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JOURNAL ARTICLE
Jinfeng Liu, Sijie Liu, Dan Li, Hongbin Li, Fan Zhang
Background NFE2L2 (nuclear factor erythroid-2-related factor-2) encodes a basic leucine zipper (bZIP) transcription factor and exhibits variations in various tumor types, including lung cancer. In this study, we comprehensively investigated the impact of simultaneous mutations on the survival of NFE2L2 -mutant lung cancer patients within specific subgroups. Methods A cohort of 1,103 lung cancer patients was analyzed using hybridization capture-based next-generation sequencing. Results The NFE2L2 gene had alterations in 3...
June 2024: Global medical genetics
#2
JOURNAL ARTICLE
Roman Jaksik, Kamila Szumała, Khanh Ngoc Dinh, Jarosław Śmieja
Lung cancer is a global health challenge, hindered by delayed diagnosis and the disease's complex molecular landscape. Accurate patient survival prediction is critical, motivating the exploration of various -omics datasets using machine learning methods. Leveraging multi-omics data, this study seeks to enhance the accuracy of survival prediction by proposing new feature extraction techniques combined with unbiased feature selection. Two lung adenocarcinoma multi-omics datasets, originating from the TCGA and CPTAC-3 projects, were employed for this purpose, emphasizing gene expression, methylation, and mutations as the most relevant data sources that provide features for the survival prediction models...
March 25, 2024: International Journal of Molecular Sciences
#3
JOURNAL ARTICLE
Yuzhi Wang, Yunfei Xu, Yuqin Deng, Liqiong Yang, Dengchao Wang, Zhizhen Yang, Yi Zhang
BACKGROUND: Early research indicates that cancer patients are more vulnerable to adverse outcomes and mortality when infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonetheless, the specific attributes of SARS-CoV-2 in lung Adenocarcinoma (LUAD) have not been extensively and methodically examined. METHODS: We acquired 322 SARS-CoV-2 infection-related genes (CRGs) from the Human Protein Atlas database. Using an integrative machine learning approach with 10 algorithms, we developed a SARS-CoV-2 score (Cov-2S) signature across The Cancer Genome Atlas and datasets GSE72094, GSE68465, and GSE31210...
2024: Frontiers in Immunology
#4
JOURNAL ARTICLE
Yalei Zhang, Dongmei Li
Aneuploidy is a hallmark of cancers, but the role of aneuploidy-related genes in lung adenocarcinoma (LUAD) and their prognostic value remain elusive. Gene expression and copy number variation (CNV) data were enrolled from TCGA and GEO database. Consistency clustering analysis was performed for molecular cluster. Tumor microenvironment was assessed by the xCell and ESTIMATE algorithm. Limma package was used for selecting differentially expressed genes (DEGs). LASSO and stepwise multivariate Cox regression analysis were used to establish an aneuploidy-related riskscore (ARS) signature...
April 7, 2024: Scientific Reports
#5
JOURNAL ARTICLE
Vincenzo L'Imperio, Giorgio Cazzaniga, Mauro Mannino, Davide Seminati, Francesco Mascadri, Joranda Ceku, Gabriele Casati, Francesca Bono, Catarina Eloy, Elena Guerini Rocco, Chiara Frascarelli, Matteo Fassan, Umberto Malapelle, Fabio Pagni
The estimation of tumor cellular fraction (TCF) is a crucial step in predictive molecular pathology, representing an entry adequacy criterion also in the next-generation sequencing (NGS) era. However, heterogeneity of quantification practices and inter-pathologist variability hamper the robustness of its evaluation, stressing the need for more reliable results. Here, 121 routine histological samples from non-small cell lung cancer (NSCLC) cases with complete NGS profiling were used to evaluate TCF interobserver variability among three different pathologists (pTCF), developing a computational tool (cTCF) and assessing its reliability vs ground truth (GT) tumor cellularity and potential impact on the final molecular results...
March 26, 2024: Virchows Archiv: An International Journal of Pathology
#6
JOURNAL ARTICLE
Caiming Li, Nan Kang, Shun Ye, Weihang Huang, Xia Wang, Cheng Wang, Yuchen Li, Yan-Fei Liu, Ying Lan, Liang Ma, Yuhang Zhao, Yong Han, Jun Fu, Danhua Shen, Lianhua Dong, Wenbin Du
Digital PCR (dPCR) holds immense potential for precisely detecting nucleic acid markers essential for personalized medicine. However, its broader application is hindered by high consumable costs, complex procedures, and restricted multiplexing capabilities. To address these challenges, an all-in-one dPCR system is introduced that eliminates the need for microfabricated chips, offering fully automated operations and enhanced multiplexing capabilities. Using this innovative oscillation-induced droplet generation technique, OsciDrop, this system supports a comprehensive dPCR workflow, including precise liquid handling, pipette-based droplet printing, in situ thermocycling, multicolor fluorescence imaging, and machine learning-driven analysis...
March 22, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
#7
JOURNAL ARTICLE
Shaodi Wen, Renrui Zou, Xiaoyue Du, Rongtian Pan, Rutao Li, Jingwei Xia, Cong Xu, Ruotong Wang, Feng Jiang, Guoren Zhou, Jifeng Feng, Miaolin Zhu, Xin Wang, Bo Shen
BACKGROUND: Malignant tumours, particularly non-small cell lung cancer (NSCLC), pose a significant threat to human health due to their prevalence and lethality. Treatment methods for NSCLC vary greatly among individuals, making it crucial to identify predictive markers. Moreover, during tumour initiation and progression, tumour cells can release signaling molecules to induce polarization of macrophages towards a more tumour friendly M2 phenotype, which can promote tumour growth, metastasis, and drug resistance...
March 30, 2024: Heliyon
#8
MULTICENTER STUDY
Wei Lin, Siming Zhang, Chunyan Gu, Haixia Zhu, Yuan Liu
BACKGROUND: Glioma pathogenesis related-2 (GLIPR2), an emerging Golgi membrane protein implicated in autophagy, has received limited attention in current scholarly discourse. METHODS: Leveraging extensive datasets, including The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), Human Protein Atlas (HPA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC), we conducted a comprehensive investigation into GLIPR2 expression across diverse human malignancies...
2024: Frontiers in Immunology
#9
JOURNAL ARTICLE
Wenguang Pang, Longlong Gong, Wangpan Shi, Hongbo Zheng, Min Ye, Jiarong Chen, Ronggang Li, Xin Zhang, Dong Ren, Zheng Wang
Next generation sequencing (NGS) is typically used to reveal tumor gene variation feature for targeted therapy of various types of human cancers, including non-small cell lung cancer (NSCLC). Here, we report the role and potential applicable value of combining DNA and RNA sequencing in gene variation detection in NSCLC. 386 NSCLC patients with stage II-IV were enrolled and detected using NGS sequencing of DNA and RNA panels that covered all well-documented target driver genes from the Chinese Society of Clinical Oncology (CSCO)...
March 6, 2024: Discover. Oncology
#10
JOURNAL ARTICLE
Yupei Lin, Bryan M Burt, Hyun-Sung Lee, Thinh T Nguyen, Hee-Jin Jang, Claire Lee, Wei Hong, Robert Taylor Ripley, Christopher I Amos, Chao Cheng
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...
February 23, 2024: NPJ Precision Oncology
#11
JOURNAL ARTICLE
Zhifeng Ye, Ting Huang, Keke Hu, HeRan Zhou, Ling Huang, Lu Wang
Lung cancer remains a leading cause of global cancer-related mortality, and the exploration of innovative therapeutic approaches, such as PD1/PDL1 immunotherapy, is critical. This study leverages comprehensive data from the Cancer Genome Atlas (TCGA) to investigate the differential expression of PD1/PDL1 in lung cancer patients and explores its implications. Clinical data, RNA expression, somatic mutations, and copy number variations of 1017 lung cancer patients were obtained from TCGA. Patients were categorized into high (HE) and low (LE) PD1/PDL1 expression groups based on mRNA levels...
February 16, 2024: Journal of Applied Genetics
#12
JOURNAL ARTICLE
Yue Zang, Xia Ran, Jie Yuan, Hao Wu, Youya Wang, He Li, Huajing Teng, Zhongsheng Sun
Hyperactive ribosome biogenesis (RiboSis) fuels unrestricted cell proliferation, whereas genomic hallmarks and therapeutic targets of RiboSis in cancers remain elusive, and efficient approaches to quantify RiboSis activity are still limited. Here, we have established an in silico approach to conveniently score RiboSis activity based on individual transcriptome data. By employing this novel approach and RNA-seq data of 14 645 samples from TCGA/GTEx dataset and 917 294 single-cell expression profiles across 13 cancer types, we observed the elevated activity of RiboSis in malignant cells of various human cancers, and high risk of severe outcomes in patients with high RiboSis activity...
January 22, 2024: Briefings in Bioinformatics
#13
JOURNAL ARTICLE
Lingxue Shi, Xiaohong Wang, Shang Guo, Hongyan Gou, Haiyun Shang, Xiaojia Jiang, Chunxian Wei, Jia Wang, Chao Li, Lihong Wang, Zengren Zhao, Weifang Yu, Jun Yu
Copy number alterations are crucial for the development of gastric cancer (GC). Here, we identified Transmembrane Protein 65 (TMEM65) amplification by genomic hybridization microarray to profile copy-number variations in GC. TMEM65 mRNA level was significantly up-regulated in GC compared to adjacent normal tissues, and was positively associated with TMEM65 amplification. High TMEM65 expression or DNA copy number predicts poor prognosis (P < 0.05) in GC. Furtherly, GC patients with TMEM65 amplification (n = 129) or overexpression (n = 78) significantly associated with shortened survival...
February 10, 2024: Oncogene
#14
JOURNAL ARTICLE
Qianhui Wei, Jing Zhou, Xinyue Wang, Zhaona Li, Xiuqiong Chen, Kaidi Chen, Richeng Jiang
BACKGROUND: Nucleophosmin/nucleoplasmin 3 ( NPM3 ), a member of the NPM protein family, is widely expressed in various human tissues. Although previous studies identified elevated NPM3 expression in several cancers, a systematic pan-cancer analysis remains lacking. In this study, we conducted a comprehensive analysis of NPM3 to determine its role in tumorigenesis and tumor development. METHODS: Using data from The Cancer Genome Atlas (TCGA) and various bioinformatics analysis tools, we conducted a pan-cancer analysis of NPM3 ...
October 2023: Cancer Pathog Ther
#15
JOURNAL ARTICLE
Glowi Alasiri, Bahauddeen Alrfaei, Ali M Alaseem, Osama A AlKhamees, Jehad A Aldali, Ala M Aljehani, Abdulaziz Alfahed, Mohammad Azhar Aziz, Ghadir Almuhaini, Mana M Alshehri
The protein kinase TAOK3, belongs to the MAP kinase family, is one of three closely related members, namely TAOK1, TAOK2, and TAOK3. We performed a pan-cancer investigation of TAOK3 across different cancer types, including uterine carcinosarcoma, adenocarcinoma of the stomach and pancreas, and endometrial carcinoma of the uterus, to better understand TAOK3's role in cancer. In at least 16 types of cancer, our findings indicate that TAOK3 expression levels differ considerably between normal and tumor tissues...
March 2024: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
#16
JOURNAL ARTICLE
Mingxia Zhu, Xiaping Wang, Qing Zhang, Chen Xie, Tongshan Wang, Kai Shen, Lan Zhang, Xin Zhou
Targeting Protein for Xenopus Kinesin Like Protein 2 (TPX2) serves as a microtubule associated protein for the regulation of spindle assembly and tumorigenesis. We aim to investigate the prognostic and immunological role of TPX2 in pan-cancer. TCGA database, Tumor Immune Single-cell Hub (TISCH), and Human Protein Atlas (HPA) were retrieved to evaluate the expression pattern of TPX2 as well as its diagnostic and prognostic value in solid tumors. Genomic alterations of TPX2 were assessed with cBioPortal database...
February 2, 2024: Aging
#17
JOURNAL ARTICLE
Long Xu, Renquan Ding, Shuxi Song, Junling Liu, Jingyu Li, Xing Ju, Baozhao Ju
BACKGROUND: Aberrant activation of the phosphatidlinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway has been shown to play an important role in lung adenocarcinoma (LUAD). The effect of KRAS mutations, one of the important signatures of LUAD, on the PI3K/AKT/mTOR pathway in LUAD remains unclear. METHODS: The Seurat package and principal component analysis were used for cell categorization of single-cell RNA sequencing data of LUAD...
January 2024: Journal of Gene Medicine
#18
JOURNAL ARTICLE
Edwin Roger Parra, Jiexin Zhang, Dzifa Yawa Duose, Edgar Gonzalez-Kozlova, Mary W Redman, Hong Chen, Ganiraju C Manyam, Gayatri Kumar, Jianhua Zhang, Xingzhi Song, Rossana Lazcano, Mario L Marques-Piubelli, Caddie Laberiano-Fernandez, Frank Rojas, Baili Zhang, Len Taing, Aashna Jhaveri, Jacob Geisberg, Jennifer Altreuter, Franziska Michor, James Provencher, Joyce Yu, Ethan Cerami, Radim Moravec, Kasthuri Kannan, Rajyalakshmi Luthra, Gheath Alatrash, Hsin-Hui Huang, Hui Xie, Manishkumar Patel, Kai Nie, Jocelyn Harris, Kimberly Argueta, James Lindsay, Roshni Biswas, Stephen Van Nostrand, Seunghee Kim-Schulze, Jhanelle E Gray, Roy Herbst, Ignacio I Wistuba, Scott Gettinger, Karen Kelly, Lyudmila Bazhenova, Sacha Gnjatic, J Jack Lee, Jianjun Zhang, Cara Haymaker
BACKGROUND: Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. METHODS: Tissue and longitudinal blood specimens from phase III trial S1400I in metastatic lung squamous cell carcinoma (SqNSCLC) patients treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink...
January 26, 2024: Clinical Cancer Research
#19
JOURNAL ARTICLE
Yalei Zhang, Yan Hao, Hui Pan, Hongbo Zheng, Jiaqi Zhou
BACKGROUND: Chemotherapy has been the standard treatment for small-cell lung cancer (SCLC) for decades. Nonetheless, patients are usually responsive to initial chemotherapy but quickly suffer from relapse, resulting in a poor long-term outcome. Treating advances that greatly ameliorate survival outcomes are historically finite, and credible biomarkers for therapeutic evaluation are deficient. As the genetic biology emerges, investigating biomarkers to optimize individualized treatment for SCLC is necessary...
December 30, 2023: Journal of Thoracic Disease
#20
JOURNAL ARTICLE
Bjarne Daenekas, Eilís Pérez, Fabio Boniolo, Sabina Stefan, Salvatore Benfatto, Martin Sill, Dominik Sturm, David T W Jones, David Capper, Marc Zapatka, Volker Hovestadt
MOTIVATION: Copy-number variations (CNVs) are common genetic alterations in cancer and their detection may impact tumor classification and therapeutic decisions. However, detection of clinically relevant large and focal CNVs remains challenging when sample material or resources are limited. This has motivated us to create a software tool to infer CNVs from DNA methylation arrays which are often generated as part of clinical routines and in research settings. RESULTS: We present our R package, conumee 2...
January 19, 2024: Bioinformatics
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