Integrins are heterodimeric receptors important for cell adhesion and signaling. Integrin α5β1 is a key mediator of angiogenesis and its dysregulation is associated with tumor progression and metastasis. Despite numerous efforts, α5β1-targeting therapeutics have been unsuccessful due to poor efficacy and off-target effects. A contributing factor is our limited understanding of how integrin conformation influences interactions with therapeutics. Using cell-based functional assays, patient-derived xenografts, biophysics, X-ray crystallography, and electron microscopy, we shed light on these relationships by characterizing two anti-α5β1 antibodies, BIIG2 and MINT1526A. We show that both antibodies bind α5β1 with nanomolar affinity, reduce tube formation in vitro, and bind overlapping epitopes that block fibronectin binding. However, using electron microscopy, we reveal that while BIIG2 binding does not substantially alter the conformational states, MINT1526A preferentially recognizes the bent conformation and restricts the conformational ensemble. These insights can guide which aspects to prioritize to improve the design of future integrin-targeted therapeutics.

Since they were first described in the late nineteenth century, antibodies have become widely recognized as being able to serve mechanistic functions in both "protective," as well as "pathogenic" adaptive immune responses. Due to their critical roles in a wide range of disease states, there has been significant interest in the fields of immunology and medicine in identifying individual antibody-cognate antigens. However, numerous technical and logistical challenges associated with older cognate antigen identification strategies limited their widespread utilization in these fields. To meet this critical need, we recently developed an optimized, high-throughput, affinity chromatography-based, shotgun immunoproteomics pipeline which we have previously demonstrated resolves many of the identified weaknesses of past methodologies. This chapter provides a comprehensive protocol for each step of this shotgun immunoproteomics pipeline, from input protein sample preparation through data analysis and antigen identification. This high-throughput methodology for antibody-cognate antigen identification is both a user-friendly and cost-effective procedure which could potentially facilitate novel discoveries in basic, translational, and clinical research settings.

Introduction: Extracranial carotid artery pathology accounts for 15-20% of ischemic strokes. Advancements in magnetic resonance angiography (MRA) with vessel wall imaging (VWI) have enabled the identification of vulnerable plaques, aiding in risk stratification for neurovascular events. This pilot study aimed to identify proteins in plaques with and without vulnerable features on MRA with VWI. Hypothesis: There is a differential proteomic profile of vulnerable and non-vulnerable, thus, these can serve as potential biomarkers for disease progression, stroke prevention, and therapeutic targets. Methods: Consecutive patients undergoing carotid endarterectomy (CEA) were included in the study cohort with pre-operative MRA with VWI. A retrospective chart review was conducted to extract pertinent clinical data including cardiovascular risk factors and medications. The proteomic analysis involved Tandem Mass Tag (TMTpro) labeling of peptides, basic pH HPLC fractionation, and NanoLC-tandem mass spectrometry. Results: A total of sixteen plaques were retrieved from fifteen patients. There were 73.3% male patients. The most common comorbidities were hyperlipidemia (93.3%) and hypertension (80%). 31.2% of patients had symptomatic disease. Eleven plaques were vulnerable in preoperative MRI with VWI. From those, intraplaque hemorrhage was the most common feature (81.1%) . Proteomic analysis revealed 23 relevant proteins significantly elevated in vulnerable plaques, including Proteinase 3 (PRTN3), Phospholipid Transfer Protein (PLTP), and S100 Calcium-Binding Protein A12 (S100A12), with increased abundance exceeding two-fold changes or above (P<0.001). Conversely, three proteins exhibited reduced abundance in vulnerable plaques including Dynamin-3 (DNM3), Transmembrane Protein 181 (TMEM181), and Adducin-3 (ADD3) (P<0.05). All results are summarized in Figure 1A-C and Table I and II. Conclusion: This study contributes to the understanding of protein biomarkers associated with carotid plaque vulnerability, offering insights into disease progression, stroke prevention, and identification of potential therapeutic targets (Figure 1D) . Furthermore, these patients could benefit from early surgical intervention if these biomarkers were to be detected. We present a comprehensive study of multiple proteins with significant bioavailability in explanted plaque specimens that can serve as a foundation for identifying blood biomarkers for future validation studies.

UFMylation is an understudied ubiquitin-like post-translational modification (PTM). Like ubiquitin, UFM1 is conjugated to substrates via a catalytic cascade involving a UFM1-specific E1 (UBA5), E2 (UFC1), and an E3 ligase complex (UFL1, DDRGK1 and CDK5RAP3). UFMylation is reversible, and this is mediated by UFSP2. UFMylation plays essential roles in several biological processes including the DNA damage response, endoplasmic reticulum homeostasis, unfolded protein response, autophagic functions, and immune response. Importantly, UFMylation is also crucial for healthy brain development. Alzheimer’s disease (AD), a complex neurodegenerative disorder, is characterized by the accumulation of pathologic tau and beta-amyloid proteins and has been associated with abnormalities in the aforementioned processes. Intriguingly, the potential link between AD and UFMylation has not been investigated yet. Considering that pathological tau plays a critical role in AD, and tau also plays an important role for the DNA damage response in neurons under physiological conditions, we speculated that tau itself could be modified with UFM1. We performed Western blot and Meso Scale Discovery based ELISA to measure the protein level of UFM1, UFSP2 and other UFMylation pathway components in RIPA-soluble and insoluble fraction in human post-mortem frontal cortex. To test whether tau can be modified by UFM1, we performed co-immunoprecipitation (Co-IP), Proximity Ligation Assays (PLA) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). We found a significant reduction of soluble UFSP2, but an increase of soluble total UFM1 in AD compared to controls. We found that tau interacts with UFL1 and DDRGK1. In addition, using immunoprecipitation of denaturing lysates we found that tau can indeed be covalently modified by UFM1 when overexpressed. We detected strong signal of HA-UFM1-tau in neurons but not in negative controls using PLA. Furthermore, we immunoprecipitated denatured UFM1 from human autopsy brain, and detected two specific UFM1-tau bands with tau antibodies. Together, this data strongly indicates that tau is UFMylated under endogenous conditions. Using LC-MS/MS, we identified 17 UFMylation sites in tau proteins. UFMylation is dysregulated in AD; tau protein can be modified by UFM1 both in vitro and in vivo , which enables a more comprehensive understanding of tau PTMs.

INTRODUCTION:Proliferative glomerulonephritis with monoclonal immunoglobulin deposits (PGNMID) is classified within the spectrum of monoclonal gammopathy of renal significance (MGRS). However, PGNMID features an unexpected low rate of detectable monoclonal gammopathy, questioning the reality of an underlying clonal disorder in most cases. METHODS:We reviewed a cohort of 56 patients with PGNMID focusing on hematological characteristics. To detect discrete underlying clones, we used a highly sensitive high-throughput immunoglobulin (Ig) repertoire sequencing assay from RNA bone marrow (RACE-RepSeq). We also challenged the monoclonality of kidney deposits using immunofluorescence with antibodies specific for light chain (LC) variable region subgroups. RESULTS:RACE-RepSeq detected a bone marrow clone corresponding to the deposited Ig in only 23% of the whole cohort. As previously reported, PGNMID-IgG3 was the predominant subtype (41/56, 73%), with an over-representation of IgG3 kappa deposits (33/56, 59%). The low prevalence of clonal disorders was driven by PGNMID-IgG3 cases, with only 4/41 (9.8%) patients showing an IgG3-secreting bone marrow clone by RACE-RepSeq. In all seven clone-negative PGNMID-IgG3 kappa cases studied by immunofluorescence with anti-LC variable domain antibodies, glomerular deposits stained for all tested Vκ subgroups, ruling out their monoclonal nature. Compared to control individuals, immunoglobulin repertoire analyses in 24 patients without a detectable clone failed to detect any bias toward the deposited isotype, but showed increased IgG1 representation, suggesting an infectious trigger. CONCLUSIONS:Our results suggest that PGNMID is a heterogeneous condition. The predominant subtype most often involves oligoclonal or polyclonal production of nephrotoxic IgG3 and may not derive from a clonal B-cell disorder. Such cases should no longer be classified as MGRS.

BACKGROUND:Kidney aging is characterized by a loss of glomeruli, predominately in the superficial cortex, with a resultant decline in glomerular filtration rate and an increased risk of various kidney-related diseases. The early molecular alterations in glomeruli associated with the aging process are not well studied. METHODS:We combined laser capture microdissection and mass spectrometry-based unbiased proteomic analysis of non-sclerosed, non-ischemic glomeruli in the superficial cortex from young and old adults who underwent a radical nephrectomy for a tumor to understand the age-related molecular changes in glomeruli. 24 young and 30 old adults were used for the discovery dataset and the significant differentially expressed proteins were further validated using an independent set comprising 6 young and 8 old adults. RESULTS:Kidneys from older adults had lower eGFR, less kidney parenchyma on CT imaging, and more glomerulosclerosis and arteriosclerosis on histology. Quantitative proteomic analysis of non-sclerosed, non-ischemic glomeruli identified increased expression of TIMP3, GPC6, SNCG, APOA4 and NT5E in old adults that were further validated in an independent set. Pathway analysis indicated that proteins with increased expression in old adults were enriched in mitochondrial translational processes, aerobic respiration, and TCA cycle, whereas proteins with decreased expression in old adults were enriched in mRNA splicing, mRNA processing, and nonsense mediated decay. Further, Spearman correlation of validated differentially expressed proteins did not show any significant correlation with the kidney pathology independent of age group. CONCLUSIONS:Overall, this study identified proteins that are specifically associated with the aging process in otherwise normal-appearing glomeruli.

The preservation of tissue architecture and morphology in formalin-fixed paraffin-embedded (FFPE) tissues enables spatial resolution at the cellular and sub-cellular levels. Laser capture microdissection (LCM) combined with liquid chromatography tandem mass spectrometry analysis permits collection of tissue areas with spatial context for proteome profiling from FFPE slides. In this study, we performed proteome profiling of non-diseased renal tubulointerstitial tissue in a cohort of young (< 40 years) and old (> 70 years) individuals with the goal of spatially correlating the histomorphology to the proteomic profile. To perform in-depth characterization of renal tubulointerstitium and to identify renal aging-associated proteins, a multiplexing strategy using tandem mass tags (TMT) was employed, resulting in the quantitation of 7,355 proteins. Our approach allowed for identification of proteins with low abundance such as fibrocystin and ninein-like protein. Notably, 162 solute carrier proteins from 47 solute carrier families were identified, which were enriched in proximal and distal tubule cells. Finally, we discovered a proteomic signature associated with renal aging, which includes metalloproteinase inhibitor 3, nicotinamide N-methyltransferase, matrix metallopeptidase 7, phenazine biosynthesis-like domain-containing protein and solute carrier family 23 member 1. Overall, our study demonstrates the power of LCM combined with proteomics to leverage archived FFPE tissue samples for investigating proteomic alterations in the renal tubulointerstitium with age at a high depth of proteome coverage.

C3 glomerulopathy (C3G) is a rare disease resulting from dysregulation of the alternative pathway of complement. C3G includes C3 glomerulonephritis (C3GN) and dense deposit disease (DDD), both of which are characterized by bright glomerular C3 staining on immunofluorescence studies. However, on electron microscopy (EM), DDD is characterized by dense osmiophilic mesangial and intramembranous deposits along the glomerular basement membranes (GBM), while the deposits of C3GN are not dense. Why the deposits appear dense in DDD and not in C3GN is not known. We performed laser microdissection (LCM) of glomeruli followed by mass spectrometry (MS) in 12 cases each of DDD, C3GN, and pretransplant kidney control biopsies. LCM/MS showed marked accumulation of complement proteins C3, C5, C6, C7, C8, C9 and complement regulating proteins CFHR5, CFHR1, and CFH in C3GN and DDD compared to controls. C3, CFH and CFHR proteins were comparable in C3GN and DDD. Yet, there were significant differences. First, there was a six-to-nine-fold increase of C5-9 in DDD compared to C3GN. Secondly, an unexpected finding was a nine-fold increase in apolipoprotein E (ApoE) in DDD compared to C3GN. Most importantly, immunohistochemical and confocal staining for ApoE mirrored the dense deposit staining in the GBM in DDD but not in C3GN or control cases. Validation studies using 31 C3G cases confirmed the diagnosis of C3GN and DDD in 80.6 % based on ApoE staining. Overall, there is a higher burden of terminal complement pathway proteins in DDD compared to C3GN. Thus, our study shows that dense deposits in DDD are enriched with ApoE compared to C3GN and control cases. Hence, ApoE staining may be used as an adjunct to EM for the diagnosis of DDD and might be valuable when EM is not available.

Membranous nephropathy (MN) results from accumulation of antigen-antibody immune-complexes along the subepithelial region of the glomerular basement membranes. Over the last years, 13 target antigens have been discovered and include PLA2R, THSD7A, EXT1 and EXT2, NELL1, SEMA3B, NCAM1, CNTN1, HTRA1, FAT1, PCDH7, NTNG1, PCSK6 and NDNF, accounting for 80-90% of MN antigens. MN associated with many of these antigens have distinctive clinicopathologic findings. It is important to accurately identify the antigen in MN. Immunohistochemical (IHC) and/or immunofluorescence (IF) methods are currently used to detect PLA2R, THSD7A, NELL1, SEMA3B and EXT1/EXT2. However, for the remaining antigens, IHC/IF methods do not exist and are not practical for detection. Here, we developed laser microdissection-based mass spectrometry methodology (LMD/MS) as a one-stop clinical test for the detection of MN antigens using paraffin-embedded kidney biopsy tissue. The LMD/MS test was validated in two steps. LMD/MS was used to detect the antigen in 75 cases of MN with known antigens and correctly identified the antigen in all these cases. Next, LMD/MS was used to identify the antigen in 61 MN cases where the antigen was unknown and identified one of the known antigens in 40 of 61 cases including many of the less common antigens. This lower-than-expected detection rate is explained by intentional enrichment of the cohort with PLA2R-negative MN. Overall, PLA2R was identified in 16.4%, one of the other antigens detected in 49.1%, and in the remaining 34.5% of cases, none of the above antigens was detected. Thus, LMD/MS is an extremely useful and reliable method for the detection of known MN antigens and possibly indicating an unknown MN antigen for eventual discovery.

Objective: We sought to identify differentially expressed proteins in serum, plasma, and plaque samples of patients with carotid atherosclerotic lesions. Methods: We performed a systematic review of the proteomic profile of serum, plasma, and plaque samples of patients with carotid artery disease. We included full-length peer-reviewed studies of adult humans and reported them using PRISMA guidelines. The quality of the design and content of the articles included in the review was assessed using the Newcastle-Ottawa scale. Results: We included six peer-reviewed articles reporting protein expression in serum, plasma, or plaque samples from patients with carotid atherosclerosis. Three were single-center cross-sectional studies, two were single-center case-control studies, and one was a single-center cohort study. Thirty-six proteins were found to be expressed differentially when comparing samples from healthy subjects and individuals with diseased carotid vessels and between patients with symptomatic and asymptomatic carotid artery atherosclerotic lesions. Some of these were shown to be related to inflammatory or anti-inflammatory pathways in atherogenesis. CD5L and S100A12 were both found to be upregulated in patients with unstable plaque, the former owing to its anti-inflammatory properties and the latter for its pro-oxidant effects in atherosclerosis. ACTB is involved in cellular structure and integrity and was found to be downregulated in patients with ruptured carotid plaques. Conclusions: Atherosclerotic carotid disease places the patient at increased risk of ischemic neurological events. Proteomics may help to understand their pathophysiological processes and can identify differential protein expression in blood samples from healthy subjects and patients with carotid artery plaques. This patient-centered approach will allow for the timely identification of individuals at higher risk of experiencing stroke.

Laser capture microdissection and mass spectrometry (LCM/MS) is a technique that involves dissection of glomeruli from paraffin-embedded biopsy tissue, followed by digestion of the dissected glomerular proteins by trypsin, and subsequently mass spectrometry to identify and semiquantitate the glomerular proteins. LCM/MS has played a crucial role in the identification of novel types of amyloidosis, biomarker discovery in fibrillary GN, and more recently discovery of novel target antigens in membranous nephropathy (MN). In addition, LCM/MS has also confirmed the role for complement proteins in glomerular diseases, including C3 glomerulopathy. LCM/MS is now widely used as a clinical test and considered the gold standard for diagnosis and typing amyloidosis. For the remaining glomerular diseases, LCM/MS has remained a research tool. In this review, we discuss the usefulness of LCM/MS in other glomerular diseases, particularly MN, deposition diseases, and diseases of complement pathways, and advocate more routine use of LCM/MS at the present time in at least certain diseases, such as MN, for target antigen detection. We also discuss the limitations of LCM/MS, particularly the difficulties faced from moving from a research-based technique to a clinical test. Nonetheless, the role of LCM/MS in glomerular diseases is expanding. Currently, LCM/MS may be used to identify the etiology in certain glomerular diseases, but in the future, LCM/MS can play a valuable role in determining pathways of complement activation, inflammation, and fibrosis.

Background Glycosylation is an enzyme-catalyzed post-translational modification that is distinct from glycation and is present on a majority of plasma proteins. N-glycosylation occurs on asparagine residues predominantly within canonical N-glycosylation motifs (Asn-X-Ser/Thr) although non-canonical N-glycosylation motifs Asn-X-Cys/Val have also been reported. Albumin is the most abundant protein in plasma whose glycation is well-studied in diabetes mellitus. However, albumin has long been considered a non-glycosylated protein due to absence of canonical motifs. Albumin contains two non-canonical N-glycosylation motifs, of which one was recently reported to be glycosylated.Methods We enriched abundant serum proteins to investigate their N-linked glycosylation followed by trypsin digestion and glycopeptide enrichment by size-exclusion or mixed-mode anion-exchange chromatography. Glycosylation at canonical as well as non-canonical sites was evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) of enriched glycopeptides. Deglycosylation analysis was performed to confirm N-linked glycosylation at non-canonical sites. Albumin-derived glycopeptides were fragmented by MS3 to confirm attached glycans. Parallel reaction monitoring was carried out on twenty additional samples to validate these findings. Bovine and rabbit albumin-derived glycopeptides were similarly analyzed by LC-MS/MS.Results Human albumin is N-glycosylated at two non-canonical sites, Asn68 and Asn123. N-glycopeptides were detected at both sites bearing four complex sialylated glycans and validated by MS3-based fragmentation and deglycosylation studies. Targeted mass spectrometry confirmed glycosylation in twenty additional donor samples. Finally, the highly conserved Asn123 in bovine and rabbit serum albumin was also found to be glycosylated.Conclusions Albumin is a glycoprotein with conserved N-linked glycosylation sites that could have potential clinical applications.

Introduction: Membranous nephropathy (MN) is the most common glomerular disease associated with sarcoidosis. The target antigen M-type phospholipase A2 receptor 1 (PLA2R) has been identified in a subset of sarcoidosis-associated MN. The target antigen is not known in the remaining sarcoidosis-associated MN. Methods: Data of patients with history of sarcoidosis and biopsy-proven MN were retrieved and analyzed. Mass spectrometry (MS/MS) was performed on all kidney biopsies of sarcoidosis-associated MN to detect the target antigens. Immunohistochemistry (IHC) studies were performed to confirm and localize the target antigens along the glomerular basement membrane (GBM). Results: Eighteen patients with history of sarcoidosis and biopsy-proven MN were identified, of whom 3 were known to be PLA2R-negative, and in the remaining patients the target antigen was unknown. Thir-teen (72%) patients were males; the median age at MN diagnosis was 54.5 years. The median proteinuria at presentation was proteinuria 9.8 g/24 h. Eight patients (44.4%) had concurrent sarcoidosis. Using MS/ MS, we detected PLA2R and neural epidermal growth factor-like-1 protein (NELL1) in 7 (46.6%) and 4 (22.2%) patients, respectively. In addition, 1 case each (5.5%) was positive for thrombospondin type 1 domain-containing 7A (THSD7A), protocadherin-7 (PCDH7), and putative antigen Serpin B12. No known target antigen was detected in the remaining 4 patients (22.2%). Conclusion: Patients with sarcoidosis and MN exhibit heterogeneous target antigens. We identified, along with PLA2R, the presence of previously unreported antigens, including NELL1, PCDH7, and THSD7A. The incidence of the target antigens in sarcoidosis appears to mirror the overall incidence of target antigens in MN. MN in sarcoidosis may be the result of a heightened immune response and is not associated with a single target antigen.