title: Gene expression analysis on a photodiode array-based bioluminescence analyzer by using sensitivity-improved SRPP.
abstract: Most methods used for gene expression analysis are based on dye-labeling, which requires costly instruments. Recently a dye-free gene expression analysis method-SRPP (Sequence-tagged reverse-transcription polymerase chain reaction coupled with pyrosequencing) was developed to compare relative gene expression levels in different tissues, but the throughput of the SRPP assay is very limited due to the use of a photomultiplier tube (PMT)-based pyrosequencer for the detection. To increase the throughput of the SRPP assay, an inexpensive photodiode (PD) array-based bioluminescence analyzer (termed as "PD-based pyrosequencer") was coupled to SRPP; however the low sensitivity of PD limited the wide application of SRPP. To enable SRPP analyzing low abundance genes in clinical samples, sequence-tagged gene-specific primers instead of sequence-tagged poly (T)(n) primers were used for reverse-transcription, and the SRPP sensitivity was thus improved more than 10 times. This improvement compensates the sensitivity loss due to the use of PD in a pyrosequencer. The accurate determination of the expression levels of ten prognostic marker genes (AL080059, MMP9, EXT1, ORC6L, AF052162, C9orf30, FBXO31, IGFBP5, ESM1, and RUNDC1) differing between normal tissues and tumor tissues of breast cancer patients demonstrated that SRPP using gene-specific RT primers coupled with the PD array-based bioluminescence analyzer is reliable, inexpensive, and sensitive in gene expression analysis.
authors.affiliation: Huadong Research Institute for Medicine and Biotechnics, Nanjing, 210002, China.
authors.forename: Qinxin
authors.initials: Q
authors.lastname: Song
authors.forename: Hua
authors.initials: H
authors.lastname: Jing
authors.forename: Haiping
authors.initials: H
authors.lastname: Wu
authors.forename: Guohua
authors.initials: G
authors.lastname: Zhou
authors.forename: Tomoharu
authors.initials: T
authors.lastname: Kajiyama
authors.forename: Hideki
authors.initials: H
authors.lastname: Kambara
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D004396:Coloring Agents / Q000737:chemistry; D005260:Female; D005786:Gene Expression Regulation; D006801:Humans; D008163:Luminescent Measurements / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013194:Staining and Labeling
chemical_list: D014408:Biomarkers, Tumor; D004396:Coloring Agents