Quantitative label-free proteomic analysis of human urine to identify novel candidate protein biomarkers for schistosomiasis

Onile, Olugbenga Samson; Calder, Bridget; Soares, Nelson C.; Anumudu, Chiaka I.; Blackburn, Jonathan M.

doi:10.1371/journal.pntd.0006045

Cited by 26 publications

(25 citation statements)

References 45 publications

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“…Advanced proteomic analysis has led to high-throughput profiling of bladder cancer-related proteins with both high sensitivity and specificity, which has resulted in a wealth of informative biomarkers [16]. A similar strategy was utilized in a recent study that identified 54 potential protein biomarkers of bladder schistosomiasis by quantitatively comparing urinary samples from humans [17]. Other types of omics applications, such as genomics, epigenomics, transcriptomics and metabolomics, were also applied to determine biomarkers of bladder schistosomiasis.…”

Section: Multi-omics Application For Bladder Bio-marker Developmentmentioning

confidence: 99%

Biomarker discovery and beyond for diagnosis of bladder diseases

Jung

Kim

2020

Bladder

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Molecular biosignatures of altered cellular landscapes and functions have been casually linked with pathological conditions, which imply the promise of biomarkers specific to bladder diseases, such as bladder cancer and other dysfunctions. Urinary biomarkers are particularly attractive due to costs, time, and the minimal and noninvasive efforts acquiring urine. The evolution of omics platforms and bioinformatics for analyzing the genome, epigenome, transcriptome, proteome, lipidome, metabolome, etc., have enabled us to develop more sensitive and disease-specific biomarkers. These discoveries broaden our understanding of the complex biology and pathophysiology of bladder diseases, which can ultimately be translated into the clinical setting. In this short review, we will discuss current efforts on identification of promising urinary biomarkers of bladder diseases and their roles in diagnosis and monitoring. With these considerations, we also aim to provide a prospective view of how we can further utilize these bladder biomarkers in developing ideal and smart medical devices that would be applied in the clinic.

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Section: Multi-omics Application For Bladder Bio-marker Developmentmentioning

confidence: 99%

Biomarker discovery and beyond for diagnosis of bladder diseases

Jung

Kim

2020

Bladder

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“…This study was performed to establish homology of the 36 biomarker proteins evaluated in a previous study (Onile et al, 2017) in other schistosome species. It was found that protein homologues of the 36 S. mansoni biomarker proteins are present in S. haematobium and S.…”

Section: Potential Therapeutic Targetsmentioning

confidence: 99%

“…Phosphopyruvate hydratase, elongation factor 1-alpha and putative actin-1 protein have been identified as eggshell protein markers that can induce cellular or antibody responses and may be useful schistosomiasis diagnostic candidates. They have also been identified as putative S. mansoni biomarker proteins (Onile et al, 2017). They all have homologues in both S. haematobium and S. japonicum with many conserved regions and semi conserved regions in the multiple sequence alignment ( Figure 4.10).…”

Section: Potential Therapeutic Targetsmentioning

confidence: 99%

“…Identification of biomarker proteins is important in early diagnosis of both schistosomiasis and schistosomiasis associated bladder cancer and has been evaluated in recent studies (Onile et al, 2017); it may also have application in drug and vaccine development for the treatment of the disease. These biomarker proteins were found using S. mansoni database, which is the best curated schistosome species.…”

Section: Introductionmentioning

confidence: 99%

“…Zheng et al, (2012) strongly suggest that SjSP-216, a highly expressed gene in the young worm stage, could serve as a potential biomarker for the early immunodiagnosis of S. japonicum infections in vertebrate hosts The aim of the study is to contribute to the development of protein biomarkers for schistosomiasis diagnosis using a bioinformatics approach. This will be achieved by identifying the homologues of the 36 biomarker proteins from Schistosoma mansoni evaluated in recent study (Onile et al, 2017) in other Schistosoma species using bioinformatics tools. These biomarker protein sequences from S. mansoni will be compared with those from other Schistosoma species to visualize similarities and differences.…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatics evaluation of the homologues ofSchistosoma mansonibiomarker proteins of bladder cancer in otherSchistosomaspecies

Folayowon

Adebayo²,

Isokpehi

et al. 2020

Preprint

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Schistosomiasis remains a public health problem in developing countries. An ideal diagnostic test capable of detecting parasites as early as possible after the onset of infection is therefore highly desired. The identification of biomarker proteins associated with active infection and immune response may constitute the basis for the development of a successful diagnostic test. The aim of this study is to contribute to the development of protein biomarkers for schistosomiasis using a bioinformatics approach. The homologues of 36 previously identified urine biomarker proteins from a Schistosoma mansoni database, were identified in other Schistosoma species using SMARTBLAST and analyzed for similarities and differences using multiple sequence alignment. Of the 36 S. mansoni biomarker proteins, 29 had homologues with both S. haematobium and S. japonicum or either of S. haematobium and S . japonicum . Most of the 29 S. mansoni biomarker proteins aligned with their homologues with many conserved regions. However, some vital biomarker proteins like venom allergen-like proteins, which had been proposed as a putative drug and vaccine target, showed more semi conserved regions in which the amino acids had similar shape but weakly similar properties. The predictions of 12 markers found in all three species also show that treatment of infections may possibly benefit from the investigational drug Artenimol and specific nutraceuticals or supplements. Experimental evaluation is needed to confirm the potential of the proteins as biomarkers for early diagnosis of schistosomiasis and associated bladder cancer.

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MS1 ion current‐based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts

Wang¹,

Shen²,

Rasam

et al. 2019

Mass Spectrometry Reviews

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The rapidly‐advancing field of pharmaceutical and clinical research calls for systematic, molecular‐level characterization of complex biological systems. To this end, quantitative proteomics represents a powerful tool but an optimal solution for reliable large‐cohort proteomics analysis, as frequently involved in pharmaceutical/clinical investigations, is urgently needed. Large‐cohort analysis remains challenging owing to the deteriorating quantitative quality and snowballing missing data and false‐positive discovery of altered proteins when sample size increases. MS1 ion current‐based methods, which have become an important class of label‐free quantification techniques during the past decade, show considerable potential to achieve reproducible protein measurements in large cohorts with high quantitative accuracy/precision. Nonetheless, in order to fully unleash this potential, several critical prerequisites should be met. Here we provide an overview of the rationale of MS1‐based strategies and then important considerations for experimental and data processing techniques, with the emphasis on (i) efficient and reproducible sample preparation and LC separation; (ii) sensitive, selective and high‐resolution MS detection; iii)accurate chromatographic alignment; (iv) sensitive and selective generation of quantitative features; and (v) optimal post‐feature‐generation data quality control. Prominent technical developments in these aspects are discussed. Finally, we reviewed applications of MS1‐based strategy in disease mechanism studies, biomarker discovery, and pharmaceutical investigations.

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Quantitative label-free proteomic analysis of human urine to identify novel candidate protein biomarkers for schistosomiasis

Cited by 26 publications

References 45 publications

Biomarker discovery and beyond for diagnosis of bladder diseases

Biomarker discovery and beyond for diagnosis of bladder diseases

Bioinformatics evaluation of the homologues ofSchistosoma mansonibiomarker proteins of bladder cancer in otherSchistosomaspecies

MS1 ion current‐based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts

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