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Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis

Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. We analysed 83 progressive lesions, 41 regressive and 33 normal epithelial control samples. DNA methylation and gene expression profiles were further validated using publicly available lung cancer data. Results: Somatic mutation burden was higher in progressive lesions than regressive CIS lesions, across base substitutions, rearrangements, and copy number changes. Driver mutations were present in both progressive and regressive CIS lesions, but were more numerous in progressive cases. Progressive and regressive CIS lesions had distinct epigenomic and transcriptional profiles, with a strong chromosomal instability signature. Gene expression, methylation and copy number profiles can all predict accurately which CIS lesions will progress to lung cancer. Conclusion: Pre-invasive CIS lesions that will subsequently progress to invasive lung cancer can be distinguished from those that will regress using molecular profiling. Progression is associated with a strong chromosomal instability signature. These findings inform the development of novel therapeutic targets.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001000837 Cancer Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00000765169 cram 47.8 GB
EGAF00000765171 cram 43.1 GB
EGAF00000765172 cram 43.5 GB
EGAF00000765173 cram 41.7 GB
EGAF00000765174 cram 41.6 GB
EGAF00000765175 cram 43.3 GB
EGAF00000765176 cram 43.2 GB
EGAF00000765177 cram 43.1 GB
EGAF00000765178 cram 41.6 GB
EGAF00000765179 cram 46.1 GB
EGAF00000765180 cram 46.9 GB
EGAF00000765181 cram 43.3 GB
EGAF00000765182 cram 44.4 GB
EGAF00000765183 cram 39.4 GB
EGAF00000765184 cram 38.6 GB
EGAF00000765185 cram 39.3 GB
EGAF00000765186 cram 39.1 GB
EGAF00000765187 cram 39.0 GB
EGAF00000765188 cram 37.8 GB
EGAF00000765189 cram 47.1 GB
EGAF00000765190 cram 48.9 GB
EGAF00000765191 cram 45.6 GB
EGAF00000765213 cram 44.6 GB
EGAF00000765214 cram 49.0 GB
EGAF00000765215 cram 41.8 GB
EGAF00000765217 cram 40.8 GB
EGAF00000765218 cram 42.3 GB
EGAF00000765219 cram 40.0 GB
EGAF00000765220 cram 39.5 GB
EGAF00000765221 cram 40.2 GB
EGAF00000765222 cram 42.3 GB
EGAF00000765223 cram 41.9 GB
EGAF00000765224 cram 42.3 GB
EGAF00000765225 cram 42.0 GB
EGAF00000765226 cram 42.7 GB
EGAF00000765227 cram 43.0 GB
EGAF00000765228 cram 43.0 GB
EGAF00000765229 cram 48.2 GB
EGAF00000765230 cram 47.7 GB
EGAF00000765231 cram 47.3 GB
EGAF00000765232 cram 45.0 GB
EGAF00000765233 cram 46.1 GB
EGAF00000765234 cram 46.3 GB
EGAF00000765235 cram 47.2 GB
EGAF00000765238 cram 47.0 GB
EGAF00000765239 cram 40.8 GB
EGAF00000765289 cram 41.9 GB
EGAF00000765290 cram 40.4 GB
EGAF00000765630 cram 39.8 GB
EGAF00000765631 cram 46.2 GB
EGAF00000765632 cram 42.0 GB
EGAF00000765633 cram 39.4 GB
EGAF00000765634 cram 39.4 GB
EGAF00000765635 cram 38.8 GB
EGAF00000765636 cram 48.5 GB
EGAF00000765637 cram 47.2 GB
EGAF00000765638 cram 50.0 GB
EGAF00000765639 cram 44.4 GB
EGAF00000765641 cram 44.5 GB
EGAF00000765642 cram 42.1 GB
EGAF00000765643 cram 39.3 GB
EGAF00000765644 cram 43.3 GB
EGAF00000765645 cram 48.5 GB
EGAF00000765646 cram 46.4 GB
EGAF00000765647 cram 45.1 GB
EGAF00000765650 cram 43.3 GB
EGAF00000765651 cram 40.9 GB
EGAF00000765652 cram 40.8 GB
EGAF00000765653 cram 43.1 GB
EGAF00000765654 cram 43.9 GB
EGAF00000774115 cram 53.2 GB
EGAF00000948840 cram 32.2 GB
EGAF00000948841 cram 36.1 GB
EGAF00000948842 cram 34.7 GB
EGAF00000948843 cram 33.5 GB
EGAF00000948844 cram 36.2 GB
EGAF00000948845 cram 37.2 GB
EGAF00001008032 cram 37.5 GB
EGAF00001008033 cram 36.9 GB
EGAF00001013285 cram 36.9 GB
EGAF00002044769 cram 5.8 GB
EGAF00002044770 cram 5.5 GB
EGAF00002044771 cram 5.7 GB
EGAF00002044772 cram 6.0 GB
EGAF00002044773 cram 6.2 GB
EGAF00002044774 cram 6.5 GB
EGAF00002044775 cram 5.8 GB
EGAF00002044776 cram 5.6 GB
EGAF00002044777 cram 5.7 GB
EGAF00002044778 cram 6.0 GB
EGAF00002044779 cram 6.2 GB
EGAF00002044780 cram 6.5 GB
EGAF00002044781 cram 5.9 GB
EGAF00002044782 cram 5.6 GB
EGAF00002044783 cram 5.8 GB
EGAF00002044784 cram 6.0 GB
EGAF00002044785 cram 6.3 GB
EGAF00002044786 cram 6.5 GB
EGAF00002044787 cram 5.8 GB
EGAF00002044788 cram 5.5 GB
EGAF00002044789 cram 5.7 GB
EGAF00002044790 cram 5.9 GB
EGAF00002044791 cram 6.1 GB
EGAF00002044792 cram 6.3 GB
EGAF00002044793 cram 9.4 GB
EGAF00002044794 cram 9.0 GB
EGAF00002044795 cram 8.1 GB
EGAF00002044796 cram 8.3 GB
EGAF00002044797 cram 9.4 GB
EGAF00002044798 cram 9.0 GB
EGAF00002044799 cram 8.1 GB
EGAF00002044800 cram 8.4 GB
EGAF00002044801 cram 9.3 GB
EGAF00002044802 cram 9.0 GB
EGAF00002044803 cram 8.0 GB
EGAF00002044804 cram 8.3 GB
EGAF00002044805 cram 9.5 GB
EGAF00002044806 cram 9.2 GB
EGAF00002044807 cram 8.3 GB
EGAF00002044808 cram 8.6 GB
EGAF00002044809 cram 6.6 GB
EGAF00002044810 cram 6.2 GB
EGAF00002044811 cram 6.7 GB
EGAF00002044812 cram 6.7 GB
EGAF00002044813 cram 5.9 GB
EGAF00002044814 cram 6.9 GB
EGAF00002044815 cram 6.4 GB
EGAF00002044816 cram 6.9 GB
EGAF00002044817 cram 6.9 GB
EGAF00002044818 cram 6.1 GB
EGAF00002044819 cram 6.9 GB
EGAF00002044820 cram 6.4 GB
EGAF00002044821 cram 6.8 GB
EGAF00002044822 cram 6.9 GB
EGAF00002044823 cram 6.0 GB
EGAF00002044824 cram 6.8 GB
EGAF00002044825 cram 6.3 GB
EGAF00002044826 cram 6.8 GB
EGAF00002044827 cram 6.8 GB
EGAF00002044828 cram 6.0 GB
EGAF00002044829 cram 6.7 GB
EGAF00002044830 cram 6.3 GB
EGAF00002044831 cram 6.7 GB
EGAF00002044832 cram 6.9 GB
EGAF00002044833 cram 6.0 GB
EGAF00002044834 cram 9.0 GB
EGAF00002044835 cram 8.7 GB
EGAF00002044836 cram 6.7 GB
EGAF00002044837 cram 8.1 GB
EGAF00002044838 cram 9.1 GB
EGAF00002044839 cram 8.8 GB
EGAF00002044840 cram 6.8 GB
EGAF00002044841 cram 8.2 GB
EGAF00002044842 cram 9.2 GB
EGAF00002044843 cram 8.9 GB
EGAF00002044844 cram 6.8 GB
EGAF00002044845 cram 8.2 GB
EGAF00002044846 cram 5.7 GB
EGAF00002044847 cram 5.3 GB
EGAF00002044848 cram 5.5 GB
EGAF00002044849 cram 5.8 GB
EGAF00002044850 cram 6.0 GB
EGAF00002044851 cram 6.2 GB
EGAF00002044852 cram 5.6 GB
EGAF00002044853 cram 5.3 GB
EGAF00002044854 cram 5.5 GB
EGAF00002044855 cram 5.7 GB
EGAF00002044856 cram 6.0 GB
EGAF00002044857 cram 6.1 GB
EGAF00002044858 cram 9.6 GB
EGAF00002044859 cram 9.4 GB
EGAF00002044860 cram 7.1 GB
EGAF00002044861 cram 8.5 GB
173 Files (4.1 TB)