Identification of hypoxia-related gene signatures based on multi-omics analysis in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) is the most common type of lung cancer and one of the malignancies with the highest incidence rate and mortality worldwide. Hypoxia is a typical feature of tumour microenvironment (TME), which affects the progression of LUAD from multiple molecular levels. However, the underlying molecular mechanisms behind LUAD hypoxia are not fully understood. In this study, we estimated the level of hypoxia by calculating a score based on 15 hypoxia genes. The hypoxia scores were relatively high in LUAD patients with poor prognosis and were bound up with tumour node metastasis (TNM) stage, tumour size, lymph node, age and gender. By comparison of high hypoxia score group and low hypoxia score group, 1820 differentially expressed genes were identified, among which up-regulated genes were mainly about cell division and proliferation while down-regulated genes were primarily involved in cilium-related biological processes. Besides, LUAD patients with high hypoxia scores had higher frequencies of gene mutations, among which TP53, TTN and MUC16 had the highest mutation rates. As for DNA methylation, 1015 differentially methylated probes-related genes were found and may play potential roles in tumour-related neurobiological processes and cell signal transduction. Finally, a prognostic model with 25 multi-omics features was constructed and showed good predictive performance. The area under curve (AUC) values of 1-, 3- and 5-year survival reached 0.863, 0.826 and 0.846, respectively. Above all, our findings are helpful in understanding the impact and molecular mechanisms of hypoxia in LUAD.

A heterogeneous tumor immune microenvironment of uncommon epidermal growth factor receptor mutant non-small cell lung cancer.

Common epidermal growth factor receptor (EGFR) mutations are usually not considered for immunotherapy in non-small cell lung cancer (NSCLC) due to poor efficacy. However, whether uncommon EGFR mutations are suitable for immunotherapy has not been thoroughly studied. Thus, we explored the tumor immune microenvironment (TME) features in uncommon EGFR mutant NSCLC. In this study, a total of 41 patients with EGFR mutations were included, the majority (85.4%) of whom were stage I. Among them, 22 patients harbored common mutations, while 19 patients presented with uncommon mutations. Compared with common mutations, uncommon mutations exhibited more infiltrating T cells and fewer M2 macrophages, upregulated expression of antigen processing and a presentation pathway. Unsupervised clustering based on the mIF profile identified two classes with heterogeneous TME in uncommon mutations. Class 1 featured the absence of PD-1+ cytotoxic T cell infiltration, and class 2 displayed a hotter TME because of the downregulated expression of hypoxia (p < 0.001), oxidative phosphorylation (p = 0.009), and transforming growth factor beta signaling (p = 0.01) pathways as well as increased expression of CTLA4 (p = 0.001) and PDCD1 (p = 0.004). The association of CTLA4 and PDCD1 with TME profiles was validated in a TCGA lung adenocarcinoma cohort with uncommon EGFR mutations. Our study reveals the distinct and heterogeneous TME features in uncommon EGFR mutant NSCLC.

[18F]FDG PET-CT radiomics signature to predict pathological complete response to neoadjuvant chemoimmunotherapy in non-small cell lung cancer: a multicenter study.

OBJECTIVES: This study aims to develop and validate a radiomics model based on 18F-fluorodeoxyglucose positron emission tomography-computed tomography ([18F]FDG PET-CT) images to predict pathological complete response (pCR) to neoadjuvant chemoimmunotherapy in non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: One hundred eighty-five patients receiving neoadjuvant chemoimmunotherapy for NSCLC at 5 centers from January 2019 to December 2022 were included and divided into a training cohort and a validation cohort. Radiomics models were constructed via the least absolute shrinkage and selection operator (LASSO) method. The performances of models were evaluated by the area under the receiver operating characteristic curve (AUC). In addition, genetic analyses were conducted to reveal the underlying biological basis of the radiomics score. RESULTS: After the LASSO process, 9 PET-CT radiomics features were selected for pCR prediction. In the validation cohort, the ability of PET-CT radiomics model to predict pCR was shown to have an AUC of 0.818 (95% confidence interval [CI], 0.711, 0.925), which was better than the PET radiomics model (0.728 [95% CI, 0.610, 0.846]), CT radiomics model (0.732 [95% CI, 0.607, 0.857]), and maximum standard uptake value (0.603 [95% CI, 0.473, 0.733]) (p < 0.05). Moreover, a high radiomics score was related to the upregulation of pathways suppressing tumor proliferation and the infiltration of antitumor immune cell. CONCLUSION: The proposed PET-CT radiomics model was capable of predicting pCR to neoadjuvant chemoimmunotherapy in NSCLC patients. CLINICAL RELEVANCE STATEMENT: This study indicated that the generated 18F-fluorodeoxyglucose positron emission tomography-computed tomography radiomics model could predict pathological complete response to neoadjuvant chemoimmunotherapy, implying the potential of our radiomics model to personalize the neoadjuvant chemoimmunotherapy in lung cancer patients. KEY POINTS: • Recognizing patients potentially benefiting neoadjuvant chemoimmunotherapy is critical for individualized therapy of lung cancer. • [18F]FDG PET-CT radiomics could predict pathological complete response to neoadjuvant immunotherapy in non-small cell lung cancer. • [18F]FDG PET-CT radiomics model could personalize neoadjuvant chemoimmunotherapy in lung cancer patients.

LncRNA FOXD3-AS1 promoted chemo-resistance of NSCLC cells via directly acting on miR-127-3p/MDM2 axis.

BACKGROUND: This study aims to investigate the mechanism underlying the high level of long non-coding RNA FOXD3-AS1 in cisplatin-resistant NSCLC cells. METHODS: Cisplatin-resistant cells were generated from A549 cells. CCK-8 were used to evaluate cell proliferation. The FOXD3-AS1, miR-127-3p, MDM2 and MRP1 mRNA expression levels were confirmed by qRT-PCR. Protein levels of MDM2 and MRP1 were determined by western blot assay. Luciferase reporter and RNA pull-down assays were evaluated the relationship between miR-127-3p and FOXD3-AS1/MDM2. In vivo tumor growth was evaluated in a xenograft nude mice model. RESULTS: FOXD3-AS1 was up-regulated in cisplatin-resistant NSCLC cells (A549/DDP and H1299/DDP cells) in comparison with their parental cell lines. Overexpression of FOXD3-AS1 promoted cisplatin-resistance in A549 and H1299 cells; while FOXD3-AS1 knockdown sensitized A549/DDP and H1299/DDP cells to cisplatin treatment. FOXD3-AS1 regulated miR-127-3p expression by acting as a competing endogenous RNA, and miR-127-3p repressed MDM2 expression via targeting the 3'UTR. MiR-127-3p overexpression and MDM2 knockdown both increased the chemo-sensitivity in A549/DDP cells; while miR-127-3p knockdown and MDM2 overexpression both promoted chemoresistance in A549 cells. Further rescue experiments revealed that miR-127-3p knockdown or MDM2 overexpression counteracted the suppressive effects of FOXD3-AS1 knockdown on chemo-resistance and MRP1 expression in A549/DDP cells. In vivo studies showed that FOXD3-AS1 knockdown potentiated the antitumor effects of cisplatin treatment. Inspection of clinical samples showed the upregulation of FOXD3-AS1 and MDM2, and down-regulation of miR-127-3p in NSCLC tissues compared to normal adjacent tissues. CONCLUSION: In conclusion, our results suggest that LncRNA FOXD3-AS1 promotes chemo-resistance of NSCLC cells via directly acting on miR-127-3p/MDM2 axis. Our findings may provide novel perspectives for the treatment of NSCLC in patients resistant to chemotherapy.

[Research Advances in Regeneration of Soft Tissue with Small Intestinal Submucosa].

Small intestinal submucosa(SIS)is a natural decellularized extracellular matrix material.Due to its excellent biocompatibility,unique biomechanical properties and biological activity,it has been widely used as a scaffold in regenerative medicine.This article reviews the recent progress in the characterization and medical application of SIS respectively.The specific biological properties of the SIS,as well as its interaction with cells,are highlighted.Some of the SIS products and clinical cases are also reviewed and discussed.

Meta-analyses of methylation markers for prostate cancer.

Prostate cancer (PCa) is the most frequently diagnosed non-cutaneous cancer that has become the sixth leading cause of mortality in both the developed and developing countries. Accumulating evidence showed a number of genes with aberrant DNA methylation in the pathogenesis of PCa. Here, we conducted a systematic meta-analysis to evaluate the contribution of aberrantly methylated genes to the risk of PCa. Relevant methylation studies were retrieved from PubMed and Wanfang literature databases. In the meta-analysis, Mantel-Haenszel odds ratios (ORs) and 95 % confidence intervals (CIs) were calculated for each methylation event under appropriate models. A total of 594 publications were initially retrieved from PubMed and Wanfang literature database. After a three-step filtration, we harvested 39 case-control articles investigating the role of gene methylation in the prediction of PCa risk. Among the 31 genes involved, 24 genes were shown to be significantly hypermethylated in the PCa patients. Our meta-analyses identified strong associations of four aberrantly methylated genes (GSTP1, RASSF1, p16, and RARB) with PCa. Further research is needed to strengthen our findings in the future.

A novel PIBF1-RET gene fusion identified from a stage IA lung adenocarcinoma: A case report.

INTRODUCTION: Rearranged during transfection (RET) gene fusions occur in 0.7% to 2% in lung cancer and 1% to 2% in non-small cell lung cancer. Systemic therapies for RET fusion-positive non-small cell lung cancer consist mostly of targeted therapy with RET inhibitors such as selpercatinib and pralsetinib. To date, approximately 40 fusion partners have been reported. Herein, we report a novel progesterone immunomodulatory binding factor 1 (PIBF1)-RET gene fusion identified from a stage IA lung adenocarcinoma and was further validated by RNA sequencing analysis. PATIENT CONCERNS: A 55-year-old male smoker was found by chest computed tomography to have a solid nodule in the right lower lobe of the lung and enlarged mediastinal lymph nodes. DIAGNOSES: The patient was then diagnosed with stage IA lung adenocarcinoma (T1N0M0). INTERVENTION: The patient then underwent thoracoscopic lobectomy of the right lower lobe and mediastinal lymph node dissection. Molecular testing with a targeted panel of 8 lung cancer-associated driver genes detected a novel PIBF1-RET (P16:R12) fusion, which putatively encodes a gene in which the first 16 exons of PIBF1 was concatenated to RET exon 13 and its downstream sequence, retaining the RET kinase domain. The genomic translocation was further validated by RNA sequencing with a panel of 115 cancer-associated genes, which found no other aberrations. OUTCOMES: The patient was discharged 3 days after surgery. CONCLUSION: We report a novel PIBF1-RET fusion in early-stage lung adenocarcinoma. This finding expands the spectrum of RET fusion partners and warrants further studies in characterizing the oncogenic role of this genomic aberration and response to RET-targeted therapies.

Cellular Senescence in Non-Small Cell Lung Cancer.

Lung cancer has the highest mortality rate amongst all malignancies worldwide, and is the second-highest incidence of cancer in women. Non-small cell lung cancer (NSCLC) is responsible for approximately 80% of lung cancer cases. Recent studies indicate that cellular senescence may be a promising cancer biomarker. However, the regulation of cellular senescence and its underlying mechanisms in NSCLC are not yet fully understood. Here, we present a comprehensive analysis of the genes linked to cellular senescence in NSCLC. We also describe the secretory phenotype associated with NSCLC and examine its immune profile and prognostic potential. Our findings offer novel insights into the development of effective NSCLC treatments.

LncRNA RP11­805J14.5 functions as a ceRNA to regulate CCND2 by sponging miR­34b­3p and miR­139­5p in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) is the most common lung cancer with high incidence. The prognosis of LUAD is poor due to its aggressive behavior. Long non­coding RNAs (lncRNAs) have been reported as a key modulator on LUAD progression. Therefore, the present study aimed to clarify the molecular mechanism of lncRNAs in LUAD development. The expression of lncRNA RP11­805J14.5 (RP11­805J14.5) in LUAD tissues and cells was quantified based on the data in The Cancer Genome Atlas (TCGA). Cell viability was determined using Cell Counting Kit­8 method. Apoptotic cells were sorted and determined by flow cytometry. Cell migration and invasion abilities were detected by the Transwell assay. Luciferase reporter experiment and RNA pull­down assay were utilized to determine the interactions between RP11­805J14.5, microRNA (miR)­34b­3p, miR­139­5p, and cyclin D2 (CCND2). A xenograft tumor was established to determine tumor growth in vivo. RP11­805J14.5 was highly expressed in LUAD and associated with poor survival of LUAD patients. Knockdown of RP11­805J14.5 suppressed LUAD cell growth, invasion, migration and tumor growth, indicating that RP11­805J14.5 is an important regulator of LUAD. Our study demonstrated that the regulation of RP11­805J14.5 on LUAD was mediated by CCND2 whose expression was regulated by sponging miR­34b­3p and miR­139­5p. The expression of RP11­805J14.5 was increased in LUAD, and the knockdown of RP11­805J14.5 expression suppressed LUAD cell growth, invasion and migration by downregulating CCND2 by sponging miR­34b­3p and miR­139­5p, indicating that RP11­805J14.5 could be a prospective target for LUAD therapy.

Research progress on the relationship between the TOR signaling pathway regulator, epigenetics, and tumor development.

Almost all cellular activities depend on protein folding, signaling complex assembly/disassembly, and epigenetic regulation. One of the most important regulatory mechanisms responsible for controlling these cellular processes is dynamic protein phosphorylation/dephosphorylation. Alterations in phosphorylation networks have major consequences in the form of disorders, including cancer. Many signaling cascades, including the target of rapamycin (TOR) signaling, are important participants in the cell cycle, and dysregulation in their phosphorylation/dephosphorylation status has been linked to malignancies. As a TOR signaling regulator, protein phosphatase 2A (PP2A) is responsible for most of the phosphatase activities inside the cells. On the other hand, TOR signaling pathway regulator (TIPRL) is an essential PP2A inhibitory protein. Many other physiological roles have also been suggested for TIPRL, such as modulation of TOR pathways, apoptosis, and cell proliferation. It is also reported that TIPRL was increased in various carcinomas, including non-small-cell lung carcinoma (NSCLC) and hepatocellular carcinomas (HCC). Considering the function of PP2A as a tumor suppressor and also the effect of the TIPRL/PP2A axis on apoptosis and proliferation of cancer cells, this review aims to provide a complete view of the role of TIPRL in cancer development in addition to describing TIPRL/PP2A axis and its epigenetic regulation.

A rare survival case of blunt left ventricular rupture caused by a low-energy pedestrian collision with a stationary forklift: a case report.

Blunt cardiac rupture (BCR) is a rare injury with a high mortality rate. It is usually caused by high-energy traumatic accidents, such as motor vehicle collisions. For the first time, we report a rare case of BCR caused by a pedestrian collision with a stationary motor vehicle, which is a low-energy traumatic accident. This is also the first surgical survival BCR case to be reported of a contralateral ventricular rupture at the direct stress site. A 45-year-old formerly healthy Chinese woman, with no family history of heart disease, was walking in a hurry when she accidentally hit a forklift that was parked on the side of the road. The patient gradually lost consciousness, and was admitted to Hwa Mei Hospital Emergency Center 1 hour later. An ultrasound revealed a pericardial effusion about 1 cm deep and a small amount of peritoneal -35 effusion. Emergency computed tomography (CT) scans revealed a small amount of fluid accumulation in the right thoracic cavity, fractures of the 5th and 6th ribs on the right side, and pericardial effusion. The patient's blood pressure remained unstable after 1 hour of endotracheal intubation, B-ultrasound-guided pericardiocentesis, and antishock therapy; thus, open-heart surgery was deemed necessary. A large amount of blood accumulation was found in the intact pericardium. There was a small blood clot at the apex of the left ventricle near the interventricular septum. The removal of the clot revealed a tear about 1 cm in diameter. The patient's BCR was successfully repaired in the surgery. By the end of the 18-month follow-up period, the patient was found to have recovered well without significant complications. The internal mechanism of the case report was deceleration. Prompt diagnosis and emergency thoracotomy when BCR is suspected are key to rescuing patients, regardless of whether the accident is high energy or low energy, or if there is evidence of a direct force acting on the precordium, or the presence of pericardial rupture.

A patient with metastatic non-small cell lung cancer who received pembrolizumab monotherapy after stereotactic body radiotherapy had progression-free survival of nearly 5 years: a case report.

Lung cancer is a malignancy with the highest morbidity and mortality in the world. Radiotherapy, chemotherapy, targeted therapy, and immunotherapy have been widely used to treat metastatic non-small cell lung cancer (NSCLC). Stereotactic body radiotherapy (SBRT), also known as stereotactic ablation radiotherapy (SABR), can precisely deliver a high dose of radiation to a target in a limited area. SBRT has been established as the standard treatment for patients with early NSCLC who are unsuitable for operation or refuse surgery and patients with oligometastatic NSCLC who are not suitable for surgery. As an immunologic agent, pembrolizumab has been approved to treat metastatic NSCLC in certain countries, including China and the United States. Increased tumor proportion score (TPS) can reduce pembrolizumab's immunotherapeutic effect, while SBRT can reduce TPS and enhance immunotherapy efficacy. However, there have been no reports in China on metastatic NSCLC patients who have received pembrolizumab monotherapy after stereotactic body radiotherapy (SBRT). Here, we present a case of progression-free survival (PFS) of nearly 5 years with pembrolizumab monotherapy after SBRT for metastatic NSCLC. This case is the patient with the most prolonged medication duration and who experienced the most efficacious treatment among the patients with metastatic NSCLC reported in the Chinese literature.

Multi-omics Data Analyses Construct TME and Identify the Immune-Related Prognosis Signatures in Human LUAD.

Lung cancer has been the focus of attention for many researchers in recent years for the leading contribution to cancer-related death worldwide, in which lung adenocarcinoma (LUAD) is the most common histological type. However, the potential mechanism behind LUAD initiation and progression remains unclear. Aiming to dissect the tumor microenvironment of LUAD and to discover more informative prognosis signatures, we investigated the immune-related differences in three types of genetic or epigenetic characteristics (expression status, somatic mutation, and DNA methylation) and considered the potential roles that these alterations have in the immune response and both the immune-related metabolic and neural systems by analyzing the multi-omics data from The Cancer Genome Atlas (TCGA) portal. Additionally, a four-step strategy based on lasso regression and Cox regression was used to construct the prognostic prediction model. For the prognostic predictions on the independent test set, the performance of the trained models (average concordance index [C-index] = 0.839) is satisfied, with average 1-year, 3-year, and 5-year areas under the curve (AUCs) equal to 0.796, 0.786, and 0.777. Finally, the overall model was constructed based on all samples, which comprised 27 variables and achieved a high degree of accuracy on the 1-year (AUC = 0.861), 3-year (AUC = 0.850), and 5-year (AUC = 0.916) survival predictions.

Knockdown of TOR signaling pathway regulator suppresses cell migration and invasion in non-small cell lung cancer via the regulation of epithelial-to-mesenchymal transition.

Non-small cell lung cancer (NSCLC) is one of the most common cancer types worldwide. Previous studies have indicated that TOR signaling pathway regulator (TIPRL) is involved in the progression of NSCLC. However, the underlying mechanisms of the role of TIPRL in regulating NSCLC metastasis have remained largely elusive. In the present study, the expression pattern of TIPRL in NSCLC was analyzed using The Cancer Genome Atlas (TCGA) dataset. Furthermore, Kaplan-Meier curve analysis was performed to evaluate the prognostic value of TIPRL in NSCLC, using the Kaplan-Meier Plotter and TCGA datasets. Loss-of-function assays were performed to determine the effects of TIPRL on cell migration and invasion. The results suggested that TIPRL was upregulated in NSCLC and positively associated with an advanced Tumor-Node-Metastasis stage. A higher expression level of TIPRL was associated with shorter overall and disease-free survival times in patients with NSCLC. To the best of our knowledge, the present study was the first to report that TIPRL acts as a metastasis promoter in NSCLC. Silencing of TIPRL suppressed A549 cell migration and invasion. Mechanistically, the present study indicated that TIPRL knockdown significantly promoted epithelial-cadherin expression, whereas it suppressed twist and vimentin expression in A549 cells. In conclusion, the present analysis suggested that TIPRL may serve as a biomarker for the prognosis of NSCLC and as a future target for its treatment.

Estrogen and promoter methylation in the regulation of PLA2G7 transcription.

In the current study, cell lines including HEK293, SW480, HPASMC, HPCASMC and HAEC were cultured with 5-aza-2-deoxycytidine (DAC) and 17-ß-estradiol to investigate whether PLA2G7 transcription was under the control of promoter methylation and 17-ß-estradiol. Luciferase reporter gene assays were used to evaluate whether reporter gene activity was enhanced by PLA2G7 promoter fragment. Gene expression and methylation were detected using RT-PCR and pyrosequencing methods, respectively. Endogenous PLA2G7 transcription levels were found to be significantly lower in vascular related cell lines than in the other cell lines. Luciferase reporter gene assays indicated that gene activity was significantly enhanced by PLA2G7 promoter fragment. PLA2G7 transcription was found to be up-regulated with the treatment of DAC. The 17-ß-estradiol was found to down-regulate PLA2G7 transcription in all the cell lines. However, 17-ß-estradiol did not have significant effect on PLA2G7 methylation. Further chromatin immunoprecipitation assay showed that 17-ß-estradiol might regulate gene transcription by affecting the acetylated histone H3 and H4 marks on PLA2G7 promoter. Our results showed that PLA2G7 gene expression was co-regulated by 17-ß-estradiol and promoter methylation. Our findings might provide molecular clues for gender disparity in the contribution of PLA2G7 to vascular related diseases such as coronary heart disease.

DNA methylation and leukemia susceptibility in China: Evidence from an updated meta-analysis.

Mounting evidence supports a role for DNA methylation in the pathogenesis of leukemia; however, there no overview of these results in the Chinese population. The present study performed a comprehensive meta-analysis to establish candidate genes with an altered methylation status in Chinese leukemia patients. Eligible studies were identified through searching the National Center of Biotechnology Information PubMed and Wanfang databases. Studies were pooled and overall odds ratios with corresponding confidence intervals were calculated. A total of 4,325 leukemia patients and 2,010 controls from 94 studies on 53 genes were included in this meta-analysis, and 47 genes were found to be aberrantly methylated in leukemia patients. A further subgroup meta-analysis by leukemia subtype demonstrated that hypermethylation of 5 genes, namely cyclin-dependent kinase (CDKN)2A, DNA-binding protein inhibitor-4, CDKN2B, glioma pathogenesis-related protein 1 and p73, contributed to the risk of various subtypes of leukemia. In addition, a strong association between CDKN2A and leukemia was identified in Chinese (P<0.00001) but not in European patients. The aberrantly methylated genes identified in the present meta-analysis may help elucidate the mechanisms underlying the development of leukemia in Chinese patients.

The diagnostic value of DNA methylation in leukemia: a systematic review and meta-analysis.

BACKGROUND: Accumulating evidence supports a role of DNA methylation in the pathogenesis of leukemia. The aim of our study was to evaluate the potential genes with aberrant DNA methylation in the prediction of leukemia risk by a comprehensive meta-analysis of the published data. METHODS: A series of meta-analyses were done among the eligible studies that were harvested after a careful filtration of the searching results from PubMed literature database. Mantel-Haenszel odds ratios and 95% confidence intervals were computed for each methylation event assuming the appropriate model. RESULTS: A total of 535 publications were initially retrieved from PubMed literature database. After a three-step filtration, we harvested 41 case-control articles that studied the role of gene methylation in the prediction of leukemia risk. Among the involving 30 genes, 20 genes were shown to be aberrantly methylated in the leukemia patients. A further subgroup meta-analysis by subtype of leukemia showed that CDKN2A, CDKN2B, ID4 genes were significantly hypermethylated in acute myeloid leukemia. CONCLUSIONS: Our meta-analyses identified strong associations between a number of genes with aberrant DNA methylation and leukemia. Further studies should be required to confirm the results in the future.