Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma

Shimwell, Neil J.; Bryan, Richard T.; Wei, Wenbin; James, Nicholas D.; Cheng, Kar Keung; Zeegers, Maurice P.; Johnson, Philip J.; Martin, Ashley; Ward, Douglas G.

doi:10.1038/bjc.2013.157

Cited by 40 publications

(53 citation statements)

References 47 publications

(53 reference statements)

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“…In this context, urine could prove to be an important proximal fluid in providing biomarkers that could be tested noninvasively [2]. The choice of urine is particularly useful in the context of kidney and urinary system related diseases such as acute and chronic kidney diseases, diseases with either the urinary bladder or prostrate, and kidney transplantation [2][3][4][5][6][7][8][9]. Circulating peptides in urine are to be considered potentially useful as biomarkers as they are both abundant and easily accessible.…”

Section: Introductionmentioning

confidence: 99%

Optimization for Peptide Sample Preparation for Urine Peptidomics

Sigdel

Nicora

Qian

et al. 2017

Methods in Molecular Biology

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Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput 'peptidomics' methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regards to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements that it hampers both the identification of peptides and the depth of the peptidomics read when utilizing LC-MS based peptidome analysis. We report on a novel adaptation of the standard solid phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. Expense and time requirements were comparable for both SPE and mSPE, but more interfering contaminants from the urine matrix were evident in the SPE preparations (e.g., clogging of the LC-MS columns, yellowish background coloration of prepared samples due to retained urobilin, lower peptide yields) when compared to the mSPE method. When we compared data from technical replicates of 4 runs, the mSPE method provided significantly improved efficiencies for the preparation of samples from urine (e.g., mSPE peptide identification 82% versus 18% with SPE; p = 8.92E-05). Additionally, peptide identifications, when applying the mSPE method, highlighted the biology of differential activation of urine peptidases during acute renal transplant rejection with distinct laddering of specific peptides, which was obscured for most proteins when utilizing the conventional SPE method. In conclusion, the mSPE method was found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis due to the optimized sample clean up that provided improved experimental inference from the confidently identified peptides.

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Section: Introductionmentioning

confidence: 99%

Optimization for Peptide Sample Preparation for Urine Peptidomics

Sigdel

Nicora

Qian

et al. 2017

Methods in Molecular Biology

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“…The recent introduction of new high-throughput technologies resulted in the discovery of many new substances, which may be detected in urine and used for a noninvasive detection as tumor markers [16,17]. Combination of individual markers facilitates higher sensitivity of tests [18].…”

Section: Introductionmentioning

confidence: 99%

Panel of Urinary Diagnostic Markers for Non-Invasive Detection of Primary and Recurrent Urothelial Urinary Bladder Carcinoma

Soukup¹,

Kalousová²,

Čapoun³

et al. 2015

Urol Int

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Objectives: To determine the combination of urinary protein markers for noninvasive detection of primary and recurrent urothelial bladder carcinomas. Methods: Urinary concentrations of 27 biomarkers (NSE, ATT, AFABP, Resistin, Midkine, Clusterin, Uromodulin, ZAG2, HSP27, HSP 60, NCAM1/CD56, Angiogenin, Calreticulin, Chromogranin A, CEACAM1, CXCL1, IL13Ra2, Progranulin, VEGFA, CarbAnhydIX, Annexin-V, TIM4, Galectin1, Cystatin B, Synuclein G, ApoA1 and ApoA2) were assessed by enzyme-linked immunosorbent assay or by electrochemiluminiscence immunoassay. Results: During the primary diagnostics, a group of 70 patients with primary occurrence of bladder cancer and 49 healthy control subjects were compared. For this clinical situation, the most accurate combination proved to be the combination of cytology with markers Midkine and Synuclein G (sensitivity 91.8%, specificity 97.5%). During the monitoring of patients with non-muscle invasive bladder cancer (NMIBC), a group of 44 patients with cancer recurrence was compared with the group of 61 patients with a history of NMIBC without current disease. For this clinical situation, the most accurate combination proved to be the combination of cytology and erythrocytes count in urine sediment with markers Midkine, ZAG2, CEACAM1, and Synuclein G (sensitivity 92.68%, specificity 90.16%). A lower accuracy of the diagnostic panel and the necessity to use more markers in the case of recurrence was connected with a different structure of patients. Conclusions: Multi-marker test can significantly improve the bladder cancer detection both during the primary diagnostics and monitoring of patients with NMIBC. This outcome should result in other, larger studies.

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“…5,19 However, the latest generation of experimental platforms shows significant promise in the field of urinary biomarker discovery, identifying protein-, DNA-and RNA-based biomarkers with potential clinical utility. 20,21 A number of studies are ongoing, although for the foreseeable future it is likely that these biomarkers will only reduce the frequency of cystoscopic surveillance and not replace cystoscopy altogether, especially for high-risk NMIBC. However, we are hopeful that the future will see the development of a multi-biomarker urinary test with utility for both the diagnosis and surveillance of UBC.…”

Section: Urinary Biomarkersmentioning

confidence: 99%