Review
Cell Biology
Junichi Yuasa-Kawada, Mariko Kinoshita-Kawada, Yoshio Tsuboi, Jane Y. Wu
Summary: Neurons migrate and extend axons to their synaptic targets by sensing extracellular cues. Guidance genes play critical roles in neural development and also regulate cell migration and communication outside the nervous system. Understanding the signaling mechanisms of guidance genes and their involvement in human diseases is important for therapeutic potentials in neural repair.
Article
Biochemical Research Methods
Brandon M. Gassaway, Jiaming Li, Ramin Rad, Julian Mintseris, Kyle Mohler, Tyler Levy, Mike Aguiar, Sean A. Beausoleil, Joao A. Paulo, Jesse Rinehart, Edward L. Huttlin, Steven P. Gygi
Summary: Iterative Synthetically Phosphorylated Isomers (iSPI) is a proteome-scale library of human-derived phosphoserine-containing phosphopeptides with precisely known positions of phosphorylation. It serves as a valuable resource for optimization, standardization, and benchmarking in phosphoproteomics workflows, and addresses the lack of inexpensive and diverse phosphopeptides with ground-truth phosphorylation positions.
Article
Biochemistry & Molecular Biology
Ross A. Robinson, Samuel C. Griffiths, Lieke L. van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, Lina Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, Ozge Dudukcu, Anna A. De Ruiter, Dianne M. A. Van den Heuvel, Benjamin Bishop, Jonathan Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Summary: The study reveals that Neogenin (NEO1) can be simultaneously affected by both Netrin-1 (NET1) and repulsive guidance molecule (RGM) ligands, forming a ternary NEO1-NET1-RGM complex that triggers reciprocal silencing of downstream signaling. This complex, existing in the cell membrane as a trimer-of-trimers super-assembly, inhibits cell growth and migration by preventing the formation of signaling-compatible complexes and clustering of NEO1 ectodomains.
Article
Biochemistry & Molecular Biology
Lili Niu, Philipp E. Geyer, Rajat Gupta, Alberto Santos, Florian Meier, Sophia Doll, Nicolai J. Wewer Albrechtsen, Sabine Klein, Cristina Ortiz, Frank E. Uschner, Robert Schierwagen, Jonel Trebicka, Matthias Mann
Summary: This study quantified protein composition differences among liver cell types and analyzed dynamic proteome changes in primary cell cultures, providing valuable insights for biological and pharmaceutical research.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Livia Goto-Silva, Michele Martins, Jimmy Rodriguez Murillo, Leticia R. Q. Souza, Gabriela Vitoria, Julia T. Oliveira, Juliana M. Nascimento, Erick Correia Loiola, Fabio C. S. Nogueira, Gilberto B. Domont, Marilia Zaluar P. Guimaraes, Fernanda Tovar-Moll, Stevens Kastrup Rehen, Magno Junqueira
Summary: This study identified quantitative changes in the proteome of neurospheres during differentiation, showing that human neurospheres have a molecular profile resembling the fetal brain. Upregulated pathways during differentiation include neuronal development, differentiation, cell adhesion, and axonal guidance, while cell proliferation pathways are downregulated.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2021)
Article
Biochemical Research Methods
Maria Ryaboshapkina, Kevin Saitoski, Ghaith M. Hamza, Andrew F. Jarnuczak, Severine Pechberty, Claire Berthault, Kaushik Sengupta, Christina Rye Underwood, Shalini Andersson, Raphael Scharfmann
Summary: In this study, the representativeness of EndoC-beta H1 cells as a translational human beta cell model was verified through omics analysis. The secretome of EndoC-beta H1 cells was characterized, revealing similarities and differences compared to human beta cells and insulinomas. The study also identified a high proportion of extracellular vesicle proteins in the secretome of EndoC-beta H1 cells. These findings provide valuable insights into the secretion regulation of human beta cells and warrant further investigation.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Pavel Sinitcyn, Alicia L. Richards, Robert J. Weatheritt, Dain R. Brademan, Harald Marx, Evgenia Shishkova, Jesse G. Meyer, Alexander S. Hebert, Michael S. Westphall, Benjamin J. Blencowe, Juergen Cox, Joshua J. Coon
Summary: Deep proteome sequencing provides an 80% coverage of the human proteome. Shotgun proteomics experiments detect about 10,000 human proteins from a single sample, but fail to distinguish protein variants and isoforms. Our study using various methods identifies a million unique peptides and provides evidence for the translation of nonsynonymous variants.
NATURE BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Michael Fish, Delaney Nash, Alexandru German, Alyssa Overton, Masoud Jelokhani-Niaraki, Simon D. X. Chuong, Matthew D. Smith
Summary: Plastids, specialized organelles in plant cells, originated from ancient cyanobacteria. As genes encoding plastid proteins were transferred to the nuclear genome during evolution, eukaryotic cells developed targeting pathways and protein machinery to direct these proteins back to the plastids. Chloroplasts, the most well-studied plastids, play essential roles in photosynthesis and metabolism. Understanding the pathways and regulation of protein targeting is vital for chloroplast biogenesis and function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
Emily Holt, Danielle Stanton-Turcotte, Angelo Iulianella
Summary: This article discusses the importance of integrating sensory information for an animal's movement through their environment and maintenance of homeostatic physiology. It covers the origins and development of the dorsal root ganglia (DRG) and the cells that populate it, as well as the diverse developmental and molecular processes that control sensory connectivity to the spinal cord.
Article
Biochemistry & Molecular Biology
Hironao Nakayama, Hidetaka Ohnuki, Masako Nakahara, Hisayo Nishida-Fukuda, Tomohisa Sakaue, Shinji Fukuda, Shigeki Higashiyama, Yuki Doi, Masahiro Mitsuyoshi, Takashi Okimoto, Giovanna Tosato, Chiaki Kusumoto
Summary: Netrin-1 expression is significantly reduced in colorectal cancer tissues compared to normal tissues, and DNA methylation plays a role in the repression of NTN1 transcription in CRC. NTN1 DNA hypermethylation is associated with advanced CRC disease.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Navratan Bagwan, Henrik H. El Ali, Alicia Lundby
Summary: Post translational modifications (PTMs) are covalent modifications of proteins that regulate protein function and increase proteome diversity. In human hearts, high-resolution mass spectrometry measurements and PTM identification algorithms identified over 150 different PTMs, highlighting the diversity of cardiac protein modifications.
SCIENTIFIC REPORTS
(2021)
Article
Engineering, Biomedical
Bo Liu, Yunfan Kong, Wen Shi, Mitchell Kuss, Ke Liao, Guoku Hu, Peng Xiao, Jagadesan Sankarasubramanian, Chittibabu Guda, Xinglong Wang, Yuguo Lei, Bin Duan
Summary: This study reported the potential value of dExo derived from hADMSCs in modulating various functions of peripheral nerve-related cells, suggesting their promising application in neural regeneration.
BIOACTIVE MATERIALS
(2022)
Review
Neurosciences
Alexandre Dumoulin, Esther T. Stoeckli
Summary: The molecular mechanisms of neural circuit formation have been a topic of interest for Santiago Ramo acute accent n y Cajal and many other neuroscientists. Cajal's observations on neuronal connections and morphology have provided valuable insights into the adult and developing nervous system. Technological advancements now allow us to manipulate gene expression and study the effects on axon guidance in situ, leading to a better understanding of the molecular basis of axon guidance. This review summarizes the progress made in modern live-imaging approaches used to study axon guidance.
Article
Developmental Biology
Nikole R. Zuniga, Alexandre Dumoulin, Giuseppe Vaccaro, Esther T. Stoeckli
Summary: During neural circuit formation, the switch in receptor expression is crucial for axons to navigate from one intermediate target to the next. We identified Cables1 as a key linker that regulates receptor phosphorylation and controls axon navigation in the developing spinal cord.
Article
Multidisciplinary Sciences
Anzelika Rubina, Mihil Patel, Katie Nightingale, Martin Potts, Ceri A. Fielding, Simon Kollnberger, Betty Lau, Kristin Ladell, Kelly L. Miners, Jenna Nichols, Luis Nobre, Dawn Roberts, Terrence M. Trinca, Jason P. Twohig, Virginia-Maria Vlahava, Andrew J. Davison, David A. Price, Peter Tomasec, Gavin W. G. Wilkinson, Michael P. Weekes, Richard J. Stanton, Eddie C. Y. Wang
Summary: Human cytomegalovirus (HCMV) impairs host immune defenses by targeting the protease ADAM17, which leads to the regulation of multiple surface receptors. This provides a paradigm for viral-encoded immunomodulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Allergy
Joana Costa, Simona Lucia Bavaro, Sara Benede, Araceli Diaz-Perales, Cristina Bueno-Diaz, Eva Gelencser, Julia Klueber, Colette Larre, Daniel Lozano-Ojalvo, Roberta Lupi, Isabel Mafra, Gabriel Mazzucchelli, Elena Molina, Linda Monaci, Laura Martin-Pedraza, Cristian Piras, Pedro M. Rodrigues, Paola Roncada, Denise Schrama, Tanja Cirkovic-Velickovic, Kitty Verhoeckx, Caterina Villa, Annette Kuehn, Karin Hoffmann-Sommergruber, Thomas Holzhauser
Summary: This research searched for evidence on how different physicochemical properties affect the allergenicity of food proteins, and found consistent effects on protein allergenicity within the same protein family. Molecular stability was identified as the most common characteristic promoting plant protein allergenicity. However, there is still a lack of systematic approach to link physicochemical properties with clinical allergenicity.
CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Vittoria Disciglio, Paola Sanese, Candida Fasano, Claudio Lotesoriere, Anna Maria Valentini, Giovanna Forte, Martina Lepore Signorile, Katia De Marco, Valentina Grossi, Ivan Lolli, Filomena Cariola, Cristiano Simone
Summary: This study reports a variant in the promoter of the PTEN gene that may affect the expression of PTEN protein. The variant was found to be associated with cancer risk in patients based on analysis of tissue samples.
Article
Medicine, General & Internal
Darja Kanduc
Summary: This study aimed to investigate the specificity of sequences used in serological and PCR tests for detecting SARS-CoV-2. The results showed that there is a significant peptide sequence sharing between the spike glycoprotein of SARS-CoV-2 and the human proteome. Only a limited number of peptides were found to be specific to SARS-CoV-2, and the genetic differences between the virus and humans were almost negligible. These findings have implications for understanding the issue of viral versus human specificity and can explain the occurrence of false positives in SARS-CoV-2 tests.
JOURNAL OF LABORATORY PHYSICIANS
(2023)
Article
Genetics & Heredity
Darja Kanduc
Summary: This study analyzed the molecular mimicry and cross-reactivity between the SARS-CoV-2 proteome and human immunoregulatory proteins. The findings suggest that this molecular mimicry syndrome may underlie the decay of adaptive immune responses following SARS-CoV-2 infection. The severity of immunosuppression is determined by the extent of immune responses and higher titers of immune responses can result in more severe cross-reactions against human immunodeficiency-related proteins. Booster doses of SARS-CoV-2 vaccines may have unexpected results.
GLOBAL MEDICAL GENETICS
(2022)
Article
Oncology
Martina Lepore Signorile, Valentina Grossi, Candida Fasano, Giovanna Forte, Vittoria Disciglio, Paola Sanese, Katia De Marco, Francesca La Rocca, Raffaele Armentano, Anna Maria Valentini, Gianluigi Giannelli, Cristiano Simone
Summary: c-MYC is a crucial factor in the development of colorectal cancer, with high expression in most sporadic cases. In this study, researchers discovered that the kinase p38 alpha contributes to the stability of c-MYC protein, which is involved in CRC metabolism and survival. Furthermore, p38 alpha prevents ubiquitination of c-MYC, leading to increased levels of the protein. These findings suggest that p38 alpha could be a potential therapeutic target for countering CRC proliferation, metastasis, and chemoresistance mediated by c-MYC.
Article
Genetics & Heredity
Darja Kanduc
Summary: This study explores the translation mechanisms of the EBNA1 protein in human hosts during Epstein-Barr virus latency and reactivation. It finds that the biased codon usage of EBNA1 cannot be translated due to noncompliance with human codon usage patterns and tRNA pools. Additionally, it highlights the importance of cell proliferation in modifying the host's tRNA pool to meet the translational needs of EBNA1 during viral reactivation. This work provides a biochemical mechanism for the pathogen's transition from latency to reactivation and underscores the role of human codon usage in innate immunity.
GLOBAL MEDICAL GENETICS
(2022)
Review
Food Science & Technology
Wieneke Dijk, Caterina Villa, Sara Benede, Emilia Vassilopoulou, Isabel Mafra, Maria Garrido-Arandia, Monica Martinez Blanco, Gregory Bouchaud, Tamara Hoppenbrouwers, Simona Lucia Bavaro, Linda Giblin, Karen Knipping, Ana Maria Castro, Susana Delgado, Joana Costa, Shanna Bastiaan-Net
Summary: New types of protein sources entering our diet require a straightforward in vitro screening model to predict the safety and potential risk for allergic sensitization. However, there is no consensus on the in vitro model to study protein translocation and epithelial activation, which are crucial events in allergic sensitization. INFOGEST members have highlighted critical features and defined indispensable and optional intestinal cell types for a consensus model to study epithelial protein transport in the context of allergic sensitization.
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2023)
Article
Chemistry, Medicinal
Marco Daniele Parenti, Marina Naldi, Elisabetta Manoni, Edoardo Fabini, Daniela Cederfelt, Vladimir O. Talibov, Valeria Gressani, Ummu Guven, Valentina Grossi, Candida Fasano, Paola Sanese, Katia De Marco, Alexander A. Shtil, Alexander V. Kurkin, Andrea Altieri, U. Helena Danielson, Giuseppina Caretti, Cristiano Simone, Greta Varchi, Manuela Bartolini, Alberto Del Rio
Summary: Recent findings suggest that inhibiting SMYD3 methyltransferase could be a therapeutic strategy for certain deadly cancer types. This study designed active site-selective covalent SMYD3 inhibitors and demonstrated their ability to attenuate tumor biology at the cellular and genetic levels, inhibiting important genes and cell proliferation.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Darja Kanduc
Summary: This study investigated the molecular mimicry between respiratory syncytial virus (RSV) F glycoprotein (gp) antigen and the human proteome. The results showed that the viral antigen shares a significant number of pentapeptides with human proteins, with 525 out of 570 common sequences. These viral sequences are widely distributed among 3,762 human proteins involved in crucial cellular functions. These findings have implications for the development of anti-RSV vaccines, suggesting the need for safer vaccination protocols based on pentapeptide sequences unique to the viral antigen.
GLOBAL MEDICAL GENETICS
(2023)
Review
Biochemistry & Molecular Biology
Martina Lepore Signorile, Valentina Grossi, Candida Fasano, Cristiano Simone
Summary: Colorectal cancer (CRC) is a deadly form of cancer that can be prevented through early detection and chemoprevention. Various approaches, including screening and the use of preventive agents, have been researched. The ideal chemopreventive agent should be well tolerated, easily administered, and cost-effective. However, further investigation is required to develop a comprehensive and effective strategy for CRC chemoprevention.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Darja Kanduc
Summary: This study examines the immune response of newborns and children to SARS-CoV-2 after prophylactic immunization, and suggests that the immune response may not only target the virus but also human proteins associated with infantile diseases through molecular mimicry and cross-reactivity. The findings reveal a potential link between exposure to SARS-CoV-2 and pediatric diseases, highlighting the role of immunologic memory and the child's infection history in determining the immune response and autoimmune complications.
GLOBAL MEDICAL GENETICS
(2023)
Article
Genetics & Heredity
Darja Kanduc
Summary: This study examined the peptide sharing between KISS1, its receptor KISSR, and SARS-CoV-2. The results showed that SARS-CoV-2 shares multiple minimal immune pentapeptide determinants with KISSR only. This peptide sharing has a high immunologic potential and may contribute to the development of hypogonadotropic hypogonadism syndrome associated with altered KISSR.
GLOBAL MEDICAL GENETICS
(2023)
Article
Oncology
Antonino Pantaleo, Giovanna Forte, Filomena Cariola, Anna Maria Valentini, Candida Fasano, Paola Sanese, Valentina Grossi, Antonia Lucia Buonadonna, Katia De Marco, Martina Lepore Signorile, Anna Filomena Guglielmi, Andrea Manghisi, Gianluigi Gigante, Raffaele Armentano, Vittoria Disciglio, Cristiano Simone
Summary: This study clinically and molecularly characterized CRC patients with LS features. The majority of patients had pathogenic or likely pathogenic variants in MMR genes, highlighting the importance of personalized medicine in LS and hereditary cancer syndromes.
Article
Genetics & Heredity
Darja Kanduc
Summary: This study highlights molecular mimicry and its resulting autoimmune cross reactivity as the molecular mechanism behind adverse events following meningococcal B vaccination. It also warns against active immunizations based on entire antigens.
GLOBAL MEDICAL GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Candida Fasano, Martina Lepore Signorile, Katia De Marco, Giovanna Forte, Paola Sanese, Valentina Grossi, Cristiano Simone
Summary: This study screened the affinity of a tripeptide library to SMYD3 and identified new SMYD3-interacting proteins through computational analysis. These findings are important for understanding the role of SMYD3 in cancer development and for developing therapeutic strategies.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
