Relapse-related molecular signature in early-stage lung adenocarcinomas based on base excision repair, stimulator of interferon genes pathway and tumor-infiltrating lymphocytes

Clinical application of ctDNA in early diagnosis, treatment and prognosis of patients with non-small cell lung cancer

Lung cancer is one of the most common malignancies worldwide, with non-small cell lung cancer (NSCLC) being the most common type. As understanding of precise treatment options for NSCLC deepens, circulating tumor DNA (ctDNA) has emerged as a potential biomarker that has become a research hotspot and may represent a new approach for the individualized diagnosis and treatment of NSCLC. This article reviews the applications of ctDNA for the early screening of patients with NSCLC, guiding targeted therapy and immunotherapy, evaluating chemotherapy and postoperative efficacy, assessing prognosis and monitoring recurrence. With the in-depth study of the pathogenesis of NSCLC, plasma ctDNA may become an indispensable part of the precise treatment of NSCLC, which has great clinical application prospects.

Stimulator of Interferon Genes Protein (STING) Expression in Cancer Cells: A Tissue Microarray Study Evaluating More than 18,000 Tumors from 139 Different Tumor Entities

Stimulator of interferon genes protein (STING) activates the immune response in inflammatory cells. STING expression in cancer cells is less well characterized, but STING agonists are currently being evaluated as anticancer drugs. A tissue microarray containing 18,001 samples from 139 different tumor types was analyzed for STING by immunohistochemistry. STING-positive tumor cells were found in 130 (93.5%) of 139 tumor entities. The highest STING positivity rates occurred in squamous cell carcinomas (up to 96%); malignant mesothelioma (88.5%-95.7%); adenocarcinoma of the pancreas (94.9%), lung (90.3%), cervix (90.0%), colorectum (75.2%), and gallbladder (68.8%); and serous high-grade ovarian cancer (86.0%). High STING expression was linked to adverse phenotypes in breast cancer, clear cell renal cell carcinoma, colorectal adenocarcinoma, hepatocellular carcinoma, and papillary carcinoma of the thyroid (p < 0.05). In pTa urothelial carcinomas, STING expression was associated with low-grade carcinoma (p = 0.0002). Across all tumors, STING expression paralleled PD-L1 positivity of tumor and inflammatory cells (p < 0.0001 each) but was unrelated to the density of CD8+ lymphocytes. STING expression is variable across tumor types and may be related to aggressive tumor phenotype and PD-L1 positivity. The lack of relationship with tumor-infiltrating CD8+ lymphocytes argues against a significant IFN production by STING positive tumor cells.

APE1 promotes radiation resistance against radiation-induced pyroptosis by inhibiting the STING pathway in lung adenocarcinoma

Mammalian apurinic/apyrimidinic endonuclease 1 (APE1, APEX1) is a multifunctional enzyme that maintains cellular homeostasis. It is involved in the base excision repair (BER) pathway and plays a key role in radiation-induced DNA damage response. However, the relationship between APE1-driven radiation resistance and pyroptosis in lung adenocarcinoma (LUAD) cells and the underlying molecular mechanisms remain unclear. We found that APE1 was significantly upregulated in LUAD tissues compared to para-carcinoma tissues and promoted the proliferation and invasion of LUAD cells in vitro and in vivo. Mechanistically, APE1 inhibited pyroptosis by inactivating the interferon gene stimulator (STING) pathway via direct interaction with AIM2 and DDX41, as detected by RNA-seq and co-immunoprecipitation. APE1 protects LUAD cells against radiation-induced damage and induces radio-resistance by targeting the STING pathway. It can induce pyroptosis and is negatively regulated by interactions with AIM2 and DDX41. Therefore, APE1 inhibitors should be considered to enhance the radiosensitivity of LUAD cells and improve patient prognosis and therapeutic outcomes. Thus, APE1 play a role in the tumor immune microenvironment and in tumor immunotherapy.

The prognostic impact of tumor-infiltrating B lymphocytes in patients with solid malignancies: A systematic review and meta-analysis

This study reviewed the prognostic effect of tumor-infiltrating B lymphocytes (TIBLs) on solid malignancies, to determine the potential role of TIBLs in predicting cancer patient's prognosis and their response to immunotherapy. A total of 45 original papers involving 11,099 individual patients were included in this meta-analysis covering 7 kinds of cancer. The pooled results suggested that high levels of TIBLs were correlated with favorable OS in lung, esophageal, gastric, colorectal, liver, and breast cancer; improved RFS in lung cancer; and improved DFS in gastrointestinal neoplasms. Additionally, TIBLs were significantly correlated with negative lymphatic invasion in gastric cancer, small tumor size in hepatocellular carcinoma, and negative distant metastasis in colorectal cancer. Additionally, TIBLs were reported as a discriminative feature of patients treated with immunotherapy with improved survival. We concluded that TIBLs play a favorable prognostic role among the common solid malignancie, providing theoretical evidence for further prognosis prediction for solid tumors.

Integrated Analysis of Multi-Omics Data to Establish a Hypoxia-Related Prognostic Model in Osteosarcoma

Background:

Osteosarcoma (OS) is the most common malignant bone tumor in clinical practice, and currently, the ability to predict prognosis in the diagnosis of OS is limited. There is an urgent need to find new diagnostic methods and treatment strategies for OS.

Material and methods:

We downloaded the multi-omics data for OS from the TARGET database. Prognosis-associated methylation sites were used to identify clustered subtypes of OS, and OS was classified into 3 subtypes (C1, C2, C3). Survival analysis showed significant differences between the C3 subtype and the other subtypes. Subsequently, differentially expressed genes (DEGs) across subtypes were screened and subjected to pathway enrichment analysis.

Results:

A total of 249 DEGs were screened from C3 subtype to other subtypes. Metabolic pathway enrichment analysis showed that DEGs were significantly enriched to the hypoxic pathway. Based on univariate and multivariate COX regression analysis, 12 genes from the hypoxia pathway were further screened and used to construct hypoxia-related prognostic model (HRPM). External validation of the HRPM was performed on the GSE21257 dataset. Finally, differences in survival and immune infiltration between high and low risk score groups were compared.

Conclusion:

In summary, we proposed a hypoxia-associated risk model based on a 12-gene expression signature, which is potentially valuable for prognostic diagnosis of patients with OS.

[Consensus on Postoperative Recurrence Prediction of Non-small Cell Lung Cancer Based on Molecular Markers]

Significant progress has been made in lung cancer screening, surgery, chemoradiation, targeted therapy, and immunotherapy recently. Surgical resection is the most important treatment for localized non-small cell lung cancer (NSCLC) so far, but there are still many patients who develop local recurrence or distant metastases within 5 years of surgery. Currently, the risk factors of recurrence in patients with NSCLC are mainly based on clinical and pathological features, which hardly identify patients at high risk of recurrence accurately. With the development of new detection technologies, a number of molecular markers that may have a predictive risk of recurrence in NSCLC have been discovered over the years. In order to summarize the molecular markers related to postoperative recurrence in NSCLC patients, we have formulated a consensus on the prediction of postoperative recurrence of NSCLC based on molecular markers. This consensus mainly focuses on the early stage NSCLC patients, discusses and summarizes the risk factors of disease recurrence from the molecular level. It is hoped that more and more valuable information can be provided for the management of patients, so as to provide more guidance for the perioperative management of the patients with early stage NSCLC in the future.
.

Evaluation of tumor microenvironmental immune regulation and prognostic in lung adenocarcinoma from the perspective of purinergic receptor P2Y13

Tumor-infiltrating immune cells (TICs) can serve as an important indicator to evaluate the prognosis and therapeutic response in lung adenocarcinoma (LUAD). The identification of mutated genes that can affect the abundance of TICs and prognosis has practical implications. In the presented study, tumor microenvironment (TME) scoring was performed by the ESTIMATE scoring system on 598 RNA transcripts selected from the TCGA database to determine the proportions of immune cells and stromal cells. The infiltration difference of TICs in LUAD samples was obtained by CIBERSORT. The 'immuneeconv' R software package, which integrates six latest algorithms, including TIMER, xCell, MCP-counter, CIBERSORT, EPIC and quanTIseq were used to verify the correlation between purinergic receptor P2Y13 (P2RY13) and immune cells. Based on RNA sequencing analysis of the Lewis lung cancer-bearing model in C57BL/6 mice and immunohistochemistry (IHC) of human LUAD tissues, the expression of P2RY13 and associated pathways were verified. It was shown that differentially expressed genes (DEGs) obtained by interactive analysis based on Immunescore and Stromalscore were significantly enriched in immune-related pathways. The expression of P2RY13 was significantly associated with prognosis and clinicopathological characteristics of LUAD patients. More importantly, this gene played an important role in maintaining the immune dominant environment and changing the regulation of TICs. P2RY13 expression was positively correlated with the infiltration of dendritic cells (DCs) in various of tumor tissues as validated by the PanglaoDB scRNA-seq database. Therefore, P2RY13 is expected to be a potential biomarker for predicting TME and the prognosis of LUAD after verification.

Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery

Background

The widespread use of low-dose chest CT screening has improved the detection of early lung adenocarcinoma. Radical surgery is the best treatment strategy for patients with early lung adenocarcinoma; however, some patients present with postoperative recurrence and poor prognosis. Through this study, we hope to establish a model that can identify patients that are prone to recurrence and have poor prognosis after surgery for early lung adenocarcinoma.

Materials and Methods

We screened prognostic and relapse-related genes using The Cancer Genome Atlas (TCGA) database and the GSE50081 dataset from the Gene Expression Omnibus (GEO) database. The GSE30219 dataset was used to further screen target genes and construct a risk prognosis signature. Time-dependent ROC analysis, calibration degree analysis, and DCA were used to evaluate the reliability of the model. We validated the TCGA dataset, GSE50081, and GSE30219 internally. External validation was conducted in the GSE31210 dataset.

Results

A novel four-gene signature (INPP5B, FOSL2, CDCA3, RASAL2) was established to predict relapse-related survival outcomes in patients with early lung adenocarcinoma after surgery. The discovery of these genes may reveal the molecular mechanism of recurrence and poor prognosis of early lung adenocarcinoma. In addition, ROC analysis, calibration analysis and DCA were used to verify the genetic signature internally and externally. Our results showed that our gene signature had a good predictive ability for recurrence and prognosis.

Conclusions

We established a four-gene signature and predictive model to predict the recurrence and corresponding survival rates in patients with early lung adenocarcinoma after surgery. These may be helpful for reforumulating post-operative consolidation treatment strategies.

Association of postoperative recurrence with radiological and clinicopathological features in patients with stage IA-IIA lung adenocarcinoma

OBJECTIVES

To retrospectively investigate whether radiological and clinicopathological characteristics were associated with the presence of stage IA-IIA lung adenocarcinoma in patients at high risk for a postoperative recurrence.

MATERIALS AND METHODS

Three hundred twelve patients with biopsy-proven node-negative early-stage (IA-IIA) lung adenocarcinoma met the inclusion criteria for this study. Demographics data and histopathological findings were collected from medical records. Computed tomography (CT) performed approximately 1 month before surgery was manually scored using 23 CT descriptors. Univariate analyses were applied to demonstrate an association between clinicopathological and radiological features and 2-/5-year recurrences. Multivariate logistic regression was performed to assess the ability of radiological and clinicopathological features to discriminate low and high-risk factors for recurrence. A ROC curve was used to evaluate prediction performance.

RESULTS

Univariate analysis revealed that the 2-year recurrence was associated with six radiological features and two clinicopathological features, while 5-year recurrence was associated with five radiological features and two clinicopathological features. A multivariate logistic regression model of combined clinicopathological and radiological features showed that stage IIA (OR = 2.87), solid texture (solid part > 50 %: OR = 4.81; solid part = 100 %: OR = 3.61), pleural attachment (OR = 3.97) and bronchovascular bundle thickening (OR = 2.16) were associated with the independent predictors of 2-year recurrence, and stage IIA (OR = 3.52), solid texture (solid part > 50 %: OR = 3.56; solid part = 100 %: OR = 2.44) and pleural attachment (OR = 4.57) were associated with 5-year recurrence. Combined radiological and clinicopathological features could be significant indicators of 2- and 5-year recurrences (AUC = 0.784 and AUC = 0.815, respectively).

CONCLUSIONS

The combination of radiological and clinicopathological features has the potential to help predict postoperative recurrence in patients with stage IA-IIA lung adenocarcinomas and guide oncologists and patients whether to undergo additional treatment after surgery.

Relapse-related molecular signature in early-stage lung adenocarcinomas based on base excision repair, stimulator of interferon genes pathway and tumor-infiltrating lymphocytes

Approximately 30% of patients with early-stage non-small cell lung cancer (NSCLC) relapse within 5 years after surgery. Therefore, it is necessary to identify a robust and reliable prognostic signature for early-stage NSCLC. Immunohistochemistry data from 147 patients with stage I lung adenocarcinoma (stage I-LUAD) were analyzed for the protein expression of base excision repair (BER), stimulator of interferon genes (STING) and tumor-infiltrating lymphocytes (TIL) to explore the relationship between protein expression and prognosis. A prediction model was further established by nomogram and externally verified using The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases. XRCC1 and H2AX are negative prognostic markers for relapse-free survival (RFS), while CD8, CD20 and STING are positive prognostic markers for RFS. Nomograms for RFS share common prognostic markers, including XRCC1, H2AX, STING, CD8 and CD20. The c-index was 0.724 and 0.698 in the training cohort and the internal validation cohort, respectively. It was externally verified that the nomogram model had a good prediction for recurrence of stage I-LUAD. Correlation analysis showed that APE1 and H2AX were negatively correlated with STING, while STING was positively correlated with TIL. BER, the STING pathway and TIL were associated with early recurrence and were correlated with the tissue expression of stage I-LUAD. Our nomogram model was a good predictor for recurrence of stage I-LUAD.