Alveolar progenitor cells and the origin of lung cancer

Aja, Julio Sainz de; Dost, Antonella F M; Kim, Carla F.

doi:10.1111/joim.13201

Cited by 59 publications

(39 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5 e; Additional file 3 : Table S2). For example, surfactant homeostasis, which is a kind of chemical homeostasis important for the lungs, is a characteristic biological process of alveolar cells [ 37 ], a confirmed cell of origin of LUAD [ 38 , 39 ]. Since alveolar cells become more and more poorly differentiated and gradually lose their cell identity as LUAD progresses [ 40 ], these results implied that the epigenetic heterogeneity at the proximal HVRs across the LUAD patients may be connected with their different tumor progression stages.…”

Section: Resultsmentioning

confidence: 99%

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

Chen

Yuan

et al. 2022

Genome Biol

View full text Add to dashboard Cite

Identifying genomic regions with hypervariable ChIP-seq or ATAC-seq signals across given samples is essential for large-scale epigenetic studies. In particular, the hypervariable regions across tumors from different patients indicate their heterogeneity and can contribute to revealing potential cancer subtypes and the associated epigenetic markers. We present HyperChIP as the first complete statistical tool for the task. HyperChIP uses scaled variances that account for the mean-variance dependence to rank genomic regions, and it increases the statistical power by diminishing the influence of true hypervariable regions on model fitting. A pan-cancer case study illustrates the practical utility of HyperChIP.

show abstract

Section: Resultsmentioning

confidence: 99%

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

Chen

Yuan

et al. 2022

Genome Biol

View full text Add to dashboard Cite

show abstract

“…5E and Supplementary Table 2). For example, surfactant homeostasis, which is a kind of chemical homeostasis important for the lungs, is a characteristic biological process of alveolar cells [37], a confirmed cell of origin of LUAD [38,39]. Since alveolar cells become more and more poorly differentiated and gradually lose their cell identity as LUAD progresses [40], these results implied that the epigenetic heterogeneity at the proximal HVRs across the LUAD patients may be connected with their different tumor progression stages.…”

Section: Biological Interpretation Of Hvrs and Lvrsmentioning

confidence: 86%

HyperChIP for identifying hypervariable signals across ChIP/ATAC-seq samples

Chen

Yuan

et al. 2021

Preprint

View full text Add to dashboard Cite

With the reduction in sequencing costs, studies become prevalent that profile the chromatin landscape for tens or even hundreds of human individuals by using ChIP/ATAC-seq techniques. Identifying genomic regions with hypervariable ChIP/ATAC-seq signals across given samples is essential for such studies. In particular, the hypervariable regions (HVRs) across tumors from different patients indicate their heterogeneity and can contribute to revealing potential cancer subtypes and the associated epigenetic markers. We present HyperChIP as the first complete statistical tool for the task. HyperChIP uses scaled variances that account for the mean-variance dependence to rank genomic regions, and it increases the statistical power by diminishing the influence of true HVRs on model fitting. Applying it to a large pan-cancer ATAC-seq data set, we found that the identified HVRs not only provided a solid basis to uncover the underlying similarity structure among the involved tumor samples, but also led to the identification of transcription factors pertaining to the similarity structure when coupled with a motif-scanning analysis.

show abstract

“…Although there are different research directions, the ultimate goal is to diagnose and treat lung cancer. Basal cells are stem/ progenitor cells that maintain airway homeostasis and repair after epithelial injury and are candidate source genes for lung squamous cell carcinoma (23), while alveolar type 2 (AT2) cells are the origin cells for lung adenocarcinoma (24). Circulating tumor cells (CTCs) are considered a valuable marker for early diagnosis, prognosis, and risk stratification in cancer patients, and they have been found to predict survival in patients with various types of cancer, including lung cancer (25).…”

Section: Discussionmentioning

confidence: 99%

SMOX expression predicts the prognosis of non-small cell lung cancer

Huang¹,

Zhang²,

Shi³

2021

Ann Transl Med

View full text Add to dashboard Cite

Background: The development of non-small cell lung cancer (NSCLC) is very rapid, and the effect of its treatment is often closely related to the diagnosis time of the disease. Therefore, simple and convenient tumor biomarkers are helpful for the timely diagnosis and prevention of NSCLC.Methods: Through univariate and multivariate Cox regression analyses, SMOX was determined as an independent prognostic factor of GSE42127, GSE41271, GSE68465, and TCGA datasets. Furthermore, western blot, reverse transcription-polymerase chain reaction (RT-PCR), and immunohistochemical analysis were performed to confirm the predictive efficiency of SMOX expression in NSCLC.Results: Patients were divided into high and low expression groups according to the median value of SMOX expression, and Kaplan-Meier curves of multiple datasets indicated that patients with low SMOX expression had a better survival rate. According to the analysis of immune infiltration, the immune microenvironment, and immune checkpoints, SMOX expression of the high and low groups showed differences in immunity in NSCLC. By comparing cancer and adjacent tissues using western blot analysis, RT-PCR and immunohistochemical analysis, we found that SMOX was highly expressed in tumor tissues and had low expression in adjacent tissues. Simultaneously, the Kaplan-Meier curve suggested that among the 155 NSCLC patients, those with low SMOX expression had better survival.Conclusions: SMOX can be used as an effective predictive target for NSCLC.

show abstract

Alveolar progenitor cells and the origin of lung cancer

Cited by 59 publications

References 56 publications

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

HyperChIP for identifying hypervariable signals across ChIP/ATAC-seq samples

SMOX expression predicts the prognosis of non-small cell lung cancer

Contact Info

Product

Resources

About