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. 2017 Dec 30;21(4):259–266. doi: 10.5114/wo.2017.72382

Table 1.

Characteristic of global lncRNA profiling studies in HNSCC

Study Analysis Results description
Zou et al. [62, 63] Bioinformatic analysis of RNA-seq data sets (TCGA data from UCSC Cancer Genomics Hub) of 40-tumour-adjacent normal pairs and 363 additional unpaired tumors

  • – 9681 lncRNA transcripts significantly changed; 596 lincRNAs of them strong dysregulated in HNSCC (up or downregulated)

  • – Confirmation of GAS5 and MEG3 down-regulation and identification of H19 and PCAT-1 dysregulation (all tumor sites)

  • – Different tumor sites analysis of 39 matched samples revealed:

    1. OSCC – 777 lncRNAs changed

    2. TSCC – 1020 lncRNAs changed

    3. LSCC – 657 lncRNAs changed

  • – 276 lincRNAs significantly predict patients’ OS (over and underexpression depends on lincRNA);

  • – 256 associated with TP53 mutation and 269 with TP53-3p co-occurrence
Nohata et al. [64] Bioinformatic analysis of RNA-seq data sets (TCGA data from The Atlas of Noncoding RNAs in Cancer – TANRIC) of 468 tumor samples Analysis of sequencing data of OPC-22 panel (cell lines)

  • – 728 lncRNA transcripts changed between normal and tumor samples (212 up- and 516 down-regulated)

  • – Significant connection of 55 lncRNAs with patient’s prognosis in OS or DFS (reduced or increased OS or DFS – depending on type of lncRNA)

  • – 27 upregulated lncRNAs in HPV+ cell lines and 140 up-regulated in HPV+ tumors from TCGA

  • – 30 lncRNAs downregulated in TP53 mutated tumors
Yang and Deng [65] Microarray analysis (mRNA and lncRNA) of 6 pairs of NPC and chronic nasopharyngitis (CNP) samples and qRT-PCR validation

  • – 856 lncRNA transcripts changed between NPC and CNP (425 up- and 431 down-regulated)

  • – Changed lncRNA connected with apoptosis, cell growth and proliferation revealed by lncRNA-mRNA interaction analysis, migration and movement or cell differentiation and interaction with JAK-STAT signaling pathway
Zhang et al. [69] Microarray analysis of randomly paired 3 metastatic and 4 primary NPC tumor samples and qRT-PCR validation

  • – 8088 lncRNA transcripts changed between metastatic and primary samples (3778 up-and 4310 down-regulated)

  • – Expression level of ENST00000438550 as an independent indicator of disease progression in NPC patients
Zhou et al. [74] Microarray analysis of 3 paired tumor and adjacent noncancerouse samples from hypopharyngeal squamose cell carcinoma (HSCC) patients and qRT-PCR validation

  • – AB209630 and AB019562 indicated as changed in HNSCC (AB209630 low expressed, AB019562 high expressed), which influence on cell growth, colony formation, invasion and apoptosis/cell death in FaDu

  • – High expression of AB209630 correlated with better OS
Ren et al. [70] Next generation sequencing and qRT-PCR validation

  • – 2670 known and 4820 novel lncRNAs changed in paclitaxel-resistant CNE-2 compared to parental CNE-2 cell line

  • – n375709 – the most overexpressed lncRNA; influence on sensitivity to paciltaxel in vivo
Zhang et al. [66] Bioinformatic analysis of microarray data sets (GSE25099 from Gene Expression Omnibus database) of 57 OSCC samples and 22 normal sample

  • – 160 lncRNA transcripts changed between OSCC and normal samples (41 up- and 119 down-regulated)

  • – Up-regulated targets of lncRNA connected with immune response, response to wounding, inflammatory response and regulation of proliferation; down-regulated targets of lncRNA connected with epidermis development
Li et al. [73] Next generation sequencing and qRT-PCR of radio-resistant CNE-2-Rs and parental CNE-2 cell lines (nasopharengynal) and qRT-PCR validation

  • – 310 up-regulated and 471 down-regulated of known lncRNAs in radioresistant CNE-2-Rs compared to parental CNE-2 cell line

  • – 3 novel lncRNA Unigene8485, Unigene8588 and down-regulated Unigene3434

  • – 13 pairs of lncRNA-mRNA associated with radioresistance in CNE-2-Rs cell line
Zhang et al. [75] Microarray analysis (lncRNA and mRNA) of 7 NPC tumor samples and adjacent non-tumor samples and qRT-PCR validation

  • – 481 lncRNA transcripts changed between NPC and normal samples (231 up- and 250 down-regulated) as well as 766 mRNA transcripts (323 up- and 443 down-regulated)

  • – Up-regulated lncRNAs mainly localized on chromosomes: 12, 2, 1 (8.7% of lncRNA transcripts)

  • – LncRNA-mRNA pairs implicated in processes such as: regulation of transcription, macromolecule metabolic and biosynthesis, nerve development, immunological synapse or signaling pathways: B and T cell receptor transmembrane and TGF-β receptor