TCGA Tumor Research Articles

Identification of anoikis related subtypes and construction of prognostic model in hepatocellular carcinoma.

Anoikis resistance, the acquired ability of tumor cells to resist detachment-induced cell death, has been linked to loss of cellular homeostasis, cancer growth, and metastasis. After cancer cells acquire this ability, they can spread to other tissues or organs in the body through the blood circulation system, promoting the distant metastasis of cancer. Therefore, studying the molecular mechanism of anti-anoikis is one of the effective methods for discovering the treatment of human malignant tumors. This article aims to explore the expression of anoikis genes in hepatocellular carcinoma, identify and characterize the molecular subtypes based on anoikis genes, screen key features, construct a prognostic signature, and explore the treatment response of patients with different risks. This study utilized the TCGA tumor database to calculate differential expression between hepatocellular carcinoma and adjacent tissues using the limma package. A protein interaction network was constructed using the STRING database for gene GO enrichment analysis. Consensus clustering analysis was performed on anoikis apoptotic genes using TCGA tumor sample data as a training set to identify molecular subtypes. Principal component analysis was also performed, along with survival difference analysis on different groups. Additionally, immune cellular infiltration was analyzed using CIBERSORT, XCELL, SSGSEA, and ESTIMATE analysis tools. Finally, univariate cox screening was used to identify prognostic related genes based on differentially expressed genes between subtypes.Based on the analysis of prognostic genes, we utilized the LASSO cox algorithm to eliminate redundant genes and construct a prognostic model using characteristic genes. The prognostic performance was evaluated through training and verification sets, and patients were classified into high and low risk groups based on the median score of the model. Survival differences were then compared between these groups. Univariate and multivariate cox analyses were conducted to confirm that the signature genes were independent prognostic factors. Lastly, relevant molecular responses and potential drug treatment effects were predicted. Most anoikis genes were broadly dysregulated in the TCGA-LIHC cohort; molecular subtypes were identified using unsupervised clustering, and samples were divided into 2 subtypes with significant prognostic differences between subtypes difference; 13 key prognostic genes were finally screened and a risk scoring model was built. The prognostic model had a higher AUC and had a better predictive effect; drug efficacy prediction had a better curative effect in the low-risk group. In this study, a prognostic model of anoikis-related genes in liver hepatocellular carcinoma was constructed, and the model has good predictive performance.

An alternatively spliced PD-L1 isoform PD-L1∆3, and PD-L2 expression in breast cancers: implications for eligibility scoring and immunotherapy response.

Targeting PD-1/PD-L1 has shown substantial therapeutic response and unprecedented long-term durable responses in the clinic. However, several challenges persist, encompassing the prediction of treatment effectiveness and patient responses, the emergence of treatment resistance, and the necessity for additional biomarkers. Consequently, we comprehensively explored the often-overlooked isoforms of crucial immunotherapy players, leveraging transcriptomic analysis, structural modeling, and immunohistochemistry (IHC) data. Our investigation has led to the identification of an alternatively spliced isoform of PD-L1 that lacks exon 3 (PD-L1∆3) and the IgV domain required to interact with PD-1. PD-L1∆3 is expressed more than the canonical isoform in a subset of breast cancers and other TCGA tumors. Using the deep learning-based protein modeling tool AlphaFold2, we show the lack of a possible interaction between PD-L1∆3 and PD-1. In addition, we present data on the expression of an additional ligand for PD-1, PD-L2. PD-L2 expression is widespread and positively correlates with PD-L1 levels in breast and other tumors. We report enriched epithelial-mesenchymal transition (EMT) signature in high PD-L2 transcript expressing (PD-L2 > PD-L1) tumors in all breast cancer subtypes, highlighting potential crosstalk between EMT and immune evasion. Notably, the estrogen gene signature is downregulated in ER + breast tumors with high PD-L2. The data on PD-L2 IHC positivity but PD-L1 negativity in breast tumors, together with our results on PD-L1∆3, highlight the need to utilize PD-L2 and PD-L1 isoform-specific antibodies for staining patient tissue sections to offer a more precise prediction of the outcomes of PD-1/PD-L1 immunotherapy.

Exploring the role of macrophages in the progression from atypical hyperplasia to endometrial carcinoma through single-cell transcriptomics and bulk transcriptomics analysis.

In this study, we aimed to identify key genes in endometrial cancer by conducting single-cell analysis of macrophages. We sourced clinical data from the TCGA database as well as supplementary datasets GSE201926 and GSE173682. Using bulk-seq data of atypical endometrial hyperplasia and endometrial cancer, we pinpointed key differentially expressed genes. Single-cell RNA sequencing was utilized for further gene expression analysis. Cluster analysis was conducted on TCGA tumor data, identifying two distinct subtypes. Statistical methods employed included LASSO regression for diagnostic modeling and various clustering algorithms for subtype identification. We found that subtype B was closely related to cellular metabolism. A diagnostic model was established using LASSO regression and was based on the genes CDH18, H19, PAGE2B, PXDN, and THRB. This model effectively differentiated the prognosis of cervical cancer. We also constructed a prognosis model and a column chart based on these key genes. Through CIBERSORT analysis, CDH18 and PAGE2B were found to be strongly associated with macrophage M0. We propose that these genes influence the transformation from atypical endometrial hyperplasia to endometrial cancer by affecting macrophage M0. In conclusion, these key genes may serve as therapeutic targets for endometrial cancer. A new endometrial cancer risk prognosis model and column chart have been constructed based on these genes, offering a reliable direction for future cervical cancer treatment.

A high-throughput test enables specific detection of hepatocellular carcinoma

High-throughput tests for early cancer detection can revolutionize public health and reduce cancer morbidity and mortality. Here we show a DNA methylation signature for hepatocellular carcinoma (HCC) detection in liquid biopsies, distinct from normal tissues and blood profiles. We developed a classifier using four CpG sites, validated in TCGA HCC data. A single F12 gene CpG site effectively differentiates HCC samples from other blood samples, normal tissues, and non-HCC tumors in TCGA and GEO data repositories. The markers were validated in a separate plasma sample dataset from HCC patients and controls. We designed a high-throughput assay using next-generation sequencing and multiplexing techniques, analyzing plasma samples from 554 clinical study participants, including HCC patients, non-HCC cancers, chronic hepatitis B, and healthy controls. HCC detection sensitivity was 84.5% at 95% specificity and 0.94 AUC. Implementing this assay for high-risk individuals could significantly decrease HCC morbidity and mortality.

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.

The expression profiling and clinical significance of a chronic pain-related gene IL1R1.

Chronic pain is a disease that existed during cancer treatment for a long time. It has been reported that interleukin (IL)-1 is involved in the inflammatory response during tumor development. IL1R1 and IL1R2 are members of the IL-1 receptor family of cytokine receptors. However, few studies have reported the role of chronic pain-related genes, IL1R1, in pan-cancer. In this study, 8 lumbar disc prolapse (LDP) patients and 8 controls with differentially expressed genes were investigated to find chronic pain-related genes. Then, IL1R1 was analyzed using the TCGA database. The clinical survival data from TCGA were used to analyze the prognostic value of IL1R1. This study further evaluated the relationship between IL1R1 and immune checkpoints, immune-activating genes, immunosuppressive genes, chemokines, and chemokine receptors. IL1R1 was expressed in varying degrees in most TCGA tumor types, indicating a better survival status. The expression of IL1R1 is closely related to T cell infiltration, immune checkpoints, immune-activating genes, immunosuppressive genes, chemokines, and chemokine receptors. The results show that IL1R1 is a kind of potential cancer biomarker. Coordination with other immune checkpoints IL1R1k may adjust the immune microenvironment, immunotherapy can be applied to the development of new targeted drugs.

Identification of New Key Genes and Their Association with Breast Cancer Occurrence and Poor Survival Using In Silico and In Vitro Methods.

Breast cancer is one of the most prevalent types of cancer diagnosed globally and continues to have a significant impact on the global number of cancer deaths. Despite all efforts of epidemiological and experimental research, therapeutic concepts in cancer are still unsatisfactory. Gene expression datasets are widely used to discover the new biomarkers and molecular therapeutic targets in diseases. In the present study, we analyzed four datasets using R packages with accession number GSE29044, GSE42568, GSE89116, and GSE109169 retrieved from NCBI-GEO and differential expressed genes (DEGs) were identified. Protein-protein interaction (PPI) network was constructed to screen the key genes. Subsequently, the GO function and KEGG pathways were analyzed to determine the biological function of key genes. Expression profile of key genes was validated in MCF-7 and MDA-MB-231 human breast cancer cell lines using qRT-PCR. Overall expression level and stage wise expression pattern of key genes was determined by GEPIA. The bc-GenExMiner was used to compare expression level of genes among groups of patients with respect to age factor. OncoLnc was used to analyze the effect of expression levels of LAMA2, TIMP4, and TMTC1 on the survival of breast cancer patients. We identified nine key genes, of which COL11A1, MMP11, and COL10A1 were found up-regulated and PCOLCE2, LAMA2, TMTC1, ADAMTS5, TIMP4, and RSPO3 were found down-regulated. Similar expression pattern of seven among nine genes (except ADAMTS5 and RSPO3) was observed in MCF-7 and MDA-MB-231 cells. Further, we found that LAMA2, TMTC1, and TIMP4 were significantly expressed among different age groups of patients. LAMA2 and TIMP4 were found significantly associated and TMTC1 was found less correlated with breast cancer occurrence. We found that the expression level of LAMA2, TIMP4, and TMTC1 was abnormal in all TCGA tumors and significantly associated with poor survival.

A pan-cancer analysis of the oncogenic role of YKT6 in human tumors.

YKT6, as a Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein with vesicle trafficking, plays an essential role in the development and progression of tumor. However, the gene of YKT6 has not been fully assessed in pan-cancer studies. We aim to investigate the gene of YKT6 across 33 different types of tumor by using the Cancer Genome Atlas, Gene Expression Omnibus database, and other several kinds of bioinformatic tools. YKT6 is significantly up-regulated in most tumors, and we found that overexpression of YKT6 is positively associated with poor prognosis of overall survival and poor disease-free survival prognosis in several tumors, such as Adrenocortical carcinoma, Bladder Urothelial Carcinoma, Head and Neck squamous cell carcinoma. We also detected distinct associations exist between YKT6 and tumor mutational burden or microsatellite instability with tumors. YKT6 expression was positively related to cancer-associated fibroblasts for TCGA tumors of colon adenocarcinoma and LGG. Furthermore, we discovered a significantly positively correlation between YKT6 expression and endothelial cell in tumors of colon adenocarcinoma, HNSC-HPV+, OV, READ and THCA. While a negative relationship was obtained between YKT6 expression and endothelial cell in KIRC. Moreover, "Syntaxin binding," "SNARE complex," "vesicle fusion" and "DNA replication" are involved in the influence of YKT6 on tumor pathogenesis. Our pan-cancer analysis offers a deep comprehending the gene of YKT6 in tumoeigenesis from viewpoint of clinical tumor samples.

Abstract 6418: xWU-NK-101 as salvage therapy post immune checkpoint blockade (ICB)

Abstract ICB therapy has transformed cancer treatment; durable responses in difficult-to-treat cancers have been observed. Despite this most patients (pts) don’t respond to ICB (primary resistance), and many pts who initially respond eventually relapse (acquired resistance). Primary resistance is associated with tumor cell extrinsic factors, e.g., the immunosuppressive nature of the tumor microenvironment (TME), while acquired resistance is associated with tumor intrinsic factors, e.g., downregulation of MHC1, preventing T cell recognition. Treatments to overcome ICB resistance are necessary. WU-NK-101 is a PBMC-derived, cytokine-reprogrammed, expanded, and cryopreserved off-the-shelf memory NK cell product. WU-NK-101 cells capture the memory-like NK cell biology of cytokine-induced memory-like (CIML) NK cells, exhibiting enhanced cytotoxicity, metabolic fitness/flexibility, and resistance to TME immunosuppression (Muth et al. EHA 2022; Rutella et al. ESMO 2022). Bone marrow biopsies, collected from R/R AML pts who received CIML-NK cells (NCT01898793), were interrogated using immune gene expression (GE) profiling and spatially resolved proteomics (IO360® panel, n = 740 genes, and GeoMx® DSP; NanoString Technologies). Higher T-cell infiltration was noted post CIML-NK. CIBERSORT deconvoluted GE data inferred higher abundance of macrophages, γδT cells and activated dendritic cells on day 28 post-treatment. GE signatures showed downregulation of NFIL3 and FAM30A (log2 fold-change <1.0; p<0.05) post CIML-NK. TIDE algorithm modelling indicated that lower expression of NFIL3 and FAM30A correlated with high CTL infiltration and improved outcomes in many TCGA tumors (Jiang et al. Nat. Med. 2018). Hence, CIML-NK treatment led to modifications in the TME towards a more T-cell amenable environment. Deleting MHC1 on NALM6 cells significantly improved WU-NK-101 killing compared to WT (p<0.0001), highlighting one mechanism whereby WU-NK-101 overcomes acquired ICB resistance. In transwell assays, co-incubation of tumor cells with WU-NK-101 in the lower chamber led to dose dependent killing; in the upper chamber (tumor cells alone), viability was preserved but a dose-dependent increase of MHC1/PDL1 expression was noted. Similar results were observed using cell-free conditioned media from WU-NK-101 cytotoxicity assays, suggesting that soluble factors released from WU-NK-101 augment MHC1/PDL1 expression. Treatment of tumor cells with IFNγ alone led to similar increases in MHC1/PDL1 expression. Importantly, in vivo experiments revealed that residual tumor cells post WU-NK-101 treatment exhibited higher levels of MHC1/PDL1. Overall, these data highlight a further mechanism through which WU-NK-101 overcomes acquired ICB resistance. In summary, WU-NK-101 has the potential to reverse primary and acquired mechanisms of ICB resistance. A Phase 1b clinical trial of WU-NK-101 as salvage therapy post-ICB is in development. Citation Format: Tom A. Leedom, Barbara Muz, Jaykumar Vadakekolathu, John J. Muth, Xiao-Hua Li, Gregory Watson, Kristaan Magee, Ryan P. Sullivan, Melissa Berrien-Elliott, Todd Fenigher, Sergio Rutella, Matthew L. Cooper, Ayman Kabakibi, Jan K. Davidson-Moncada. xWU-NK-101 as salvage therapy post immune checkpoint blockade (ICB) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6418.

Abstract 5907: The tumor microbiome associates with features of the tumor microenvironment, treatment outcomes, and histologies: A national collaboration of the exORIEN Consortium

Abstract A tumor microbiome has recently been established as present in many cancer types. Further study is needed to define the scope of its role in cancer tumorigenesis, progression, and treatment outcomes. The Oncology Research Information Exchange Network (ORIEN) established a collaboration among eight member institutions to study the tumor microbiome and clinical features across several cancers. We evaluated RNAseq data from n = 2,892 tumors, including colorectal adenocarcinomas, lung adeno- and squamous cell carcinomas, pancreatic adenocarcinomas, sarcomas, melanomas, and thyroid carcinomas, using the tool {exotic}. Matched cancers from the Cancer Genome Atlas were processed by the same method (n = 2,720 samples). Clinical data, including treatment information, lab values, detailed histology, and long-term follow-up, were collected and harmonized across sites. Microbe abundances (bacteria, fungi, and viruses) were associated with clinical features and human gene expression, which was deconvolved into immune cell composition using {CIBERSORT} and {TIMEx}, and aggregated into expression signatures using {tmesig} and {IOSig}. Microbes were found in all tumors and associated with treatment outcomes for all modalities tested, including radiation in colorectal cancer, chemotherapy in pancreatic cancer, and immunotherapy in melanoma. In the case of radiation treatment in colorectal cancer, the microbes also affected outcomes in preclinical model systems and were modified by altering hypoxia levels with the drug atovaquone. Virus prevalence associated with histological subtypes in lung cancer. Similar microbes in ORIEN and TCGA tumors associated with overall survival in subtypes of sarcoma (dedifferentiated liposarcoma, leiomyosarcoma, and others). Finally, microbes associated with expression-based indicators of the tumor microenvironment across cancer types. These results suggest that the tumor microbiome may have broad clinical utility as a biomarker of treatment outcomes and as a target for rational manipulation. Citation Format: Rebecca Hoyd, Caroline E. Wheeler, Samuel Coleman, Louis Denko, Carlos Chan, Yousef Zakharia, Rebecca Dodd, Cornelia M. Ulrich, Sheetal Hardikar, Jennifer Ose, Michelle Churchman, Ahmad Tarhini, Lary A. Robinson, Eric Singer, Alexandra P. Ikeguchi, Martin McCarter, Kyra Anderson, John Carpten, Gabriel Tinoco, Marium Hussain, Nicolas Denko, YunZhou Liu, Ning Jin, Youngchul Kim, Asgeir Masson, Naomi Fei, Martin Benej, McKenzie Kreamer, Dennis Dennis Grencewicz, Ahmed Hussein, Aik Choon Tan, Daniel Spakowicz. The tumor microbiome associates with features of the tumor microenvironment, treatment outcomes, and histologies: A national collaboration of the exORIEN Consortium. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5907.

Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements.

Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors to create new TE-chimeric transcripts, which can produce immunogenic antigens. We performed a comprehensive screen for these TE exaptation events in 33 TCGA tumor types, 30 GTEx adult tissues and 675 cancer cell lines, and identified 1,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Whole-lysate and HLA-pulldown mass spectrometry data confirmed that TS-TEAs are presented on the surface of cancer cells. In addition, we highlight tumor-specific membrane proteins transcribed from TE promoters that constitute aberrant epitopes on the extracellular surface of cancer cells. Altogether, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that could potentially be therapeutically exploited and targeted.

Vacuolar protein sorting 35 (VPS35) acts as a tumor promoter via facilitating cell cycle progression in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is insidious and highly malignant with extremely poor prognosis and drug resistance to current chemotherapies. Therefore, there is a critical need to investigate the molecular mechanism underlying PDAC progression to develop promising diagnostic and therapeutic interventions. In parallel, vacuolar protein sorting (VPS) proteins, involved in the sorting, transportation, and localization of membrane proteins, have gradually attracted the attention of researchers in the development of cancers. Although VPS35 has been reported to promote carcinoma progression, the specific molecular mechanism is still unclear. Here, we determined the impact of VPS35 on the tumorigenesis of PDAC and explored the underlying molecular mechanism. We performed a pan-cancer analysis of 46 VPS genes using RNAseq data from GTEx (control) and TCGA (tumor) and predicted potential functions of VPS35 in PDAC by enrichment analysis. Furthermore, cell cloning experiments, gene knockout, cell cycle analysis, immunohistochemistry, and other molecular and biochemical experiments were used to validate the function of VPS35. Consequently, VPS35 was found overexpressed in multiple cancers and correlated with the poor prognosis of PDAC. Meanwhile, we verified that VPS35 could modulate the cell cycle and promote tumor cell growth in PDAC. Collectively, we provide solid evidence that VPS35 facilitates the cell cycle progression as a critical novel target in PDAC clinical therapy.

Pan-cancer analysis reveals signal transducer and activator of transcription (STAT) gene family as biomarkers for prognostic prediction and therapeutic guidance.

Background: The signal transducer and activator of transcription (STAT) gene family have been widely found to regulate cell proliferation, differentiation, apoptosis, and angiogenesis through complex signaling pathways, and thus impacting tumor formation and development in different types of tumor. However, the roles of STATs on prognostic prediction and therapeutic guidance in pan-cancer remain unexplored. Materials and Methods: The dataset of 33 types of TCGA tumor, para-carcinoma and normal tissues, was obtained from the UCSC Xena database, including the gene expression profiles in the formats of FPKM value, demographic characteristics, clinical information, and survival data of STATs. Differential expression and co-expression analyses, WGCNA, clinical relevance analysis, immune subtype analysis, tumor stemness analysis, tumor purity analysis, immune infiltration analysis, immunotherapy related analysis, tumor mutation related analysis, and drug sensitivity analysis were performed by R software. Results: Differential expression of STAT1 was found between normal and BRCA tissues (p < 0.001, log2FC = 0.895). Additionally, the strongest correlation among STATs lied between STAT1 and STAT2 (correlation coefficient = 0.6). Moreover, high expression levels of STAT1 (p = 0.031) were revealed to be notably correlated with poor prognosis in KIRP. In addition, STAT1 expressed the highest value in immune subtypes C1, C2, C3, and C6 in LUAD. What's more, strong negative correlations were demonstrated between expression of STAT6 and mDNAss and mRNAss of TGCT. Additionally, STAT4 expression was characterized to be significantly negatively correlated with tumor purity of the majority of cancer types. Moreover, STAT1 and STAT3 were shown to be generally high-expressed in pan-cancer myeloid cells, and STATs all had positive correlation with the infiltration of the majority of immune cells. In addition, STATs were revealed to be closely linked with immunotherapy response. What's more, STAT4 expression was identified to have a strong negative correlation with TMB value in DLBC. Last but not least, positive correlations were accessed between STAT5 and sensitivity of Nelarabine (cor = 0.600, p < 0.001). Conclusion: In the present study, we identified STATs as biomarkers for prognostic prediction and therapeutic guidance in pan-cancer. Hopefully our findings could provide a valuable reference for future STATs research and clinical applications.

Pervasiveness of HLA allele-specific expression loss across tumor types

BackgroundEfficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune-mediated killing of cancer cells. According to recent reports, patient HLA-I genotypes can impact the efficacy of cancer immunotherapy, and the somatic loss of HLA-I heterozygosity has been established as a factor in immune evasion. While global deregulated expression of HLA-I has also been reported in different tumor types, the role of HLA-I allele-specific expression loss — that is, the preferential RNA expression loss of specific HLA-I alleles — has not been fully characterized in cancer.MethodsHere, we use RNA and whole-exome sequencing data to quantify HLA-I allele-specific expression (ASE) in cancer using our novel method arcasHLA-quant.ResultsWe show that HLA-I ASE loss in at least one of the three HLA-I genes is a pervasive phenomenon across TCGA tumor types. In pancreatic adenocarcinoma, tumor-specific HLA-I ASE loss is associated with decreased overall survival specifically in the basal-like subtype, a finding that we validated in an independent cohort through laser-capture microdissection. Additionally, we show that HLA-I ASE loss is associated with poor immunotherapy outcomes in metastatic melanoma through retrospective analyses.ConclusionsTogether, our results highlight the prevalence of HLA-I ASE loss and provide initial evidence of its clinical significance in cancer prognosis and immunotherapy treatment.

Pan-cancer analysis reveals DDX21 as a potential biomarker for the prognosis of multiple tumor types.

DExD-box helicase 21 (DDX21) is an essential member of the RNA helicase family. DDX21 is involved in the carcinogenesis of various malignancies, but there has been no comprehensive research on its involvement in different types of cancer. This study used TCGA, CPTAC, GTEx, GEO, FANTOM5, BioGRID, TIMER2, GEPIA2, cBioPortal, STRING, and Metascape databases and Survival ROC software to evaluate DDX21 gene expression, protein expression, immunohistochemistry, gene mutation, immune infiltration, and protein phosphorylation in 33 TCGA tumor types, as well as the prognostic relationship between DDX21 and different tumors, by survival analysis and similar gene enrichment analysis. Furthermore, Cell Counting Kit-8 (CCK-8) and Transwell studies were employed to assess the effect of DDX21 expression on lung adenocarcinoma (LUAD) cell proliferation and migration. The DDX21 gene was highly expressed in most cancers, and overexpression was associated with poor overall survival (OS) and disease-free survival (DFS). DDX21 mutations were most common in uterine corpus endometrial carcinoma (UCEC; >5%), and DDX21 expression was positively correlated with the degree of infiltration of CAF and CD8+ cells in several tumor types. Numerous genes were co-expressed with DDX21. Gene enrichment analysis revealed close links between DDX21, RNA metabolism, and ribosomal protein production. In vitro analysis of LUAD cells showed that DDX21 expression was positively correlated with cell proliferation and migration capacity, consistent with prior bioinformatics studies. DDX21 is overexpressed in a variety of cancers, and overexpression in some cancers is associated with poor prognosis. Immune infiltration and DDX21-related gene enrichment analyses indicated that DDX21 may affect cancer development through mechanisms that regulate tumor immunity, RNA metabolism, and ribosomal protein synthesis. This pan-cancer study revealed the prognostic value and the oncogenic role of DDX21.

Landscape of immune-related signatures induced by targeting of different epigenetic regulators in melanoma: implications for immunotherapy

BackgroundImprovement of efficacy of immune checkpoint blockade (ICB) remains a major clinical goal. Association of ICB with immunomodulatory epigenetic drugs is an option. However, epigenetic inhibitors show a heterogeneous landscape of activities. Analysis of transcriptional programs induced in neoplastic cells by distinct classes of epigenetic drugs may foster identification of the most promising agents.MethodsMelanoma cell lines, characterized for mutational and differentiation profile, were treated with inhibitors of DNA methyltransferases (guadecitabine), histone deacetylases (givinostat), BET proteins (JQ1 and OTX-015), and enhancer of zeste homolog 2 (GSK126). Modulatory effects of epigenetic drugs were evaluated at the gene and protein levels. Master molecules explaining changes in gene expression were identified by Upstream Regulator (UR) analysis. Gene set enrichment and IPA were used respectively to test modulation of guadecitabine-specific gene and UR signatures in baseline and on-treatment tumor biopsies from melanoma patients in the Phase Ib NIBIT-M4 Guadecitabine + Ipilimumab Trial. Prognostic significance of drug-specific immune-related genes was tested with Timer 2.0 in TCGA tumor datasets.ResultsEpigenetic drugs induced different profiles of gene expression in melanoma cell lines. Immune-related genes were frequently upregulated by guadecitabine, irrespective of the mutational and differentiation profiles of the melanoma cell lines, to a lesser extent by givinostat, but mostly downregulated by JQ1 and OTX-015. GSK126 was the least active drug. Quantitative western blot analysis confirmed drug-specific modulatory profiles. Most of the guadecitabine-specific signature genes were upregulated in on-treatment NIBIT-M4 tumor biopsies, but not in on-treatment lesions of patients treated only with ipilimumab. A guadecitabine-specific UR signature, containing activated molecules of the TLR, NF-kB, and IFN innate immunity pathways, was induced in drug-treated melanoma, mesothelioma and hepatocarcinoma cell lines and in a human melanoma xenograft model. Activation of guadecitabine-specific UR signature molecules in on-treatment tumor biopsies discriminated responding from non-responding NIBIT-M4 patients. Sixty-five % of the immune-related genes upregulated by guadecitabine were prognostically significant and conferred a reduced risk in the TCGA cutaneous melanoma dataset.ConclusionsThe DNMT inhibitor guadecitabine emerged as the most promising immunomodulatory agent among those tested, supporting the rationale for usage of this class of epigenetic drugs in combinatorial immunotherapy approaches.

High expression of TTC21A predicts unfavorable prognosis and immune infiltrates in clear cell renal cell carcinoma.

Background: Clear cell renal cell carcinoma (ccRCC) is the most common pathological type of renal cell carcinoma. Tetratricopeptide repeat domain 21A (TTC21A), known as a component of intraflagellar transport complex A which is essential for the function of cilia, However, the role of TTC21A remains unclear in ccRCC. For the first time, we explore the role and potential mechanism of TTC21A in ccRCC based on multiple databases. Methods: TTC21A expression across all TCGA tumor was analyzed via Tumor Immune Estimation Resource (TIMER) site. The correlation between TTC21A and clinicopathologic characteristics of ccRCC was analyzed with TCGA database. The diagnostic and prognostic value of TTC21A was evaluated by receiver operation characteristic curve, Kaplan-Meier plotter and Cox regression respectively. Moreover, functional enrichment analysis of TTC21A and the co-expression genes were performed by Gene Set Enrichment Analysis. The correlation of TTC21A and immune infiltration were evaluated by single sample Gene Set Enrichment Analysis. Results: Pan-cancer analysis indicated that TTC21A was highly expressed in ccRCC and other cancer. In addition, elevated expression of TTC21A was associated with worse overall survival in ccRCC patients. Functional enrichment analysis showed that TTC21A and the co-expressed genes enriched in glucose metabolism and energy metabolism. Moreover, TTC21A expression was associated with infiltrating levels of dendritic cell, nature killer cell and other immune marker sets. Conclusion: The results of analysis indicate that expression of TTC21A is associated with poor prognosis and immune infiltrating in ccRCC, which suggested TTC21A might be used as a potential predictor and target of treatment in ccRCC.

Bioinformatic analysis of the LCN2-SLC22A17-MMP9 network in cancer: The role of DNA methylation in the modulation of tumor microenvironment.

Several features of cancer cells such as proliferation, invasion, metastatic spreading, and drug resistance are affected by their interaction with several tumor microenvironment (TME) components, including neutrophil gelatinase-associated lipocalin (NGAL), solute carrier family 22 member 17 (SLC22A17), and matrix metallopeptidase 9 (MMP9). These molecules play a key role in tumor growth, invasion, and iron-dependent metabolism of cancer cells. However, the precise epigenetic mechanisms underlying the gene regulation of Lipocalin 2 (LCN2), SLC22A17, and MMP9 in cancer still remain unclear. To this purpose, computational analysis was performed on TCGA and GTEx datasets to evaluate the expression and DNA methylation status of LCN2, SLC22A17, and MMP9 genes in different tumor types. Correlation analysis between gene/isoforms expression and DNA methylation levels of LCN2, SLC22A17, and MMP9 was performed to investigate the role of DNA methylation in the modulation of these genes. Protein network analysis was carried out using reverse phase protein arrays (RPPA) data to identify protein–protein interactions of the LCN2–SLC22A17–MMP9 network. Furthermore, survival analysis was performed according to gene expression and DNA methylation levels. Our results demonstrated that LCN2 and MMP9 were mainly upregulated in most tumor types, whereas SLC22A17 was largely downregulated, representing a specific hallmark signature for all gastrointestinal tumors. Notably, the expression of LCN2, SLC22A17, and MMP9 genes was negatively affected by promoter methylation. Conversely, intragenic hypermethylation was associated with the overexpression of SLC22A17 and MMP9 genes. Protein network analysis highlighted the role of the LCN2–SLC22A17–MMP9 network in TME by the interaction with fibronectin 1 and claudin 7, especially in rectal tumors. Moreover, the impact of expression and methylation status of LCN2, SLC22A17, and MMP9 on overall survival and progression free interval was tumor type–dependent. Overall, our analyses provide a detailed overview of the expression and methylation status of LCN2, SLC22A17, and MMP9 in all TCGA tumors, indicating that the LCN2–SLC22A17–MMP9 network was strictly regulated by DNA methylation within TME. Our findings pave the way for the identification of novel DNA methylation hotspots with diagnostic and prognostic values and suitable for epi-drug targeting.

Prognostic microRNAs associated with phosphoserine aminotransferase 1 in gastric cancer as markers of bone metastasis.

This study analyzed PSAT1-targeted miRNAs as a prognostic predictor for gastric cancer. The relationship between the clinical manifestations of gastric cancer in patients and phosphoserine aminotransferase 1 (PSAT1) was analyzed using correlation analysis. PSAT1 was highly expressed in gastric cancer, and its low expression was associated with a poor prognosis. By pan-cancer analysis, PSAT1 could affect the tumor immune microenvironment by immune infiltration analysis. Nine microRNAs targeting PSAT1 and associated with gastric cancer were screened by miRwalk and microRNA expression in TCGA tumor tissues. Six microRNAs were obtained by survival curve analysis, including hsa-miR-1-3p, hsa-miR-139-5p, hsa-miR-145-5p, hsa-miR-195-5p, hsa-miR-218-5p, and hsa-miR-497-5p. Based on the above six microRNAs, a model for bone metastasis prediction in gastric cancer prediction was constructed. An analysis of a decision curve was performed based on the microRNAs obtained to predict bone metastasis from gastric cancer. It had a positive area under the curve (AUC) value of 0.746, and the decision curve analysis (DCA) indicated that it was clinically significant. Dual-luciferase reporter genes indicated that hsa-miR-497-5p and PSAT1 were targeted, and qRT-PCR results confirmed that hsa-miR-497-5p could down-regulate PSAT1 expression. MicroRNAs targeting the regulation of PSAT1 expression can well predict the prognosis of gastric cancer.

Immune Gene Signature Expression Differs between African American and Caucasian Patients with Renal Cell Carcinoma

BACKGROUND: Predictive immune signatures such as the T-effector, the 26-gene “Renal 101 Immuno signature” and the 18-gene T-cell inflamed gene expression profile were developed in clinical trials enrolling predominantly Caucasians and there is a dearth of literature comparing tumor biology between African American (AA) and Caucasian patients. OBJECTIVE: To compare the immune gene signature expression in AA (n = 55) and Caucasian (n = 457) patients. METHODS: Raw gene expression count data were downloaded from the TCGA KIRC dataset and tumor samples from “white” and “black or AA” patients were selected. The gene expression values of the immune signatures were VST-transformed normalized counts and compared between the groups. RESULTS: There were 457 Caucasian and 55 AA patients in the TCGA. The immune gene expression in all three signatures was significantly lower in AA patients compared to Caucasians (p &lt; 0.05). We validated our findings in an independent dataset using Nanostring Immune Profile Panel. Since the majority of AA tumors in TCGA were stage I (71%), we compared gene expression between stage I AA tumors (n = 39) with stage I Caucasian tumors (n = 220). Once again, the immune gene expression was significantly lower in AA patients compared to Caucasians (p &lt; 0.05), indicating differences in tumor biology between the races. CONCLUSIONS: Low expression of predictive immune gene signatures in AA compared to Caucasian patients indicates a possible difference in the biology of their tumors. Future studies are needed to validate our findings in other datasets and to study the predictive role of these signatures in AA patients.