Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach

Despite years of research, we are still unraveling crucial stages of gene expression regulation in cancer. On the basis of major biological hallmarks, we hypothesized that there must be a uniform gene expression pattern and regulation across cancer types. Among non-coding genes, long non-coding RNAs (lncRNAs) are emerging as key gene regulators playing powerful roles in cancer. Using TCGA RNAseq data, we analyzed coding (mRNA) and non-coding (lncRNA) gene expression across 15 and 9 common cancer types, respectively. 70 significantly differentially expressed genes common to all 15 cancer types were enlisted. Correlating with protein expression levels from Human Protein Atlas, we observed 34 positively correlated gene sets which are enriched in gene expression, transcription from RNA Pol-II, regulation of transcription and mitotic cell cycle biological processes. Further, 24 lncRNAs were among common significantly differentially expressed non-coding genes. Using guilt-by-association method, we predicted lncRNAs to be involved in same biological processes. Combining RNA-RNA interaction prediction and transcription regulatory networks, we identified E2F1, FOXM1 and PVT1 regulatory path as recurring pan-cancer regulatory entity. PVT1 is predicted to interact with SYNE1 at 3′-UTR; DNAJC9, RNPS1 at 5′-UTR and ATXN2L, ALAD, FOXM1 and IRAK1 at CDS sites. The key findings are that through E2F1, FOXM1 and PVT1 regulatory axis and possible interactions with different coding genes, PVT1 may be playing a prominent role in pan-cancer development and progression.

isoform of ASF1 and encodes a member of H3 and H4 family of histone chaperone proteins. It is involved in histone deposition, exchange, and removal during nucleosome assembly and disassembly as well as histone modification. ASF1B is implicated as a prognostic value in breast cancer cells, and ASF1B mRNA expression level is significantly associated with disease progression, metastasis and poor or shorter survival (1).

CHAF1A (Chromatin Assembly Factor 1 Subunit A) is a primary component of the chromatin
assembly factor 1 (CAF1) involved in bringing histones H3 and H4 to replicating DNA and also involved in heterochromatin maintenance (2,3). CHAF1A inhibits differentiation and promotes an aggressive form of neuroblastoma and elevated levels of CHAF1A strongly correlates with poor prognosis and survival in glioblastoma patients (4). Overexpression of CHAF1A promotes cell proliferation and inhibits apoptosis. CHAF1A is identified as a prognostic biomarker and potential therapeutic target for epithelial ovarian cancer, colon cancer and hepatocellular carcinoma (5,6,7). DNAJC9 (DnaJ Heat Shock Protein Family (Hsp40) Member C9), a novel human type C DnaJ/HSP40 member, contains a typical N-terminal J domain. It can interact with HSP70s through the J domain (Nterminal 98 residues) activating HSP70 ATPase activity (8). The precise role of DNAJC9 in cancer is not investigated. E2F1 acts as a tumor suppressor in the presence of inactivated RB protein. Dysregulated E2F1 in transformed cells induces apoptosis signaling cascade through activation of an intrinsic p53/p73 cell death pathway. Upon overexpression of E2F1, oncogenic E2F1 target genes, such as EGFR, androgen receptor, EZH2 and CoF are upregulated. Consequent activation of cytoplasmic (PI3K/AKT and RAS/MAPK/ERK) and nuclear signaling cascades related to invasion and metastasis leads to further damages. E2F1 cofactors are also lost which are required for proper activation of apoptotic genes (9). ACTR/AIB1, an E2F1 coactivator, is required for E2F1-mediated gene expression and the consequent proliferation of ER-negative breast cancer cells (10).
DNA Flap Endonuclease 1 (FEN1) plays a role in both DNA replication and repair thereby maintaining stability and integrity of the genome. Suppression of FEN1 in breast and lung cancers leads to the retardation of DNA replication, DNA double-strand breaks (DSBs) and apoptosis. FEN1 is established as a potential therapeutic treatment for breast cancer and as well as in other cancer types (11, 12).
Forkhead Box M1 (FoxM1) is a transcription factor essential for cell proliferation and cell cycle progression and is associated with proliferation. FOXM1 is involved in tumorigenesis and its elevated levels are associated with tumor progression, invasion and angiogenesis by increasing expression of MAD2L1 (Mitotic Arrest Deficient 2 Like 1) is a mitotic spindle assembly checkpoint protein involved in the spindle-kinetochore attachment and it prevents anaphase till there is proper alignment of all chromosomes on metaphase plate (45). Higher expression of MAD2L1 is associated with tumor progression and poor disease survival in breast cancer and lung adenocarcinoma (46,47).
NOP2 or p120 functions in the cell cycle during tumor proliferation and is identified as a biomarker in lung cancer (48). Upregulated PXNA3 is involved in tumor progression and angiogenesis in breast cancer (52).
Germline mutation in the exonuclease domain of POLE and POLD1 predispose to breast cancer, oligodendroglioma, endometrial cancer and colorectal adenomas (53,54).
PPP1R14B is significantly overexpressed in ovarian clear cell carcinoma (62). KAT2B/ PCAF a histone acetyltransferase protein acetylates core histones (H3 and H4) and also promotes transcriptional activation by acetylating non-histone proteins. PCAF is induced and activated by ATRA (all-trans-retinoic acid) and PCAF substrates' acetylation promotes granulocytic differentiation in leukemia cells and autophagy by inhibiting Akt/mTOR signaling pathway in hepatocellular carcinoma (72,73). PCAF blocks up-regulation of TIMP-1 by acetylating STAT3 which modulates crosstalk between tumor cells and CAFs (cancer-associated fibroblasts) in HCC microenvironment (74). Among our list of lncRNA genes, PVT1 protects MYC protein, which is a major cancer protein, from phosphorylation-mediated degradation by inhibiting phosphorylation of threonine58 (75). PVT1 was found to be up-regulated in gastric cancer through FOXM1 positive feedback loop mechanism involved in growth and invasion (76). From our studies, PVT1 was found to be up-regulated in all nine types of tumors and FOXM1 was up-regulated in all 15 types of cancers, providing a major prominent role of these two genes (table 7 and (82). SNHG1 is predicted as a poor prognostic marker and promotes cell proliferation and invasion, and reduces apoptosis, in hepatocellular carcinoma, glioma, non-small cell lung cancer (NSCLC) and gastric cancer by promoting DNMT1 expression (83)(84)(85).
Overexpression of lncRNA ZNFX1-AS1 o r ZFAS1 (zinc finger antisense 1) enhances epithelialmesenchymal transition in glioma and gastric cancer (86,87). It is also involved in tumor progression, invasion and metastasis in acute myeloid leukemia cell, colorectal cancer by modulating ZEB1, in gastric cancer through exosomes-mediated transfer of ZFAS1 and in glioma by activation of the Notch signaling pathway (88)(89)(90)(91)(92). Over-expression of ZFAS1 induces hepatocellular carcinoma development by upregulating miR-9 and reducing methylation at CpG island of miR-9 promoter (93). ZFAS1 may function as oncogene in colorectal cancer by destabilizing p53 and interacting with CDK1/cyclin B1 complex leading to cell cycle control and inhibition of apoptosis (94). Surprisingly, in a dual action mode, ZFAS1 is identified as a putative tumor suppressor in breast cancer (95). In epithelial ovarian cancer, ZFAS1 inhibits proliferation, migration, and chemoresistance by upregulating Sp1 through inhibiting miR-150-5p (96).
LncRNA GAS5 promotes cell proliferation and inhibits apoptosis in prostate cancer and is identified as a potential diagnostic biomarker and therapeutic target (97). GAS5 expression was significantly reduced in non-small cell lung cancer, and colorectal cancer; overexpression of GAS5 inhibits cell proliferation, induces G0/G1 arrest and apoptosis (98)(99)(100)(101).
The snoRNA host gene-11 (SNHG11) expression was determined in cells exposed to ionizing radiation, SNHG11 expression was found to be induced in TK6 (p53 positive) and reduced or repressed in WTK1 (p53 negative) cells; this altered expression is part of stress response complex system in radiated cell and its response depends upon p53 function (102).