MALDI imaging mass spectrometry in glomerulonephritis: feasibility study

Proteomics for the study of new biomarkers in Fabry disease: State of the art

Nephropathy represents a major complication of Fabry Disease and its accurate characterization is of paramount importance in predicting the disease progression and assessing the therapeutic responses. The diagnostic process still relies on performing renal biopsy, nevertheless many efforts have been made to discover early reliable biomarkers allowing us to avoid invasive procedures. In this field, proteomics offers a sensitive and fast method leading to an accurate detection of specific pathological proteins and the discovery of diagnostic and prognostic biomarkers that reflect disease progression and facilitate the evaluation of therapeutic responses. Here, we report a review of selected literature focusing on the investigation of several proteomic techniques highlighting their advantages, limitations and future perspectives in their application in the routine study of Fabry Nephropathy.

Matrix-assisted laser desorption/ionization mass spectrometry imaging to uncover protein alterations associated with the progression of IgA nephropathy

IgA nephropathy (IgAN) is one of the most diffuse glomerulonephrites worldwide, and many issues still remain regarding our understanding of its pathogenesis. The disease is diagnosed by renal biopsy examination, but potential pitfalls still persist with regard to discriminating its primary origin and, as a result, determining patient outcome remains challenging. In this pilot study, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) was performed on renal biopsies obtained from patients with IgAN (n = 11) and other mesangioproliferative glomerulonephrites (MesPGN, n = 6) in order to enlighten proteomic alterations that may be associated with the progression of IgAN. Differences in the proteomic profiles of IgAN and MesPGN tissue could clearly be detected using this approach and, furthermore, 14 signals (AUC ≥ 0.8) were observed to have an altered intensity among the different CKD stages within the IgAN group. In particular, large increases in the intensity of these signals could be observed at CKD stages II and above. These signals primarily corresponded to proteins involved in either inflammatory and healing pathways and their increased intensity was localized within regions of tissue with large amounts of inflammatory cells or sclerosis. Despite much work in recent years, our molecular understanding of IgAN progression remains incomplete. This pilot study represents a promising starting point in the search for novel protein markers that can assist clinicians in better understanding the pathogenesis of IgAN and highlighting those patients who may progress to end-stage renal disease.

Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology

In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.

Metabolomics profiling of methamphetamine addicted human serum and three rat brain areas

Methamphetamine (METH) has already been a serious problem all over the world. The identification of related biomarkers and pathways is helpful to evaluate the degree of METH addiction, develop appropriate treatment during abstinence, and explore the mechanism. Here, it is the first time to perform metabolomics profiling of METH addicted human serum and three regions of METH-induced conditioned place preference (CPP) rat brain by using UHPLC-MS/MS and matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI), respectively. Untargeted metabolomics analysis demonstrated clear differences between METH abusers and the healthy control by finding 35 distinct expressed metabolites in serum, including 5 TCA intermediates, 17 amino acids and 13 other biomolecules, 15 of which were newly identified following METH exposure. By using MALDI-MSI, the relative quantification and distribution of 14 metabolites were investigated in the nucleus accumbens (NAc), dorsal hippocampus (dHPC) and ventral hippocampus (vHPC) of CPP rat brain. Taken together, METH addiction could influence energy metabolism, amino acids metabolism, and phospholipids metabolism. A multi-parameter model consisting of these related metabolites can be established as a METH addiction biomarker in the future. The mapping of phospholipids provided new insights into the mechanism of METH addiction. Notably, the trend of metabolite changes in NAc and dHPC was almost the same, while it was opposite between dHPC and vHPC. It seems that NAc and dHPC were the two regions more susceptible to METH administration in the brain. And dHPC and vHPC play different roles in METH addiction proved by metabolites mapping.

To explore the mechanism of METH addiction, the metabolomics profiling of METH addicted human serum and rat brain were performed using UHPLC-MS/MS and MALDI-MSI, respectively. 35 differentially expressed metabolites were identified in the serum.

Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations

Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.

MALDI-MSI Pilot Study Highlights Glomerular Deposits of Macrophage Migration Inhibitory Factor as a Possible Indicator of Response to Therapy in Membranous Nephropathy

PURPOSE

Membranous nephropathy (MN) is the most frequent cause of nephrotic syndrome in adults and the disease course is characterized by the "rule of third", with one-third of patients experiencing complete remission and the remaining experiencing relapses or progression of the disease. Additionally, the therapeutic approach is not standardized, leading to further heterogeneity in terms of response and outcome.

EXPERIMENTAL DESIGN

In this pilot study, MALDI-MSI analysis is performed on renal biopsies (n = 13) obtained from two homogeneous groups of patients, which differentially responded to the immunosuppressive treatments (Ponticelli regimen).

RESULTS

A signal at m/z 1303 displays the greatest discriminatory power when comparing the two groups and is observed to be of higher intensity in the glomeruli of the non-responding patients. The corresponding tryptic peptide is identified as macrophage migration inhibitory factor (MIF).

CONCLUSIONS AND CLINICAL RELEVANCE

Despite much effort being made in recent years to understand the pathogenesis of MN, a biomarker able to predict the outcome of these patients following therapeutic treatment is still lacking. Here, a protein (MIF), verified by immunohistochemistry, that can differentiate between these MN patients and could be a valuable starting point for a further study focused on verifying its predictive role in therapy response is highlighted.

Nephropathology: A Cornerstone for Understanding and Estimation of Recent Advances in Glomerular Diseases

The developments in the field of kidney pathology are major objectives for nephrology worldwide, since the histopathologic diagnosis is a cornerstone for all glomerulopathies (either primary or secondary related to systemic diseases-for tubulointerstitial and vascular lesions as well as renal allograft nephropathy). Moreover, the correct interpretation of kidney tissue samples is a challenge for pathologists too. Consequently, a new subspecialty - nephropathology, was accepted by many medical schools in various universities, while dedicated scientific meetings, journals and websites were also created. In the following few pages, a short overview on the history, classic and novel meanings of the renal pathology for the understanding of glomerular pathophysiology will be discussed.

MALDI-MS Imaging in the Study of Glomerulonephritis

Glomerulonephritis (GNs) are one of the most frequent causes of chronic kidney disease (CKD), a renal condition that often leads to end-stage renal failure, and a careful assessment of these diseases is essential for prognostic and therapeutic purposes. The application of MALDI-MSI directly on bioptic renal tissue represents a new stimulating perspective and facilitates the detection of specific proteomic indicators that are directly correlated with the pathological alterations that occur within the glomeruli during the development of glomerulonephritis. Here, we describe the standard workflow for the MALDI-MSI analysis of clinical fresh-frozen and FFPE renal biopsies and highlight how the obtained molecular information, when combined with histology, can be used to detect specific protein markers of GNs.

The putative role of MALDI-MSI in the study of Membranous Nephropathy

Membranous Nephropathy (MN) is an immunocomplex mediated renal disease that represents one of the most frequent glomerulopathies worldwide. This glomerular disease can manifest as primary (idiopathic) or secondary and this distinction is crucial when choosing the most appropriate course of treatment. In secondary cases, the best strategy involves treating the underlying disease, whereas in primary forms, the identification of confirmatory markers of the idiopathic etiology underlining the process is requested by clinicians. Among those currently reported, the positivity to circulating antigens (PLA2R, IgG4 and THSD7A) was demonstrated in approximately 75% of iMN patients, while approximately 1 in 4 patients with iMN still lack a putative diagnostic marker. Ultimately, the discovery of biomarkers to help further stratify these two different forms of glomerulopathy seems mandatory. Here, MALDI-MSI was applied to FFPE renal biopsies from histologically diagnosed primary and secondary MN patients (n=20) in order to detect alterations in their tissue proteome. MALDI-MSI was able to generate molecular signatures of primary and secondary MN, with one particular signal (m/z 1459), identified as Serine/threonine-protein kinase MRCK gamma, being over-expressed in the glomeruli of primary MN patients with respect to secondary MN. Furthermore, a number of signals that could differentiate the different forms of iMN that were positive to PLA2R or IgG4 were detected, as well as a further set of signals (m/z 1094, 1116, 1381 and 1459) that could distinguish these patients from those who were negative to both. These signals could potentially represent future targets for the further stratification of iMN patients. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.

Proteomics in thyroid cytopathology: Relevance of MALDI-imaging in distinguishing malignant from benign lesions

Several proteomic strategies are used extensively for the purpose of biomarker discovery and in order to obtain insights into the molecular aspects of cancers, using either body fluids or tissue as samples. Among them, MALDI-imaging can be applied to cytological thyroid specimens to investigate the molecular signatures of different pathological conditions and highlight differences in the proteome that are of relevance for diagnostic and pathogenetic research. In this study, 26 ex-vivo fine needle aspirations from benign thyroid nodules (n = 13) and papillary thyroid carcinomas (n = 13) were analyzed by MALDI-imaging. Based on the specific protein signatures capable of distinguishing the aforementioned patients, MALDI-imaging was able to correctly assign, in blind, the specimens from ten additional FNABs to a malignant or benign class, as later confirmed by the morphological classification. Moreover, some proteins presented a progressive overexpression in malignant phenotypes when compared with Hashimoto's thyroiditis and hyperplastic/follicular adenoma. This data not only suggests that a MALDI-imaging based approach can be a valuable tool in the diagnosis of thyroid lesions but also in the detection of proteins that have a possible role in the promotion of tumorigenic activity.

α-1-Antitrypsin detected by MALDI imaging in the study of glomerulonephritis: Its relevance in chronic kidney disease progression

Idiopathic glomerulonephritis (GN), such as membranous glomerulonephritis, focal segmental glomerulosclerosis (FSGS), and IgA nephropathy (IgAN), represent the most frequent primary glomerular kidney diseases (GKDs) worldwide. Although the renal biopsy currently remains the gold standard for the routine diagnosis of idiopathic GN, the invasiveness and diagnostic difficulty related with this procedure highlight the strong need for new diagnostic and prognostic biomarkers to be translated into less invasive diagnostic tools. MALDI-MS imaging MALDI-MSI was applied to fresh-frozen bioptic renal tissue from patients with a histological diagnosis of FSGS (n = 6), IgAN, (n = 6) and membranous glomerulonephritis (n = 7), and from controls (n = 4) in order to detect specific molecular signatures of primary glomerulonephritis. MALDI-MSI was able to generate molecular signatures capable to distinguish between normal kidney and pathological GN, with specific signals (m/z 4025, 4048, and 4963) representing potential indicators of chronic kidney disease development. Moreover, specific disease-related signatures (m/z 4025 and 4048 for FSGS, m/z 4963 and 5072 for IgAN) were detected. Of these signals, m/z 4048 was identified as α-1-antitrypsin and was shown to be localized to the podocytes within sclerotic glomeruli by immunohistochemistry. α-1-Antitrypsin could be one of the markers of podocyte stress that is correlated with the development of FSGS due to both an excessive loss and a hypertrophy of podocytes.

A MALDI-Mass Spectrometry Imaging method applicable to different formalin-fixed paraffin-embedded human tissues

The paper shows a new method for the application of Matrix Assisted Laser Desorption/Ionisation (MALDI) Mass Spectrometry Imaging (MSI) technology on formalin-fixed paraffin-embedded (FFPE) tissue samples.

MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review)

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.