Lerink Lente J S, Sutton Christopher W, Otten Henny G, Faro Letizia Lo, Ploeg Rutger J, Lindeman Jan H N, Shaheed Sadr
Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
Department of Surgery, Transplant Centre, Leiden University Medical Centre, Leiden, The Netherlands.
Clin Proteomics. 2024 Aug 17;21(1):54. doi: 10.1186/s12014-024-09504-6.
Proteomics and metabolomics offer substantial potential for advancing kidney transplant research by providing versatile opportunities for gaining insights into the biomolecular processes occurring in donors, recipients, and grafts. To achieve this, adequate quality and numbers of biological samples are required. Whilst access to donor samples is facilitated by initiatives such as the QUOD biobank, an adequately powered biobank allowing exploration of recipient-related aspects in long-term transplant outcomes is missing. Rich, yet unverified resources of recipient material are the serum repositories present in the immunological laboratories of kidney transplant centers that prospectively collect recipient sera for immunological monitoring. However, it is yet unsure whether these samples are also suitable for -omics applications, since such clinical samples are collected and stored by individual centers using non-uniform protocols and undergo an undocumented number of freeze-thaw cycles. Whilst these handling and storage aspects may affect individual proteins and metabolites, it was reasoned that incidental handling/storage artifacts will have a limited effect on a theoretical network (pathway) analysis. To test the potential of such long-term stored clinical serum samples for pathway profiling, we submitted these samples to discovery proteomics and metabolomics.
A mass spectrometry-based shotgun discovery approach was used to obtain an overview of proteins and metabolites in clinical serum samples from the immunological laboratories of the Dutch PROCARE consortium. Parallel analyses were performed with material from the strictly protocolized QUOD biobank.
Following metabolomics, more than 800 compounds could be identified in both sample groups, of which 163 endogenous metabolites were found in samples from both biorepositories. Proteomics yielded more than 600 proteins in both groups. Despite the higher prevalence of fragments in the clinical, non-uniformly collected samples compared to the biobanked ones (42.5% vs 26.5% of their proteomes, respectively), these fragments could still be connected to their parent proteins. Next, the proteomic and metabolomic profiles were successfully mapped onto theoretical pathways through integrated pathway analysis, which showed significant enrichment of 79 pathways.
This feasibility study demonstrated that long-term stored serum samples from clinical biorepositories can be used for qualitative proteomic and metabolomic pathway analysis, a notion with far-reaching implications for all biomedical, long-term outcome-dependent research questions and studies focusing on rare events.
蛋白质组学和代谢组学通过提供多种机会来深入了解供体、受体和移植物中发生的生物分子过程，为推进肾移植研究提供了巨大潜力。要实现这一点，需要足够质量和数量的生物样本。虽然诸如QUOD生物样本库等举措有助于获取供体样本，但目前缺少一个有足够样本量的生物样本库来探索与受体相关的长期移植结果方面。丰富但未经验证的受体材料资源是肾移植中心免疫实验室中的血清库，这些血清库前瞻性地收集受体血清用于免疫监测。然而，尚不确定这些样本是否也适用于组学应用，因为此类临床样本由各个中心按照非统一方案收集和存储，并且经历了数量不明的冻融循环。虽然这些处理和存储方面可能会影响单个蛋白质和代谢物，但据推测，偶然的处理/存储假象对理论网络（通路）分析的影响有限。为了测试此类长期存储的临床血清样本用于通路分析的潜力，我们将这些样本提交进行发现蛋白质组学和代谢组学分析。
采用基于质谱的鸟枪法发现方法，以全面了解荷兰PROCARE联盟免疫实验室临床血清样本中的蛋白质和代谢物。对来自严格遵循方案的QUOD生物样本库的材料进行了平行分析。
代谢组学分析后，在两个样本组中均可鉴定出800多种化合物，其中163种内源性代谢物在两个生物样本库的样本中均有发现。蛋白质组学分析在两组中均产生了600多种蛋白质。尽管与生物样本库中的样本相比，临床中非统一收集的样本中片段的比例更高（分别占其蛋白质组的42.5%和26.5%），但这些片段仍可与其亲本蛋白质相连。接下来，通过综合通路分析将蛋白质组学和代谢组学谱成功映射到理论通路上，结果显示有79条通路显著富集。
这项可行性研究表明，临床生物样本库中长期存储的血清样本可用于定性蛋白质组学和代谢组学通路分析，这一观点对所有生物医学、长期结果依赖的研究问题以及关注罕见事件的研究都具有深远意义。
