Article
Chemistry, Physical
Liangjia Qiu, Ying Zhang, Genxia Wei, Chen Wang, Yinhua Zhu, Tong Yang, Zheng Chu, Peng Gao, Guangqing Cheng, Ang Ma, Yin Kwan Wong, Junzhe Zhang, Chengchao Xu, Jigang Wang, Huan Tang
Summary: Nanoparticles have great potential in biomedicine due to their unique physical and chemical properties. When nanoparticles enter biological fluids, they interact with proteins and form a protein corona. Understanding and characterizing the protein corona is crucial for the clinical translation of nanomedicine.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Yangyang Qiu, Jianan Wang, Fang He, Xiaoyan Wu, Ruitong Dan, Philip R. Hardwidge, Nengzhang Li, Yuanyi Peng
Summary: This study identified the secreted proteins of bovine P. multocida using LC-MS/MS and bioinformatics analysis. Tuf protein was found to be highly expressed in infected tissues and exhibited a protective effect against P. multocida infection.
Article
Veterinary Sciences
Paul Cann, Chrystelle Le Danvic, Chantal Porte, Didier Chesneau, Matthieu Keller, Patricia Nagnan-Le Meillour
Summary: This study aimed to test whether sexually active males can modify the composition of ewes' olfactory secretome and their estrous cycle. The results showed that after male introduction, O-GlcNAcylation, which was previously only detected in sexual activity, appeared in just 30 minutes. This provides a basis for further experiments.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Giovanni Chiappetta, Tania Gamberi, Fiorella Faienza, Xhesika Limaj, Salvatore Rizza, Luigi Messori, Giuseppe Filomeni, Alessandra Modesti, Joelle Vinh
Summary: This study investigated the effects of Auranofin (AF) on protein expression and protein oxidation in A2780 cancer cells using a strategy based on simultaneous expression proteomics and redox proteomics determinations. The results demonstrated that AF affected the cellular redox state, mitochondrial functions, and induced ER stress, which were extensively validated. The study suggests that AF exerts its effects through a multitarget mechanism, mainly affecting redox metabolism and mitochondrial functions.
Article
Biochemistry & Molecular Biology
J. A. Moleon Baca, A. Ontiveros Ortega, A. Aranega Jimenez, S. Granados Principal
Summary: The surface charge of cells is influenced by the ionic medium, which is particularly important in tumor cells as it affects their aggregation and adhesion in different organs. This study examines the changes in surface charge of tumor cells when pH, electrolytes, and their concentration are modified, and suggests that these changes can modify the behavior and aggregation state of tumor cells, potentially aiding in the prognosis and treatment of various tumors.
BIOELECTROCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Ambra Costa, Davide Ceresa, Antonella De Palma, Rossana Rossi, Sara Turturo, Sara Santamaria, Carolina Balbi, Federico Villa, Daniele Reverberi, Katia Cortese, Pierangela De Biasio, Dario Paladini, Domenico Coviello, Silvia Ravera, Paolo Malatesta, Pierluigi Mauri, Rodolfo Quarto, Sveva Bollini
Summary: This study provides a detailed characterization of the total secretome and extracellular vesicles of human amniotic-fluid derived stem cells (hAFS), comparing fetal and perinatal cells. Both sources of cells offer formulations enriched with factors promoting regeneration, with fetal hAFS showing a more pronounced pro-vasculogenic and anti-aging profile. The study confirms that hAFS represent a promising source of regenerative paracrine factors for potential therapy consideration based on specific clinical scenarios.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Fredrick J. Rosario, Sammy Pardo, Trond M. Michelsen, Kathryn Erickson, Lorna Moore, Theresa L. Powell, Susan T. Weintraub, Thomas Jansson
Summary: By studying the secreted proteins of PHT cells isolated from normal term placental villus tissue, a total of 1,344 previously unknown proteins were identified, involving processes such as energy metabolism, carbon metabolism, and glycolysis. Some proteins have slow synthesis rates, and there is significant overlap with proteins actually secreted by the placenta.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Benjamin Neuditschko, A. Paden King, Zhouyang Huang, Lukas Janker, Andrea Bileck, Yasmin Borutzki, Sierra C. Marker, Christopher Gerner, Justin J. Wilson, Samuel M. Meier-Menches
Summary: This study presents an improved approach for prioritizing candidate protein targets in inorganic drug discovery. It identifies TRIP as a first-in-class modulator of the scaffold protein NUBP2, disrupting Fe-S cluster biogenesis at sub-cytotoxic concentrations in ovarian cancer cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Analytical
Nina M. Culum, Tyler T. Cooper, Gilles A. Lajoie, Thamara Dayarathna, Stephen H. Pasternak, Jiahui Liu, Yangxin Fu, Lynne-Marie Postovit, Francois Lagugne-Labarthet
Summary: This study focuses on utilizing extracellular vesicles (EVs) as cancer biomarkers for early diagnosis of ovarian cancer, using gold nanohole arrays and surface-enhanced Raman spectroscopy for characterization. Through principal component analysis and a machine learning method, different EVs secreted by various cell lines were successfully discriminated with around 99% accuracy, sensitivity, and specificity, representing a significant progress towards quick, facile, and non-invasive cancer diagnosis.
Article
Biochemistry & Molecular Biology
Vladimir D. Manyilov, Nikolay S. Ilyinsky, Semen V. Nesterov, Baraa M. G. A. Saqr, Guy W. Dayhoff, Egor V. Zinovev, Simon S. Matrenok, Alexander V. Fonin, Irina M. Kuznetsova, Konstantin K. Turoverov, Valentin Ivanovich, Vladimir N. Uversky
Summary: This article examines the impact of intrinsically disordered proteins and regions on aging-related processes. The findings indicate that these disordered components play significant roles in aging, particularly in genome regulation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Review
Biochemical Research Methods
Rebecca Elizabeth Kattan, Deena Ayesh, Wenqi Wang
Summary: During intracellular signal transduction, protein-protein interactions (PPIs) play a critical role in regulating protein localization and function. Mass spectrometry-based interactome analysis has become a popular method for studying PPI networks, but the analysis of large datasets can be challenging. In this review, we discuss the methods and resources commonly used for analyzing large interactome-related proteomic data and propose a guideline for identifying novel interacting proteins.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Lucia Santos, Rui Nascimento, Aires Duarte, Violeta Railean, Margarida D. D. Amaral, Patrick T. T. Harrison, Margarida Gama-Carvalho, Carlos M. M. Farinha
Summary: The study combines transcriptome and proteome analysis to investigate the global gene expression patterns associated with five prototypical CFTR mutations in Cystic Fibrosis (CF) patients. Differentially expressed genes and proteins reveal common and mutation-specific changes, highlighting functional signatures that are more associated with the specific molecular defects of each mutation rather than the CFTR loss-of-function phenotype. The analysis of translated-transcripts detected specifically in each mutation provides valuable insights into the pathophysiology of CF and may contribute to the identification of new therapeutic targets and biomarkers for CF.
CELL AND BIOSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Felicie Kieffer, Fahd Hilal, Anne-Sophie Gay, Delphine Debayle, Marie Pronot, Gwenola Poupon, Iliona Lacagne, Barbara Bardoni, Stephane Martin, Carole Gwizdek
Summary: This study identifies the nuclear interactome of the FMRP protein in mammalian neurons, revealing potential central regulatory functions in mRNA biogenesis. By combining subcellular fractionation, affinity purification, and mass spectrometry analysis, the study identified 55 candidate nuclear partners, expanding the understanding of FMRP's role in neuronal physiology and FXS etiology.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Food Science & Technology
Yanyan Yi, Zhili Hao, Panpan Sun, Kuohai Fan, Wei Yin, Jianhua Guo, Xiaozhong Zheng, Na Sun, Hongquan Li
Summary: This study reveals that Scu can protect ovarian granulosa cells from ZEA-induced damage by regulating multiple targets and pathways, and possibly by inhibiting apoptosis of GCs.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maria Laura Lara, Marcos Gomides Carvalho, Fabiana Ferreira de Souza, Rubia Alves Schmith, Viviane Maria Codognoto, Bruna De Vita, Camila de Paula Feitas Dell 'Aqua, Fernada da Cruz Landim, Marina Landim e Alvarenga
Summary: This study aimed to examine the secretome of feline adipose tissue-derived mesenchymal stem cells (AD-MSCs) and compare the effects of different culture conditions on AD-MSC proteomics. The results showed that AD-MSCs cultured without fetal bovine serum (FBS) had more identified proteins compared to those cultured with FBS. Hypoxic conditions did not significantly affect protein abundance. The proteins in the secretome were involved in extracellular matrix modulation, cell signaling pathways, and promoting cell proliferation and maintenance, as well as cell adhesion, migration, and morphogenesis.
Article
Biochemical Research Methods
Virginia Campos Silvestrini, Carolina Hassibe Thome, Daniele Albuquerque, Camila de Souza Palma, Germano Aguiar Ferreira, Guilherme Pauperio Lanfredi, Ana Paula Masson, Lara Elis Alberici Delsin, Fernanda Ursoli Ferreira, Felipe Canto de Souza, Lyris Martins Franco de Godoy, Adriano Aquino, Emanuel Carrilho, Rodrigo Alexandre Panepucci, Dimas Tadeu Covas, Vitor Marcel Faca
JOURNAL OF PROTEOMICS
(2020)
Article
Biochemistry & Molecular Biology
Jonathas Rodrigo dos Santos, Mariza Bortolanza, Gustavo Duarte Ferrari, Guilherme Pauperio Lanfredi, Glauce Crivelaro do Nascimento, Ana Elisa Calereiro Seixas Azzolini, Elaine Del Bel, Alline Cristina de Campos, Vitor Marcel Faca, Anderson Vulczak, Luciane Carla Alberici
Article
Biochemistry & Molecular Biology
Michael C. Lanz, Kumar Yugandhar, Shagun Gupta, Ethan J. Sanford, Vitor M. Faca, Stephanie Vega, Aaron M. N. Joiner, J. Christopher Fromme, Haiyuan Yu, Marcus B. Smolka
Summary: This study assembled a dataset of 30,902 phosphosites from 75 independent phosphoproteomic experiments using Saccharomyces cerevisiae. By aggregating this dataset with others, over 46,000 budding yeast phosphosites were identified. Computational positioning of phosphorylation sites on protein structures revealed numerous sites predicted to disrupt protein complex architecture, providing insights into potential functional phosphorylation events.
Article
Biochemistry & Molecular Biology
Israel C. Vasconcelos, Raquel M. Campos, Hanna K. Schwaemmle, Ana P. Masson, Gustavo D. Ferrari, Luciane C. Alberici, Vitor M. Fac, Norberto Garcia-Cairasco, Adriano Sebollela
Summary: Tau protein plays a crucial role in neurological diseases, but freeze-and-thaw treatment of extracts may lead to artifact results. Freeze-and-thaw treatment of rodent brain homogenates results in the appearance of a 25 kDa Tau fragment. This phenomenon was not observed in human samples under the same conditions.
BIOSCIENCE REPORTS
(2021)
Article
Oncology
Lucas Eduardo Botelho de Souza, Fernanda Ursoli Ferreira, Carolina Hassibe Thome, Heloisa Brand, Maristela Delgado Orellana, Vitor Marcel Faca, Aparecida Maria Fontes, Dimas Tadeu Covas
Summary: Melanoma cells have the capability to activate an EMT-like program and acquire metastatic traits through distinct pathways induced by MSCs' secretome, both in mouse and human cells.
Article
Cell Biology
Andrea Gutierrez Maria, Kleiton Silva Borges, R. C. P. Lira, Carolina Hassib Thome, Annabel Berthon, Ludivine Drougat, Katja Kiseljak-Vassiliades, Margaret E. Wierman, Fabio R. Faucz, Vitor Marcel Faca, Luiz Gonzaga Tone, Constantine A. Stratakis
Summary: A combination of aurora kinase inhibitor and beta-catenin pathway blocker showed decreased cell proliferation and viability in ACC cell lines, suggesting a potential combinatorial approach for targeting ACC tumors.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ethan J. Sanford, William J. Comstock, Vitor M. Faca, Stephanie C. Vega, Robert Gnugge, Lorraine S. Symington, Marcus B. Smolka
Summary: The Mec1/ATR kinase plays a crucial role in genome maintenance in response to genotoxic insults by promoting context-dependent signaling and DNA repair. This study highlights a distinct Mec1 signaling response triggered by hyper-resection, which influences the outcomes of DNA recombination.
Article
Biochemical Research Methods
Natalia Silva da Trindade, Thais Cunha de Sousa Cardoso, Giulliana Galdini Costa, Gabriela Freitas Cruvinel, Ana Paula Masson, Guilherme Pauperio Lanfredi, Silmara Marques Allegretti, Vitor Faca, Matheus de Souza Gomes, Enyara Rezende Morais, Fernanda Janku Cabral
Summary: This study investigated the role of epigenetic mechanisms, particularly the interaction of Heterochromatin Protein 1 (HP1) with nuclear proteins, in regulating gene expression in the cercariae stage of Schistosoma mansoni. The findings suggest that these mechanisms are crucial for gene silencing, heterochromatin formation, and translational regulation. This research sheds light on the nuclear interactors in S. mansoni cercariae, providing insights into the regulation of gene expression in this infective stage of the parasite.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Carolina Hassibe Thome, Germano Aguiar Ferreira, Diego Antonio Pereira-Martins, Guilherme Augusto dos Santos, Douglas R. Almeida-Silveira, Isabel Weinhauser, Gustavo Antonio de Souza, Roos Houtsma, Jan Jacob Schuringa, Eduardo M. Rego, Vitor M. Faca
Summary: The depletion of non-T cell activation linker (NTAL) membrane protein from lipid rafts by alkylphospholipids or downregulation by shRNA knockdown decreases cell viability through the Akt/PI3K pathway in mantle cell lymphoma and acute promyelocytic leukemia cells. Knockdown of NTAL in acute myeloid leukemia (AML) cell lines results in decreased cell proliferation and survival, potentially making NTAL and its protein interactors potential therapeutic targets for AML.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Guilherme P. Lanfredi, Carolina H. Thome, Germano A. Ferreira, Virginia C. Silvestrini, Ana P. Masson, Alessandra P. Vargas, Mariana L. Grassi, Aline Poersch, Francisco J. Candido dos Reis, Vitor M. Faca
Summary: Ovarian cancer, especially High Grade Serous Ovarian Carcinoma, is a deadly gynecologic malignancy with poor prognosis mainly due to metastasis. Epithelial to Mesenchymal Transition plays a key role in cellular changes during metastasis.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2021)
Article
Chemistry, Analytical
Evair D. Nascimento, Wilson T. Fonseca, Tassia R. de Oliveira, Camila R. S. T. B. de Correia, Vitor M. Faca, Beatriz P. de Morais, Virginia C. Silvestrini, Henrique Pott-Junior, Felipe R. Teixeira, Ronaldo C. Faria
Summary: An ultrasensitive magneto-assay using magnetic beads and gold nanoparticles has been developed for detecting SARS-CoV-2 Spike protein in human saliva. The technique exhibits an ultralow limit of detection and high diagnostic efficiency.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biology
Jennie R. Sims, Vitor M. Faca, Catalina Pereira, Carolline Ascencao, William Comstock, Jumana Badar, Gerardo A. Arroyo-Martinez, Raimundo Freire, Paula E. Cohen, Robert S. Weiss, Marcus B. Smolka
Summary: The kinase ATR plays a crucial role in mammalian meiosis by promoting meiotic progression and coordinating key events in DNA repair and quality control. This study used phosphoproteomics to identify ATR signaling events and found ATR-dependent phosphorylation in DNA repair proteins and mRNA regulatory proteins. The study also highlighted the importance of ATR signaling in the proper localization of CDK2 in spermatocytes.
Article
Biology
Catalina Pereira, Gerardo A. Arroyo-Martinez, Matthew Z. Guo, Michael S. Downey, Emma R. Kelly, Kathryn J. Grive, Shantha K. Mahadevaiah, Jennie R. Sims, Vitor M. Faca, Charlton Tsai, Carl J. Schiltz, Niek Wit, Heinz Jacobs, Nathan L. Clark, Raimundo Freire, James Turner, Amy M. Lyndaker, Miguel A. Brieno-Enriquez, Paula E. Cohen, Marcus B. Smolka, Robert S. Weiss
Summary: DNA damage response mechanisms play important roles in meiotic processes, ensuring successful gamete formation. A study found that disruption of RAD1 in mice resulted in impaired DSB repair, germ cell depletion, and infertility, as well as defects in homolog synapsis, phosphorylation of ATR targets, and meiotic sex chromosome inactivation.
Article
Biochemistry & Molecular Biology
Leticia B. C. Penariol, Carolina H. Thome, Patricia A. Tozetti, Carlos R. K. Paier, Fabiana O. Buono, Kamila C. Peronni, Maristela D. Orellana, Dimas T. Covas, Maria E. A. Moraes, Wilson A. Silva, Julio C. Rosa-e-Silva, Rui A. Ferriani, Vitor M. Faca, Omero B. Poli-Neto, Daniel G. Tiezzi, Juliana Meola
Summary: This study used multi-omics approaches to analyze the transcriptome and proteome data of endometriosis MenSCs, and identified several genes and proteins related to the disease, as well as modulated signaling pathways. The findings suggest that the chronic inflammatory endometrial microenvironment can regulate MenSCs, providing insights into the pathogenesis of endometriosis and its implications for regenerative medicine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Jadson C. Santos, Mariangela Dametto, Ana Paula Masson, Vitor M. Faca, Rodrigo Bonacin, Eduardo A. Donadi, Geraldo Aleixo Passos
Summary: The AIRE protein interacts with partner proteins to form a complex that plays a crucial role in gene expression in the thymus. The interaction with SIRT1 is important for the progression of transcription. The study investigates the effect of a mutation in the AIRE protein on its interaction with SIRT1.
FRONTIERS IN IMMUNOLOGY
(2022)
