01848nas a2200253 4500008004100000022001400041245005200055210005200107260007700159300001000236490000600246520106800252653001701320653002401337653001901361653002101380653000901401100001701410700001601427700002001443700002001463700002501483856008601508 2014 eng d a1862-834600aImmune response to chemically modified proteome0 aImmune response to chemically modified proteome aBOSCHSTRASSE 12, D-69469 WEINHEIM, GERMANYbWILEY-V C H VERLAG GMBHcFEB a19-340 v83 a

Both enzymatic and nonenzymatic PTMs of proteins involve chemical modifications. Some of these modifications are prerequisite for the normal functioning of cell, while other chemical modifications render the proteins as neo-self antigens, which are recognized as non-self leading to aberrant cellular and humoral immune responses. However, these modifications could be a secondary effect of autoimmune diseases, as in the case of type I diabetes, hyperglycemia leads to protein glycation. The enigma of chemical modifications and immune response is akin to the chick-and-egg paradox. Nevertheless, chemical modifications regulate immune response. In some of the well-known autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, and multiple sclerosis, chemically modified proteins act as autoantigens forming immune complexes. In some instances, chemical modifications are also involved in regulating immune response during pathogen infection. Further, the usefulness of proteomic analysis of immune complexes is briefly discussed.

10aAutoantibody10aAutoimmune diseases10aImmune complex10aImmunoproteomics10aPTMs1 aBhat, Shweta1 aMary, Sheon1 aBanarjee, Reema1 aGiri, Ashok, P.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/immune-response-chemically-modified-proteome-000717nas a2200193 4500008004100000022001400041245012400055210006900179260000800248300001200256490000800268100002000276700001900296700002000315700002000335700001700355700002500372856012600397 2016 eng d a1355-603700aUnderstanding endothelial dysfunction in diabetic cardiovascular complications using mass spectrometry-based proteomics0 aUnderstanding endothelial dysfunction in diabetic cardiovascular cOCT aA16-A170 v1021 aBanarjee, Reema1 aSharma, Akshay1 aBai, Shakuntala1 aDeshmukh, Arati1 aKazi, Rubina1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/understanding-endothelial-dysfunction-diabetic-cardiovascular-complications-using-mass02820nas a2200241 4500008004100000245011400041210006900155260000800224300001400232490000700246520197800253100002402231700002002255700001502275700002102290700002002311700002402331700002402355700002202379700002302401700002502424856012902449 2017 eng d00aMethylglyoxal attenuates insulin signaling and downregulates the enzymes involved in cholesterol biosynthesis0 aMethylglyoxal attenuates insulin signaling and downregulates the cNOV a2338-23490 v133 a

Methylglyoxal (MG) is a highly reactive dicarbonyl known to be elevated under the hyperglycemic conditions of diabetes and is implicated in the development of diabetic complications. Therefore, the current study investigates the role of MG in exacerbating insulin resistance at the insulin signaling level, as well as its effect on the global proteomic level. By using insulin sensitive rat muscle cells (L6) and Chinese hamster ovary (CHO) cells stably expressing the insulin receptor (IR) and a glucose transporter fused with green fluorescent protein (GLUT4-GFP), we have observed that MG impairs insulin signaling, inhibits GLUT4 translocation and reduces glucose uptake. SWATH MS analysis, a label-free quantitative mass spectrometric approach, showed altered expression of 99 proteins out of 2404 identified in response to MG treatment. These proteins are mainly involved in stress response, protein folding and proteolysis. Some of the deregulated proteins such as thioredoxin 2, glutathione S transferase, T complex protein 1 subunit beta (tcbp1), heat shock protein 90 and E3 ubiquitin ligase were previously reported to be associated with either diabetes or insulin resistance. Interestingly, aminoguanidine (AMG), a potent dicarbonyl scavenger, restored the deleterious effects of MG. For the first time, we report that MG induces downregulation of enzymes involved in cholesterol biosynthesis such as acetyl-CoA acetyltransferase, hydroxymethylglutaryl-CoA synthase, farnesyl pyrophosphate synthetase, squalene monooxygenase, and lanosterol synthase. GC MS analysis for sterol metabolites corroborated the proteomic results; MG significantly reduced cholesterol production whereas AMG treatment restored cholesterol production to levels similar to the control. Thus, MG leads to primary defects in insulin signaling and cellular abnormalities at the proteomic and metabolic levels, both of which may contribute to the development of insulin resistance.

1 aDeshmukh, Arati, B.1 aBai, Shakuntala1 aAarthy, T.1 aKazi, Rubina, S.1 aBanarjee, Reema1 aRathore, Rajeshwari1 aVijayakumar, M., V.1 aThulasiram, H. V.1 aBhat, Manoj, Kumar1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/methylglyoxal-attenuates-insulin-signaling-and-downregulates-enzymes-involved-cholesterol01873nas a2200193 4500008004100000245017900041210006900220260000800289300001300297490000600310520111700316100002101433700002001454700002001474700001801494700002501512700002501537856011701562 2018 eng d00aAdvanced glycation end products modulate amyloidogenic APP processing and tau phosphorylation: a mechanistic link between glycation and the development of alzheimer's disease0 aAdvanced glycation end products modulate amyloidogenic APP proce cMAY a988-10000 v93 aAdvanced glycation end products (AGEs) are implicated in the pathology of Alzheimer's disease (AD), as they induce neurodegeneration following interaction with the receptor for AGE (RAGE). This study aimed to establish a mechanistic link between AGE-RAGE signaling and AD pathology. AGE-induced changes in the neuro2a proteome were monitored by SWATH-MS. Western blotting and cell-based reporter assays were used to investigate AGE-RAGE regulated APP processing and tau phosphorylation in primary cortical neurons. Selected protein expression was validated in brain samples affected by AD. The AGE-RAGE axis altered proteome included increased expression of cathepsin B and asparagine endopeptidase (AEP), which mediated an increase in A beta(1-)(42) formation and tau phosphorylation, respectively. Elevated cathepsin B, AEP, RAGE, and pTau levels were found in human AD brain, coincident with enhanced AGEs. This study demonstrates that the AGE-RAGE axis regulates A beta(1-)(42) formation and tau phosphorylation via increased cathepsin B and AEP, providing a new molecular link between AGEs and AD pathology.1 aBatkulwar, Kedar1 aGodbole, Rashmi1 aBanarjee, Reema1 aKassaar, Omar1 aWilliams, Robert, J.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/advanced-glycation-end-products-modulate-amyloidogenic-app-processing-and-tau02974nas a2200181 4500008004100000245012600041210006900167260000800236300001000244490000800254520230300262100002002565700001902585700002002604700002002624700002502644856012302669 2018 eng d00aProteomic study of endothelial dysfunction induced by Ages and its possible role in diabetic cardiovascular complications0 aProteomic study of endothelial dysfunction induced by Ages and i cSEP a69-790 v1873 a

Endothelial dysfunction is one of the primary steps in the development of diabetes associated cardiovascular diseases. Hyperglycemic condition in diabetes promotes accumulation of advanced glycation end products (AGEs) in the plasma, that interact with the receptor for AGEs (RAGE) present on the endothelial cells and negatively affect their function. Using Human umbilical vascular endothelial cells (HUVECs) in culture, the effect of glycated human serum albumin on global proteomic changes was studied by SWATH-MS, a label free quantitative proteomic approach. Out of the 1860 proteins identified, 161 showed higher abundance while 123 showed lesser abundance in cells treated with glycated HSA. Bioinformatic analysis revealed that the differentially regulated proteins were involved in various processes such as apoptosis, oxidative stress etc. that are associated with endothelial dysfunction. Furthermore, the iRegulon analysis and immunofuorescence studies indicated that several of the differentially regulated proteins were transcriptionally regulated by NF-kappa B, that is downstream to AGE-RAGE axis. Some of the important differentially regulated proteins include ICAM1, vWF, PAI-1 that affect important endothelial functions like cell adhesion and blood coagulation. qPCR analysis showed an increase in expression of the AGE receptor RAGE along with other genes involved in endothelial function. AGE treatment to HUVEC cells led to increased oxidative stress and apoptosis. This is the first proteomics study that provides insight into proteomic changes downstream to AGE-RAGE axis leading to endothelial dysfunction and predisposing to cardiovascular complications. Significance: Cardiovascular disease (CVD) is a major pathological outcome in diabetic patients and it is important to address ways that target its development before the onset. Elevated plasma AGEs in diabetes can affect endothelial function and can continue to show their effects even after blood glucose levels are back to normal. Since endothelial dysfunction acts as one of the initiating factors for the development of CVD, understanding how AGEs affect the endothelial cell proteome to cause dysfunction will provide insight into the mechanisms involved and aid designing new therapeutic approaches.

1 aBanarjee, Reema1 aSharma, Akshay1 aBai, Shakuntala1 aDeshmukh, Arati1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/proteomic-study-endothelial-dysfunction-induced-ages-and-its-possible-role-diabetic02264nas a2200217 4500008004100000022001400041245011500055210006900170260000900239300001600248490000600264520148300270100002001753700003201773700002001805700002201825700001801847700002901865700002501894856012701919 2020 eng d a2470-134300aCD44, a predominant protein in methylglyoxal-induced secretome of muscle cells, is elevated in diabetic plasma0 aCD44 a predominant protein in methylglyoxalinduced secretome of  cOCT  a25016-250280 v53 a

Methylglyoxal (MG), a glycolytic intermediate and reactive dicarbonyl, is responsible for exacerbation of insulin resistance and diabetic complication. In this study, NIG-induced secretome of rat muscle cells was identified and relatively quantified by SWATH-MS. A total of 643 proteins were identified in MG induced' secretome, of which 82 proteins were upregulated and 99 proteins were downregulated by more than 1.3-fold in SWATH analysis. Further, secretory proteins from the dassical secretory pathway and nonclassical secretory pathway were identified using SignalP and SecretomeP, respectively. A total of 180 proteins were identified with SignalP, and 113 proteins were identified with SecretomeP. The differentially expressed proteins were functionallyannotated by KEGG pathway analysis using Cytoscape soft ware with plugin clusterMaker. The differentially expressed proteins were'sfound to he involved m various pathways like extracellular matrix (ECM) receptor interaction, leukocyte transendothelial migration, fluid shear tress and atherosclerosis, complement and coagulation cascades, and lysosomal pathway. Since the MG levels are high in diabetic conditions, the presence of MG-induced isecreted proteins was inspected `by profiling human plasma of healthy and diabetic subjects (n = 10 each). CD44, a predominant MG -induced secreted protein, was found to be elevated in the diabetic plasma and to have a role in the development of insulin resistance.

1 aBai, Shakuntala1 aChaurasiya, Arvindkumar, H.1 aBanarjee, Reema1 aWalke, Prachi, B.1 aRashid, Faraz1 aUnnikrishnan, Ambika, G.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/cd44-predominant-protein-methylglyoxal-induced-secretome-muscle-cells-elevated-diabetic02789nas a2200289 4500008004100000022001400041245015800055210006900213260000800282300001400290490000700304520175600311653002102067653001702088653003302105653002102138653002002159100002502179700002102204700003202225700002202257700002002279700002502299700002202324700002402346856012902370 2020 eng d a0721-759500aEnzymatic and non-enzymatic detoxification of reactive carbonyl compounds improves the oxidative stress tolerance in cucumber, tobacco and rice seedlings0 aEnzymatic and nonenzymatic detoxification of reactive carbonyl c cSEP a1359-13720 v393 a

Detoxification of reactive carbonyl compounds (RCC) is crucial to sustain cellular activity to improve plant growth and development. Seedling growth is highly affected by accumulation of RCC under stress. We report non-enzymatic, enzymatic mechanisms of detoxification of RCC in the cucumber, tobacco and rice seedling systems exposed to glucose, NaCl, methyl viologen (MV) induced oxidative stress. The cucumber seedlings exposed to carbonyl stress had higher levels of malondialdehyde (MDA), protein carbonyls (PCs) and advanced glycation end-product N-carboxymethyl-lysine (AGE-CML) that negatively affected the seedling growth. The overexpression of enzyme encoding aldo-keto reductase-1 (AKR1) in tobacco and rice showed detoxification of RCC, MDA and methylglyoxal (MG) with improved seedling growth under glucose, NaCl and MV-induced oxidative stress. Further, small molecules like acetylsalicylic acid (ASA), aminoguanidine (AG), carnosine (Car), curcumin (Cur) and pyridoxamine (PM) showed detoxification of RCC non-enzymatically and rescued the cucumber seedling growth from glucose, NaCl and MV-stress. In autotrophically grown rice seedlings these molecules substantially improved seedling growth under MV-induced oxidative stress. Seedlings treated with the small molecules sustained higher guaiacol peroxidase (GPX) enzyme activity signifying the role of small molecules in reducing carbonyl stress-induced protein inactivation and AGE-CML protein modifications. The results showed that besides enzymatic detoxification of RCC, the small molecules also could reduce cytotoxic effect of RCC under stress. The study demonstrates that small molecules are attractive compounds to improve the seedling growth under stress conditions.

10aOxidative stress10aplant growth10aReactive carbonyl scavengers10aSeed germination10asmall molecules1 aNareshkumar, Ambekar1 aSubbarao, Sindhu1 aVennapusa, Amarnatha, Reddy1 aAshwin, Vargheese1 aBanarjee, Reema1 aKulkarni, Mahesh, J.1 aRamu, Vemanna, S.1 aUdayakumar, Makarla uhttps://library.ncl.res.in/content/enzymatic-and-non-enzymatic-detoxification-reactive-carbonyl-compounds-improves-oxidative01874nas a2200337 4500008004100000022001400041245012900055210006900184260001100253300001100264490000700275520074300282653002601025653002001051653003101071653004201102653001501144100001701159700001901176700001901195700002101214700002001235700001701255700002701272700002001299700002401319700001801343700001701361700002701378856013101405 2021 eng d a2234-943X00aPlasma-derived extracellular vesicles reveal galectin-3 binding protein as potential biomarker for early detection of glioma0 aPlasmaderived extracellular vesicles reveal galectin3 binding pr cNOV 26 a7787540 v113 a{Gliomas are the most common type of the malignant brain tumor, which arise from glial cells. They make up about 40% of all primary brain tumors and around 70% of all primary malignant brain tumors. They can occur anywhere in the central nervous system (CNS) and have a poor prognosis. The average survival of glioma patients is approximately 6-15 months with poor aspects of life. In this edge, identification of proteins secreted by cancer cells is of special interest because it may provide a better understanding of tumor progression and provide early diagnosis of the diseases. Extracellular vesicles (EVs) were isolated from pooled plasma of healthy controls (n=03) and patients with different grades of glioma (Grade I or II or III10ablood-based biomarker10aearly detection10agalectin-3 binding protein10aplasma-derived extracellular vesicles10aproteomics1 aRana, Rashmi1 aChauhan, Kirti1 aGautam, Poonam1 aKulkarni, Mahesh1 aBanarjee, Reema1 aChugh, Parul1 aChhabra, Satnam, Singh1 aAcharya, Rajesh1 aKalra, Samir, Kumar1 aGupta, Anshul1 aJain, Sunila1 aGanguly, Nirmal, Kumar uhttps://library.ncl.res.in/content/plasma-derived-extracellular-vesicles-reveal-galectin-3-binding-protein-potential-biomarker02486nas a2200277 4500008004100000022001400041245017700055210006900232260000900301300001400310490000700324520149400331653001201825653001301837653001801850653002201868653003301890653002501923100001901948700002001967700002301987700001502010700002602025700002502051856013202076 2024 eng d a0739-110200aDe novo structure prediction of meteorin and meteorin-like protein for identification of domains, functional receptor binding regions, and their high-risk missense variants0 aDe novo structure prediction of meteorin and meteorinlike protei cJUN  a4522-45360 v423 a

Meteorin (Metrn) and Meteorin-like (Metrnl) are homologous secreted proteins involved in neural development and metabolic regulation. In this study, we have performed de novo structure prediction and analysis of both Metrn and Metrnl using Alphafold2 (AF2) and RoseTTAfold (RF). Based on the domain and structural homology analysis of the predicted structures, we have identified that these proteins are composed of two functional domains, a CUB domain and an NTR domain, connected by a hinge/loop region. We have identified the receptor binding regions of Metrn and Metrnl using the machine-learning tools ScanNet and Masif. These were further validated by docking Metrnl with its reported KIT receptor, thus establishing the role of each domain in the receptor interaction. Also, we have studied the effect of non-synonymous SNPs on the structure and function of these proteins using an array of bioinformatics tools and selected 16 missense variants in Metrn and 10 in Metrnl that can affect the protein stability. This is the first study to comprehensively characterize the functional domains of Metrn and Metrnl at their structural level and identify the functional domains, and protein binding regions. This study also highlights the interaction mechanism of the KIT receptor and Metrnl. The predicted deleterious SNPs will allow further understanding of the role of these variants in modulating the plasma levels of these proteins in disease conditions such as diabetes.

10adomains10aMeteorin10ameteorin-like10amissense variants10aprotein-protein interactions10astructure prediction1 aShankar, Shiva1 aBanarjee, Reema1 aJathar, Swaraj, M.1 aRajesh, S.1 aRamasamy, Sureshkumar1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/de-novo-structure-prediction-meteorin-and-meteorin-protein-identification-domains-functional02515nas a2200277 4500008004100000022001400041245011700055210006900172260000800241300001100249490000800260520162800268653001301896653002201909653001201931653001201943653002201955100001501977700001901992700002002011700001902031700002002050700001902070700002502089856012302114 2025 eng d a1046-592800aSimple freeze-thaw based method for efficient purification of recombinant human proinsulin from inclusion bodies0 aSimple freezethaw based method for efficient purification of rec cMAR a1066450 v2273 a

Insulin is a pivotal peptide hormone essential for regulating glucose homeostasis. It has been known for over 100 years, but its production and purification methods are still under improvement. Escherichia coli based bacterial expression system is primarily used for insulin production. The human insulin protein expressed in bacteria usually forms inclusion bodies, complicating the purification process. Traditionally, insulin purification is a timeconsuming process involving urea-based denaturation methods, and various refolding techniques, followed by extensive chromatographic methods. Here, we report an easy and efficient purification of human proinsulin involving freeze-thaw based solubilization method. The extracted proinsulin inclusion bodies are treated with different concentrations of urea, followed by a freeze-thaw based solubilization. The freezing was carried out at various temperatures, mainly -80 degrees C, -20 degrees C, and -196 degrees C to determine the optimum condition for solubilization. Highest solubilization of proinsulin from the inclusion body was achieved with 0.5M urea and -20 degrees C. Further Nickel NTA-based purification was performed, and the purified protein was characterized for disulfide mapping by high-resolution mass spectrometer (HRMS). We also performed glucose uptake assays to validate the functional properties of purified proinsulin. This freeze-thaw based mild solubilization approach is a fast and effective method for getting bioactive proinsulin, which will help further design better purification and processing strategies for insulin production.

10aDiabetes10aDisulfide mapping10aglucose10ainsulin10aMass spectrometry1 aRajesh, S.1 aJathar, Swaraj1 aBanarjee, Reema1 aSharma, Monika1 aPalkar, Shivani1 aShankar, Shiva1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/simple-freeze-thaw-based-method-efficient-purification-recombinant-human-proinsulin