Differential Gene Expression Landscape of Co-Existing Cervical Pre-Cancer Lesions Using RNA-seq

Abstract

Genetic changes occurring in different stages of pre-cancer lesions reflect causal events initiating and promoting the progression to cancer. Co-existing pre-cancerous lesions including low- and high-grade squamous intraepithelial lesion (LGSIL and HGSIL), and adjacent “normal” cervical epithelium from six formalin-fixed paraffin-embedded samples were selected. Tissues from these 18 samples were isolated using laser-capture microdissection, RNA was extracted and sequenced. RNA-sequencing generated 2.4 billion raw reads in 18 samples, of which ~50.1% mapped to known and annotated genes in the human genome. There were 40 genes up-regulated and 3 down-regulated (normal to LGSIL) in at least one-third of the sample pairs (same direction and FDR p < 0.05) including S100A7 and KLK6. Previous studies have shown that S110A7 and KLK7 are up-regulated in several other cancers, whereas CCL18, CFTR, and SLC6A14, also differentially expressed in two samples, are up-regulated specifically in cervical cancer. These differentially expressed genes in normal to LGSIL progression were enriched in pathways related to epithelial cell differentiation, keratinocyte differentiation, peptidase, and extracellular activities. In progression from LGSIL to HGSIL, two genes were up-regulated and five down-regulated in at least two samples. Further investigations using co-existing samples, which account for all internal confounders, will provide insights to better understand progression of cervical pre-cancer.

Emerging role of cystic fibrosis transmembrane conductance regulator - an epithelial chloride channel in gastrointestinal cancers

“…In addition, further investigation by the Peng et al [61] indicated that the upregulated CFTR in pre-cancerous and cervical cancer tissues resulted from aberrantly increased NF-kB p65 translocation [62] . RNA sequencing results obtained from samples co-existing with pre-cancerous lesions and adjacent normal cervical tissue demonstrated that CFTR was also significantly up-regulated in cervical cancer [63] , which is in agreement with the findings from Peng et al [61] and Wu et al [62] . These findings are opposite of those from other types of cancers which demonstrated the tumor suppressive roles of CFTR, indicating that the role of CFTR in cancer is organ/system specific.…”

“…When the CFTR is functional, it is possible ion transportation activities do not account for the main aspect of the tumorigenesis. CFTR has also recently been related to cervical cancer [61][62][63] . A series of studies from Peng et al [61] demonstrated that the expression of CFTR is gradually increased from normal to pre-cancerous cervical tissue and cervical cancer tissues, and it is also positively correlated to histological grades, tumor stage, and metastatic grades.…”

Identification of biomarker and HPV strain for Cervical Cancer from pre-existing RNAseq data

“…Considering the protein nature of this biomarker, the experiment was designed to detect the differentially expressed gene, associating with this protein function group, in RNA-seq data from two articles. Compare to the findings from Royse et al (2014), confirmatory result was reproduced that comparisons between both groups yielded insignificant outcome. Since data from single article was insufficient to provide meaningful clue, final dataset was collected from multiple sources.…”

“…According to Bethesda classification system, precancerous cervical lesions, also known as cervical intraepithelial neoplasia (CIN), can be categorized into Atypical squamous cells (ASC), low grade squamous intraepithelial lesion (LGSIL), encompassing CIN 1; and high grade squamous intraepithelial lesion (HGSIL), encompassing CIN 2 and 3 (Royse et al, 2014). Most precancerous lesions, particularly LGSIL, can regress due to the immune system, but some persisted and eventually developed into carcinoma.…”

Adiponectin plays a role in energy metabolism for musk secretion in scent glands of muskrats (<i>Ondatra zibethicus</i>)

“…The sequencing was performed using an Illumina HiSeq H2000 (Illumina, San Diego, CA, USA) at 50 base pairs, paired end, and 25 million paired reads per sample, following the manufacturer's protocol. Multiplexed single-read runs were conducted with a total of 10 7 cycles [17]. The unigenes were annotated by comparison with deposited sequences in the NR, Swiss-Prot, Go, COG, Kegg database using BLAST software.…”