Prognosis Of Adenocarcinoma Research Articles

An immunogenic cell death-related gene expression signature in predicting prognosis of pancreatic ductal adenocarcinoma

BackgroundImmunogenic cell death (ICD) has been identified as regulated cell death, which is sufficient to activate the adaptive immune response. This study aimed to research ICD-related genes and create a gene model to predict pancreatic ductal adenocarcinoma (PAAD) patients’ prognosis.MethodsThe RNA sequencing and clinical data were downloaded from the TGCA and GEO databases. The PAAD samples were classified into two subtypes based on the expression levels of ICD-related genes using consensus clustering. Based on the differentially expressed genes (DEGs), a prognostic scoring model was constructed using LASSO regression and Cox regression, and the scoring model was used to predict the prognosis of PAAD patients. Moreover, colony formation assay was performed to confirm the prognostic value of those genes.ResultsWe identified two ICD cluster by consensus clustering, and found that the the ICD-high group was closely associated with immune-hot phenotype, favorable clinical outcomes. We established an ICD-related prognostic model which can predict the prognosis of pancreatic ductal adenocarcinoma. Moreover, depletion of NT5E, ATG5, FOXP3, and IFNG inhibited the colony formation ability of pancreatic cancer cell.ConclusionWe identified a novel classification for PAAD based on the expression of ICD-related genes, which may provide a potential strategy for therapeutics against PAAD.

Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma

Malignant pleural mesothelioma (MPM) is a rare but lethal pleural cancer with high intratumor heterogeneity (ITH). A recent study in lung adenocarcinoma has developed a clonal gene signature (ORACLE) from multiregional transcriptomic data and demonstrated high prognostic values and reproducibility. However, such a strategy has not been tested in other types of cancer with high ITH. We aimed to identify biomarkers from multi-regional data to prognostically stratify MPM patients. We generated a multiregional RNA-seq dataset for 78 tumor samples obtained from 26 MPM patients, each with one sample collected from a superior, lateral, and inferior region of the tumor. By integrating this dataset with the Cancer Genome Atlas MPM RNA-seq data, we selected 29 prognostic genes displaying high variability across different tumors but low ITH, which named PRACME (Prognostic Risk Associated Clonal Mesothelioma Expression). We evaluated PRACME in two independent MPM datasets and demonstrated its prognostic values. Patients with high signature scores are associated with poor prognosis after adjusting established clinical factors. Interestingly, the PRACME and the ORACLE signatures defined respectively from MPM and lung adenocarcinoma cross-predict prognosis between the two cancer types. Further investigation indicated that the cross-prediction ability might be explained by the high similarity between the two cancer types in their genomic regions with copy number variation, which host many clonal genes. Overall, our clonal signature PRACME provided prognostic stratification in MPM and this study emphasized the importance of multi-regional transcriptomic data for prognostic stratification based on clonal genes.

Prognostic significance of serum tumor markers in various pathologic subtypes of gastric cancer

PurposeThis study aimed to assess the utility of 6 serum tumor markers in prognosis between gastric adenocarcinoma and gastric signet ring cell carcinoma (SRCC). MethodsA cohort of 3131 cases of gastric adenocarcinoma and 275 cases of gastric SRCC was assembled. The serum levels of carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), carbohydrate antigen 125, alpha fetoprotein (AFP), carbohydrate antigen 242 (CA242), and carbohydrate antigen 724 (CA724) were measured in all cases. The study analyzed the association between the levels of these 6 tumor markers and the prognosis of gastric adenocarcinoma and SRCC. ResultsThe study revealed that gastric SRCC exhibited lower concentrations of CEA (P < .001) and CA19-9 (P = .002), along with reduced positive rates of CEA (P = .041), CA19-9 (P = .003), AFP (P < .001), and CA242 (P = .006), while displaying higher positive rates of CA724 (P = .024) than gastric adenocarcinoma. Nevertheless, the receiver operating characteristic curve demonstrated that serum tumor markers did not hold clinical significance in differentiating between gastric adenocarcinoma and SRCC. Survival analysis substantiated that the combined criteria of serum tumor markers stood as an independent risk factor for both gastric adenocarcinoma and SRCC. Notably, the nomogram indicated that serum tumor markers exerted a more substantial influence on the prognosis of gastric adenocarcinoma than on gastric SRCC. ConclusionThe study concluded that the combined criteria of serum tumor markers emerge as independent risk factors for both subtypes of gastric cancer. Furthermore, this combined approach exhibited enhanced efficacy in prognosticating the outcome of gastric adenocarcinoma compared with gastric SRCC.

Effects of different KRAS mutants and Ki67 expression on diagnosis and prognosis in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) is a prevalent form of non-small cell lung cancer with a rising incidence in recent years. Understanding the mutation characteristics of LUAD is crucial for effective treatment and prediction of this disease. Among the various mutations observed in LUAD, KRAS mutations are particularly common. Different subtypes of KRAS mutations can activate the Ras signaling pathway to varying degrees, potentially influencing the pathogenesis and prognosis of LUAD. This study aims to investigate the relationship between different KRAS mutation subtypes and the pathogenesis and prognosis of LUAD. A total of 63 clinical samples of LUAD were collected for this study. The samples were analyzed using targeted gene sequencing panels to obtain sequencing data. To complement the dataset, additional clinical and sequencing data were obtained from TCGA and MSK. The analysis revealed significantly higher Ki67 immunohistochemical scores in patients with missense mutations compared to controls. Moreover, the expression level of KRAS was found to be significantly correlated with Ki67 expression. Enrichment analysis indicated that KRAS missense mutations activated the SWEET_LUNG_CANCER_KRAS_DN and CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 pathways. Additionally, patients with KRAS missense mutations and high Ki67 IHC scores exhibited significantly higher tumor mutational burden levels compared to other groups, which suggests they are more likely to be responsive to ICIs. Based on the data from MSK and TCGA, it was observed that patients with KRAS missense mutations had shorter survival compared to controls, and Ki67 expression level could more accurately predict patient prognosis. In conclusion, when utilizing KRAS mutations as biomarkers for the treatment and prediction of LUAD, it is important to consider the specific KRAS mutant subtypes and Ki67 expression levels. These findings contribute to a better understanding of LUAD and have implications for personalized therapeutic approaches in the management of this disease.

Deciphering disulfidptosis: Uncovering a lncRNA-based signature for prognostic assessment, personalized immunotherapy, and therapeutic agent selection in lung adenocarcinoma patients

BackgroundDisulfidptosis, a recently identified type of regulated cell death, plays critical roles in various biological processes of cancer; however, whether they can impact the prognosis of lung adenocarcinoma (LUAD) remains to be fully elucidated. We aimed to adopt this concept to develop and validate a lncRNA signature for LUAD prognostic prediction. MethodsFor this study, the TCGA-LUAD dataset was used as the training cohort, and multiple datasets from the GEO database were pooled as the validation cohort. Disulfidptosis regulated genes were obtained from published studies, and various statistical methods, including Kaplan-Meier (KM), Cox, and LASSO, were used to train our gene signature DISULncSig. We utilized KM analysis, COX analysis, receiver operating characteristic analysis, time-dependent AUC analysis, principal component analysis, nomogram predictor analysis, and functional assays in our validation process. We also compared DISULncSig with previous studies. We performed analyses to evaluate DISULncSig's immunotherapeutic ability, focusing on eight immune algorithms, TMB, and TIDE. Additionally, we investigated potential drugs that could be effective in treating patients with high-risk scores. Additionally qRT-PCR examined the expression patterns of DISULncSig lncRNAs, and the ability of DISULncSig in pan-cancer was also assessed. ResultsDISULncSig containing twelve lncRNAs was trained and showed strong predictive ability in the validation cohort. Compared with previous similar studies, DISULncSig had more prognostic ability advantages. DISULncSig was closely related to the immune status of LUAD, and its tight relationship with checkpoints KIR2DL3, IL10, IL2, CD40LG, SELP, BTLA, and CD28 may be the key to its potential immunotherapeutic ability. For the high DISULncSig score population, we found ten drug candidates, among which epothilone-b may have the most potential. The pan-cancer analysis found that DISULncSig was a risk factor in multiple cancers. Additionally, we discovered that some of the DISULncSig lncRNAs could play crucial roles in specific cancer types. ConclusionThe current study established a powerful prognostic DISULncSig signature for LUAD that was also valid for most pan-cancers. This signature could serve as a potential target for immunotherapy and might help the more efficient application of drugs to specific populations.

Uncovering the ceRNA Network Related to the Prognosis of Stomach Adenocarcinoma Among 898 Patient Samples.

Stomach adenocarcinoma (STAD) patients are often associated with significantly high mortality rates and poor prognoses worldwide. Among STAD patients, competing endogenous RNAs (ceRNAs) play key roles in regulating one another at the post-transcriptional stage by competing for shared miRNAs. In this study, we aimed to elucidate the roles of lncRNAs in the ceRNA network of STAD, uncovering the molecular biomarkers for target therapy and prognosis. Specifically, a multitude of differentially expressed lncRNAs, miRNAs, and mRNAs (i.e., 898 samples in total) was collected and processed from TCGA. Cytoplasmic lncRNAs were kept for evaluating overall survival (OS) time and constructing the ceRNA network. Differentially expressed mRNAs in the ceRNA network were also investigated for functional and pathological insights. Interestingly, we identified one ceRNA network including 13 lncRNAs, 25 miRNAs, and 9 mRNAs. Among them, 13 RNAs were found related to the patient survival time; their individual risk score can be adopted for prognosis inference. Finally, we constructed a comprehensive ceRNA regulatory network for STAD and developed our own risk-scoring system that can predict the OS time of STAD patients by taking into account the above.

ScRNA-seq revealed high stemness epithelial malignant cell clusters and prognostic models of lung adenocarcinoma

Lung adenocarcinoma (LUAD) is one of the sole causes of death in lung cancer patients. This study combined with single-cell RNA-seq analysis to identify tumor stem-related prognostic models to predict the prognosis of lung adenocarcinoma, chemotherapy agents, and immunotherapy efficacy. mRNA expression-based stemness index (mRNAsi) was determined by One Class Linear Regression (OCLR). Differentially expressed genes (DEGs) were detected by limma package. Single-cell RNA-seq analysis in GSE123902 dataset was performed using Seurat package. Weighted Co-Expression Network Analysis (WGCNA) was built by rms package. Cell differentiation ability was determined by CytoTRACE. Cell communication analysis was performed by CellCall and CellChat package. Prognosis model was constructed by 10 machine learning and 101 combinations. Drug predictive analysis was conducted by pRRophetic package. Immune microenvironment landscape was determined by ESTIMATE, MCP-Counter, ssGSEA analysis. Tumor samples have higher mRNAsi, and the high mRNAsi group presents a worse prognosis. Turquoise module was highly correlated with mRNAsi in TCGA-LUAD dataset. scRNA analysis showed that 22 epithelial cell clusters were obtained, and higher CSCs malignant epithelial cells have more complex cellular communication with other cells and presented dedifferentiation phenomenon. Cellular senescence and Hippo signaling pathway are the major difference pathways between high- and low CSCs malignant epithelial cells. The pseudo-temporal analysis shows that cluster1, 2, high CSC epithelial cells, are concentrated at the end of the differentiation trajectory. Finally, 13 genes were obtained by intersecting genes in turquoise module, Top200 genes in hdWGCNA, DEGs in high- and low- mRNAsi group as well as DEGs in tumor samples vs. normal group. Among 101 prognostic models, average c-index (0.71) was highest in CoxBoost + RSF model. The high-risk group samples had immunosuppressive status, higher tumor malignancy and low benefit from immunotherapy. This work found that malignant tumors and malignant epithelial cells have high CSC characteristics, and identified a model that could predict the prognosis, immune microenvironment, and immunotherapy of LUAD, based on CSC-related genes. These results provided reference value for the clinical diagnosis and treatment of LUAD.

Comparison of postoperative survival between early-onset and late-onset adenocarcinoma of esophagogastric junction: a population-based study.

The prognosis of early-onset adenocarcinoma of esophagogastric junction (AEG) remains unclear. This research aimed at comparing the prognosis between early-onset and late-onset AEGs. We extracted eligible patients with surgically resected, pathologically confirmed, nonmetastatic AEG from the Surveillance, Epidemiology, and End Results database from 2004 to 2015. The cutoff age of early-onset AEG was set at ≤50years old. Univariate and multivariate Cox analysis as well as competing risk model were adopted for comparing overall survival (OS) and cancer-specific survival (CSS) between early-onset and late-onset AEGs. In addition, multiple imputation and propensity score matching (PSM) were also carried out for sensitivity analysis. In total, 4610 eligible AEG patients were collected in this study, including 610 early-onset AEGs and 4000 late-onset AEGs. Kaplan-Meier curves revealed significantly better survival in early-onset AEGs than late-onset AEGs. After interpolating missing data by multiple imputation, multivariate Cox regression analysis similarly showed better OS and CSS in early-onset AEGs. By using PSM analysis at a ratio of 1:1, we matched 610 early-onset AEG patients with 610 late-onset AEG patients. After PSM, univariate Cox regression model still revealed favorable prognosis in early-onset AEGs. Similar results were confirmed by performing PSM analysis at a ratio of 1:2 and 1:3. In addition, competing risk model demonstrated significantly lower cancer-specific death in early-onset AEGs compared to late-onset AEGs before and after matching. By applying several effective sensitivity analyses, we reported significantly favorable OS and CSS in early-onset AEGs compared to late-onset AEGs.

Development of the ARDS-derived gene panel for lung adenocarcinoma prognosis stratification and experiment validation of CCL20 expression.

Acute respiratory distress syndrome (ARDS) is a life-threatening condition characterized by lung inflammation and high mortality rates. Lung cancer, specifically lung adenocarcinoma (LUAD), is a major cause of cancer-related deaths worldwide. Patients with LUAD, particularly those undergoing chemotherapy, are more likely to develop ARDS. ARDS inflicts major malfunctioning in the immune system. We suspected a certain shared pathogenic mechanism between these diseases. This study analyzed 503 LUAD patients from the TCGA-LUAD cohort as the training set, 85 LUAD cases from the GSE30219 cohort as the validation set, and 24 RNA-seq samples from ARDS mice model and control groups in the GSE2411 cohort. The differentially expressed genes (DEGs) of ARDS were analyzed using the limma package and screened by Cox and Lasso analysis. ssGSEA and xCell algorithms were utilized for immune landscaping. RT-qPCR analysis was used to determine the mRNA levels of key genes in both the LPS-induced ARDS model and human LUAD cell lines. We identified DEGs between ARDS and control groups, which were highly associated with cytokine production and leukocyte migration. A prognosis model for LUAD patients was developed based on the expressions of the key genes in the ARDS-derived DEGs, including FMO3, IL1R2, CCL20, CFTR, and GADD45G. A satisfactory efficacy was observed in both the training and validation cohorts. The model demonstrated increased effectiveness in predicting the intratumor immune profile and mutation status of LUAD. Moreover, we utilized LPS to induce the ARDS model, which resulted in elevated expressions of IL1R2 and CCL20. Additionally, CCL20 was upregulated in cancerous LUAD cell lines. We developed an ARDS-based model for stratifying LUAD prognosis. CCL20 was found to be elevated in both the ARDS model and LUAD, suggesting a shared underlying mechanism of these two diseases.

MAP4 acts as an oncogene and prognostic marker and affects radioresistance by mediating epithelial–mesenchymal transition in lung adenocarcinoma

PurposeTo explore the effect of microtubule-associated protein 4 (MAP4) on lung adenocarcinoma cells in vitro and evaluate its prognostic value. Radioresistance, indicated by reduced efficiency of radiotherapy, is a key factor in treatment failure in lung adenocarcinoma (LADC). This study aims to explore the primary mechanism underlying the relationship between MAP4 and radiation resistance in lung adenocarcinoma.MethodsWe analysed the expression of MAP4 in lung adenocarcinoma by real-time quantitative polymerase chain reaction (RT‒qPCR), immunohistochemistry (IHC) and bioinformatics online databases, evaluated the prognostic value of MAP4 in lung adenocarcinoma and studied its relationship with clinicopathological parameters. Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis identified independent prognostic factors associated with lung adenocarcinoma that were used to construct a nomogram, internal validation was performed. We then evaluated the accuracy and clinical validity of the model using a receiver operating characteristic (ROC) curve, time-dependent C-index analysis, a calibration curve, and decision curve analysis (DCA). Scratch assays and transwell assays were used to explore the effect of MAP4 on the migration and invasion of lung adenocarcinoma cells. Bioinformatics analysis, RT‒qPCR, Cell Counting Kit-8 (CCK-8) assays and Western blot experiments were used to study the relationship between MAP4, epithelial–mesenchymal transition (EMT) and radiation resistance in lung adenocarcinoma.ResultsMAP4 expression in lung adenocarcinoma tissues was significantly higher than that in adjacent normal lung tissues. High expression of MAP4 is associated with poorer overall survival (OS) in patients with lung adenocarcinoma. Univariate Cox regression analysis showed that pT stage, pN stage, TNM stage and MAP4 expression level were significantly associated with poorer OS in LADC patients. Multivariate Cox regression analysis and LASSO regression analysis showed that only the pT stage and MAP4 expression level were associated with LADC prognosis. The nomogram constructed based on the pT stage and MAP4 expression showed good predictive accuracy. ROC curves, corrected C-index values, calibration curves, and DCA results showed that the nomogram performed well in both the training and validation cohorts and had strong clinical applicability. The results of in vitro experiments showed that the downregulation of MAP4 significantly affected the migration and invasion of lung adenocarcinoma cells. MAP4 was strongly correlated with EMT-related markers. Further studies suggested that the downregulation of MAP4 can affect the viability of lung adenocarcinoma cells after irradiation and participate in the radiation resistance of lung adenocarcinoma cells by affecting EMT.ConclusionMAP4 is highly expressed in lung adenocarcinoma; it may affect prognosis by promoting the migration and invasion of cancer cells. We developed a nomogram including clinical factors and MAP4 expression that can be used for prognosis prediction in patients with lung adenocarcinoma. MAP4 participates in radiation resistance in lung adenocarcinoma by regulating the radiation-induced EMT process. MAP4 may serve as a biomarker for lung adenocarcinoma prognosis evaluation and as a new target for improving radiosensitivity.

Single-cell and Bulk RNA-Seq reveal angiogenic heterogeneity and microenvironmental features to evaluate prognosis and therapeutic response in lung adenocarcinoma.

Angiogenesis stands as a pivotal hallmark in lung adenocarcinoma (LUAD), intricately shaping the tumor microenvironment (TME) and influencing LUAD progression. It emerges as a promising therapeutic target for LUAD, affecting patients' prognosis. However, its role in TME, LUAD prognosis, and its clinical applicability remain shrouded in mystery. We employed integrated single-cell and bulk transcriptome sequencing to unravel the heterogeneity of angiogenesis within LUAD cells. Through "consensus clustering", we delineated distinct angiogenic clusters and deciphered their TME features. "Monocle2" was used to unravel divergent trajectories within malignant cell subpopulations of LUAD. Additionally, regulon submodules and specific cellular communication patterns of cells in different angiogenic states were analyzed by "pyscenic" and "Cellchat" algorithms. The "univariate Cox" and "LASSO" algorithms were applied to build angiogenic prognostic models. Immunohistochemistry (IHC) on clinical samples validated the role of model factors in LUAD angiogenesis. We utilized CTRP 2.0 and PRISM databases for pinpointing sensitive drugs against lung adenocarcinoma. Two clusters for the activation of angiogenesis were identified, with Cluster 1 showing a poor prognosis and a pro-cancerous TME. Three differentiated states of malignant epithelial LUAD cells were identified, which had different degrees of angiogenic activation, were regulated by three different regulon submodules, and had completely different crosstalk from other cells in TME. The experiments validate that SLC2A1 promotes angiogenesis in LUAD. ARS (Angiogenesis related score) had a high prognostic value; low ARSs showed immunotherapy benefits, whereas high ARSs were sensitive to 15 chemotherapeutic agents. The assessment of angiogenic clusters helps to determine the prognostic and TME characteristics of LUAD. Angiogenic prognostic models can be used to assess the prognosis, immunotherapeutic response, and chemotherapeutic drug sensitivity of LUAD.

Comparative prognosis and risk assessment in gallbladder neuroendocrine neoplasms versus adenocarcinomas.

Gallbladder neuroendocrine neoplasms (GB-NENs) are a rare malignant disease, with most cases diagnosed at advanced stages, often resulting in poor prognosis. However, studies regarding the prognosis of this condition and its comparison with gallbladder adenocarcinomas (GB-ADCs) have yet to yield convincing conclusions. We extracted cases of GB-NENs and GB-ADCs from the Surveillance, Epidemiology, and End Results (SEER) database in the United States. Firstly, we corrected differences in clinical characteristics between the two groups using propensity score matching (PSM). Subsequently, we visualized and compared the survival outcomes of the two groups using the Kaplan-Meier method. Next, we employed the least absolute shrinkage and selection operator (LASSO) regression and Cox regression to identify prognostic factors for GB-NENs and constructed two nomograms for predicting prognosis. These nomograms were validated with an internal validation dataset from the SEER database and an external validation dataset from a hospital. Finally, we categorized patients into high-risk and low-risk groups based on their overall survival (OS) scores. A total of 7,105 patients were enrolled in the study, comprising 287 GB-NENs patients and, 6,818 GB-ADCs patients. There were substantial differences in clinical characteristics between patients, and GB-NENs exhibited a significantly better prognosis. Even after balancing these differences using PSM, the superior prognosis of GB-NENs remained evident. Independent prognostic factors selected through LASSO and Cox regression were age, histology type, first primary malignancy, tumor size, and surgery. Two nomograms for prognosis were developed based on these factors, and their performance was verified from three perspectives: discrimination, calibration, and clinical applicability using training, internal validation, and external validation datasets, all of which exhibited excellent validation results. Using a cutoff value of 166.5 for the OS nomogram score, patient mortality risk can be identified effectively. Patients with GB-NENs have a better overall prognosis compared to those with GB-ADCs. Nomograms for GB-NENs prognosis have been effectively established and validated, making them a valuable tool for assessing the risk of mortality in clinical practice.

The development and implementation of pathological parameters and molecular testing impact prognosis of colorectal adenocarcinoma

ObjectiveThis study aims to analyze how changes in pathological diagnosis practice and molecular detection technology have affected clinical outcomes for colorectal cancer (CRC) patients in Fudan University Shanghai Cancer Center (FUSCC). MethodsThis retrospective cohort study analyzed 21,141 pathologically confirmed CRC cases diagnosed at FUSCC from 2008 to 2020. Patients were divided into five groups for different analytical purposes: (1) the before vs. since 2014 groups to analyze the influence of the changes in the classification criteria of pT3 and pT4 staging on the survival of patients; (2) the partial vs. total mesorectal excision (TME) groups to analyze whether evaluation of completeness of the mesorectum have impact on the survival of patients; (3) the tumor deposit (TD)(+)N0 vs. TD(+)N1c groups to analyze the influence of the changes in the pN staging on the survival of patients with positive TD and negative regional lymph node metastasis (LNM); (4) the before vs. since 2013 groups to analyze the influence of the changes in the testing process of deficient mismatch repair on the survival of patients; and (5) the groups with vs. without RAS/BRAF gene mutation testing to analyze the influence of these testing on the survival of patients. Patients’ clinicopathological parameters, including age at diagnosis, sex, tumor size, location, differentiation, mucinous subtype, TD, lymphovascular invasion, perineural invasion, tumor depth, LNM and distant metastasis, and tumor-node-metastasis (TNM) stage, were compared between groups. Kaplan-Meier analysis with log rank method was performed for patients’ overall survival (OS) and disease-free survival (DFS) analyses. ResultsIn pathological reports, there were three parameter changes that impacted patient outcomes. Firstly, changes in the pT staging criteria led to a shift of the ratio of patients with stage pT3 to stage pT4 from 1: 110.9 to 1: 0.26. In comparison to patients admitted before 2014 (n = 4,754), a significant difference in prognosis between pT3 and pT4 stages was observed since 2014 (n = 9,965). Secondly, we began to evaluate the completeness of the mesorectum since 2016. As a result, 91.0% of patients with low rectal cancer underwent TME (n = 4,111) surgery, and patients with TME had significantly better OS compared with partial mesorectal excision (PME, n = 409). Thirdly, we began to stage TD (+) LNM (-) as N1c since 2017. The results showed that N1c (n = 127) but not N0 (n = 39) can improve the prognosis of patients without LNM and distal metastasis. In molecular testing, there have been three and five iterations of updates regarding mismatch repair (MMR)/microsatellite instability (MSI) status and RAS/BRAF gene mutation detection, respectively. The standardization of MMR status testing has sharply decreased the proportion of deficient MMR (dMMR) patients (from 32.5% to 7.4%) since 2013. The prognosis of patients underwent MMR status testing since 2013 (n = 867) were significantly better than patients before 2013 (n = 1,313). In addition, detection of RAS/BRAF gene mutation status (n = 5,041) resulted in better DFS but not OS, for patients with stage I-III disease (n = 16,557). ConclusionOver the past few decades, updates in elements in pathological reports, as well as the development of standardized tests for MMR/MSI status and RAS/BRAF gene mutations have significantly improved patient outcomes.

Clinicopathological characteristics and outcomes of colorectal mucinous adenocarcinoma: a retrospective analysis from China.

Mucinous adenocarcinoma (MAC) is a unique subtype of colorectal cancer and its prognostic value remains controversial. This study aimed to compare the clinicopathological characteristics and prognostic differences between patients with MAC and non-mucinous adenocarcinoma (NMAC). 674 patients with NMAC, 110 patients with adenocarcinoma with mucinous component (ACWM) and 77 patients with MAC between 2016-2019 were enrolled in the study. Univariate and multivariate Cox regression were performed to analyze the factors associated with prognosis. Predictive nomograms of overall survival (OS) and cancer-specific survival (CSS) for patients with colorectal adenocarcinoma were constructed. Confounding factors were eliminated by propensity score matching (PSM). Compared with patients with NMAC, patients with MAC were more likely to have a tumor located at the proximal colon, present with a larger tumor diameter, more advanced T stage, higher frequency of metastasis, deficiency of mismatch repair, and elevated preoperative carcinoembryonic antigen. Patients with MAC were related to worse OS (HR=2.53, 95%CI 1.73-3.68, p<0.01) and CSS (HR=3.09, 95%CI 2.10-4.57, p<0.01), which persisted after PSM. Subgroup analysis demonstrated that patients with left-sided or stage III/IV MAC exhibited a comparatively worse OS and CSS than those with NMAC. Furthermore, in patients with stage II with a high-risk factor and stage III MAC, adjuvant chemotherapy was associated with an improved OS, CSS, and RFS. Compared with the NMAC phenotype, the MAC phenotype was an independent risk factor for poor prognosis in colorectal adenocarcinoma with worse OS and CSS, particularly patients with left-sided colorectal cancer and stage III/IV. However, patients with MAC can still benefit from adjuvant chemotherapy.

Programmed Cell Death Ligand 1 Expression in CD163 + Tumor-associated Macrophages in Cancer Gland Rupture Microenvironment.

In this study, we aimed to examine the relationship among cancer gland rupture microenvironment, programmed cell death ligand 1 (PD-L1) expression in CD163 + tumor-associated macrophages (TAMs), and prognosis in colon adenocarcinoma. A total of 122 patients were diagnosed with colon adenocarcinoma between 2010 and 2019. PD-L1 + (clone 22C3) "macrophage scores" in the microenvironment of cancer gland rupture were calculated. The effects of these variables on prognosis were statistically analyzed. CD163 + TAMs were denser in the cancer gland rupture microenvironment. PD-L1 + TAMs were observed in the tumor periphery, and there was a significant difference between the rates of PD-L1 expression in TAMs and survival time (log-rank = 10.46, P = 0.015), clinical stage 2 ( P = 0.038), and primary tumor 3 and primary tumor 4 cases ( P = 0.004, P = 0.013). The risk of mortality was 4.070 times higher in patients with a PD-L1 expression rate of ≥1% in CD163 + TAMs. High PD-L1 expression in CD163 + TAMs is associated with poor overall survival. Therefore, blocking PD-L1 in CD163 + TAMs can be used as a target for immunotherapy.

Mutational signature and prognosis in adenocarcinoma of bladder.

655 Background: Adenocarcinoma of bladder is a rare urinary bladder carcinoma with limited therapy options due to lack of molecular characterization. Here we aim to reveal mutational and transcriptomic landscapes of adenocarcinoma of bladder and their relationship with prognosis. Methods: Between February 2015 and June 2021, a total of 23 patients with adenocarcinoma of bladder were included. These included 16 patients with primary bladder adenocarcinomas and 7 patients with urachal adenocarcinoma. Whole exome sequencing, whole genome sequencing, bulk RNA-Seq and single-cell RNA-Seq were conducted for the specimens. Correlation analysis, survival analysis and t tests were also performed. Results: Prevalent T&gt;A substitutions were observed among somatic mutations, and major tri-nucleotide contexts included 5′-CTC-3′and 5′-CTG-3′. This pattern was mainly contributed by COSMIC Signature 22 related to chemical carcinogen exposure (probably aristolochic acid), which has not been reported in bladder adenocarcinoma. Moreover, genes with copy number changes also enriched KEGG term “chemical carcinogenesis”. Transcriptomic analysis implied high immune infiltration and luminal-like feature in majority of samples. Interestingly, a small fraction of samples with APOBEC-derived mutational signature exhibited higher risk of disease progression compared with samples with only chemical carcinogen-related signature, confirming molecular and prognosis heterogeneity in bladder adenocarcinoma. Conclusions: This study presents mutational and transcriptomic landscapes of bladder adenocarcinoma, and chemical carcinogen-related mutational signature indicates good prognosis in adenocarcinoma of bladder.

Macrophage-Related Gene Signatures for Predicting Prognosis and Immunotherapy of Lung Adenocarcinoma by Machine Learning and Bioinformatics.

In recent years, the immunotherapy of lung adenocarcinoma has developed rapidly, but the good therapeutic effect only exists in some patients, and most of the current predictors cannot predict it very well. Tumor-infiltrating macrophages have been reported to play a crucial role in lung adenocarcinoma (LUAD). Thus, we want to build novel molecular markers based on macrophages. By non-negative matrix factorization (NMF) algorithm and Cox regression analysis, we constructed macrophage-related subtypes of LUAD patients and built a novel gene signature consisting of 12 differentially expressed genes between two subtypes. The gene signature was further validated in Gene-Expression Omnibus (GEO) datasets. Its predictive effect on prognosis and immunotherapy outcome was further evaluated with rounded analyses. We finally explore the role of TRIM28 in LUAD with a series of in vitro experiments. Our research indicated that a higher LMS score was significantly correlated with tumor staging, pathological grade, tumor node metastasis stage, and survival. LMS was identified as an independent risk factor for OS in LUAD patients and verified in GEO datasets. Clinical response to immunotherapy was better in patients with low LMS score compared to those with high LMS score. TRIM28, a key gene in the gene signature, was shown to promote the proliferation, invasion and migration of LUAD cell. Our study highlights the significant role of gene signature in predicting the prognosis and immunotherapy efficacy of LUAD patients, and identifies TRIM28 as a potential biomarker for the treatment of LUAD.

Abstract B022: A gradient expression of integrin αvβ6 expression in human cancer cells associates with TGFβ mediated immune evasion

Abstract Our previous results demonstrate an integrin-mediated mechanism of immune evasion in colorectal cancer. Increased levels of latent TGFβ in the experimental tumor environment led to the upregulation of the immune checkpoint marker PD-L1 in HCT116WT cells, facilitating escape from T-cell killing. This effect was rescued in immune co-cultures by pretreating cancer cells with the broad-spectrum integrin inhibitor GLPG-0187. To further elucidate this system, we investigated the TGFβ-integrin axis. Integrin αvβ6 is a major activator of the inert latent TGFβ into the active, immunosuppressive form. With its high specificity within malignant tissue, inhibition of αvβ6 poses an attractive therapeutic target for disrupting TGFβ signaling while avoiding the toxicities of systemic blockade. To identify an endogenous in vitro model of integrin αvβ6-expressing cancer, computational analysis of publicly available mRNA expression data was performed to determine cancer types with high αvβ6 upregulation. This investigation revealed a strong presence of αvβ6 in pancreatic, bladder, head and neck, and cervical cancer tissues. Further in-silico work identified the head and neck squamous cell carcinoma cell lines CAL-27 and FaDu, as well as the pancreatic adenocarcinoma line Capan-2, as suitable models for in vitro study. Flow cytometry of these cell lines was performed to determine the surface expression of integrin αvβ6, revealing that protein expression correlated with the mRNA data from the previous computational studies. Capan-2 and CAL-27 exhibited high levels αvβ6 of expression, while FaDu expressed moderate levels, and HCT116WT exhibited low αvβ6 expression. These cell lines were pretreated with latent TGFβ, simulating sequestered latent TGFβ in the extracellular matrix, and subsequently co-cultured with TALL-104 T-cells. Quantitative fluorescence microscopy revealed that resistance to killing by T-cells correlated with αvβ6 expression across cell lines. These findings are consistent with the hypothesis that upregulated expression of integrin αvβ6 functions as an immunosuppressive resistance mechanism by increasing tumor microenvironment levels of active TGFβ. Analysis of mRNA sequencing data from the TCGA Pancreatic Adenocarcinoma Firehose database revealed that integrin αvβ6 is a strong marker of poor prognosis in pancreatic adenocarcinoma. Future co-culture experiments will investigate the dynamics of TGFβ activation in the tumor microenvironment in relation to αvβ6 expression. Further in vivo studies can facilitate translation of our findings to therapeutic clinical trials. Citation Format: William J. MacDonald, Praveen R. Srinivasan, Vida Tajiknia, Maximilian Pinho-Schwermann, Connor Purcell, Brooke Verschleiser, Wafik S. El-Deiry. A gradient expression of integrin αvβ6 expression in human cancer cells associates with TGFβ mediated immune evasion [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B022.

Clinicopathological Characteristics, Treatment and Prognosis in Duodenal Adenocarcinoma with Liver Metastasis: A SEER-Based Study.

Duodenal adenocarcinoma (DAC) is a rare tumor that is often accompanied by liver metastasis in advanced stages. The aim of this study was to evaluate the correlation between clinicopathological characteristics and survival in DAC patients with liver metastasis, and to explore appropriate treatment options. 482 DAC patients with liver metastasis were retrospectively identified from the Surveillance, Epidemiology and End Results (SEER) database (2011-2020). Univariate and multivariate Cox regression analyses were performed to explore the clinicopathological factors related to survival. The Kaplan-Meier method was used to identify the independent risk factors associated with survival. The 1-year overall survival (OS) and cancer-specific survival (CSS) rates for the entire cohort were 25.4% and 28.3%, and the 5-year OS and CSS rates were 2.4% and 2.9% respectively. Univariable analysis and multivariate analysis identified chemotherapy and surgery as the independent risk factors for OS and CSS. Patients who underwent chemotherapy and surgery had better CSS and OS rates, whereas radiotherapy failed to improve outcomes. We identified several prognostic factors of DAC with liver metastasis. Chemotherapy and surgery can prolong the survival of DAC patients with liver metastasis, which lays the foundation for identifying the optimal treatment strategy.

Identification of necroptosis-associated miRNA signature for predicting prognosis and immune landscape in stomach adenocarcinoma

PurposeThis study aims to identify the potential necroptosis related genes (NRGs)-associated miRNAs signature and explore the impact on the prognosis of stomach adenocarcinoma (STAD). MethodsEmploying rigorous methodologies, we utilized univariate Cox, Lasso and multivariate Cox regression analyses to develop a prognostic signature. Kaplan-Meier (K-M) and ROC curves were applied to assess the prognostic value of signature in a training group and an independent test group. Furthermore, we conducted Gene Set Enrichment Analysis (GSEA) for enrichment of tumor-related pathways. The risk score was calculated for each patient based on the expression of miRNAs which were enrolled in the signature. Patients were stratified into high- and low-risk groups. The immune cell infiltration and immunotherapy were compared between the two groups. Finally, the diagnostic potential of the miRNA was explored by RT-qPCR. ResultsWe constructed a prognostic model based on 6 NRGs-associated miRNAs. K-M plots underscored superior survival outcomes in the low-risk group. GSEA results revealed the enrichment of several tumor-related pathways in the high-risk group. Notably, CD8+ T cells, Tregs and activated memory CD4+ T cells exhibited negative correlations with the risk score. Additionally, a few immune checkpoint genes, such as CTLA4, PD1 and PD-L1, were significantly upregulated in the low-risk group. Furthermore, the serum expression levels of all these 6 miRNAs were significantly elevated in STAD patients. ConclusionsOur study identified a robust risk score derived from a signature of 6 NRGs-associated miRNAs, demonstrating high efficacy for prognosis of STAD. These results not only contributed to our understanding of STAD pathogenesis, but also held promise for potential clinical applications, particularly in the realm of personalized immunotherapy for STAD patients.