Article
Cell Biology
Devasahayam Arokia Balaya Rex, Yashwanth Subbannayya, Prashant Kumar Modi, Akhina Palollathil, Lathika Gopalakrishnan, Yashodhar P. Bhandary, Thottethodi Subrahmanya Keshava Prasad, Sneha M. Pinto
Summary: Interleukin-33 (IL-33) is an important cytokine involved in innate and adaptive immune responses. Aberrant IL-33 signaling has been shown to play a defensive role in infectious and inflammatory diseases. This study used quantitative phosphoproteomics analysis to investigate the temporal signaling dynamics of IL-33 in THP-1 monocytes, and identified differentially regulated proteins and pathways involved in IL-33 signaling.
Article
Biochemical Research Methods
Nuttiya Kalpongnukul, Rungnapa Bootsri, Piriya Wongkongkathep, Pornchai Kaewsapsak, Chaiyaboot Ariyachet, Trairak Pisitkun, Naphat Chantaravisoot
Summary: This study investigated the abnormal mTORC2 signaling pathway in GBM cells and found that mTORC2 inhibition might be involved in DNA repair and cancer cell survival. Additionally, it was discovered that mTORC2 controls the phosphorylation of γH2AX to repair DNA. These findings provide important insights into the function of mTORC2 in oncogenic DNA damage response and offer potential mTORC2 treatments for brain cancer patients.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Genetics & Heredity
Yuejing Jiang, Xiaoji Cong, Shangwen Jiang, Ying Dong, Lei Zhao, Yi Zang, Minjia Tan, Jia Li
Summary: AMP-activated protein kinase (AMPK) plays regulatory roles in DNA repair through phosphorylation of various substrates and modulation of histone acetylation. Specifically, AMPK promotes apoptosis through phosphorylation of apoptosis-stimulating of p53 protein 2 (ASPP2), and regulates histone acetylation through phosphorylation of histone deacetylase 9 (HDAC9). Additionally, disrupting histone acetylation enhances the sensitivity of AMPK-deficient cells to irradiation.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Sapir Schlam-Babayov, Ariel Bensimon, Michal Harel, Tamar Geiger, Ruedi Aebersold, Yael Ziv, Yosef Shiloh
Summary: This study conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells to reveal the fine-tuned dynamics and relationships between PIKKs in the response to genotoxic stress. The results highlight the complex interactions among ATM, ATR, and DNA-PK in the DDR.
Article
Medicine, Research & Experimental
Jia Liu, Jingyi Li, Zhao Sun, Yangmiao Duan, Fengqin Wang, Guangwei Wei, Jing-Hua Yang
Summary: DNA damage response is crucial in tumor pathogenesis and radiotherapy resistance. Phosphorylation of BCLAF1 at Ser290 is significantly upregulated in gastric cancer, associated with poor prognosis. Upregulation of pBCLAF1 (Ser290) leads to increased DNA damage repair response and inhibits cancer cell apoptosis induced by irradiation.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Nutrition & Dietetics
Rebecca Hetz, Erik Beeler, Alexis Janoczkin, Spencer Kiers, Ling Li, Belinda B. Willard, Mohammed S. Razzaque, Ping He
Summary: In this study, proteomics and phosphoproteomics were used to analyze the effects of Pi on protein abundance and phosphorylation. The results revealed that Pi affected signaling pathways and various biological processes. Western blot analysis confirmed changes in protein level and phosphorylation of key regulators involved in pre-mRNA alternative splicing. The global proteome and phospho-profiling provided insights into the cell signaling networks rewired by excessive Pi and improved our understanding of the molecular mechanisms of phosphate toxicity.
FRONTIERS IN NUTRITION
(2022)
Article
Oncology
Ishwar N. Kohale, Danielle M. Burgenske, Ann C. Mladek, Katrina K. Bakken, Jenevieve Kuang, Judy C. Boughey, Liewei Wang, Jodi M. Carter, Eric B. Haura, Matthew P. Goetz, Jann N. Sarkaria, Forest M. White
Summary: This study presents a highly sensitive method for analyzing pTyr signaling networks from small amounts of FFPE tissue, enabling in-depth insights into patient tumors. The findings suggest that FFPE tissues preserve pTyr signaling characteristics in tumors, indicating potential for personalized therapies.
Article
Multidisciplinary Sciences
Michael Schmalz, Xiao- Xuan Liang, Ines Wieser, Caroline Gruschel, Lukas Muskalla, Martin Thomas Stoeckl, Roland Nitschke, Norbert Linz, Alfred Leitenstorfer, Alfred Vogel, Elisa Ferrando-May, Wei Yang
Summary: Understanding and predicting the outcome of light-DNA interaction is crucial for DNA repair and radiotherapy. This study combines laser microirradiation, imaging, and modeling to investigate the damage pathways in live cells. The results show that photochemical damage dominates at 515 nm, while electron-mediated damage dominates at wavelengths ≥620 nm. The study provides a conceptual framework for interpreting the wavelength-dependent DNA damage induced by laser and electron interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
L. Armbrecht, G. Hallegraeff, C. J. S. Bolch, C. Woodward, A. Cooper
Summary: By using hybridisation capture techniques and bioinformatic tools, we successfully increased the relative abundance of marine eukaryote sedaDNA and established a new proxy for evaluating its authenticity. This approach opens up new avenues for studying the long-term changes and evolution of marine eukaryotes over geological timescales.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Rui-Jun Eveline Li, Aram de Haas, Ernesto Rodriguez, Hakan Kalay, Anouk Zaal, Connie R. Jimenez, Sander R. Piersma, Thang V. Pham, Alex A. Henneman, Richard R. de Goeij-de Haas, Sandra J. van Vliet, Yvette van Kooyk
Summary: This study revealed a specific alteration in the JAK-STAT pathway in DCs upon simultaneous stimulation with alpha 2-3sia and LPS, leading to changes in IL10:IL-12 cytokine secretion profile associated with inflammation reduction. Targeted control of STAT phosphorylation status could be a potential strategy to overcome immune escape mechanisms imposed by bacteria or tumors on the host.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Mahmoud Hallal, Sophie Braga-Lagache, Jovana Jankovic, Cedric Simillion, Remy Bruggmann, Anne-Christine Uldry, Ramanjaneyulu Allam, Manfred Heller, Nicolas Bonadies
Summary: Despite the limited predictive power of genomics in myeloid malignancies, a novel Kinase-Activity Enrichment Analysis (KAEA) pipeline was developed to analyze differential phosphoproteomics profiles. The KAEA pipeline successfully identified over- and under-active kinases in human myeloid cell lines and characterized targets of kinase-inhibitors. This approach provides researchers with an improved tool to study kinase behavior in response or resistance to targeted treatments.
Article
Cell Biology
Bharath Sampadi, Leon H. F. Mullenders, Harry Vrieling
Summary: The influence of phosphoproteomics sample preparation methods on the biological interpretation of signaling outcome is unclear. Two commonly used methods show a strong bias in phosphorylation signaling targets, each method has advantages in analyzing IR-responsive phosphoproteins, and they respectively reveal different phosphorylation signaling events.
Article
Pharmacology & Pharmacy
Sandra M. Martin-Guerrero, Paula Alonso, Alba Iglesias, Marta Cimadevila, Jose Brea, M. Isabel Loza, Pedro Casado, David Martin-Oliva, Pedro R. Cutillas, Javier Gonzalez-Maeso, Juan F. Lopez-Gimenez
Summary: Antipsychotic drugs induce phosphorylation of multiple pathways downstream of 5-HT2AR, and the single nucleotide polymorphism encoding 5-HT2AR-H452Y affects these drug-induced phosphorylation-dependent signaling networks.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Peripheral Vascular Disease
A. Augusto B. Peluso, Stefan J. Kempf, Thiago Verano-Braga, Lucas Rodrigues-Ribeiro, Lene Egedal Johansen, Mie Rytz Hansen, Gitte Kitlen, Andreas Houe Haugaard, Colin Sumners, Henrik J. Ditzel, Robson A. Santos, Michael Bader, Martin R. Larsen, U. Muscha Steckelings
Summary: This study mapped the changes in the phosphorylation status of human aortic endothelial cells in response to AT(2)-receptor stimulation and identified HDAC1 inhibition and p53 activation as novel signaling mechanisms. The study also created a dataset of AT(2)-receptor induced phospho-modified proteins, which can be used for further discoveries.
Article
Biochemistry & Molecular Biology
Chelsea L. Blankenchip, Justin Nguyen, Rebecca K. Lau, Qiaozhen Ye, Yajie Gu, Kevin D. Corbett
Summary: Bacteria utilize diverse immune systems to defend against viruses, with the transcription factor CapW associated with regulating the CBASS bacterial immune system response. CapW represses CBASS gene expression in uninfected cells and its activation is not necessary for strong anti-phage activity, suggesting it may play a role in response to signals other than phage infection. CapW is part of a family of universal defense signaling proteins, similar to the BrxR transcription factor associated with the BREX anti-phage system.
NUCLEIC ACIDS RESEARCH
(2022)
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
Biochemical Research Methods
Shayne D. Wierbowski, Siqi Liang, Yuan Liu, You Chen, Shagun Gupta, Nicole M. Andre, Steven M. Lipkin, Gary R. Whittaker, Haiyuan Yu
Summary: The emergence of new viral agents is driven by evolution of interactions between viral proteins and host targets, leading to increased infectivity of viruses such as SARS-CoV-2 through rapid evolution. State-of-the-art interface prediction and molecular docking were used to construct a three-dimensional structural interactome between SARS-CoV-2 and human, facilitating the study of how pathogen-host interactions impact transmission and virulence. The resource provided aims to aid in the development and testing of informed hypotheses for understanding the etiology and treatments of SARS-CoV-2.
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
Biotechnology & Applied Microbiology
Yadi Zhou, Yuan Liu, Shagun Gupta, Mauricio Paramo, Yuan Hou, Chengsheng Mao, Yuan Luo, Julius Judd, Shayne Wierbowski, Marta Bertolotti, Mriganka Nerkar, Lara Jehi, Nir Drayman, Vlad Nicolaescu, Haley Gula, Savas Tay, Glenn Randall, Peihui Wang, John T. Lis, Cedric Feschotte, Serpil C. Erzurum, Feixiong Cheng, Haiyuan Yu
Summary: Studying the interaction between viral and host proteins can help discover therapies for viral infections. In this study, a comprehensive network of interactions between SARS-CoV-2 and human proteins was generated using high-throughput techniques, validating known host factors and identifying new ones. The network showed the highest overlap with differentially expressed genes in COVID-19 patients and revealed an interaction between a viral protein and a human transcription factor. Additionally, network-based screening of FDA-approved or investigational drugs identified several candidates with significant proximity to SARS-CoV-2 host factors, including a drug called carvedilol which showed clinical benefits and antiviral properties.
NATURE BIOTECHNOLOGY
(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)