Alzheimer's disease CSF biomarkers correlate with early pathology and alterations in neuronal and glial gene expression.

INTRODUCTION: Normal pressure hydrocephalus (NPH) patients undergoing cortical shunting frequently show early AD pathology on cortical biopsy, which is predictive of progression to clinical AD. The objective of this study was to use samples from this cohort to identify CSF biomarkers for AD-related CNS pathophysiologic changes using tissue and fluids with early pathology, free of post-mortem artifact. METHODS: We analyzed Simoa, proteomic, and metabolomic CSF data from 81 patients with previously documented pathologic and transcriptomic changes. RESULTS: AD pathology on biopsy correlates with CSF ß-amyloid-40/42, neurofilament light chain (NfL), and phospho-tau-181(p-tau181)/ß-amyloid-42, while several gene expression modules correlate with NfL. Proteomic analysis highlights 7 core proteins that correlate with pathology and gene expression changes on biopsy, and metabolomic analysis of CSF identifies disease-relevant groups that correlate with biopsy data.. DISCUSSION: As additional biomarkers are added to AD diagnostic panels, our work provides insight into the CNS pathophysiology these markers are tracking.

Glycation and drug binding by serum albumin.

Accumulation of glycation products in patients with hyperglycaemic conditions can lead to their reaction with the proteins in the human system such as serum albumin, haemoglobin, insulin, plasma lipoproteins, lens proteins and collagen among others which have important biological functions. Therefore, it is important to understand if glycation of these proteins affects their normal action not only qualitatively, but also importantly quantitatively. Glycation of human serum albumin can easily be carried out over period of weeks and its drug transportability may be examined, in addition to characterisation of the amadori products. A combination of ultrasensitive isothermal titration calorimetry, differential scanning calorimetry, spectroscopy and chromatography provides structure-property-energetics correlations which are important to obtain mechanistic aspects of drug recognition, conformation of the protein, and role of amadori products under conditions of glycation. The role of advance glycation end products is important in recognition of antidiabetic drugs. Further, the extent of glycation of the protein and its implication on drug transportability investigated by direct calorimetric methods enables unravelling mechanistic insights into role of functionality on drug molecules in the binding process, and hinderance in the recognition process, if any, as a result of glycation. It is possible that the drug binding ability of the protein under glycation conditions may not be adversely affected, or may even lead to strengthened ability. Rigorous studies on such systems with diverse functionality on the drug molecules is required which is essential in deriving guidelines for improvements in the existing drugs or in the synthesis of new molecular entities directed towards addressing diabetic conditions.

Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry.

The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.

Liposome-encapsulated mannose-1-phosphate therapy improves global N-glycosylation in different congenital disorders of glycosylation.

Phosphomannomutase 2 (PMM2) converts mannose-6-phospahate to mannose-1-phosphate; the substrate for GDP-mannose, a building block of the glycosylation biosynthetic pathway. Pathogenic variants in the PMM2 gene have been shown to be associated with protein hypoglycosylation causing PMM2-congenital disorder of glycosylation (PMM2-CDG). While mannose supplementation improves glycosylation in vitro, but not in vivo, we hypothesized that liposomal delivery of mannose-1-phosphate could increase the stability and delivery of the activated sugar to enter the targeted compartments of cells. Thus, we studied the effect of liposome-encapsulated mannose-1-P (GLM101) on global protein glycosylation and on the cellular proteome in skin fibroblasts from individuals with PMM2-CDG, as well as in individuals with two N-glycosylation defects early in the pathway, namely ALG2-CDG and ALG11-CDG. We leveraged multiplexed proteomics and N-glycoproteomics in fibroblasts derived from different individuals with various pathogenic variants in PMM2, ALG2 and ALG11 genes. Proteomics data revealed a moderate but significant change in the abundance of some of the proteins in all CDG fibroblasts upon GLM101 treatment. On the other hand, N-glycoproteomics revealed the GLM101 treatment enhanced the expression levels of several high-mannose and complex/hybrid glycopeptides from numerous cellular proteins in individuals with defects in PMM2 and ALG2 genes. Both PMM2-CDG and ALG2-CDG exhibited several-fold increase in glycopeptides bearing Man6 and higher glycans and a decrease in Man5 and smaller glycan moieties, suggesting that GLM101 helps in the formation of mature glycoforms. These changes in protein glycosylation were observed in all individuals irrespective of their genetic variants. ALG11-CDG fibroblasts also showed increase in high mannose glycopeptides upon treatment; however, the improvement was not as dramatic as the other two CDG. Overall, our findings suggest that treatment with GLM101 overcomes the genetic block in the glycosylation pathway and can be used as a potential therapy for CDG with enzymatic defects in early steps in protein N-glycosylation.

Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach.

Many studies have demonstrated the manner in which ANS interacts with bovine serum albumin (BSA), although they are limited by the extremely low solubility of dye. The present study demonstrates the binding of ANSA dye with BSA, and since this dye can easily replace ANS, it not only simplifies research but also improves sensor accuracy for serum albumin. A combination of calorimetry and spectroscopy has been employed to establish the thermodynamic signatures associated with the interaction of ANSA with the protein and the consequent conformational changes in the latter. The results of differential scanning calorimetry reveal that when the concentration of ANSA in solution is increased, the thermal stability of the protein increases substantially. The fluorescence data demonstrated a decrease in the binding affinity of ANSA with the protein when pH increased but was unable to identify a change in the mode of interaction of the ligand. ITC has demonstrated that the mode of interaction between ANSA and the protein varies from a single set of binding sites at pH 5 and 7.4 to a sequential binding site at pH 10, emphasizing the potential relevance of protein conformational changes. TCSPC experiments suggested a dynamic type in the presence of ANSA. Molecular docking studies suggest that ANSA molecules are able to find ionic centers in the hydrophobic pockets of BSA. The findings further imply that given its ease of use in experiments, ANSA may be a useful probe for tracking the presence of serum albumin and partially folded protein states.

Defining albumin as a glycoprotein with multiple N-linked glycosylation sites.

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.

A complement C4-derived glycopeptide is a biomarker for PMM2-CDG.

BACKGROUNDDiagnosis of PMM2-CDG, the most common congenital disorder of glycosylation (CDG), relies on measuring carbohydrate-deficient transferrin (CDT) and genetic testing. CDT tests have false negatives and may normalize with age. Site-specific changes in protein N-glycosylation have not been reported in sera in PMM2-CDG.METHODSUsing multistep mass spectrometry-based N-glycoproteomics, we analyzed sera from 72 individuals to discover and validate glycopeptide alterations. We performed comprehensive tandem mass tag-based discovery experiments in well-characterized patients and controls. Next, we developed a method for rapid profiling of additional samples. Finally, targeted mass spectrometry was used for validation in an independent set of samples in a blinded fashion.RESULTSOf the 3,342 N-glycopeptides identified, patients exhibited decrease in complex-type N-glycans and increase in truncated, mannose-rich, and hybrid species. We identified a glycopeptide from complement C4 carrying the glycan Man5GlcNAc2, which was not detected in controls, in 5 patients with normal CDT results, including 1 after liver transplant and 2 with a known genetic variant associated with mild disease, indicating greater sensitivity than CDT. It was detected by targeted analysis in 2 individuals with variants of uncertain significance in PMM2.CONCLUSIONComplement C4-derived Man5GlcNAc2 glycopeptide could be a biomarker for accurate diagnosis and therapeutic monitoring of patients with PMM2-CDG and other CDGs.FUNDINGU54NS115198 (Frontiers in Congenital Disorders of Glycosylation: NINDS; NCATS; Eunice Kennedy Shriver NICHD; Rare Disorders Consortium Disease Network); K08NS118119 (NINDS); Minnesota Partnership for Biotechnology and Medical Genomics; Rocket Fund; R01DK099551 (NIDDK); Mayo Clinic DERIVE Office; Mayo Clinic Center for Biomedical Discovery; IA/CRC/20/1/600002 (Center for Rare Disease Diagnosis, Research and Training; DBT/Wellcome Trust India Alliance).

Data-Independent Acquisition and Label-Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid.

This article presents a practical guide to mass spectrometry-based data-independent acquisition and label-free quantification for proteomics analysis applied to cerebrospinal fluid, offering a robust and scalable approach to probing the proteomic composition of the central nervous system. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Cerebrospinal fluid sample collection and preparation for mass spectrometry analysis Basic Protocol 2: Mass spectrometry sample analysis with data-independent acquisition Support Protocol: Data-dependent mass spectrometry and spectral library construction Basic Protocol 3: Analysis of mass spectrometry data.

Hospital corneal retrieval program: A long way to go.

PURPOSE: The Hospital Corneal Retrieval Program (HCRP) aims to counsel and encourage the family of a critically ill or deceased person in the hospital for eye donation. Adequately sensitized health-care workers (HCWs) may play a pivotal role in boosting HCRP. STUDY DESIGN: Multicentric, cross-sectional, descriptive study. METHODS: Study participants included all HCWs of three medical colleges, including one with eye bank and corneal transplant services. A pretested, structured questionnaire was used to record the awareness, knowledge, and attitude about eye donation among HCWs. The expected outcome was to seek differences in awareness, if any, among medical and paramedical workers of medical colleges with (group A) or without (group B) eye bank and corneal transplant facilities. RESULTS: Of the 4060 study participants, 2100 HCWs were in group A and the rest (1960) were in group B. For eight out of 13 questions assessing awareness and perception, a statistically insignificant difference in responses was observed between the two groups. Regarding questions related to attitude, although the majority of HCWs in both groups were comfortable talking about eye donation, they did feel that counseling relatives of a terminally ill patient about eye donation was insensitive. Less than half of HCWs showed a willingness to donate eyes, and about half of the participants wanted to acquire more knowledge about eye donation. CONCLUSION: Awareness regarding eye donation among HCWs was mostly found to be at dismal levels, irrespective of whether they worked in an institute with or without eye bank and corneal transplant services. This warrants an accelerated effort at sensitizing HCWs as a strengthening measure for HCRP.

Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies.

Nitrotyrosine, or 3-nitrotyrosine, is an oxidative post-translational modification induced by reactive nitrogen species. Although nitrotyrosine is considered a marker of oxidative stress and has been associated with inflammation, neurodegeneration, cardiovascular disease, and cancer, identification of nitrotyrosine-modified proteins remains challenging owing to its low stoichiometric levels in biological samples. To facilitate a comprehensive analysis of proteins and peptides containing nitrotyrosine, we optimized an immunoprecipitation-based enrichment workflow using a cell line model. The identification of proteins and peptides containing nitrotyrosine residues was carried out after peroxynitrite treatment of cell lysates, which generated modified nitrotyrosine residues on susceptible sites on proteins. We evaluated the efficacy of enriching nitrotyrosine-modified proteins and peptides by employing four different commercially available monoclonal antibodies directed against nitrotyrosine. LC-MS/MS analysis resulted in the identification of 1377 and 1624 nitrotyrosine-containing peptides from protein- and peptide-based enrichment experiments, respectively. Although the yield of nitrotyrosine-containing peptides was higher in experiments where peptides rather than proteins were enriched, we found a substantial proportion (37-65%) of identified nitrotyrosine-containing peptides contained nitrotyrosine at the N-terminus. However, in protein-based immunoprecipitation <9% of nitrotyrosine-containing peptides had nitrotyrosine modification at the N-terminus of the peptide. Overall, our study resulted in the identification of 2603 nitrotyrosine-containing peptides of which >2000 have not previously been reported. We synthesized 101 novel nitrotyrosine-containing peptides identified in our analysis and analyzed them by LC-MS/MS to validate our findings. We have confirmed the validity of 70% of these peptides, as they demonstrated a similarity score exceeding 0.7 when compared to peptides identified through experimental methods. Finally, we also validated the presence of nitrotyrosine modification on PKM and EF2 proteins in peroxynitrite-treated samples by immunoblot analysis. The large catalog presented in this study along with the workflow should facilitate the investigation of nitrotyrosine as an oxidative modification in a variety of settings in greater detail.

Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology.

For precision in clinical oncology practice, detection of tumor-derived peptides and proteins in urine offers an attractive and noninvasive alternative for diagnostic or screening purposes. In this study, we report comparative quantitative proteomic profiling of urine samples from patients with gastric cancer and healthy controls using tandem mass tags-based multiplexed mass spectrometry approach. We identified 1504 proteins, of which 246 were differentially expressed in gastric cancer cases. Notably, ephrin A1 (EFNA1), pepsinogen A3 (PGA3), sortilin 1 (SORT1), and vitronectin (VTN) were among the upregulated proteins, which are known to play crucial roles in the progression of gastric cancer. We also found other overexpressed proteins, including shisa family member 5 (SHISA5), mucin like 1 (MUCL1), and leukocyte cell derived chemotaxin 2 (LECT2), which had not previously been linked to gastric cancer. Using a novel approach for targeted proteomics, SureQuant, we validated changes in abundance of a subset of proteins discovered in this study. We confirmed the overexpression of vitronectin and sortilin 1 in an independent set of urine samples. Altogether, this study provides molecular candidates for biomarker development in gastric cancer, and the findings also support the promise of urinary proteomics for noninvasive diagnostics and personalized/precision medicine in the oncology clinic.

Thermodynamics of modulation of interaction of α-helix inducer 2, 2, 2-trifluoroethanol with lysozyme in presence of cationic, anionic and non-ionic surfactants.

The interactions of anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB) and nonionic triton X-100 (TX-100) surfactants with lysozyme at pH = 2.4 have been studied individually as well as in combination with 2,2,2-trifluoroetanol (TFE). Urea has also been used in combination with surfactants. By using these combinations, efforts have been made to obtain partially folded conformations of the protein in the presence of surfactants and effect of α-helix inducer 2,2,2-trifluoroethanol on these intermediate states. Thermodynamic analysis of all these interactions has been done employing a combination of UV-visible, fluorescence and circular dichroism spectroscopies. The results have been correlated with each other and characterized qualitatively as well as quantitatively. At lower concentration of surfactant, the thermodynamic parameters indicated the destabilizing effect of SDS, stabilizing effect of CTAB and unappreciable destabilizing impact of TX-100 on lysozyme. The enhancement in destabilization effect or reduction in stabilization effect of surfactants on lysozyme in the presence of TFE and urea has also been indicated.Communicated by Ramaswamy H. Sarma.

Comparison of Keratometric Change Following Various Conjunctival Autografting Techniques in Pterygium Surgery.

Aim To compare the postoperative keratometric changes and duration of surgery for different techniques of conjunctival autografting in pterygium surgery. Methods Patients with primary pterygium attending the outpatient department and having appropriate indications for surgery were enrolled. Preoperative ophthalmic examination included visual acuity assessment, refraction, keratometry, slit lamp, and fundus evaluation. Pterygium excision surgery with conjunctival autografting was performed on all patients using one of the four different techniques, namely, sutures, fibrin glue, and the autologous blood and bridge techniques. Duration of surgery was recorded for all patients. Postoperatively, all patients were followed up on Day 1, Day 7, and Months 1, 3, and 6. Duration of surgery, keratometric changes, and recurrence rates were analyzed in all four groups. Results Sixty-eight eyes of 66 patients completed the study protocol. There was a significant reduction in astigmatism after the autologous blood graft technique (P value 0.0055) and the glue technique (P value < 0.0001). The success rate of the autologous and glue technique was 90%. The glue technique was found to be more time efficient (mean duration 20.40 minutes) than other techniques. Conclusion After pterygium excision, conjunctival auto grafting using either autologous blood or glue plays a significant role in reducing pterygium-induced astigmatism and recurrence rates with the added advantage of a shorter operative time.

Effect of atropine 0.01% on progression of myopia.

Purpose: Myopia is the most common type of refractive error and the leading cause of functional visual loss. Increased risk of myopic maculopathy, retinal detachment, glaucoma and cataract has been seen with a myopia of as low as -1D. This study was done to determine the effect of atropine 0.01% eye drops on the progression of myopia in children >5 years. Methods: This was a single-blind, prospective, randomized case-control study which included children of 5-15 years with myopia of >2D and were divided into treatment group (group 1) and placebo group (group 2). Children under treatment group were treated with application of 0.01% atropine at night. Children with history of any ocular surgery, chronic ophthalmic illness, squint and amblyopia were excluded from the study. The follow-up for myopia progression was done for two years. Results: This study showed a significant difference in increase of spherical equivalent and axial length among treatment and placebo groups after a duration of two years. Total duration of follow up was twenty-four months. Mean increase in axial length of group 1 and 2 was 0.115 mm and 0.32 mm, respectively. Mean increase in refraction of groups 1 and 2 was -0.30 D and -0.88 D, respectively, showing significant change in axial length and refraction (P < 0.0001). Conclusion: This study supports the use of atropine 0.01% eye drops in reducing the progression of myopia.

Analysis of COVID-19-associated rhino-orbital-cerebral mucormycosis patients in a tertiary care center in Northern India.

Purpose: An unprecedented surge has been noted in rhino-orbital-Cerebral mucormycosis (ROCM) in times of current COVID-19 pandemic. The present prospective study aims to evaluate clinico-epidemiological profile, risk factors, management, and outcome of the cases of ROCM that presented to our tertiary care center during the study period from April to June 2021. Methods: All patients were subjected to complete history taking, ophthalmological examination, and imaging studies. The patients were staged and were treated with intravenous liposomal amphotericin B (AMB) and sino-nasal debridement of local necrotic tissue. Transcutaneous retrobulbar AMB (TRAMB), orbital decompression, and exenteration were instituted as indicated. All patients were followed up for a minimum of 6 months before arriving at the final outcome. Statistical analysis was performed. Results: A total of 49 patients presented during the study period, with a mean age of 42.2 years. The major risk factors included uncontrolled diabetes (89.8%), COVID-19 positivity (51.02%), and concurrent steroid use (38.77%). The most common presenting symptom was facial pain/swelling (43.65%), while the most common presenting sign was deterioration in vision (75.51%). Intravenous liposomal AMB was given to all patients along with sino-nasal debridement (85.71%), TRAMB (57.14%), orbital decompression (14.28%), and exenteration (12.24%). Overall, mortality at 6 months was 22.45% (11 patients). Age more than 60 years, intracranial extension, and HbA1c of more than 8.0% were observed to be statistically significant indicators of mortality. Conclusion: Early suspicion and timely diagnosis of mucormycosis at rhino-orbital stage is warranted in order to salvage life as well as visual function. TRAMB may prove as potentially favorable treatment modality in cases with limited orbital involvement.

Role of Oncofetal Protein CR-1 as a Potential Tumor Marker for Oral Squamous Cell Carcinoma.

Cripto-1 (CR-1) is an oncofetal protein with its role as a key factor in early process of carcinoma has been evaluated in cases of various cancers. However, very few studies have reported its role in oral cancer, which is the sixth most common cancer around the world, particularly with high prevalence in developing countries. Oral squamous cell carcinoma (OSCC) is the most predominant (90%) of all the histological types of oral cancer. Late detection, associated with increased morbidity and mortality, is mainly attributed to non-availability of a suitable biomarker for the disease. In the present pilot study, we have evaluated the role of soluble CR-1, in serum as a potential tumor marker for OSCC. CR-1 was estimated using sandwich ELISA in serum samples of 50 biopsy proven OSCC patients (pre and post treatment) along with age and gender matched healthy controls. Immunohistochemistry was also done in corresponding tumor tissue sections to check the expression of CR-1. Pre-treatment CR-1 was found to be 2.25-fold higher in serum of OSCC patients as compared to control (p < 0.0001***), which was reduced to 1.6 folds post treatment (p = 0.0006***). CR-1 levels were comparatively higher in early stage of disease. Upon IHC 80% of the cases were found to be positive for CR-1. This study provides evidence that serum levels of CR-1 are elevated in patients of Oral Squamous Cell Carcinoma, which decrease post treatment. Also, the association of expression of protein with tumor progression predicts CR-1 as a molecule that can be further evaluated as a potential tumor maker in OSCC.

Identification of potential salivary biomarker panels for oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is one of the most prevalent cancers worldwide with the maximum number of incidences and deaths reported from India. One of the major causes of poor survival rate associated with OSCC has been attributed to late presentation due to non-availability of a biomarker. Identification of early diagnostic biomarker will help in reducing the disease morbidity and mortality. We validated 12 salivary proteins using targeted proteomics, identified initially by relative quantification of salivary proteins on LC-MS, in OSCC patients and controls. Salivary AHSG (p = 0.0041**) and KRT6C (p = 0.002**) were upregulated in OSCC cases and AZGP1 (p ≤ 0.0001***), KLK1 (p = 0.006**) and BPIFB2 (p = 0.0061**) were downregulated. Regression modelling resulted in a significant risk prediction model (p < 0.0001***) consisting of AZGP1, AHSG and KRT6C for which ROC curve had AUC, sensitivity and specificity of 82.4%, 78% and 73.5% respectively for all OSCC cases and 87.9%, 87.5% and 73.5% respectively for late stage (T3/T4) OSCC. AZGP1, AHSG, KRT6C and BPIFB2 together resulted in ROC curve (p < 0.0001***) with AUC, sensitivity and specificity of 94%, 100% and 77.6% respectively for N0 cases while KRT6C and AZGP1 for N+ cases with ROC curve (p < 0.0001***) having AUC sensitivity and specificity of 76.8%, 73% and 69.4%. Our data aids in the identification of biomarker panels for the diagnosis of OSCC cases with a differential diagnosis between early and late-stage cases.