Diagnostic amyloid proteomics: experience of the UK National Amyloidosis Centre

Abstract

<jats:title>Abstract</jats:title><jats:p>Systemic amyloidosis is a serious disease which is caused when normal circulating proteins misfold and aggregate extracellularly as insoluble fibrillary deposits throughout the body. This commonly results in cardiac, renal and neurological damage. The tissue target, progression and outcome of the disease depends on the type of protein forming the fibril deposit, and its correct identification is central to determining therapy. Proteomics is now used routinely in our centre to type amyloid; over the past 7 years we have examined over 2000 clinical samples. Proteomics results are linked directly to our patient database using a simple algorithm to automatically highlight the most likely amyloidogenic protein. Whilst the approach has proved very successful, we have encountered a number of challenges, including poor sample recovery, limited enzymatic digestion, the presence of multiple amyloidogenic proteins and the identification of pathogenic variants. Our proteomics procedures and approaches to resolving difficult issues are outlined.</jats:p>

Amyloid Typing by Mass Spectrometry in Clinical Practice: a Comprehensive Review of 16,175 Samples

“…Nonetheless, when coupled with a robust quality control and quality assurance system 25 and advanced bioinformatics, 31,36 it can be applied to routine reference laboratory practice as shown in this study and in other published studies. 32,[37][38][39][40][41][42][43] In this study of routine clinical samples sent for amyloid typing to our reference laboratory, we identified 21 different amyloid types. These amyloid proteins represent the entire spectrum of common and rare amyloidrelated diseases, including hereditary (mutated ATTR, AFib, AApoAI, AApoCII, AGel, and ALys), neoplastic (AL, APro, and ACal), chronic inflammatory (AA and ALect2), iatrogenic (AIns and AEnf), and age-related (ATTRwt) diseases.…”

“…Figure 1 shows example amyloid proteomes of the 22 different types identified in our cohort. [32][33][34] In this figure, AL-kappa and ALlambda were considered separate amyloid types, whereas in the remainder of the manuscript they were combined under the heading of AL-type. These data show that proteomics can find the distinguishing amyloidogenic protein without a priori knowledge.…”

“…Numbers in the green boxes indicate total number of tandem mass spectrometry spectra matching a protein in a sample, which is a surrogate measure of its abundance. 32 Apolipoprotein E (ApoE), serum amyloid P component (SAP), and apolipoprotein A IV (ApoAIV) are generic amyloid markers. Overexpressed ApoAIV is an amyloid marker for AApoAIV type.…”

Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres

“…More recently, in view of the IHC limitations, some clinical centres have started to rely entirely on mass spectrometry (MS)-based proteomics methods for amyloid typing [7][8][9]. MS-based proteomics has become a well-established approach [9][10][11] and is employed for both basic research and clinical diagnosis of amyloidosis. The use of laser capture microdissection (LCM) allows the precise selection of amyloid material (CR positive) for MS analysis, and LCM-MS is now considered a robust method for amyloid typing [9,11].…”

Proteomics Fundamentally Advance the Diagnosis and Management of Amyloidosis

“…Sequence variability and a complex combination of post-translational modifications render the deposited proteins significantly different from their native counterpart, affecting protein identification. These issues can be overcome to some extent through the use of augmented databases and dedicated bioinformatics, as described by Dasari et al 1 A collective effort for standardization of the preanalytical phase and protocols, as well as for coping with other inherent issues of amyloid diagnostic proteomics, 6 is therefore desirable. In addition, given the fact that protein identification results are substantially dependent on the database and searching tools, harmonization of the bioinformatics resources is also a critical factor to render the results comparable across centers.…”