Open AccessPUM1 and RNase P genes as potential cell‐free DNA markers in breast cancer
Author(s) -
Murillo Carrasco Alexis,
Acosta Oscar,
Ponce Jaime,
Cotrina José,
Aguilar Alfredo,
Araujo Jhajaira,
Rebaza Pamela,
Pinto Joseph A.,
Fujita Ricardo,
Buleje José
Publication year - 2021
Publication title -
journal of clinical laboratory analysis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.536
H-Index - 50
eISSN - 1098-2825
pISSN - 0887-8013
DOI - 10.1002/jcla.23720
Subject(s) - digital polymerase chain reaction , cell free fetal dna , breast cancer , housekeeping gene , liquid biopsy , intraclass correlation , genomic dna , copy number analysis , gene , oncology , medicine , real time polymerase chain reaction , biology , cancer , microbiology and biotechnology , copy number variation , genetics , polymerase chain reaction , gene expression , genome , pregnancy , clinical psychology , fetus , prenatal diagnosis , psychometrics
Background Cell‐free DNA (cfDNA) is used in clinical research to identify biomarkers for diagnosis of and follow‐up on cancer. Here, we propose a fast and innovative approach using traditional housekeeping genes as cfDNA targets in a copy number analysis. We focus on the application of highly sensitive technology such as digital PCR (dPCR) to differentiate breast cancer (BC) patients and controls by quantifying regions of PUM1 and RPPH1 ( RNase P ) in plasma samples. Methods We conducted a case‐control study with 82 BC patients and 82 healthy women. cfDNA was isolated from plasma using magnetic beads and quantified by spectrophotometry to estimate total cfDNA. Then, both PUM1 and RPPH1 genes were specifically quantified by dPCR. Data analysis was calibrated using a reference genomic DNA in different concentrations. Results We found RNase P and PUM1 values were correlated in the patient group (intraclass correlation coefficient [ICC] = 0.842), but they did not have any correlation in healthy women (ICC = 0.519). In dPCR quantification, PUM1 showed the capacity to distinguish early‐stage patients and controls with good specificity (98.67%) and sensitivity (100%). Conversely, RNase P had lower cfDNA levels in triple‐negative BC patients than luminal subtypes ( p < 0.025 for both), confirming their utility for patient classification. Conclusion We propose the PUM1 gene as a cfDNA marker for early diagnosis of BC and RNase P as a cfDNA marker related to hormonal status and subtype classification in BC. Further studies with larger sample sizes are warranted.