Differential gene expression analysis is one of the most common applications of RNA sequencing [
60]. Samples from different backgrounds (different species, tissues and periods) can be used for RNA sequencing to identify differentially expressed genes, revealing their function and potential molecular mechanisms [
61]. More importantly, differential gene expression analysis facilitates the discovery of potential cancer biomarkers [
62]. Many studies have shown that gene fusions are closely related to oncogenesis and are appreciated as both ideal cancer biomarkers and therapeutic targets [
63]. Gene fusions in clinical samples are primarily detected by RNA-CaptureSeq. Compared to whole transcriptome sequencing, RNA-CaptureSeq has significantly higher sequencing depth [
27,
64,
65]. It has been reported that the NUP98-PHF23 fusion gene is likely to be a novel therapeutic target in acute myeloid leukemia (AML) [
66]. Recently, a variety of recurrent gene fusions, including ESR1-CCDC170, SEC16A-NOTCH1, SEC22B-NOTCH2 and ESR1-YAP1, have been identified in breast cancer, indicating that recurrent gene fusion is one of the key drivers for cancer [
67]. Several novel configurations of BRAF, NTRK3 and RET gene fusions have been identified in colorectal cancer [
68]. These fusions may promote the development of malignancy and provide new targets for personalized treatment [
68]. In addition, some special genomic factors have been discovered as biomarkers by RNA sequencing, including miRNA, lncRNA and circRNA, which are widely present in various types of cancer [
69‐
71]. A recent example is circRNA_0001178 and circRNA_0000826, which are biomarkers of colorectal cancer metastasis to the liver [
72]. By applying both RNA sequencing and small RNA sequencing, a study on pancreatic cancer identified differential expression of simple repetitive sequences (SSRs) and demonstrated that the frequency of SSR motifs changed dramatically, which is expected to become a tumor biomarker [
73]. In addition to nucleic acid biomarkers, RNA-seq combined with immunohistochemistry and western blot has also identified certain proteins as cancer biomarkers, such as nuclear COX2 (cyclooxygenase2) in combination with HER2 (human epidermal growth factor receptor type 2), which may serve as potential biomarkers for the diagnosis and prognosis of colorectal cancer [
74]. Similar examples identified using RNA-seq profiling analysis include ISG15 (Interferon-stimulated gene 15) in nasopharyngeal carcinoma [
75] and DMGDH (dimethylglycine dehydrogenase) in hepatocellular carcinoma [
76]. Data-mining analysis of RNA sequencing data and other clinical data has identified that the isoforms of peroxiredoxins also can be expected the prognostic biomarkers for predicting overall survival and relapse-free survival in breast cancer [
77]. Increasing differentially expressed genes are being identified by RNA sequencing, and new potential cancer biomarkers are being continuously discovered (Table
2). However, sufficient clinical practice is needed to confirm the diagnostic and predictive applications of these biomarkers in cancer.
Table 2
Representative potential biomarkers identified by RNA-seq in cancer
Liver cancer | tRNA-ValTAC-3/tRNA-GlyTCC-5/tRNA-ValAAC-5/tRNA-GluCTC-5 | tsRNA | Up | Diagnostic | |
| ACVR2B-AS1 | LncRNA | Up | Prognostic/therapeutic target | |
Lung cancer | LINC01537 | LncRNA | Down | Prognostic/therapeutic target | |
circFARSA | CircRNA | Up | Noninvasive biomarker | |
LINC01123 | LncRNA | Up | Prognostic/therapeutic target | |
Gastric cancer | CTD2510F5.4 | LncRNA | Up | Diagnostic/prognostic | |
MEF2C-AS1/FENDRR | LncRNA | Down | Diagnostic/prognostic | |
Prostate cancer | PSLNR | LncRNA | Down | Diagnostic/therapeutic target | |
Colorectal cancer | RAMS11 | LncRNA | Up | Therapeutic target | |
CRCAL-1/CRCAL-2 /CRCAL-3/ CRCAL-4 | LncRNA | Up | Therapeutic target | |
Colon cancer | AFAP1-AS1 | LncRNA | Up | Prognostic/ therapeutic target | |
Head and neck squamous cell carcinoma | LINC00460 | LncRNA | Up | Prognostic | |
HCG22 | LncRNA | Down | Prognostic | |
HOXA11-AS/LINC00964/MALAT1 | LncRNA | Up | Diagnostic | |
Clear cell renal cell carcinomas | SLINKY | LncRNA | Up | Prognostic | |
Leukemia | LUCAT1 | LncRNA | Up | Therapeutic target | |
circ-HIPK2 | CircRNA | Down | Diagnostic/prognostic | |
RNA-seq could detect early mutations as well as high molecular risk mutations, thus can discover novel cancer biomarkers and potential therapeutic targets, monitoring of diseases and guiding targeted therapy during early treatment decisions. Tumor mutation burden (TMB) is considered as a potential biomarker for immune checkpoint therapy and prognosis [
78,
79]. RNA-seq can be used to explore the application value of TMB in diffuse glioma [
78]. Through the RNA-seq, MET exon 14 mutation and isocitrate dehydrogenase 1 (IDH1) mutation were identified as new potential therapeutic targets in lung adenocarcinoma and chondrosarcoma patients, respectively [
80,
81]. Several studies have shown that RNA sequencing can effectively improve the detection rate on the basis of DNA sequencing, provide more comprehensive detection results and achieve a better curative effect for targeted therapy [
82]. In addition, it has been proved that IDH mutation is a good prognostic marker for glioma by RNA-seq [
83]. Targeted therapy is also considered to enhance or replace cytotoxic chemotherapy regimen in cancer including AML [
84‐
86].
ScRNA-seq also has some new discoveries in diagnosis. For example, scRNA-seq data can be used to infer copy number variations (CNV) and to distinguish malignant from non-malignant cells. The infer CNV algorithm, which was used in the study of glioblastoma, uses averaging relative expression levels over large genomic regions to infer chromosome copy number variation [
87]. Similar examples include head and neck cancer [
88] and human oligodendroglioma [
89]. It is reported that RNA sequence of tumor-educated blood platelets (TEPs) can also become a blood-based cancer diagnosis method [
90]. It should be noted that the lack of detailed functional implications of the identified RNAs in platelets in the field of platelet RNA research is also an urgent problem to be solved [
91].