Widespread changes in the genome and epigenome resulted in both localized and regional changes in gene expression are common in cancer. However, the association between changes in the genome and epigenome and changes in the three-dimensional architecture of cancer cells remains unclear. In this study, we were the first to perform the analysis of chromatin organization between lung cancer and normal tissues using Hi-C chromosome conformation capture sequencing integrated with gene expression data to determine if chromatin interactions were changed in lung cancer. Our results indicated that the overall spatial organization of chromatin in lung cancer was similar normal cells and TADs are present in both normal and cancer cells.
Due to chromosomes are folded similarly, TADs retain their physical positions within the nucleus of cancer cells on a large scale. However, we have identified several distinct differences in the three-dimensional organization of chromatin in the lung cancer. Our Hi-C data showed that chromosome 11, 15 and X had a greater number of TADs which were merged and shifted to intra -TADs boundaries in the lung cancer tissue. The sizes of the TADs in chromosome 11, 15 and X were slightly smaller in lung cancer. That cancer cells have a higher number of smaller TADs may reflect key characteristics of transformed cells.
Each chromosome consists of numerous A and B compartments, which preferentially interact in cis (A with A, and B with B). The A compartments correlate with early replicating, euchromatic regions, whereas the B compartments correlate with heterochromatin. We found that there was an increase in the number of component A/B switching locations was also found in chromosome 11, 15 and X in lung cancer. A similar TADs switching behavior has been observed during cellular differentiation of embryonic stem cells or from pre–pro-B cells to pro-B cells. An overall high conservation of TADs accompanied by frequent switching between compartments, suggesting their functional role in differentiation.
127 our experts are availableright now
We further analyzed the Hi-C and RNA sequences data from 16 patients. Results showed that there were more up-regulated lncRNAs expression than down-regulated lncRNAs expression in chromosome 15 and X in cancer tissue. GO and KEGG pathway enrichment analyses demonstrated that many genes in lung cancer were significantly enriched in biology regulation and metabolic process. Previous study had identified the differentially expressed genes between lung squamous cell carcinoma SCC and normal controls and found NFIC, BRCA1, and NFATC2 were the top 3 transcription factors in the development of lung squamous cell carcinoma. In our study, we found AKR1B10, AKR1B15, ZIC2 and ZIC5 were on the top 15 list of down-regulated genes in lung adenocarcinoma. AKR1B10 and AKR1B15 genes belong to the aldo-keto reductase family involved in detoxification of aldehydes.
AKR1B10 gene was highly correlated with smokers’ non-small cell lung carcinomas while AKR1B15 was the top 6 up-regulated gene in SCC lung squamous cell carcinoma. ZIC2 and ZIC5 genes encode a member of the ZIC family of C2H2-type zinc finger proteins. The encoded proteins may act as a transcriptional repressor which may play crucial roles in a wide array of developmental systems, including the central nervous system, muscle and skeletal development. ZIC2 may function as an oncogene in small cell lung carcinoma and ZIC5 was the top 5 up-regulated gene in SCC lung squamous cell carcinoma. In addition, a recent large-scale study had been conducted and identified 10 new susceptibility loci in lung cancer.
The new loci emphasized the heterogeneity in genetic susceptibility across histological subtypes of lung cancer. Compared with normal lung cells, the recurrent copy-number alterations in distinguished chromosomal regions have found in the genome of lung cancer cells. We also found that most of lncRNA switched their components concentrated in chromosome 1, 2, 4, 5, 7, 8, 10, 11, 12, 13, 15 and X. Berrieman et.al. in 2004 reported that chromosomes 4, 5, 8, 11, 12 and 19 were most frequently involved in inter-chromosomal translocations. The most frequently amplified genes were ZNF703, PRDM14 and MYC on chromosome 8 and the BIRC5 gene on chromosome 17 in non-small cell lung cancer.
Although gains and loss of chromosomal loci have been reported in non-small cell lung cancer, copy number changes of the genes localized in these loci have not been analyzed in lung cancer. Two loci 15q25.1 and 5p15.33 with achieved the threshold of genome-wide significance were found associated with lung cancer in African Americans. The population-based studies have identified three main susceptibility loci, at 5p156,7,8, 6p216, and 15q25 in lung cancer patients. Interestingly, the locus at 15q25 harbors genes for nicotinic acetylcholine receptor subunits (CHRNA3, CHRNA5, and CHRNB4) that have previously been associated with lung cancer risk.
We found that lncRNAs FAM83H-AS1, AFAP1-AS1 and LOC100132111 genome structure have switched from A compartment to A compartment. By analyzing RNA-Seq data from lung adenocarcinomas and luminal subtype breast cancer, FAM83H-AS1 was the top dysregulated lncRNAs and found to be overexpressed in tumors and significantly associated with worse patient. FAM83H-AS1 involved in cancer cell proliferation, migration and invasion and regulated MET/EGFR signaling pathway. FAM83H-AS1 could be potentially used as diagnostic/prognostic marker in lung cancer.
Many studies had demonstrated that lncRNA AFAP1-AS1 (actin filament-associated protein 1 antisense RNA may be necessary for development, and that its dysregulation may participate in human cancer progression. Yin et la in 2018 reported that silencing AFAP1-AS1 significantly decreases a series of genes which promoting proliferation in non-small cell lung cancer. lncRNA AFAP1-AS1 could be potentially served as a prognostic biomarker and target for new therapies in lung cancer. lncRNA LOC100132111 expression was also increased in human lung adenocarcinoma. In our study, we discovered 10 cancer specific lncRNAs that are associated with the chromosome structure including LINC01559 and DLEU1. LINC01559 was also significantly upregulated intrahepatic cholangiocarcinoma. The lncRNA DLEU1 was found involving in many solid tumors and hematological malignancies, such epithelial ovarian carcinoma and leukemia.
Targeted therapies using tyrosine kinase inhibitors against tumors with epidermal growth factor receptor mutations and anaplastic lymphoma kinase fusions have already yielded dramatic success in precision lung adenocarcinoma medicine. Therefore, additional driver oncogenes are being translated into molecular targeted therapies. Our results have outlined dysregulated genes and lncRNAs which may be potential targets and in lung cancer treatment.
However, further studies profiling the cellular functions mediated by the candidate genes and lncRNAs are required to provide understandings into the lung tumor pathogenesis. Exploration of these new targets as well other novel targets, particularly on how these targets affect chromatin higher-order structures and gene function or display differential spatial interaction across a chromosomal region with known susceptibility in lung cancer, may provide new insights into the etiology and an understanding on how structural variation in the human genome elicits cancer progression.
