Review
Biochemical Research Methods
Joselyn S. Soto, Yasaman Jami-Alahmadi, James A. Wohlschlegel, Baljit S. Khakh
Summary: This protocol provides a method for labeling and identifying cell-specific and subcompartment-specific proteins within intact astrocytes and neurons. The approach utilizes the proximity-dependent biotinylation system BioID2 to selectively label proximal proteins in cells. This protocol can be applied to any area of the central nervous system and is important for physiological and disease-related research.
Article
Neurosciences
Sahil H. Shah, Lucio M. Schiapparelli, Satoshi Yokota, Yuanhui Ma, Xin Xia, Sahana Shankar, Sarah Saturday, Michael Nahmou, Catalina Sun, John Yates, Hollis T. Cline, Jeffrey L. Goldberg
Summary: In this study, a new in vivo quantitative measure of newly synthesized proteins was developed and applied to examine the changes in the retina after optic nerve injury. The results revealed a dynamic translational response within broader proteostasis regulation, enhancing our understanding of the cellular response to injury.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Miaoxian Yang, Yu He, Yuewen Xin, Junliang Jiang, Mi Tian, Jiaying Tan, Shuixiang Deng, Ye Gong
Summary: This study identified differentially abundant proteins in the brains of septic rats and found that these proteins are related to cellular microtubule metabolism, energy production, nucleic acid metabolism, and neurological disease. Gc-globulin, ApoA1, PI3K/AKT pathway, and acute phase response proteins were suggested as potential candidates for the diagnosis and treatment of sepsis-associated encephalopathy.
Article
Oncology
Nicolai B. Palstrom, Martin Overgaard, Peter Licht, Hans C. Beck
Summary: Proteins found in pleural effusion can serve as biomarkers for the diagnosis of malignant pleural mesothelioma (MPM). The identification of these proteins can significantly improve the accuracy of MPM diagnosis. Therefore, analyzing the protein composition of pleural effusion can lead to new diagnostic methods for MPM.
Article
Biochemical Research Methods
Zi Gao, Preston Williams, Lin Li, Yinsheng Wang
Summary: DNA sequences with high G content have the potential to form G quadruplex structures, which can interact with specific proteins. Through quantitative proteomic experiments, a number of candidate G4-interacting proteins were identified, some of them being discovered for the first time. These findings highlight the complexity and importance of understanding the G4-interaction proteome in biology.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Cell Biology
Hala Guedouari, Yasmine Ould Amer, Nicolas Pichaud, Etienne Hebert-Chatelain
Summary: Using in vitro proximity-dependent biotin identification, 51 candidate proteins that may interact with c-Src within the mitochondrial matrix were identified, with potential involvement in various mitochondrial functions. Additionally, 24 tyrosine phosphorylation sites in 17 mitochondrial proteins were identified as potential substrates for intramitochondrial Src. The study suggests that intramitochondrial Src can target multiple proteins and regulate diverse mitochondrial functions.
Article
Medicine, Research & Experimental
Huiqiong Bao, Xiaobin Li, Zhixing Cao, Zhihong Huang, Li Chen, Mingbing Wang, Jiali Hu, Wenting Li, Hongwei Sun, Xue Jiang, Ping Mei, Huawen Li, Ligong Lu, Meixiao Zhan
Summary: This study identified COPA as a potential prognostic biomarker for cervical cancer and a promising pharmacological intervention target, demonstrating its role in the progression of the disease.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Cell Biology
Sujin Byeon, Bailey Werner, Reilly Falter, Kristian Davidsen, Calvin Snyder, Shao-En Ong, Smita Yadav
Summary: Sept7 plays an important role in neuronal development, and its phosphorylation-dependent interaction with 14-3-3 proteins protects it from dephosphorylation, thereby regulating neuronal development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Orthopedics
U. T. Timur, H. Jahr, J. Anderson, D. C. Green, P. J. Emans, A. Smagul, L. W. van Rhijn, M. J. Peffers, T. J. M. Welting
Summary: This study identified tissue-dependent secreted proteins from intra-articular human knee osteoarthritis tissues, which may serve as novel candidates for osteoarthritis biomarker development on a tissue-specific basis.
OSTEOARTHRITIS AND CARTILAGE
(2021)
Article
Biochemical Research Methods
Jakob Woessmann, David Kotol, Andreas Hober, Mathias Uhlen, Fredrik Edfors
Summary: Using multiple proteases and recombinant protein standards, this study investigates the effect of protease bias on accuracy and precision in label-free mass spectrometry experiments. The researchers successfully established quantification methods for multiple proteins.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Virology
Victor Acevedo-Sanchez, Roy S. Martinez-Ruiz, Sergio R. Aguilar-Ruiz, Honorio Torres-Aguilar, Pedro Chavez-Olmos, Efrain Garrido, Rafael Baltierrez-Hoyos, Maria de los A. Romero-Tlalolini
Summary: This study compared the proteomic content of extracellular vesicles (EVs) derived from cervical cancer cells and normal cells, and found that EVs play important roles in cell-cell interactions. They are involved in processes such as cell adhesion, proteolysis, lipid metabolism, and immune responses. The role of EVs in cancer may include migration, invasion, metastasis, and the activation or suppression of immune system cells.
Article
Food Science & Technology
Junpeng Gao, Yi Wang, Bo Lyu, Jian Chen, Guang Chen
Summary: Saussurea involucrata has been studied for its anti-hepatoma function, showing significant inhibitory effects on liver tumors with no toxicity at high doses. Proteomics analysis revealed the impact of ESPI on pathways related to protein metabolic processes and catalytic activities.
Article
Multidisciplinary Sciences
Gennifer E. Merrihew, Jea Park, Deanna Plubell, Brian C. Searle, C. Dirk Keene, Eric B. Larson, Randall Bateman, Richard J. Perrin, Jasmeer P. Chhatwal, Martin R. Farlow, Catriona A. McLean, Bernardino Ghetti, Kathy L. Newell, Matthew P. Frosch, Thomas J. Montine, Michael J. MacCoss
Summary: Alzheimer's disease (AD) is a complex and devastating neurodegenerative disease with limited treatment options. In order to understand the molecular changes specific to AD, researchers have constructed a unique human brain sample cohort that includes different types of AD and normal individuals. By using advanced proteomics techniques, they have generated a high-quality dataset at the peptide and protein level, providing valuable insights into the molecular signatures of the disease. The data have been deposited in a public database and are readily accessible for further analysis.
Article
Environmental Sciences
Gefei Huang, Yiming Ma, Dongying Xie, Cunmin Zhao, Lin Zhu, Guangshan Xie, Pengfei Wu, Wei Wang, Zhongying Zhao, Zongwei Cai
Summary: Plastic pollution poses a significant threat to ecosystems. While the adverse effects of microplastics have been extensively studied, the toxicity of nanoplastics remains unclear, particularly at the protein level. This study used quantitative proteomics to investigate the proteome dynamics in a soil nematode exposed to 100 nm polystyrene nanoplastics (PS-NPs). The results showed that exposure to PS-NPs led to differential expression of proteins related to various cellular processes, and these changes were consistent with the observed phenotypic defects. Overall, this study provides insights into the molecular mechanisms underlying the toxicity of nanoplastics.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Medicine, Research & Experimental
Jie Zhu, Ling Han, Ruilai Liu, Zhenghua Zhang, Qiong Huang, Xu Fang, Ke Yang, Guiqin Huang, Zhizhong Zheng, Nikhil Yawalkar, Hui Deng, Kexiang Yan
Summary: By analyzing the proteome profile of PBMCs from patients with PsA, PsO, and healthy controls, this study identified 14 potential biomarkers for PsA diagnosis. Additionally, the expression of SIRT2 was significantly higher in PsA patients compared to PsO and healthy controls, and was negatively correlated with the phosphorylation of p38MAPK.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Christian Borgo, Claudio D'Amore, Valeria Capurro, Valeria Tomati, Elvira Sondo, Federico Cresta, Carlo Castellani, Nicoletta Pedemonte, Mauro Salvi
Summary: The advent of Trikafta has revolutionized the treatment of cystic fibrosis patients with the most common misfolding mutation, F508del-CFTR. However, there is still room for improvement in its efficacy, especially in rare CFTR mutations. By targeting the misfolding detection machinery, the combination of Trikafta with a drug like TAK-243 shows promising results in improving CFTR function, including in rare CF-causing mutations.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Silvia Pietrobono, Raffaella De Paolo, Domenico Mangiameli, Andrea Marranci, Ilaria Battisti, Cinzia Franchin, Giorgio Arrigoni, Davide Melisi, Laura Poliseno, Barbara Stecca
Summary: Despite advances in BRAF kinase inhibitors (BRAFi) for BRAF-mutant melanomas, resistance development remains a major clinical problem. This study identifies p38/SOX2-mediated adaptive response mechanism to BRAFi, revealing its role in providing survival signals to melanoma cells.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Neurosciences
Susanna Cogo, James E. Tomkins, Nikoleta Vavouraki, Veronica Giusti, Federica Forcellato, Cinzia Franchin, Isabella Tessari, Giorgio Arrigoni, Laura Cendron, Claudia Manzoni, Laura Civiero, Patrick A. Lewis, Elisa Greggio
Summary: Mutations in SPG11 gene are the major cause of hereditary spastic paraplegia and thinning of the corpus callosum. Previous studies have shown that loss of function of spatacsin results in lysosomal and axonal transport impairments. This study identified 14-3-3 proteins as physiological interactors of spatacsin and revealed that the interaction is regulated by protein kinase A-dependent phosphorylation.
NEUROBIOLOGY OF DISEASE
(2022)
Article
Medical Laboratory Technology
Ada Aita, Ilaria Battisti, Nicole Contran, Serena Furlan, Andrea Padoan, Cinzia Franchin, Francesco Barbaro, Anna Maria Cattelan, Carlo-Federico Zambon, Mario Plebani, Daniela Basso, Giorgio Arrigoni
Summary: This study identified potential biomarkers in saliva for SARS-CoV-2 infection outcome through proteomic analysis. The differentially abundant proteins involved in innate immunity, taste, and viral binding to the host show potential as biomarkers and drug targets.
CLINICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
Barbara Di Camillo, Lucia Puricelli, Elisabetta Iori, Gianna Maria Toffolo, Paolo Tessari, Giorgio Arrigoni
Summary: Protein turnover rate is crucial for cellular functions and dysregulation of protein degradation can lead to various diseases. Studying protein synthesis and degradation rates is important to understand the pathophysiology of diseases. This study used a dynamic-SILAC approach to investigate protein turnover and abundance in a cellular model of diabetic nephropathy, identifying several proteins with altered turnover and abundance between diabetic nephropathic subjects and controls. These proteins could potentially serve as biomarkers or therapeutic targets for diabetic complications. The data obtained also provide valuable information on protein half-lives in human fibroblasts and contribute to basic cell biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Diana Piol, Laura Tosatto, Emanuela Zuccaro, Eric N. Anderson, Antonella Falconieri, Maria J. Polanco, Caterina Marchioretti, Federica Lia, Joseph White, Elisa Bregolin, Giovanni Minervini, Sara Parodi, Xavier Salvatella, Giorgio Arrigoni, Andrea Ballabio, Albert R. La Spada, Silvio C. E. Tosatto, Fabio Sambataro, Diego L. Medina, Udai B. Pandey, Manuela Basso, Maria Plennuto
Summary: Spinal and bulbar muscular atrophy is caused by polyglutamine expansions in androgen receptor, leading to gain-of-function toxicity. This study investigates the phosphorylation of polyglutamine-expanded receptor and its role in neurodegeneration. The researchers find that certain kinases and phosphatases can modify the function and toxicity of the receptor, and targeting these enzymes can potentially be used as a therapeutic approach.
Article
Food Science & Technology
Lucia Giagnoni, Saptarathi Deb, Alessandra Tondello, Giulia Zardinoni, Michele De Noni, Cinzia Franchin, Alice Vanzin, Giorgio Arrigoni, Antonio Masi, Piergiorgio Stevanato, Alessio Cecchinato, Andrea Squartini, Carlo Spanu
Summary: Cheese production relies on the complex dynamics of microbial groups, especially the proportion of psychrotrophic bacteria in milk, affected by refrigeration temperature. Accidental thermal variations of milk can occur during collection and transportation. A trial was conducted to analyze the impact of temperature on cheese quality and bacterial communities using DNA extraction and sequencing. Shifts in bacterial communities were observed, providing insights for improved handling of technical processing conditions in the cheese manufacturing industry.
FOOD RESEARCH INTERNATIONAL
(2023)
Letter
Oncology
Andrea Marranci, Antonella Prantera, Simona Masotti, Raffaella De Paolo, Caterina Baldanzi, Maurizio S. S. Podda, Serena Mero, Marianna Vitiello, Cinzia Franchin, Mariavittoria Laezza, Laura Comelli, Giorgio Arrigoni, Tiziana Cervelli, Giovanna Del Pozzo, Laura Poliseno
Summary: Our study reveals that PARP1 can down-regulate the translation of BRAF-X1, negatively impacting the MAPK pathway and sensitizing melanoma cells to BRAF and MEK inhibitors, both in vitro and in vivo.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Valeria Capaci, Giorgio Arrigoni, Lorenzo Monasta, Michelangelo Aloisio, Giulia Rocca, Giovanni Di Lorenzo, Danilo Licastro, Federico Romano, Giuseppe Ricci, Blendi Ura
Summary: This study focuses on the phosphoproteome of endometrial cancer (EC) and normal endometrium, aiming to identify differentially phosphorylated proteins involved in tumorigenic signaling pathways. Differentially phosphorylated proteins were analyzed using 2D-DIGE, IMAC, and mass spectrometry. Validation through Western blotting confirmed altered abundance of HBB, CKB, LDHB, and HSPB1. Bioinformatic analysis revealed tumorigenic signaling pathways. This study highlights the role of phosphoproteome in EC tumor growth and suggests potential for new drugs targeting EC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Multidisciplinary
Alice Vanzin, Cinzia Franchin, Giorgio Arrigoni, Ilaria Battisti, Antonio Masi, Andrea Squartini, Vittoria Bisutti, Diana Giannuzzi, Luigi Gallo, Alessio Cecchinato, Sara Pegolo
Summary: The study analyzed the peptidome profiles of milk samples from cows with subclinical mastitis induced by different pathogens. The results showed that the peptides that best distinguish positive from negative samples are mainly derived from abundant milk proteins such as beta- and alpha(s1)-casein, indicating the potential of these peptides as new diagnostic and therapeutic tools.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Eleanor L. Atkinson, Jessica Iegre, Claudio D'Amore, Paul Brear, Mauro Salvi, Marko Hyvonen, David R. Spring
Summary: In this study, an iterative cycle of enzymatic assays, X-ray crystallography, molecular modelling and cellular assays was used to develop a functionalisable chemical probe for the investigation of CK2α/β PPI. The lead peptide, P8C9, showed successful binding to CK2α at the PPI site, and it was found to be easily synthesizable and functionalisable. The peptide also exhibited high stability in serum and had potential for further optimization.
CHEMICAL COMMUNICATIONS
(2022)
