Integrated RNA and metabolite profiling of urine liquid biopsies for prostate cancer biomarker discovery

Abstract

Sensitive and specific diagnostic and prognostic biomarkers for prostate cancer (PCa) are urgently needed. Urine samples are a non-invasive means to obtain abundant and readily accessible "liquid biopsies". Herein we used urine liquid biopsies to identify and characterize a novel group of urineenriched RNAs and metabolites in patients with PCa and normal individuals with or without benign prostatic disease. Differentially expressed RNAs were identified in urine samples by deep sequencing and metabolites in urine were measured by mass spectrometry. mRNA and metabolite profiles were distinct in patients with benign and malignant disease. Integrated analysis of urinary gene expression and metabolite signatures unveiled an aberrant glutamate metabolism and tricarboxylic acid (TCA) cycle node in prostate cancer-derived cells. Functional validation supported a role for glutamate metabolism and glutamate oxaloacetate transaminase 1 (GOT1)-dependent redox balance in PCa, which could be exploited for novel biomarkers and therapies. In this study, we discovered cancerspecific changes in urinary RNAs and metabolites, paving the way for the development of sensitive and specific urinary PCa diagnostic biomarkers either alone or in combination. Our methodology was based on single void urine samples (i.e., without prostatic massage). The integrated analysis of metabolomic and transcriptomic data from these liquid biopsies revealed a glutamate metabolism and tricarboxylic acid cycle node that was specific to prostate-derived cancer cells and cancer-specific metabolic changes in urine.More than 180,000 men are diagnosed with prostate cancer (PCa) in U.S. in the 2016, where 26,000 of these patients will die of the disease 1 . PCa is one of the second most frequently diagnosed cancer deaths among men worldwide 2 . The radiotherapy and surgery for localized PCa are known to be effective, however the prognosis for patients with the progressive disease is poor. A test to detect PCa with high sensitivity and specificity at an early stage is a clinical imperative. Moreover, there is a vital need for novel therapeutic tactics to manage this insidious and prevalent disease. open Scientific RepoRtS | (2020) 10:3716 | https://doi.org/10.1038/s41598-020-60616-z www.nature.com/scientificreports www.nature.com/scientificreports/ Serum prostate specific antigen (PSA) levels are been used for PCa diagnosis and screening for over thirty years, and digital rectal examination (DRE) for even longer 3 . However, PSA has modest sensitivity and specificity and does not discriminate indolent from aggressive cancers 3,4 . Prostate cancer antigen 3 (PCA3), a prostate-specific non-coding RNA, was approved by the FDA in 2012 as the first PCa molecular diagnostic test for a particular clinical indication (need for recurrence prostate biopsies in men aged >50 years with assumed PSA levels and/or DRE and/or one or more earlier negative biopsies) 5 . Nevertheless, the importance of the PCA3 test is limited by substantial individual variability, better performan...

Quantitative SWATH-Based Proteomic Profiling for Identification of Mechanism-Driven Diagnostic Biomarkers Conferring in the Progression of Metastatic Prostate Cancer

“…Elevated levels of GOT1 have also been observed in malignant high Gleason score Prostate tumors when compared to controls. Thereby implying that PCa cells may be undergoing GOT1 dependent metabolism while acquiring malignant phenotype and hence pointing toward GOT1 as a potential biomarker for PCa (41). GOT1 was reported to be downregulated (Average fold −1.5) in hormonal treated androgen independent CaP xenografts (LuCaP 35V) when compared to their untreated xenografts by cDNA microarray analysis, further pointing toward the involvement of GOT1 in immune response and androgen receptor signaling (42).…”

Beyond liquid biopsy: Toward non-invasive assays for distanced cancer diagnostics in pandemics

“…Next-generation Sequencing and RNA-seq - 5510 differentially expressed transcripts; 37 genes upregulated in PCa ( Lee et al, 2020 )…”

Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection

“…In case of RNA, one usually finds concentrations of total RNA in the nanogram or even the sub-nanogram range per 10 mL of urine [15]. This is supported by indirect evidence suggesting amounts of urine RNA that can only be detected by RT-qPCR [17,18]. Usually, these concentrations are too low for detection by standard analytical methods and even after preparation, RNA solutions are extremely diluted.…”