Article
Genetics & Heredity
Liliya Fedulova, Ekaterina Vasilevskaya, Olga Tikhonova, Laura Kazieva, Galina Tolmacheva, Alexandr Makarenko
Summary: This study investigates the post-genomic markers associated with recovery from hemorrhagic stroke, revealing molecular factors that contribute to neuronal functional recovery and reduce damage factors. The study also identifies neurotrophic factors associated with nerve cell survival and differentiation in muscles.
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
Medicine, General & Internal
Aoqierbatu, Aqilatu Luo, Yuting Shi, Yuyan Na, Ya Tuo
Summary: This study identified genes and pathways associated with damaged knee cartilage tissues using microarray analysis, revealing hub genes and pathways strongly linked to cartilage injury. These findings offer new insights into potential pathological mechanisms and therapeutic strategies for cartilage injury.
Article
Biochemical Research Methods
Hongjun Chen, Yekai Zhou, Yongjing Liu, Peijing Zhang, Ming Chen
Summary: This study integrated clinical and biomedical research data to systematically mine and analyze pathological proteins and their interaction network in neurodegenerative diseases. It proposed a solution that includes protein isoforms to reveal the impact of protein binding interactions on disease. Finally, a Neurodegenerative Disease Atlas was constructed with interactive 3D molecular graphics.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Nimisha Ghosh, Indrajit Saha, Nikhil Sharma
Summary: SARS-CoV-2 has a higher chance of progression in adults with certain underlying health conditions or comorbidities, possibly leading to death. Understanding host-virus protein interactions can aid in designing effective antiviral drugs. Identifying hub proteins connected to most human proteins helps predict potential diseases and comorbidities.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Plant Sciences
Merve Yilmaz, Merle Paulic, Thorsten Seidel
Summary: This study reports a protein-protein interaction network of Arabidopsis thaliana, combining various types of information such as subcellular localization, gene ontologies, biochemical properties, and co-expression. The resulting network shows enrichment in nuclear, cytosolic, and plasma membrane proteins, while being depleted in extracellular and mitochondrial proteins. Additionally, proteins involved in transcription are highly abundant in the network.
Article
Biochemistry & Molecular Biology
Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David Garcia-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti J. Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaino
Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Xinling He, Ji Yin, Mingfang Yu, Jiao Qiu, Aiyang Wang, Haoyu Wang, Xueyi He, Xiao Wu
Summary: The hub genes LCK, JAK2, SOCS3, STAT1, and EGFR were found to play important roles in the progression of rheumatoid arthritis (RA) and may provide novel therapeutic treatments for RA.
AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH
(2022)
Article
Biochemical Research Methods
Raiha Tahir, Anil K. Madugundu, Savita Udainiya, Jevon A. Cutler, Santosh Renuse, Li Wang, Nicole A. Pearson, Christopher J. Mitchell, Nupam Mahajan, Akhilesh Pandey, Xinyan Wu
Summary: In this study, the researchers used BioID to explore the interactome of TNK2, identifying both known and novel interacting partners. They also validated the interaction between TNK2 and CLINT1 through co-immunoprecipitation and immunofluorescence analysis, highlighting the potential functional significance of these molecules in TNK2-mediated signaling.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Narumi Watanabe, Yuuto Ohnuki, Yasubumi Sakakibara
Summary: This study developed a deep learning-based method that integrates protein features, compound features, and multiple types of interactome data to predict protein-compound interactions. Performance evaluations showed that the deep learning framework outperformed state-of-the-art machine learning methods for protein-compound interaction prediction tasks. The improvement in performance was statistically significant, indicating that multi-interactome data can enhance prediction accuracy.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Immunology
Kristina Zec, Stephanie Thiebes, Jenny Bottek, Devon Siemes, Philippa Spangenberg, Duc Viet Trieu, Nils Kirstein, Nirojah Subramaniam, Robin Christ, Diana Klein, Verena Jendrossek, Maria Loose, Florian Wagenlehner, Jadwiga Jablonska, Thilo Bracht, Barbara Sitek, Bettina Budeus, Ludger Klein-Hitpass, Dirk Theegarten, Olga Shevchuk, Daniel R. Engel
Summary: This study provides novel insights into the molecular adaptations of alveolar macrophages (AM) upon lung infection with Streptococcus pneumoniae. The results reveal a strong neutrophil-associated proteomic signature in AM, and identify CD11b as a central molecular hub influencing neutrophil recruitment, activation, and migration.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Zahra Pezeshkian, Seyed Ziaeddin Mirhoseini, Shahrokh Ghovvati
Summary: In this study, candidate genes associated with divergent apparent metabolizable energy in chickens were identified through bioinformatics analysis. Important biological pathways and gene modules related to feed efficiency were successfully identified, and core genes closely related to apparent metabolizable energy in chickens were determined. These core genes can serve as biomarkers for apparent metabolizable energy and feed efficiency in chickens.
ANIMAL BIOTECHNOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Ciaran P. Seath, Aaron D. Trowbridge, Tom W. Muir, David W. C. MacMillan
Summary: Biomolecular interactions are crucial for cellular processes, with a focus on protein-protein interactions playing a key role in cellular signaling pathways. Recent advancements in creating reactive intermediates that cross-link neighboring proteins have provided insights into the biomolecular makeup of cellular environments, accelerating the understanding of PPIs and their impact on cellular physiology.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Biochemical Research Methods
Chujun Duan, Xiaojun Zhao, Xiao Li, Jiangang Xie, Yi Si, Linxiao Wang, Dan Wu, Yifan Wang, Shanshou Liu, Qianmei Wang, Ran Zhuang, Wen Yin, Junjie Li
Summary: The study investigates the pathophysiological alterations in liver transplantation (LT) by analyzing transcriptome sequencing data. The researchers identified differentially expressed genes (DEGs) and enriched pathways in the LT process. Hub genes, such as PTEN, MYC, and EIF2S1, were identified through protein-protein interaction network analysis. Furthermore, a structure-based virtual screening process (SBVS) predicted potential inhibitors for PTEN.
MOLECULAR AND CELLULAR PROBES
(2023)
Review
Chemistry, Multidisciplinary
Isabel V. L. Wilkinson, Martin Pfanzelt, Stephan A. Sieber
Summary: Cofactors are essential for enzyme reactions, and their functions and binding partners still remain partly unknown. The use of cofactor mimics and chemical proteomics approaches can help uncover their activities and biological properties. The diverse activities of cofactors have inspired various applications, such as antibiotic therapeutics, inhibitors, and biosensors.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Hematology
Javier Raboso-Gallego, Ana Casado-Garcia, Xiaoyu Jiang, Marta Isidro-Hernandez, Andrew J. Gentles, Shuchun Zhao, Yaso Natkunam, Oscar Blanco, Veronica Dominguez, Belen Pintado, Diego Alonso-Lopez, Javier De las Rivas, Carolina Vicente-Duenas, Izidore S. Lossos, Isidro Sanchez-Garcia
Summary: The study shows that constitutive enforced expression of HGAL leads to DLBCL development, and this protein is mainly present in germinal center B lymphocytes.
Article
Oncology
Ana Casado-Garcia, Marta Isidro-Hernandez, Ninad Oak, Andrea Mayado, Christine Mann-Ran, Javier Raboso-Gallego, Silvia Aleman-Arteaga, Alexandra Buhles, Dario Sterker, Elena G. Sanchez, Jorge Martinez-Cano, Oscar Blanco, Alberto Orfao, Diego Alonso-Lopez, Javier De Las Rivas, Susana Riesco, Pablo Prieto-Matos, Africa Gonzalez-Murillo, Francisco Javier Garcia Criado, Maria Begona Garcia Cenador, Thomas Radimerski, Manuel Ramirez-Orellana, Cesar Cobaleda, Jun J. Yang, Carolina Vicente-Duenas, Andreas Weiss, Kim E. Nichols, Isidro Sanchez-Garcia
Summary: This study demonstrates that early-life administration of the JAK1/2 inhibitor ruxolitinib significantly reduces the risk of B-ALL in mice. This finding presents a potential strategy for preventing the development of B-ALL.
Review
Pharmacology & Pharmacy
Joanna Kopecka, Iris C. Salaroglio, Elizabeth Perez-Ruiz, Ana Bela Sarmento-Ribeiro, Simona Saponara, Javier De Las Rivas, Chiara Riganti
Summary: Hypoxia in solid tumors leads to resistance to immunotherapy, particularly to ICPIs and CAR T-cells, by promoting immunosuppressive populations and angiogenesis. Innovative combination therapies may provide a solution to enhance the efficacy of immunotherapy against hypoxic and therapy-resistant tumors.
DRUG RESISTANCE UPDATES
(2021)
Article
Immunology
Pablo Juanes-Velasco, Alicia Landeira-Vinuela, Marina L. Garcia-Vaquero, Quentin Lecrevisse, Raquel Herrero, Antonio Ferruelo, Rafael Gongora, Fernando Corrales, Javier De Las Rivas, Jose A. Lorente, Angela-Patricia Hernandez, Manuel Fuentes
Summary: This study analyzed the immune profile of severe ARDS in COVID-19 patients using functional proteomics approaches. It found that the autoimmune profiles were correlated with disease severity and clinical progression, providing new perspectives for therapeutic development and biomarker identification in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Oncology
Raquel Alves, Ana Cristina Goncalves, Sergio Rutella, Antonio M. Almeida, Javier De Las Rivas, Ioannis P. Trougakos, Ana Bela Sarmento Ribeiro
Summary: Chronic myeloid leukemia (CML) is associated with a molecular alteration resulting in the BCR-ABL1 fusion gene, and resistance to tyrosine kinase inhibitors (TKIs) such as Imatinib may occur during treatment. Understanding the molecular mechanisms of TKI resistance, in addition to patient adherence, is crucial for managing CML effectively.
Article
Oncology
Santiago Bueno-Fortes, Julienne K. Muenzner, Alberto Berral-Gonzalez, Chuanpit Hampel, Pablo Lindner, Alexandra Berninger, Kerstin Huebner, Philipp Kunze, Tobias Baeuerle, Katharina Erlenbach-Wuensch, Jose Manuel Sanchez-Santos, Arndt Hartmann, Javier de las Rivas, Regine Schneider-Stock
Summary: In this study, a gene signature associated with the loss of CDKN1A gene in HCT116 p21-/- colorectal cancer cells is identified and shown to be related to the CMS4 subtype of colon cancer. This gene signature is associated with worse relapse-free and overall survival. The findings provide insights into the molecular mechanisms of epithelial-mesenchymal transition and contribute to our understanding of tumor progression.
Article
Biochemistry & Molecular Biology
Alicia Landeira-Vinuela, Paula Diez, Pablo Juanes-Velasco, Quentin Lecrevisse, Alberto Orfao, Javier de las Rivas, Manuel Fuentes
Summary: The Human Proteome Project systematically characterized the protein landscape using diverse techniques in this study, which focused on a B-cell lymphoma cell line. Through integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics, 5672 unique proteins were identified and further analyzed for insights into protein dynamics at the intracellular level. The study also developed a bioinformatic pipeline for the comprehensive and global characterization of intracellular protein profiles.
Article
Oncology
Mattia D'Agostino, David A. Cairns, Juan Jose Lahuerta, Ruth Wester, Uta Bertsch, Anders Waage, Elena Zamagni, Maria-Victoria Mateos, Daniele Dall'Olio, Niels W. C. J. van de Donk, Graham Jackson, Serena Rocchi, Hans Salwender, Joan Blade Creixenti, Bronno van der Holt, Gastone Castellani, Francesca Bonello, Andrea Capra, Elias K. Mai, Jan Durig, Francesca Gay, Sonja Zweegman, Michele Cavo, Martin F. Kaiser, Hartmut Goldschmidt, Jesus Maria Hernandez Rivas, Alessandra Larocca, Gordon Cook, Jesus F. San-Miguel, Mario Boccadoro, Pieter Sonneveld
Summary: In this study, the Revised International Staging system (R-ISS) for intermediate-risk multiple myeloma patients was revised based on the additive value of each single risk feature.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Economics
Francesco Cerisoli, Farzad Ali, Tamas Bereczky, Natacha Bolanos, Lars Bullinger, Sujith Dhanasiri, James Gallagher, Sonia Garcia Perez, Jan Geissler, Yann Guillevic, Kathryn Harrison, Anastasia Naoum, Carla Portulano, Ana E. Rodriguez Vicente, Renate Schulze-Rath, Gabriela Yumi Gomez, Guillermo Sanz, Jesus Maria Hernandez Rivas
Summary: The HARMONY project aims to evaluate the suitability of existing value frameworks (VFs) for assessing the clinical and societal impact of new interventions for hematologic malignancies (HMs). Through surveys and questionnaires, the project identified important outcomes and preferred data sources for each HM. The comparative analysis highlights the challenges and opportunities of existing frameworks in the context of HMs and proposes possible actions for creating or integrating a more specific, patient-focused clinical VF.
Article
Immunology
Alicia Landeira-Vinuela, Carlota Arias-Hidalgo, Pablo Juanes-Velasco, Miguel Alcoceba, Almudena Navarro-Bailon, Carlos Eduardo Pedreira, Quentin Lecrevisse, Laura Diaz-Munoz, Jose Manuel Sanchez-Santos, Angela-Patricia Hernandez, Marina L. Garcia-Vaquero, Rafael Gongora, Javier De Las Rivas, Marcos Gonzalez, Alberto Orfao, Manuel Fuentes
Summary: Chronic lymphocytic leukemia (CLL) is a lymphoid neoplasm characterized by the accumulation of mature B cells. The diagnosis is established by the detection of monoclonal B lymphocytes in peripheral blood, even in early stages [monoclonal B-cell lymphocytosis (MBLhi)], and its clinical course is highly heterogeneous. Multiple prognostic factors, such as immunoglobulin heavy chain variable region (IGHV) mutational status, del17p, and TP53 mutations, are related to the observed genetic heterogeneity. In addition, dysregulation of the immune system and the complexity of the tumor microenvironment play critical roles in the onset, progression, and therapy response of CLL.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Manuel Fuentes, Cristina Ruiz-Romero, Sara Misiego, Pablo Juanes-Velasco, Alicia Landeira-Vinuela, Adrian Torres-Roda, Hector Lorenzo-Gil, Maria Gonzalez-Gonzalez, Angela P. Hernandez, Lucia Lourido, Ronald Sjoberg, Elisa Pin, Javier de Las Rivas, Jose Manuel Sanchez-Santos, Peter Nilsson, Francisco J. Blanco
Summary: Rheumatic diseases are common and complex conditions with low sensitivity to clinical diagnosis. This study developed an early diagnosis method for personalized treatment based on the identification of relevant proteins associated with the specific pathologies. By utilizing functional proteomics screening, a panel of 30 serum proteins has been identified as potential biomarkers for rheumatic diseases such as osteoarthritis, rheumatoid arthritis, and psoriatic arthritis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Alicia Landeira-Vinuela, Miguel Alcoceba-Sanchez, Almudena Navarro-Bailon, Carlota Arias-Hidalgo, Pablo Juanes-Velasco, Jose Manuel Sanchez-Santos, Quentin Lecrevisse, Carlos Eduardo Pedreira, Marina L. Garcia-Vaquero, Angela-Patricia Hernandez, Enrique Montalvillo, Rafael Gongora, Javier de las Rivas, Marcos Gonzalez-Diaz, Alberto Orfao, Manuel Fuentes
Summary: Clonal B cell expansion in chronic lymphocytic leukemia may be triggered by persistent antigenic stimulation. Studying the dynamics of the humoral response in these patients can provide information about immunoglobulin levels and identify compromising antigens. This study offers a new perspective for patient stratification and targeted therapy selection.
Article
Biochemistry & Molecular Biology
Natalia Alonso-Moreda, Alberto Berral-Gonzalez, Enrique De La Rosa, Oscar Gonzalez-Velasco, Jose Manuel Sanchez-Santos, Javier De Las Rivas
Summary: In the past two decades, there have been many studies on complex biological samples that provide bulk expression signals but fail to identify specific genes in specific cell types due to cellular heterogeneity. To solve this problem, computational techniques have been developed to deconvolve cell mixtures and calculate the relative proportions of cellular components. This study implemented five deconvolution methods and analyzed blood, immune cells, and cancer cells in complex mixture samples. The results show that CIBERSORT is optimized for identifying immune cell types, while LINSEED provides precise gene signatures for immune cell types and cancer cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Hematology
Sandra Muntion, Silvia Preciado, Elena Sanchez-Luis, Luis Corchete, Maria Diez-Campelo, Lika Osugui, Gerardo-Javier Marti-Chillon, Maria-Belen Vidriales, Almudena Navarro-Bailon, Javier De Las Rivas, Fermin Sanchez-Guijo
Summary: This study found that Eltrombopag (EP) not only has direct effects on hematopoietic cells, but also affects the function and properties of mesenchymal stem cells (MSCs), enhancing their ability to support hematopoiesis. These findings are important for the treatment of hematopoietic disorders.
THERAPEUTIC ADVANCES IN HEMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marina L. Garcia-Vaquero, Margarida Gama-Carvalho, Francisco R. Pinto, Javier De Las Rivas
Summary: The centrality measures of individual proteins are insufficient to dissect the functional properties of cells, a more comprehensive, relational and context-specific method is needed. The study reveals tissue-specific functional diversification based on the identification of specific protein units.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)