MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker

BMC Cancer. 2021 Apr 29;21(1):473. doi: 10.1186/s12885-021-08218-4.


Introduction: Disruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to identify the differential expression of small RNAs (sRNAs) and mRNAs in formalin-fixed paraffin-embedded (FFPE) tissue of the breast cancer (BC) and normal adjacent tissue (NAT). Another aim is to determine the differential expression of miR-1275 as a novel biomarker for BC and also identify its target genes.

Methods: TrueQuant method for analysis of sRNA expression and MACE-sequencing method for analysis of gene expression were used analyzing. The RT-qPCR technique was used to confirm miR-1275 down expression. Target genes of miR-1275 were computationally identified using target prediction sites and also the expression level of them was experimentally determined among the expressed genes.

Results: TrueQuant findings showed that 1400 sRNAs were differentially expressed in the FFPE tissue of two Kurdish cases with BC, as compared to NAT. Among the sRNAs, 29 small RNAs were shown to be significantly downregulated in BC cells. The RT-qPCR results confirmed that miR-1275 was significantly down-expressed in 20 Kurdish cases with BC compared to NAT. However, Overall survival (OS) analysis revealed that the correlation between the expression level of miR-1275 and clinical significance was highly corrected in cases with BC (OS rate: P = 0.0401). The MACE-seq results revealed that 26,843 genes were differentially expressed in the BC tissue compared to NAT, but 7041 genes were displayed in a scatter plot. Furthermore, putative target genes (DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miR-1275 in several target predicted sites. The MACE-seq results revealed that the expression level of these targets was increased in BC tissue compared to NAT. The level of these targets was negatively associated with miR-1275 expression. Finally, the role of down-regulated miR-1275 on its targets in biological mechanisms of BC cells was identified; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis.

Conclusion: Down-expressed miR-1275, a tumor suppressor, is a novel biomarker for early detection of BC. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.

Keywords: And tumor suppressor; Breast cancer; Pathogenesis; Small RNA and gene expression; miR-1275 and its target genes; miRNA.

MeSH terms

  • ADAM Proteins / genetics
  • Adolescent
  • Adult
  • Aged
  • Biomarkers, Tumor / analysis*
  • Biomarkers, Tumor / genetics
  • Breast / chemistry
  • Breast Neoplasms / chemistry*
  • Breast Neoplasms / genetics
  • Breast Neoplasms / mortality
  • Cyclic AMP Response Element-Binding Protein / genetics
  • Cyclic AMP-Dependent Protein Kinase Catalytic Subunits / genetics
  • Dishevelled Proteins / genetics
  • Down-Regulation
  • Female
  • Gene Expression
  • Gene Expression Profiling
  • Gene Library
  • Humans
  • MicroRNAs / analysis*
  • MicroRNAs / genetics
  • Middle Aged
  • Protein Phosphatase 2 / genetics
  • RNA, Neoplasm / analysis*
  • RNA, Neoplasm / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, RNA / methods
  • Synaptotagmins / genetics
  • Tumor Suppressor Proteins / analysis
  • Tumor Suppressor Proteins / genetics
  • Turkey
  • Young Adult


  • Biomarkers, Tumor
  • CREB1 protein, human
  • Cyclic AMP Response Element-Binding Protein
  • DVL3 protein, human
  • Dishevelled Proteins
  • MIRN1275 microRNA, human
  • MicroRNAs
  • PPP2R2D protein, human
  • RNA, Neoplasm
  • SYT7 protein, human
  • Tumor Suppressor Proteins
  • Synaptotagmins
  • Cyclic AMP-Dependent Protein Kinase Catalytic Subunits
  • PRKACA protein, human
  • Protein Phosphatase 2
  • ADAM Proteins
  • THSD4 protein, human