Article
Rheumatology
Jean Escal, Tiphany Neel, Sophie Hodin, Karima Boussoualim, Adamah Amouzougan, Astrid Coassy, Herve Locrelle, Thierry Thomas, Xavier Delavenne, Hubert Marotte
Summary: This study aimed to identify a biomarker of MTX resistance (MTXR) by comparing differentially expressed blood proteins between patients with active RA and patients in remission after MTX treatment. Untargeted proteomics analysis revealed eight plasma proteins that were differentially expressed between the two groups, with triosephosphate isomerase (TPI-1) and glucose-6-phosphate isomerase (GPI) found down-regulated in the active group. This result was confirmed for TPI-1 in the targeted proteomics analysis.
Article
Environmental Sciences
Stephanie Chaousis, Frederic D. L. Leusch, Colin J. Limpus, Amanda Nouwens, Liesbeth J. Weijs, Antonia Weltmeyer, Adrian Covaci, Jason P. van de Merwe
Summary: All seven species of sea turtle are facing increasing pressures from human activities that are impacting their health. Changes in blood proteins can indicate adverse health outcomes. This study examines the protein abundance in sea turtle plasma, compares protein expression between different populations, and investigates markers of contaminant exposure.
ENVIRONMENTAL RESEARCH
(2023)
Article
Chemistry, Analytical
Chadanat Noonin, Chompunoot Kapincharanon, Kanyarat Sueksakit, Rattiyaporn Kanlaya, Visith Thongboonkerd
Summary: This study utilized tandem fast protein liquid chromatography to isolate THP from urine, comparing its efficiency and purity with two conventional methods. The results showed that the tandem FPLC system is most effective for selectively purifying monomeric and aggregated forms of THP, while diatomaceous earth adsorption is preferred for general purification.
ANALYTICAL METHODS
(2021)
Article
Biochemical Research Methods
Marlon D. M. Santos, Amanda C. Camillo-Andrade, Diogo B. Lima, Tatiana A. C. B. Souza, Juliana de S. da G. Fischer, Richard H. Valente, Fabio C. Gozzo, Valmir C. Barbosa, Carlos Batthyany, Julia Chamot-Rooke, Rosario Duran, Paulo C. Carvalho
Summary: DiagnoMass is a software tool that groups similar spectra into spectral clusters and then identifies those clusters that are discriminative for biological conditions. It has been successfully used to identify high-quality discriminative spectral clusters that were previously unidentified by widely adopted proteomic tools in Escherichia coli, Salmonella, and Shigella data. DiagnoMass can also classify proteomic profiles and is expected to be a vital tool for pinpointing biomarkers.
JOURNAL OF PROTEOMICS
(2023)
Article
Immunology
Peng Liu, Jianqiang Wu, Dandan Sun, Haolong Li, Zhihong Qi, Xiaoyue Tang, Wei Su, Yongzhe Li, Xuzhen Qin
Summary: This study aimed to identify and validate candidate protein biomarkers for cryoglobulinemia (CGE) using a TMT-PRM-ELISA workflow. APOA1 and PCSK9 were confirmed to be increased in CGE patients, indicating the involvement of proteins in cholesterol metabolism in the development of CGE. These findings provide valuable insights for pathogenesis research and biomarker discovery in CGE.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Natalia A. Shnayder, Victoria B. Sharavii, Marina M. Petrova, Polina Moskaleva, Elena A. Pozhilenkova, Darya S. Kaskaeva, Olga Tutynina, Tatiana E. Popova, Natalia P. Garganeeva, Regina F. Nasyrova
Summary: The research analyzed potential proteomic biomarkers in the serum and urine of chronic headache patients, identified several proteins related to MOH, and discussed their potential roles in identifying patients with MOH development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Congqi Hu, Zhao Dai, Jia Xu, Lianyu Zhao, Yanping Xu, Meilin Li, Jiahui Yu, Lu Zhang, Hui Deng, Lijuan Liu, Mingying Zhang, Jiarong Huang, Linping Wu, Guangxing Chen
Summary: This study identified the serum marker ORM1 as a significant differential expression between normal and RA patient samples, positively correlated with disease activity, offering a new perspective for future research on RA.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Endocrinology & Metabolism
Mengyan Zhang, Xiuling Shi, Chantong Wu, Jun Yang, Jiancheng Li, Mingqiu Chen
Summary: This study compared the differences in the expression levels of differentially-expressed proteins (DEPs) in serum specimens from non-small cell lung cancer (NSCLC) patients presenting with radiation pneumonia (RP) and non-pneumonia at 0, 3, and 6 weeks after radiotherapy using a quantitative proteomics approach. The results identified FETUB and PZP as optimal candidate proteins for predicting RP, providing evidence for potential predictive biomarkers of RP.
JOURNAL OF BIOLOGICAL REGULATORS AND HOMEOSTATIC AGENTS
(2023)
Article
Medicine, Research & Experimental
Hanwool Jeon, Joonho Byun, Hayeong Kang, Kyunggon Kim, Eunyeup Lee, Jeong Hoon Kim, Chang Ki Hong, Sang Woo Song, Young-Hoon Kim, Sangjoon Chong, Jae Hyun Kim, Soo Jeong Nam, Ji Eun Park, Seungjoo Lee
Summary: Background Recurrence is common in glioblastoma multiforme (GBM) due to residual infiltrative cells in the tumor margin. Standard therapy for GBM is ineffective and anti-angiogenic treatment is a common approach for recurrent GBM. However, resistance to anti-angiogenic agents remains a challenge. Therefore, this study aimed to identify novel biomarkers that can predict therapeutic response to anti-angiogenic agents in patients with recurrent GBM.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Medicine, Research & Experimental
Qi Chen, Xi Liang, Tianzhou Wu, Jing Jiang, Yongpo Jiang, Sheng Zhang, Yanyun Ruan, Huaping Zhang, Chao Zhang, Peng Chen, Yuhang Lv, Jiaojiao Xin, Dongyan Shi, Xin Chen, Jun Li, Yinghe Xu
Summary: This study used untargeted metabolomics and proteomics analysis to investigate the serum of patients with sepsis, revealing the pathological mechanisms of sepsis. The results showed widespread dysregulation of amino acid metabolism in sepsis patients, and identified predictive metabolites associated with sepsis. The study also found that the pentose phosphate pathway was related to sepsis-associated encephalopathy, and phenylalanine metabolism was associated with sepsis-associated acute kidney injury.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Environmental Sciences
Xinying Zhao, Hailin Xu, Yan Li, Ru Ma, Yi Qi, Min Zhang, Caixia Guo, Zhiwei Sun, Yanbo Li
Summary: This study provides proteomic insights into the potential molecular mechanisms underlying SiNPs-induced cardiotoxicity, with dysregulated mitochondrial complex subunits identified as core regulatory molecules. The findings contribute to the scientific understanding of the molecular actions and mechanisms of toxicity induced by SiNPs.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Sumaiya Nazli, Kip D. Zimmerman, Angelica M. Riojas, Laura A. Cox, Michael Olivier
Summary: The proteomic analysis of plasma has great potential for precision medicine and biomarker identification. However, detecting and quantifying low abundance proteins in plasma is challenging. This study developed a mass spectrometry approach using tandem mass tags (TMT) and a tissue reference sample, which successfully identified and quantified numerous proteins in nonhuman primate plasma samples. The methodology promises to increase the number of putative disease biomarkers by efficiently quantifying plasma proteins released from specific tissues.
Article
Immunology
Yiran Li, Yubin Long, Xiaojun Chen, Tao Wang, Jialiang Guo, Lin Jin, Ling Wang, Zhiyong Hou
Summary: This study investigated the patterns and dynamic changes of inflammatory cytokines in fracture blister fluid (FBF) and plasma. The results showed that there were different cytokine patterns in FBF and plasma, but 11 cytokines were significantly correlated in both sample types. There were also differences in cytokine patterns in plasma among FB patients, fracture without blister patients, and healthy subjects. Additionally, 15 cytokines were significantly different between FB patients and fracture without blister patients, indicating their potential as risk factors for the occurrence of blisters. The cytokine patterns in FBF and plasma showed a dynamic change from the inflammatory stage to the proliferative and repair stage, suggesting that FBs may have new clinical importance.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Yiwu Yan, Su Yeon Yeon, Chen Qian, Sungyong You, Wei Yang
Summary: Prostate cancer is a leading cause of morbidity and mortality among men worldwide, and advancements in multiple protein biomarkers offer hope for its diagnosis and prognosis. The identification of multi-protein biomarkers with high sensitivity and specificity, as well as their integration with clinicopathologic parameters, imaging, and other molecular biomarkers, can help achieve optimal personalized management for PC patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Stanislav Naryzhny, Natalia Ronzhina, Elena Zorina, Fedor Kabachenko, Nikolay Klopov, Victor Zgoda
Summary: The use of tumor markers is important for early detection of cancer recurrence and prognosis. Finding ideal tumor markers that are sensitive, specific, and reliable is a crucial issue. Human plasma is a commonly used sample in clinics and provides noninvasive, rapid analysis for various diseases including cancer. Proteomics plays a major role in the search for ideal tumor markers. Classic plasma proteins, which are abundant, can be used to generate tumor biomarker profiles. These profiles should include information about protein levels and proteoform distribution. Future research involves generating profiles of these proteins in different cancers and developing test systems based on this information.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pharmacology & Pharmacy
Sachin Kote, Jakub Faktor, Irena Dapic, Marcos Yebenes Mayordomo, Mikolaj Kocikowski, Alexander Kagansky, David Goodlett, Borivoj Vojtesek, Ted Hupp, David Wilcockson, Ross Piper
Article
Cell Biology
Maria Gomez-Herranz, Marta Nekulova, Jakub Faktor, Lenka Hernychova, Sachin Kote, Elizabeth H. Sinclair, Rudolf Nenutil, Borivoj Vojtesek, Kathryn L. Ball, Ted R. Hupp
CELLULAR SIGNALLING
(2019)
Review
Oncology
Sachin Kote, Artur Pirog, Georges Bedran, Javier Alfaro, Irena Dapic
Article
Biochemistry & Molecular Biology
Ruidong Li, Pavlina Zatloukalova, Petr Muller, Maria Gil-Mir, Sachin Kote, Simon Wilkinson, Alain J. Kemp, Lenka Hernychova, Yaxin Wang, Kathryn L. Ball, Kaixiong Tao, Ted Hupp, Borivoj Vojtesek
CELLULAR & MOLECULAR BIOLOGY LETTERS
(2020)
Article
Biochemistry & Molecular Biology
Jakub Faktor, Giuseppa Grasso, Filip Zavadil Kokas, Malgorzata Kurkowiak, Marcos Yebenes Mayordomo, Sachin Kote, Ashita Singh, Li Ruidong, J. Robert O'Neill, Petr Muller, David Goodlett, Borek Vojtesek, Ted Hupp
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2020)
Article
Chemistry, Multidisciplinary
Rushikesh P. Dhavale, R. P. Dhavale, S. C. Sahoo, P. Kollu, S. U. Jadhav, P. S. Patil, T. D. Dongale, A. D. Chougale, P. B. Patil
Summary: The study successfully utilized chitosan-coated magnetic nanoparticles as a carrier to load the poorly water-soluble anticancer drug TEL, achieving effective inhibition of human prostate cancer cells and demonstrating pH-responsive controlled release characteristics. The designed nanoformulation showed significant antitumor activity.
JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS
(2021)
Article
Electrochemistry
S. M. Patil, S. R. Shingte, V. C. Karade, J. H. Kim, R. M. Kulkarni, A. D. Chougale, P. B. Patil
Summary: This study aimed to improve the electrochemical performance of RGO by decorating it with MNPs and evaluated their performance in various aqueous electrolyte solutions. The results showed that MRGO exhibited higher redox peak current and lower peak potential separation in FC-PBS-KCl electrolyte solution. In addition, MRGO demonstrated superior performance in terms of specific capacitance and cyclic stability in KOH compared to Na2SO4 electrolyte solution. The enhanced electrochemical performance of MRGO was attributed to the synergistic effect of RGO conductivity and MNPs redox activity.
JOURNAL OF SOLID STATE ELECTROCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
V. C. Karade, A. Sharma, R. P. Dhavale, S. R. Shingte, P. S. Patil, J. H. Kim, D. R. T. Zahn, A. D. Chougale, G. Salvan, P. B. Patil
Summary: The study introduces a nanoformulation utilizing magnetized self-assembled magnetic nanospheres (MNS) grafted with APTES for controlled release of an anticancer drug in a cancerous environment. The nanoformulation showed promising cytotoxicity against lung cancer cells and potential for cancer therapy and other nanobiological applications.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Monikaben Padariya, Alicja Sznarkowska, Sachin Kote, Maria Gomez-Herranz, Sara Mikac, Magdalena Pilch, Javier Alfaro, Robin Fahraeus, Ted Hupp, Umesh Kalathiya
Summary: IRDS genes, a subgroup of ISGs, are upregulated in cancer types, promoting resistance to chemotherapy and radiotherapy. Strategies to suppress these genes and induce sensitivity were discussed, along with their associated pathways and regulators. Targeting IRDS genes may offer an efficient strategy to resensitize tumor cells and enhance anti-cancer treatment outcomes.
Article
Chemistry, Analytical
Artur Pirog, Jakub Faktor, Zuzanna Urban-Wojciuk, Sachin Kote, Elzbieta Chrusciel, Lukasz Arcimowicz, Natalia Marek-Trzonkowska, Borek Vojtesek, Ted R. Hupp, Sofian Al Shboul, Paul M. Brennan, Ryszard Tomasz Smolenski, David R. Goodlett, Irena Dapic
Summary: This study compared several protocols for proteomic sample preparation and found that the ISD method is highly efficient in protein and peptide identification from the whole proteome, while the FASP method is effective in identifying membrane proteins. Pressure-assisted digestion methods are gaining popularity due to their shorter digestion time, although they generally provide lower numbers of protein/peptide identifications.
Article
Chemistry, Analytical
Kenneth Weke, Sachin Kote, Jakub Faktor, Sofian Al Shboul, Naomi Uwugiaren, Paul M. Brennan, David R. Goodlett, Ted R. Hupp, Irena Dapic
Summary: Developments in quantitative proteomics and DIA methodology have enabled protein quantification in biological samples, including formalin-fixed paraffin-embedded (FFPE) tissues. In this study, a simple and precise DIA-MS workflow was established to detect and quantify immune- and glioblastoma (GBM)-relevant proteins in FFPE patient materials. The results showed successful detection and quantification of more than 1700 proteins, including GBM-relevant proteins and immune-related proteins. This strategy has great potential for routine protein quantification in FFPE tissue samples.
ANALYTICA CHIMICA ACTA
(2022)
Article
Multidisciplinary Sciences
Sukrut Kamerkar, Jagjeet Singh, Subham Tripathy, Hemangi Bhonsle, Mukesh Kumar, Roop Mallik
Summary: This study demonstrates real-time lipid and protein exchange across contacts between ER-mimicking membrane and lipid droplets (LDs) purified from rat liver, revealing a significant increase in LD-ER contacts in response to changes in metabolic state and immune system activation in vitro.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Monikaben Padariya, Sachin Kote, Marcos Mayordomo, Irena Dapic, Javier Alfaro, Ted Hupp, Robin Fahraeus, Umesh Kalathiya
Summary: The TAP1-TAP2 complex transports antigenic peptide substrates into the ER through two different channels, with shorter peptides being transported more quickly. IFN-gamma treatment in melanoma cells induces the presentation of shorter length peptides over MHC-I, which exhibit a relatively weak binding affinity with TAP.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
S. B. Parit, V. C. Karade, R. B. Patil, N. Pawar, R. P. Dhavale, M. Tawre, K. Pardesi, U. U. Jadhav, V. V. Dawkar, R. S. Tanpure, J. H. Kim, J. P. Jadhav, A. D. Chougale
MATERIALS TODAY CHEMISTRY
(2020)
Proceedings Paper
Materials Science, Multidisciplinary
A. R. Patil, M. S. Nimbalkar, P. S. Patil, A. D. Chougale, P. B. Patil
MATERIALS TODAY-PROCEEDINGS
(2020)
