusions: The PD-1 and PD-L1 immune checkpoint biomarkers have excellent prognostic factor value as predictors for patients with CKD on HD infected with HCV.

Role of CTLA-4, PD-1 and PD-L1 immune biomarkers among HCV patients undergoing hemodialysis

Introduction and Aim: One of the most prevalent diseases seen in Iraqi patients undergoing hemodialysis treatment for chronic renal disease is hepatitis C virus, also known as HCV infection (CKD). In this study, we intended to determine whether immune checkpoint biomarkers such as CTLA-4, PD-1, and PD-L1 might be utilized to predict the outcome for hemodialysis patients who had HCV infection and CKD. Materials and Methods: The study comprised 90 Iraqi patients. The participants were separated into three groups: Group I (control group) consisted of those without viral infection. Group II consisted of 30 HCV-infected patients who did not receive antiviral medication, whereas Group III consisted of 30 HCV-infected patients who had had recent/previous antiviral drug treatment. ELISA was used to evaluate the serum predictive values of immunological biomarkers in all three groups of people. The collected results were statistically analyzed. Results: Serum levels of the measured biomarkers were seen elevated among all individuals in Group I and II showing a high statistically significant difference between patients’ group and healthy controls. The area under the curve (AUC) for CTLA-4, PD-1, and PD-L1 was 93%, 99%, and 96%, respectively. Conclusion: The prognostic factor-value of immune biomarkers investigated in this study could be used as predictors in patients with CKD and infected with HCV.

Differential Spatial Gene and Protein Expression Associated with Recurrence Following Chemoradiation for Localized Anal Squamous Cell Cancer.

The identification of transcriptomic and protein biomarkers prognosticating recurrence risk after chemoradiation of localized squamous cell carcinoma of the anus (SCCA) has been limited by a lack of available fresh tissue at initial presentation. We analyzed archival FFPE SCCA specimens from pretreatment biopsies prior to chemoradiation for protein and RNA biomarkers from patients with localized SCCA who recurred (N = 23) and who did not recur (N = 25). Tumor cells and the tumor microenvironment (TME) were analyzed separately to identify biomarkers with significantly different expression between the recurrent and non-recurrent groups. Recurrent patients had higher mean protein expression of FoxP3, MAPK-activation markers (BRAF, p38-MAPK) and PI3K/Akt activation (phospho-Akt) within the tumor regions. The TME was characterized by the higher protein expression of immune checkpoint biomarkers such as PD-1, OX40L and LAG3. For patients with recurrent SCCA, the higher mean protein expression of fibronectin was observed in the tumor and TME compartments. No significant differences in RNA expression were observed. The higher baseline expression of immune checkpoint biomarkers, together with markers of MAPK and PI3K/Akt signaling, are associated with recurrence following chemoradiation for patients with localized SCCA. These data provide a rationale towards the application of immune-based therapeutic strategies to improve curative-intent outcomes beyond conventional therapies for patients with SCCA.

A systematic review and meta-analysis of long noncoding RNA 00963 expression and prognosis and clinicopathological characteristic in human cancers

Numerous studies have indicated that the aberrant expression of LINC00963 is extensively present in various human tumors, and that dysregulation of LINC00963 is implicated in the initiation and progression of human cancers. In this meta-analysis, data from diverse malignancies were analyzed to determine whether LINC00963 expression levels were associated with clinical prognosis and immune infiltration in pan-cancer. The eligible studies were identified from several electronic databases from the inception to July 2022 through systematic research. LINC00963 expression and survival were estimated using pooled odds ratios and hazard ratios with 95% CI. We used the Kaplan-Meier method and COX analysis for survival analysis. In addition, Spearman's correlation analysis was used to uncover any correlation between LINC00963 and microsatellites instability (MSI), tumor mutational burden (TMB), DNA methyltransferases (DNMTs), immune checkpoint biomarkers, and the related genes of mismatch repair (MMR). Our findings indicated that overexpression of LINC00963 was related to poor overall survival (OS) (HR =1.32, 95% CI, 1.09-1.59, P= 0.004). The TCGA database also found that abnormal expression of LINC00963 was linked to overall survival in various cancers. Moreover, there is an association between LINC00963 expression and MSI, TMB, and MMR in malignancies of various types. The results of this study indicate that LINC00963 may serve as a prognostic biomarker and a therapeutic target for cancer. By using it, cancer diagnoses can be improved, treatment targets discovered, and prognostic questions improved.

Sensitive and quantitative in vivo analysis of PD-L1 using magnetic particle imaging and imaging-guided immunotherapy.

The programmed cell death protein-1 (PD-1) and programmed cell death ligand-1 (PD-L1) expression correlate with the immunotherapeutic response rate. The sensitive and non-invasive imaging of immune checkpoint biomarkers is favorable for the accurate detection and characterization, image-guided immunotherapy in cancer precision medicine. Magnetic particle imaging (MPI), as a novel and emerging imaging modality, possesses the advantages of high sensitivity, no image depth limitation, positive contrast, and absence of radiation. Hence, in this study, we performed the pioneer investigation of monitoring PD-L1 expression using MPI and the MPI-guided immunotherapy. We developed anti-PD-L1 antibody (aPDL1)-conjugated magnetic fluorescent hybrid nanoparticles (MFNPs-aPDL1) and utilized MPI in combination with fluorescence imaging (FMI) to dynamically monitor and quantify PD-L1 expression in various tumors with different PD-L1 expression levels. The ex vivo real-time polymerase chain reaction (qPCR), western blotting, and immunofluorescence staining analysis were further performed to validate the in vivo imaging observation. Moreover, the MPI was further performed for the guidance of immunotherapy. Our data showed that PD-L1 expression can be specifically and sensitively monitored and quantified using MPI and FMI imaging methods, which were validated by ex vivo qPCR and western blotting analysis. In addition, MPI-guided PD-L1 immunotherapy can enhance the effectiveness of cancer immunotherapy. To our best knowledge, this is the pioneer study to utilize MPI in combination with a newly developed MFNPs-aPDL1 imaging probe to dynamically visualize and quantify PD-L1 expression in tumor microenvironment. This imaging strategy may facilitate the clinical optimization of immunotherapy management.

LncRNA DUXAP8 as a prognostic biomarker for various cancers: A meta-analysis and bioinformatics analysis.

Background: Dual homeoboxes A pseudogene 8 (DUXAP8) is a newly discovered long noncoding RNA that has been shown to function as an oncogene in a variety of human malignant cancers. By integrating available data, this meta-analysis sought to determine the relationship between clinical prognosis and DUXAP8 expression levels in diverse malignancies. Materials and methods: A systematic search was performed to identify eligible studies from several electronic databases from their inception to 25 October 2021. Pooled odds ratios and hazard ratios with 95% CI were used to estimate the association between DUXAP8 expression and survival. For survival analysis, the Kaplan-Meier method and COX analysis were used. Furthermore, we utilized Spearman’s correlation analysis to explore the correlation between DUXAP8 and tumor mutational burden (TMB), microsatellite instability (MSI), the related genes of mismatch repair (MMR), DNA methyltransferases (DNMTs), and immune checkpoint biomarkers. Results: Our findings indicated that overexpression of DUXAP8 was related to poor overall survival (OS) (HR = 1.63, 95% CI, 1.49–1.77, p < 0.001). In addition, elevated DUXAP8 expression was closely related to poor OS in several cancers in the TCGA database. Moreover, DUXAP8 expression has been associated with TMB, MSI, and MMR in a variety of malignancies. Conclusion: This study revealed that DUXAP8 might serve as a prognostic biomarker and potential therapeutic target for cancer. It can be used to improve cancer diagnosis, discover potential treatment targets, and improve prognosis.

Predictive value of Leukocyte ImmunoTest (LIT™) in cancer patients: a prospective cohort study

Early diagnosis of cancer is crucial to initiate prompt treatment for better patient outcomes. The host immune function and its associated modulators are considered to be potential biomarkers for early cancer diagnosis. Immune and immune-checkpoint biomarkers have been reported to contribute to cancer development, while a high neutrophil-to-lymphocyte ratio has been shown to be associated with poor survival outcomes in a variety of cancers. One hundred sixty-one cancer patients were recruited to take a cost-effective novel Leukocyte ImmuneTest (LIT). LIT was measured to objectively determine the pre-treatment immune status of patients. The correlation between LIT and other conventional diagnostic markers or tumor-related variables was then investigated. Significant correlations between LIT and white blood cell count, smoking status, and tumor stage 4 were found. In addition, the LIT score significantly differentiated between malignant and benign tumors in this study population. Our work raises the possibility to use LIT for general screening surveillance before further costly specialized equipment is applied for cancer diagnosis.

MACC1 Promotes the Progression and Is a Novel Biomarker for Predicting Immunotherapy Response in Colorectal Cancer.

Aims As one of the most prevalent malignant diseases in the world, the mechanisms of metastasis in colon cancer are poorly understood. The aim of this study was to investigate the role of the HGF/c-MET axis in the proliferation and metastasis in colon cancer. Methods The effect of MACC1 on cell proliferation and metastasis was analyzed through a series of in vitro experiments. The role of MACC1 in cancer cells was demonstrated by overexpression and silencing of MACC1 in gain or loss function experiments. To investigate the relationship between MACC1 and c-MET/HGF, we detected c-MET protein expression by disrupting with or overexpressing MACC1. The bioinformatics analysis was used to investigate the correlation between MACC1 and c-MET, and the c-MET expression after the interference of HGF with MACC1 was determined. Subsequently, the function of c-MET was verified in colon cancer cells by a series of experiments. The mouse tumor transplantation model experiment is most suitable in vivo. Results The results indicated that the overexpression of MACC1 could accelerate proliferation and facilitate metastasis in colon cancer cell lines. Furthermore, c-MET was determined to be the downstream regulator of MACC1. The addition of HGF could stimulate the expression of MACC1. With further exploration, we proved that c-MET is downstream of MACC1 in colon cancer and that overexpression of c-MET in colon cancer enhances cell proliferation and migration capability. At last, MACC1 expression level negatively correlates with the infiltration levels and several immune checkpoint biomarkers. High MACC1 expression has a lower response rate with ICIs in COAD. Conclusions We found that, under the regulation of the MACC1/HGF/c-MET axis, the proliferation and metastasis of colorectal cancer are increased by MACC1, which can be a novel biomarker for predicting ICIs response in colorectal cancer. Our findings provide a new idea for the targeted treatment of colorectal cancer.

Congress of neurological surgeons systematic review and evidence-based guidelines update on the role of neuropathology in the management of progressive glioblastoma in adults.

These recommendations apply to adult patients with progressive or recurrent glioblastoma (GBM). For adult patients with progressive glioblastoma does testing for Isocitrate Dehydrogenase (IDH) 1 or 2 mutations provide new additional management or prognostic information beyond that derived from the tumor at initial presentation? Level III: Repeat IDH mutation testing is not necessary if the tumor is histologically similar to the primary tumor and the patient's clinical course is as expected. For adult patients with progressive glioblastoma does repeat testing for MGMT promoter methylation provide new or additional management or prognostic information beyond that derived from the tumor at initial presentation and what methods of detection are optimal? Level III: Repeat MGMT promoter methylation is not recommended. For adult patients with progressive glioblastoma does EGFR amplification or mutation testing provide management or prognostic information beyond that provided by histologic analysis and if performed on previous tissue samples, does it need to be repeated? Level III: In cases that are difficult to classify as glioblastoma on histologic features EGFR amplification testing may help in classification. If a previous EGFR amplification was detected, repeat testing is not necessary. Repeat EGFR amplification or mutational testing may be recommended in patients in which target therapy is being considered. For adult patients with progressive glioblastoma does large panel or whole genome sequencing provide management or prognostic information beyond that derived from histologic analysis? Level III: Primary or repeat large panel or whole genome sequencing may be considered in patients who are eligible or interested in molecularly guided therapy or clinical trials. For adult patients with progressive glioblastoma should immune checkpoint biomarker testing be performed to provide management and prognostic information beyond that obtained from histologic analysis? Level III: The current evidence does not support making PD-L1 or mismatch repair (MMR) enzyme activity a component of standard testing. For adult patients with progressive glioblastoma are there meaningful biomarkers for bevacizumab responsiveness and does their assessment provide additional information for tumor management and prognosis beyond that learned by standard histologic analysis? Level III: No established Bevacizumab biomarkers are currently available based upon the inclusion criteria of this guideline.

UBE3A deletion enhances the efficiency of immunotherapy in non-small-cell lung cancer

ABSTRACT Immunotherapy significantly improves the prognosis of advanced lung cancer. It has become an important treatment option for advanced lung cancer. However, there remain many limitations in clinical treatment, and only a small portion of patients can benefit from immunotherapy. Our study aimed to identify markers that can precisely forecast the efficacy of immunotherapy in patients. We analyzed a non-small-cell lung cancer (NSCLC) immune checkpoint inhibitor (ICI) cohort (n=240). We used this discovery cohort to identify CNVs in genes associated with immunotherapy. We further analyzed immune biomarkers and immune infiltration in The Cancer Genome Atlas (TCGA)-NSCLC cohort and the Gene Expression Omnibus (GEO) cohorts. By analyzing an ICI dataset from MSKCC, we found that progression-free survival (PFS) was improved after UBE3A deletion (UBE3A-del). The analysis results showed that UBE3A-del had higher immunocyte infiltration levels and higher expression levels of immune checkpoint biomarkers and affected the enrichment levels of immune signaling pathways. Our results suggest that UBE3A-del can be used as a predictive biomarker of NSCLC to screen for NSCLC patients who may benefit from ICI therapy. Abbreviations: NSCLC: Non-small cell lung cancer; CNV: Copy number variation; ICIs: Immune checkpoint inhibitors; TCGA: The cancer genome atlas; GEO: Gene expression omnibus; GSEA: Gene set enrichment; PFS: Progression-free survival; OS: Overall survival; TMB: Tumor mutational burden; CTLA-4: Cytotoxic T lymphocyte antigen 4; PD-(L)1: Programmed cell death (ligand) 1; MSI: Microsatellite instability; dMMR: DNA mismatch repair; SCNAs: Somatic copy number alterations; TME: Tumor microenvironment; MSK-IMPACT: The Memorial Sloan Kettering-Integrated Mutation Profilng of Actionable; Cancer Targets; FDA: Food and Drug Administration; WES: Whole-exome sequencing; SNP: Single Nucleotide Polymorphisms; FDR: False discovery rate; DCR: Disease control rate; DDR: DNA damage response and repair; MDSCs: Myeloid-derived suppressor cells; FAO: Fatty acid oxidation

A 13-Gene Signature Based on Estrogen Response Pathway for Predicting Survival and Immune Responses of Patients With UCEC.

Background: Accumulating evidence suggests that anti-estrogens have been effective against multiple gynecological diseases, especially advanced uterine corpus endometrial carcinoma (UCEC), highlighting the contribution of the estrogen response pathway in UCEC progression. This study aims to identify a reliable prognostic signature for potentially aiding in the comprehensive management of UCEC. Methods: Firstly, univariate Cox and LASSO regression were performed to identify a satisfying UCEC prognostic model quantifying patients’ risk, constructed from estrogen-response-related genes and verified to be effective by Kaplan-Meier curves, ROC curves, univariate and multivariate Cox regression. Additionally, a nomogram was constructed integrating the prognostic model and other clinicopathological parameters. Next, UCEC patients from the TCGA dataset were divided into low- and high-risk groups according to the median risk score. To elucidate differences in biological characteristics between the two risk groups, pathway enrichment, immune landscape, genomic alterations, and therapeutic responses were evaluated to satisfy this objective. As for treatment, effective responses to anti-PD-1 therapy in the low-risk patients and sensitivity to six chemotherapy drugs in the high-risk patients were demonstrated. Results: The low-risk group with a relatively favorable prognosis was marked by increased immune cell infiltration, higher expression levels of HLA members and immune checkpoint biomarkers, higher tumor mutation burden, and lower copy number alterations. This UCEC prognostic signature, composed of 13 estrogen-response-related genes, has been identified and verified as effective. Conclusion: Our study provides molecular signatures for further functional and therapeutic investigations of estrogen-response-related genes in UCEC and represents a potential systemic approach to characterize key factors in UCEC pathogenesis and therapeutic responses.

Construction of a Novel Immune-Related mRNA Signature to Predict the Prognosis and Immune Characteristics of Human Colorectal Cancer.

Background: Anti-cancer immunotherapeutic approaches have gained significant efficacy in multiple cancer types. However, not all patients with colorectal cancer (CRC) could benefit from immunotherapy due to tumor heterogeneity. The purpose of this study was to construct an immune-related signature for predicting the immune characteristics and prognosis of CRC. Methods: RNA-sequencing data and corresponding clinical information of patients with CRC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), and immune-related genes (IRGs) were downloaded from the Immunology Database and Analysis Portal (ImmPort). Then, we utilized univariate, lasso regression, and multivariate cox regression to identify prognostic IRGs and develop the immune-related signature. Subsequently, a nomogram was established based on the signature and other prognostic factors, and its predictive capacity was assessed by receiver operating characteristic (ROC) and decision curve analysis (DCA). Finally, associations between the signature and the immune characteristics of CRC were assessed. Results: In total, 472 samples downloaded from TCGA were divided into the training cohort (236 samples) and internal validation cohort (236 samples), and the GEO cohort was downloaded as an external validation cohort (122 samples). A total of 476 differently expressed IRGs were identified, 17 of which were significantly correlated to the prognosis of CRC patients. Finally, 10 IRGs were filtered out to construct the risk score signature, and patients were divided into low- and high-risk groups according to the median of risk scores in the training cohort. The high-risk score was significantly correlated with unfavorable survival outcomes and aggressive clinicopathological characteristics in CRC patients, and the results were further confirmed in the internal validation cohort, entire TCGA cohort, and external validation cohort. Immune infiltration analysis revealed that patients in the low-risk group infiltrated with high tumor-infiltrating immune cell (TIIC) abundances compared to the high-risk group. Moreover, we also found that the immune checkpoint biomarkers were significantly overexpressed in the low-risk group. Conclusion: The prognostic signature established by IRGs showed a promising clinical value for predicting the prognosis and immune characteristics of human CRC, which contribute to individualized treatment decisions.

Comprehensive Analysis of ANLN in Human Tumors: A Prognostic Biomarker Associated with Cancer Immunity.

Background Anillin (ANLN), a ubiquitously expressed actin-binding protein, plays a critical tumor-promoting role in cell growth, migration, and cytokinesis. Numerous studies have suggested that ANLN is upregulated in many cancer types, as well as significantly associated with patient prognosis and malignant cancer characteristics. Herein, we performed an integrated pan-cancer analysis of ANLN and highlighted its underlying mechanism, which may benefit further exploration of the potential therapeutic options for cancer. Methods ANLN expression data were extracted from online databases, including TCGA, GTEx, and CCLE databases. The TIMER database was used to study the association between ANLN expression with immune checkpoint genes and immunocyte infiltration. The ScanNeo pipeline was adopted for neoantigen discovery. KEGG analysis and the STRING tool were used to elucidate the potential mechanism of ANLN in cancer development. Results ANLN is abnormally overexpressed in almost all cancer tissues compared with normal tissues. The high-ANLN expression level was positively associated with various malignant characteristics, suggesting its potential role in the immune microenvironment and poor prognosis. In addition, ANLN expression was correlated with the number of neoantigens and different phosphorylation pattern in various cancer types, revealing a functional role of genetic mutation accumulation and high phosphorylation in ANLN-mediated oncogenesis. Moreover, we found that ANLN was an important regulatory factor participating in many signaling events, especially the cell cycle and nucleocytoplasmic transport pathways. Conclusions ANLN expression is generally overexpressed in various types of cancers, and it may have an important influence on tumor progression and development. ANLN expression is significantly associated with the immune checkpoint biomarkers and tumor immunity. Together, these findings suggest that ANLN may be a predictive marker for patient prognosis across cancers.