scholarly journals Identification of CDKN3 and UBE2C mRNAs as Prognostic Biomarkers in Early-Stage Lung Adenocarcinoma Using Bioinformatics Strategy

2019 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Qiang Chen ◽  
Lutong Xu ◽  
Jing Hu ◽  
Tonglian Wang ◽  
Kang Zhang ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Early Stage ◽  
Prognostic Biomarkers

scholarly journals Non-Coding RNAs as Prognostic Biomarkers: A miRNA Signature Specific for Aggressive Early-Stage Lung Adenocarcinomas

2020 ◽  
Vol 6 (4) ◽  
pp. 48
Author(s):  
Elisa Dama ◽  
Valentina Melocchi ◽  
Francesco Mazzarelli ◽  
Tommaso Colangelo ◽  
Roberto Cuttano ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Lung Adenocarcinoma ◽  
Regulatory Networks ◽  
Early Stage ◽  
Stage I ◽  
Prognostic Biomarkers ◽  
Early Stage Disease ◽  
Ct Screening ◽  
Lung Cancer Patients ◽  
Reduction Of Mortality

Lung cancer burden can be reduced by adopting primary and secondary prevention strategies such as anti-smoking campaigns and low-dose CT screening for high risk subjects (aged >50 and smokers >30 packs/year). Recent CT screening trials demonstrated a stage-shift towards earlier stage lung cancer and reduction of mortality (~20%). However, a sizable fraction of patients (30–50%) with early stage disease still experience relapse and an adverse prognosis. Thus, the identification of effective prognostic biomarkers in stage I lung cancer is nowadays paramount. Here, we applied a multi-tiered approach relying on coupled RNA-seq and miRNA-seq data analysis of a large cohort of lung cancer patients (TCGA-LUAD, n = 510), which enabled us to identify prognostic miRNA signatures in stage I lung adenocarcinoma. Such signatures showed high accuracy (AUC ranging between 0.79 and 0.85) in scoring aggressive disease. Importantly, using a network-based approach we rewired miRNA-mRNA regulatory networks, identifying a minimal signature of 7 miRNAs, which was validated in a cohort of FFPE lung adenocarcinoma samples (CSS, n = 44) and controls a variety of genes overlapping with cancer relevant pathways. Our results further demonstrate the reliability of miRNA-based biomarkers for lung cancer prognostication and make a step forward to the application of miRNA biomarkers in the clinical routine.

scholarly journals DeepRePath: Identifying the Prognostic Features of Early-Stage Lung Adenocarcinoma Using Multi-Scale Pathology Images and Deep Convolutional Neural Networks

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3308
Author(s):  
Won Sang Shim ◽  
Kwangil Yim ◽  
Tae-Jung Kim ◽  
Yeoun Eun Sung ◽  
Gyeongyun Lee ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Early Stage ◽  
External Validation ◽  
Area Under The Curve ◽  
The Cancer Genome Atlas ◽  
Deep Convolutional Neural Networks ◽  
Prognostic Features ◽  
Multi Scale ◽  
Model Based ◽  
Number Of Patients

The prognosis of patients with lung adenocarcinoma (LUAD), especially early-stage LUAD, is dependent on clinicopathological features. However, its predictive utility is limited. In this study, we developed and trained a DeepRePath model based on a deep convolutional neural network (CNN) using multi-scale pathology images to predict the prognosis of patients with early-stage LUAD. DeepRePath was pre-trained with 1067 hematoxylin and eosin-stained whole-slide images of LUAD from the Cancer Genome Atlas. DeepRePath was further trained and validated using two separate CNNs and multi-scale pathology images of 393 resected lung cancer specimens from patients with stage I and II LUAD. Of the 393 patients, 95 patients developed recurrence after surgical resection. The DeepRePath model showed average area under the curve (AUC) scores of 0.77 and 0.76 in cohort I and cohort II (external validation set), respectively. Owing to low performance, DeepRePath cannot be used as an automated tool in a clinical setting. When gradient-weighted class activation mapping was used, DeepRePath indicated the association between atypical nuclei, discohesive tumor cells, and tumor necrosis in pathology images showing recurrence. Despite the limitations associated with a relatively small number of patients, the DeepRePath model based on CNNs with transfer learning could predict recurrence after the curative resection of early-stage LUAD using multi-scale pathology images.

scholarly journals A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhiying Chen ◽  
Jiahui Wei ◽  
Min Li ◽  
Yongjuan Zhao
Keyword(s):  
Functional Analysis ◽  
Survival Analysis ◽  
Lung Adenocarcinoma ◽  
Target Genes ◽  
Interaction Analysis ◽  
Early Stage ◽  
Gene Interaction ◽  
Gene Expression Omnibus ◽  
Circular Rnas ◽  
Cerna Network

Abstract Background This study aimed to identify potential circular ribonucleic acid (circRNA) signatures involved in the pathogenesis of early-stage lung adenocarcinoma (LAC). Methods The circRNA sequencing dataset of early-stage LAC was downloaded from the Gene Expression Omnibus database. First, the differentially expressed circRNAs (DEcircRNAs) between tumour and non-tumour tissues were screened. Then, the corresponding miRNAs and their target genes were predicted. In addition, prognosis-related genes were identified using survival analysis and further used to build a network of competitive endogenous RNAs (ceRNAs; DEcircRNA–miRNA–mRNA). Finally, the functional analysis and drug–gene interaction analysis of mRNAs in the ceRNA network was performed. Results A total of 35 DEcircRNAs (30 up-regulated and 5 down-regulated circRNAs) were identified. Moreover, 135 DEcircRNA–miRNA and 674 miRNA–mRNA pairs were predicted. The survival analysis of these target mRNAs revealed that 60 genes were significantly associated with survival outcomes in early-stage LAC. Of these, high levels of PSMA 5 and low levels of NAMPT, CPT 2 and TNFSF11 exhibited favourable prognoses. In addition, the DEcircRNA–miRNA–mRNA network was constructed, containing 5 miRNA–circRNA (hsa_circ_0092283/hsa-miR-762/hsa-miR-4685-5p; hsa_circ_0070610/hsa-let-7a-2-3p/hsa-miR-3622a-3p; hsa_circ_0062682/hsa-miR-4268) and 60 miRNA–mRNA pairs. Functional analysis of the genes in the ceRNA network showed that they were primarily enriched in the Wnt signalling pathway. Moreover, PSMA 5, NAMPT, CPT 2 and TNFSF11 had strong correlations with different drugs. Conclusion Three circRNAs (hsa_circ_0062682, hsa_circ_0092283 and hsa_circ_0070610) might be potential novel targets for the diagnosis of early-stage LAC.

Machine learning of serum metabolic patterns encodes early-stage lung adenocarcinoma

2021 ◽  
Author(s):  
Lin Huang ◽  
Kun Qian
Keyword(s):  
Machine Learning ◽  
Lung Adenocarcinoma ◽  
Cancer Detection ◽  
High Performance ◽  
Large Scale ◽  
Early Cancer ◽  
Early Stage ◽  
Early Cancer Detection ◽  
Ionization Mass ◽  
Efficient Test

Abstract Early cancer detection greatly increases the chances for successful treatment, but available diagnostics for some tumours, including lung adenocarcinoma (LA), are limited. An ideal early-stage diagnosis of LA for large-scale clinical use must address quick detection, low invasiveness, and high performance. Here, we conduct machine learning of serum metabolic patterns to detect early-stage LA. We extract direct metabolic patterns by the optimized ferric particle-assisted laser desorption/ionization mass spectrometry within 1 second using only 50 nL of serum. We define a metabolic range of 100-400 Da with 143 m/z features. We diagnose early-stage LA with sensitivity~70-90% and specificity~90-93% through the sparse regression machine learning of patterns. We identify a biomarker panel of seven metabolites and relevant pathways to distinguish early-stage LA from controls (p < 0.05). Our approach advances the design of metabolic analysis for early cancer detection and holds promise as an efficient test for low-cost rollout to clinics.

Osimertinib as neoadjuvant treatment for resectable stage II-IIIB EGFR mutant lung adenocarcinoma (NEOS).

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 8524-8524
Author(s):  
Chao Lyu ◽  
Wentao Fang ◽  
Haitao Ma ◽  
Jia Wang ◽  
Wenjie Jiao ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Surgical Resection ◽  
Interim Analysis ◽  
Kinase Inhibitors ◽  
Response Rate ◽  
Early Stage ◽  
Neoadjuvant Treatment ◽  
Complete Response ◽  
Stage Ii ◽  
Meaningful Improvement

8524 Background: Neoadjuvant treatment has demonstrated efficacy in several types of cancer and is increasingly used for the treatment of early-stage cancers with the potential of cancer downstaging to enhance complete surgical resection and to improve clinical outcomes. Recent evidences have demonstrated that the neoadjuvant use of first/second-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) may provide clinically meaningful improvement in EGFRm non-small cell lung cancer (NSCLC) patients, however, limited data were reported on osimertinib, the third-generation EGFR-TKI, in the neoadjuvant setting. Here we present an interim analysis of osimertinib as neoadjuvant treatment for resectable EGFRm NSCLC. Methods: NEOS is a prospective, multi-center, single-arm study to evaluate the efficacy and safety of osimertinib as neoadjuvant treatment in resectable EGFRm (19del/L858R) lung adenocarcinoma. Eligible patients were treated with osimertinib 80 mg orally per day for six weeks followed by surgery. Assessment of response to neoadjuvant therapy was performed according to RECIST 1.1. The primary endpoint was response rate. Secondary endpoints included safety, R0 surgical resection rate, quality of life, major pathologic response (MPR) rate, pathological complete response (pCR) rate, and N2 downstaging rate. Results: As of Dec. 17, 2020, 18 eligible patients (median age 61 [range 46-73], 27.8% male, 22.2% ECOG PS 1) have been enrolled. Patients with clinical stages IIa, IIb, and IIIa (8th AJCC) accounted for 16.7%, 22.2% and 61.1%, respectively. Half (9/18) of the patients had EGFR exon 21 L858R mutations and the other half (9/18) had EGFR exon 19del mutations. Amongst all 15 patients who completed efficacy assessment after neoadjuvant osimertinib, the response rate (RR) was 73.3% (11/15) and the disease control rate (DCR) was 100% (15/15). R0 surgical resection was performed in 93.3% (14/15) patients. Pathological downstaging occurred in 53.3% (8/15) patients. 42.9% (3/7) of the patients with confirmed N2 lymph nodes experienced downstaging to N0 disease after receiving neoadjuvant osimertinib. One patient was identified with a pCR. Adverse events (AEs) were reported in 66.7% (12/18) of patients, with the most common AE being rash (8/18, 44.4%), oral ulceration (8/18, 44.4%), and diarrhea (5/18, 27.8%). No grade 3-5 AEs or serious AEs were reported. Conclusions: Interim analysis from this study indicated neoadjuvant osimertinib as an effective and feasible treatment in patients with resectable stage II-IIIB EGFRm NSCLC. The trial is ongoing and the final results will be provided in the future. Clinical trial information: ChiCTR1800016948.

scholarly journals Two-gene signature improves the discriminatory power of IASLC/ATS/ERS classification to predict the survival of patients with early-stage lung adenocarcinoma

2016 ◽  
Vol Volume 9 ◽  
pp. 4583-4591 ◽  
Author(s):  
Wen Gao ◽  
likun Hou ◽  
Yu Yang ◽  
Huikang xie ◽  
Yang Yang ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Early Stage ◽  
Gene Signature ◽  
Discriminatory Power

scholarly journals Role of MicroRNAs in Progression and Recurrence of Early-Stage Lung Adenocarcinoma

2015 ◽  
Vol 2 (1) ◽  
pp. 52-62 ◽  
Author(s):  
Rama K. Singh ◽  
◽  
Drew C. Bethune ◽  
Zhaolin Xu ◽  
Susan E. Douglas ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Early Stage
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