Article
Cell Biology
Jiaran Li, Jifeng Wang, Yumeng Yan, Na Li, Xiaoqing Qing, Ailikemu Tuerxun, Xiaojing Guo, Xiulan Chen, Fuquan Yang
Summary: In this study, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
Article
Biochemical Research Methods
Kerry A. Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaino, Eric W. Deutsch, Andrew R. Jones
Summary: Phosphoproteomic methods are used to identify and quantify phosphorylation sites on proteins. This study introduces the concept of scoring modifications on a decoy amino acid to estimate the global false localization rate (FLR) independently.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Dominik Madej, Long Wu, Henry Lam
Summary: This study introduces a new method called CDD for FDR estimation, utilizing a fixed empirical null score distribution. Benchmarking CDD against decoy-based PeptideProphet showed similar accuracy and stability in retrieving correct PSMs. This finding highlights the potential of Big Data approaches for statistical analysis in proteomics and questions the necessity of dataset-specific target-decoy searches.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Sangjeong Lee, Heejin Park, Hyunwoo Kim
Summary: Accurately estimating the false discovery rate (FDR) is crucial in proteomics. The traditional target-decoy strategy (TDS) assumes the probabilities of spectra matching target or decoy peptides are identical, but in reality, they are not. Therefore, we propose cTDS, which estimates the FDR more accurately by considering the probability of spectra being incorrectly identified as target or decoy peptides.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Arya Ebadi, Jack Freestone, William S. Noble, Uri Keich
Summary: Controlling the false discovery rate (FDR) in proteomics experiments using target decoy competition (TDC) only controls the average proportion of false discoveries. However, the actual proportion of false discoveries (FDP) may exceed the specified FDR threshold. We demonstrate this using real data and present two methods, FDP Stepdown and TDC Uniform Band, which help bridge the gap between controlling the expected FDR and the empirical FDP.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Javier E. Flores, Lisa M. Bramer, David J. Degnan, Vanessa L. Paurus, Yuri E. Corilo, Chaevien S. Clendinen
Summary: Gas chromatography-mass spectrometry (GC-MS) is an analytic method used to identify small molecules (e.g., metabolites) in metabolomics research. However, there is a risk of false identification or discovery that is not quantified. To address this, researchers propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Biochemical Research Methods
Mitra Ebrahimpoor, Jelle J. Goeman
Summary: Volcano plots are commonly used to select interesting discoveries, but they may lead to inflated false discovery rates. We demonstrate this issue with simulation experiments and data, and propose alternative approaches for multiple testing that do not inflate the false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Kyowon Jeong, Philipp T. Kaulich, Wonhyeuk Jung, Jihyung Kim, Andreas Tholey, Oliver Kohlbacher
Summary: Top-down proteomics provides more comprehensive proteoform-level information, but reliable data analysis remains challenging. The conventional FDR estimation method may not work at the proteoform level, and the precursor deconvolution error rate should be taken into account.
Article
Biochemical Research Methods
Yan Liu, Hao Liang, Quan Zou, Zengyou He
Summary: The identification of essential proteins is an important problem in bioinformatics. Existing methods have limitations in providing context-free and easily interpretable quantifications of centrality values, specifying proper thresholds, and controlling the quality of reported essential proteins. To overcome these limitations, this study formulates the essential protein discovery problem as a multiple hypothesis testing problem and presents a significance-based method named SigEP. Experimental results demonstrate that SigEP outperforms competing algorithms.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Mathematical & Computational Biology
Xiaoya Sun, Yan Fu
Summary: The paper proposes a competition-based method, TDfdr, to accurately estimate the false discovery rate (fdr) without relying on P-values or known null distributions. Extensive simulation studies and real biomedical tasks demonstrate that TDfdr has higher discovery power.
STATISTICS IN MEDICINE
(2023)
Article
Automation & Control Systems
Xintao Xia, Zhanrui Cai
Summary: This paper proposes a differentially private adaptive FDR control method that can protect individual information and precisely control the FDR metric. By using a novel p-value transformation and a mirror peeling algorithm, privacy protection and optimal stopping technique are achieved. Empirical studies demonstrate that this method can better control FDR while reducing computation cost.
JOURNAL OF MACHINE LEARNING RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Shin June Kim, Youngjae Oh, Jaesik Jeong
Summary: With advancements in technology, analyzing complex and large-scale data requires more advanced techniques. In comparing different methods for analyzing omics data from two different groups, controlling error rates such as false discovery rate is crucial. Three methods were selected for comparison study, with Efron's approach being one-dimensional and Ploner's and Kim's approaches being two-dimensional. Variants of Ploner's approach were also considered in the performance comparison on simulated and real data.
Article
Biochemical Research Methods
Dominik Madej, Henry Lam
Summary: One of the primary objectives in mass spectrometry based peptide identification in proteomics is to validate top-scoring peptide-spectrum matches (PSMs) statistically by estimating the false discovery rate (FDR). Existing methods rely on decoys to construct a null model to estimate FDR, but this approach increases computational cost and assumes that decoy PSMs are representative of all possible incorrect target PSMs. This study proposes a novel decoy-free procedure using transformed e-value (TEV) scores and the distributions of non-top-scoring target PSMs to develop null models for top-scoring PSMs. The method shows comparable or improved performance in FDR estimation compared to popular decoy-free and decoy-based methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Statistics & Probability
Hongyuan Cao, Jun Chen, Xianyang Zhang
Summary: The article introduces a method to improve the statistical power of large-scale multiple testing by utilizing auxiliary information in high-dimensional statistical inference. By using a framework based on a two-group mixture model and imposing structural relationship constraints and an optimal rejection rule to control the false discovery rate, the method's power is enhanced. The advantages of the proposed method are verified through empirical and theoretical analysis.
ANNALS OF STATISTICS
(2022)
Article
Statistics & Probability
Yunlong Zhu
Summary: This study investigates the dependence structure of genes and proposes a new estimation method for CGGM. It formulates CGGM estimation as a multiple testing problem and introduces a new test statistic. The proposed method is shown to perform well in simulation studies and real data analysis.
COMMUNICATIONS IN STATISTICS-THEORY AND METHODS
(2022)
Article
Biochemistry & Molecular Biology
Livia Rosa-Fernandes, Carla Bandeira, Shahab Zaki Pour, Viviane de Fatima Benedetti, Daniel Ferreira, Aline R. Lorenzon, Jusciele B. Moreli, Claudio Romero Farias Marinho, Martin R. Larsen, Paolo Zanotto, Giuseppe Palmisano, Estela Bevilacqua
Summary: The study utilized quantitative proteomics analysis to investigate the impact of ZIKV infection on placental cells, revealing altered levels of proteins involved in cell proliferation, apoptosis, and inflammatory processes. The findings suggest that antibody-opsonized ZIKV particles may play a pivotal role in determining infection outcomes and the role of mixed infections, providing valuable insights for infection control strategies.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Biochemical Research Methods
Honggang Huang, Lylia Drici, Pernille S. Lassen, Giuseppe Palmisano, Martin R. Larsen
Summary: A novel strategy called TiCPG has been developed for comprehensive characterization of the proteome and three post-translational modifications (PTMs) including reversibly modified cysteines, phosphorylation, and sialylated N-linked glycosylation. This strategy combines chemical labeling and titanium dioxide chromatography. The application of TiCPG to pro-inflammatory cytokine-stimulated ll-cells revealed significant regulation of protein expression and PTMs, highlighting the involvement of these PTMs in cell apoptosis.
JOURNAL OF PROTEOMICS
(2023)
Article
Virology
Janaina Macedo-da-Silva, Livia Rosa-Fernandes, Vinicius de Morais Gomes, Veronica Feijoli Santiago, Deivid Martins Santos, Catarina Maria Stanischesk Molnar, Bruno Rafael Barboza, Edmarcia Elisa de Souza, Rodolfo Ferreira Marques, Silvia Beatriz Boscardin, Edison Luiz Durigon, Claudio Romero Farias Marinho, Carsten Wrenger, Suely Kazue Nagahashi Marie, Giuseppe Palmisano
Summary: We found that SARS-CoV-2 infection leads to increased protein arginylation, and inhibition of this process has potential therapeutic value.
Article
Oncology
Isabele Fattori Moretti, Antonio Marcondes Lerario, Paula Rodrigues Sola, Janaina Macedo-da-Silva, Mauricio da Silva Baptista, Giuseppe Palmisano, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie
Summary: This study analyzed the effects of MET combined with TMZ treatment in two GBM cell lines, U87MG and A172, stimulated with LPS. MET treatment led to mitochondrial respiration blunting and oxidative stress in both cell lines, with U87MG cells exhibiting increased apoptosis after MET + LPS + TMZ treatment and A172 cells showing cell cycle arrest after MET + TMZ treatment. The observed differential response was associated with the metabolic status of the cells. This study highlights the potential of MET as a treatment option for GPM-GBM cases with an activated TLR4 pathway and suggests the use of combination therapies, such as an IL8 inhibitor for cases with upregulated CXCL8 and an antioxidant inhibitor for MTC-GBM cases.
Article
Virology
Yasmin da Silva Santos, Thais Helena Martins Gamon, Marcela Santiago Pacheco de Azevedo, Bruna Larotonda Telezynski, Edmarcia Elisa de Souza, Danielle Bruna Leal de Oliveira, Jamille Gregorio Dombrowski, Livia Rosa-Fernandes, Giuseppe Palmisano, Leonardo Jose de Moura Carvalho, Maria Cecilia Rui Luvizotto, Carsten Wrenger, Dimas Tadeu Covas, Rui Curi, Claudio Romero Farias Marinho, Edison Luiz Durigon, Sabrina Epiphanio
Summary: Since December 2019, the COVID-19 pandemic caused by SARS-CoV-2 has been affecting the world, and now multiple variants are emerging. This study compared the effects of the wild-type (Wt) (Wuhan) strain, P.1 (Gamma) variant, and Delta variant in infected K18-hACE2 mice. The P.1-infected mice showed more severe clinical manifestations and weight loss compared to the other groups. The respiratory capacity was also reduced in P.1-infected mice. Pulmonary histological findings revealed a more aggressive disease with P.1 and Delta variants compared to the Wt strain.
Editorial Material
Immunology
Giuseppe Palmisano, Nobuko Yoshida
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Immunology
Erika Machado de Salles, Paulo Lisboa Raeder, Claudia Blanes Angeli, Veronica Feijoli Santiago, Cristiane Naffah de Souza, Theresa Ramalho, Niels Olsen Saraiva Camara, Giuseppe Palmisano, Jose Maria alvarez, Maria Regina D'Imperio Lima
Summary: This study provides evidence that P2RX7 modulates the metabolism of Th1 cells through induction of T-bet expression and aerobic glycolysis. P2RX7 signaling leads to bioenergetic mitochondrial stress and sustains the glycolytic pathway in activated CD4+ T cells responding to malaria. Inhibition of ATP synthase and subsequent reduction in oxidative phosphorylation is sufficient to promote Th1 differentiation in the absence of P2RX7.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Pharmacology & Pharmacy
Giovane de Jesus Gomes Ribeiro, Sun Liu Rei Yan, Giuseppe Palmisano, Carsten Wrenger
Summary: Malaria, mainly affecting Africa and Southeast Asia, claims over 500,000 lives annually. The disease is caused by the protozoan parasite Plasmodium, with Plasmodium vivax and Plasmodium falciparum being the main culprits in humans. The emergence of artemisinin-resistant strains in Southeast Asia underscores the urgent need for more effective and safe antimalarial drugs. This mini-review explores the potential of plant extracts and isolated natural products as antimalarial agents, focusing on in vitro studies conducted in the last five years (2018-2022).
Letter
Dermatology
Gerardo Palmisano, Carmen Orte Cano, Margot Fontaine, Clement Lenoir, Elisa Cinotti, Linda Tognetti, Pietro Rubegni, Javiera Perez-Anker, Susana Puig, Josep Malvehy, Jean-Luc Perrot, Veronique del Marmol, Ketty Peris, Mariano Suppa
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Biochemical Research Methods
Seok Heo, Taewook Kang, Alexei M. Bygrave, Martin R. Larsen, Richard L. Huganir
Summary: This study investigated the global dynamics of the hippocampal PSD proteome and phosphoproteome in mice following different types of experience, revealing the crucial role of PSD in synaptic plasticity and identifying molecular mechanisms associated with experience-dependent synaptic remodeling.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Parasitology
Mauricio S. Pena, Fenny Hui Fen Tang, Fernando Alves de Lima Franco, Alessandro Taunay Rodrigues, Guilherme Moreira Paiva Carrara, Thais Larissa Silva Araujo, Ricardo Jose Giordano, Giuseppe Palmisano, Maristela Martins de Camargo, Silvia Reni Bortolin Uliana, Beatriz Simonsen Stolf
Summary: Leishmaniases, caused by protozoan parasites, affect 12 million people worldwide. In this study, the LRR17 gene and protein were identified in Leishmania species. The protein LaLRR17 was found to increase infectivity when overexpressed in Leishmania (L.) amazonensis promastigotes. Further investigation revealed that macrophage GRP78 is a ligand for LaLRR17 and blocking this interaction prevents the increase in infection conferred by LaLRR17. These findings provide insights into the mechanism of phagocytosis in Leishmania infections.
Article
Multidisciplinary Sciences
Orlando Bonito Scudero, Veronica Feijoli Santiago, Giuseppe Palmisano, Fernando Moreira Simabuco, Armando Morais Ventura
Summary: This study investigates the interaction between the M2-2 protein from respiratory syncytial virus (RSV) and cellular proteins. Proteomic analysis reveals that M2-2 is involved in the regulation of translation, protein folding, and mRNA splicing. The study also shows that M2-2 inhibits translation and stress granule assembly, and is targeted for proteasome degradation. These findings suggest that M2-2 has additional functions to contribute to successful RSV infection.
Article
Parasitology
Marcel Ramirez, Rita de Cassia Ruiz, Gessilda de Alcantara Nogueira-Melo, Luiz Claudio Miletti, Mauro Cortez, Melyssa Negri, Giuseppe Palmisano, Jorge Gonzalez
Summary: We propose to improve learning in biomedical sciences for graduate and undergraduate courses by integrating disciplines such as molecular cell biology, biochemistry, and biophysics around the concept of pathogen interaction within hosts. Remote activities during the pandemic allow students and researchers from different places in Brazil and Latin American countries to discuss science. A multidisciplinary view of host-pathogen interaction can enhance our understanding of disease pathology and contribute to the development of diagnostic, treatment, and control strategies. Our proposal aims to strengthen and disseminate scientific knowledge in Latin America through solid theoretical training, collaboration with excellent research groups, and training within a multidisciplinary network. We will review the concept of host-pathogen interaction, teaching and research institutions, active teaching methodologies, and the current political context in science.
MEMORIAS DO INSTITUTO OSWALDO CRUZ
(2023)
Article
Biology
L. Andreone, A. F. dos Santos, R. A. M. Wailemann, L. F. Terra, V. M. Gomes, J. Macedo da Silva, L. Rosa-Fernandes, M. C. Sogayar, G. Palmisano, L. Labriola, M. J. Perone
Summary: This study investigates the use of skin spheroid-derived cells (SphCs) as a potential adjuvant for islet transplantation in type 1 diabetes. The researchers found that SphCs can improve the functionality of transplanted islets without the need for pharmacological immunosuppression.
BRAZILIAN JOURNAL OF MEDICAL AND BIOLOGICAL RESEARCH
(2023)
Article
Chemistry, Applied
Jingyuan Liu, Kasper Engholm-Keller, Mahesha M. Poojary, Marta Bevilacqua, Mogens L. Andersen, Marianne N. Lund
Summary: This study investigated the reactions of 4-methylbenzoquinone with S-lactoglobulin and amino acids at neutral pH. The results showed that Cys121 was the most modified residue in S-LG, and Michael addition occurred in all reactions with amino acids. The rate constants correlated with the pKa values of the amino acids, indicating that the amount of unprotonated amine is the major factor determining reactivity.