TY - JOUR
T1 - Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE
AU - Roberts, Matthew
AU - Ogden, Julia
AU - Hossain, A S Mukarram
AU - Chaturvedi, Anshuman
AU - Kerr, Alastair R W
AU - Dive, Caroline
AU - Beane, Jennifer Ellen
AU - Lopez-Garcia, Carlos
N1 - © 2023, Roberts et al.
PY - 2023/3/9
Y1 - 2023/3/9
N2 - Lung squamous cell carcinoma (LUSC) is a type of lung cancer with a dismal prognosis that lacks adequate therapies and actionable targets. This disease is characterized by a sequence of low- and high-grade preinvasive stages with increasing probability of malignant progression. Increasing our knowledge about the biology of these premalignant lesions (PMLs) is necessary to design new methods of early detection and prevention, and to identify the molecular processes that are key for malignant progression. To facilitate this research, we have designed XTABLE (Exploring Transcriptomes of Bronchial Lesions), an open-source application that integrates the most extensive transcriptomic databases of PMLs published so far. With this tool, users can stratify samples using multiple parameters and interrogate PML biology in multiple manners, such as two- and multiple-group comparisons, interrogation of genes of interests, and transcriptional signatures. Using XTABLE, we have carried out a comparative study of the potential role of chromosomal instability scores as biomarkers of PML progression and mapped the onset of the most relevant LUSC pathways to the sequence of LUSC developmental stages. XTABLE will critically facilitate new research for the identification of early detection biomarkers and acquire a better understanding of the LUSC precancerous stages.
AB - Lung squamous cell carcinoma (LUSC) is a type of lung cancer with a dismal prognosis that lacks adequate therapies and actionable targets. This disease is characterized by a sequence of low- and high-grade preinvasive stages with increasing probability of malignant progression. Increasing our knowledge about the biology of these premalignant lesions (PMLs) is necessary to design new methods of early detection and prevention, and to identify the molecular processes that are key for malignant progression. To facilitate this research, we have designed XTABLE (Exploring Transcriptomes of Bronchial Lesions), an open-source application that integrates the most extensive transcriptomic databases of PMLs published so far. With this tool, users can stratify samples using multiple parameters and interrogate PML biology in multiple manners, such as two- and multiple-group comparisons, interrogation of genes of interests, and transcriptional signatures. Using XTABLE, we have carried out a comparative study of the potential role of chromosomal instability scores as biomarkers of PML progression and mapped the onset of the most relevant LUSC pathways to the sequence of LUSC developmental stages. XTABLE will critically facilitate new research for the identification of early detection biomarkers and acquire a better understanding of the LUSC precancerous stages.
KW - Humans
KW - Carcinoma, Non-Small-Cell Lung/genetics
KW - Lung Neoplasms/pathology
KW - Carcinoma, Squamous Cell/genetics
KW - Gene Expression Regulation, Neoplastic
KW - Lung/pathology
KW - Precancerous Conditions/genetics
KW - Biomarkers, Tumor/genetics
U2 - 10.7554/eLife.77507
DO - 10.7554/eLife.77507
M3 - Article
C2 - 36892933
SN - 2050-084X
VL - 12
JO - eLife
JF - eLife
ER -