Review
Immunology
Jingyun Wang, Keying Liang, Li Chen, Xiaoling Su, Daoyong Liao, Jianwei Yu, Jun He
Summary: Mycoplasmas, the smallest self-replicating organisms, are capable of causing infections in humans and animals. They have developed various evasion strategies to avoid immune responses, including invasion, biofilm formation, and modulation of immune reactions.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Najla Arshad, Maudry Laurent-Rolle, Wesam S. Ahmed, Jack Chun-Chieh Hsu, Susan M. Mitchell, Joanna Pawlak, Debrup Sengupta, Kabir H. Biswas, Peter Cresswell
Summary: Two accessory proteins encoded by SARS-CoV-2, ORF3a and ORF7a, down-regulate MHC-I expression through distinct mechanisms, reducing surface MHC-I levels and enabling immune evasion by the virus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Magdalena P. Crossley, Joshua R. Brickner, Chenlin Song, Su Mon Thin Zar, Su S. Maw, Frederic Chedin, Miaw-Sheue Tsai, Karlene A. Cimprich
Summary: The study focused on imaging R-loop structures, highlighting the issues with using the S9.6 antibody and proposing GFP-dRNH1 as a more specific imaging reagent that can effectively bind to RNA-DNA hybrids without binding to dsRNA oligonucleotides and being susceptible to endogenous RNA interference. Purified GFP-dRNH1 can be used to detect RNA-DNA hybrids in fixed cells, bypassing the need for cell line engineering.
JOURNAL OF CELL BIOLOGY
(2021)
Review
Immunology
Karthik Dhatchinamoorthy, Jeff D. Colbert, Kenneth L. Rock
Summary: Loss of MHC I antigen presentation is common in many cancers, which may impair immune responses and affect the efficacy of immunotherapy. Studies have discussed underlying mechanisms through which some cancers evade immune killing by shutting down the MHC I pathway, and proposed potential strategies to overcome this limitation.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Dzana Dervovic, Ahmad A. Malik, Edward L. Y. Chen, Masahiro Narimatsu, Nina Adler, Somaieh Afiuni-Zadeh, Dagmar Krenbek, Sebastien Martinez, Ricky Tsai, Jonathan Boucher, Jacob M. Berman, Katie Teng, Arshad Ayyaz, Yiqing Lu, Geraldine Mbamalu, Sampath K. Loganathan, Jongbok Lee, Li Zhang, Cynthia Guidos, Jeffrey Wrana, Arschang Valipour, Philippe P. Roux, Juri Reimand, Hartland W. Jackson, Daniel Schramek
Summary: There is still limited understanding of the mechanisms of sensitivity/resistance to cancer immunotherapy. In this study, the authors perform CRISPR/Cas9 loss-of-function screens in mouse lung cancer models and identify Serpinb9 and Adam2 as regulators of immunotherapy response. ADAM2 functions as an oncogene by restraining cytokine signaling and expression of immune checkpoint inhibitors, leading to reduced tumor antigen presentation.
NATURE COMMUNICATIONS
(2023)
Review
Oncology
Junyang Wang, Tong Liu, Tao Huang, Mei Shang, Xudong Wang
Summary: Malignant tumors, such as gastric cancer, have the ability to evade the immune system by altering tumor-associated antigens, antigen presentation mechanisms, and the tumor microenvironment.
FRONTIERS IN ONCOLOGY
(2022)
Review
Microbiology
Joana Faria, Emma M. Briggs, Jennifer A. Black, Richard McCulloch
Summary: The survival and transmission of the African trypanosome rely on antigenic variation, which involves stochastic changes in the composition of their protective VSG coat. This process can be executed through transcriptional or recombination reactions. Understanding the cellular machinery behind this process is crucial for potential interventions.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Review
Oncology
Junyi An, Xiaohua Hu, Feng Liu
Summary: Cancer stem cells (CSCs) possess immune privilege properties to evade immune system attack. Gastrointestinal CSCs (GCSCs) are involved in tumor initiation, progression, metastasis, and recurrence, with high resistance to conventional therapies. Targeting GCSCs through immunotherapy is a promising strategy.
FRONTIERS IN ONCOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Justyna Szczykutowicz
Summary: This article discusses the immunological outcomes of human macrophage galactose-type lectin (MGL) ligand recognition, provides insights into the molecular aspects of these interactions, and reviews the MGL ligands discovered so far. It also raises the question of whether MGL-mediated interactions may be relevant in the development of maternal tolerance toward male gametes and the fetus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Hematology
Masahiro Chiba, Joji Shimono, Takashi Ishio, Norio Takei, Kohei Kasahara, Reiki Ogasawara, Takahide Ara, Hideki Goto, Koh Izumiyama, Satoko Otsuguro, Liyanage P. Perera, Hiroo Hasegawa, Michiyuki Maeda, Satoshi Hashino, Katsumi Maenaka, Takanori Teshima, Thomas A. Waldmann, Yibin Yang, Masao Nakagawa
Summary: Adult T-cell leukemia/lymphoma (ATLL) is an aggressive peripheral T-cell neoplasm with poor prognosis. This study reveals that CD48 expression in ATLL cells determines the sensitivity for NK-cell-mediated cytotoxicity against ATLL cells, suggesting CD48 as a potential molecular biomarker in NK-cell-associated immunotherapies.
Review
Immunology
Alex Bear, Thomas Locke, Sarah Rowland-Jones, Simone Pecetta, Fabio Bagnoli, Thomas C. Darton
Summary: This article discusses the mechanisms of S. aureus infection and the importance of immune evasion, with a focus on the protein SpA. Understanding the mechanisms of immune evasion is crucial for the development of effective vaccines and monoclonal antibodies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Cell Biology
Haitian Fu, Jiachen Lu, Xinxin Zhang, Bo Wang, Yifan Sun, Yao Lei, Feihu Shen, Kokouvi Kassegne, Eun-Taek Han, Yang Cheng
Summary: Plasmodium vivax-infected erythrocytes may evade splenic clearance by interacting with splenic fibroblasts (HSF) in the spleen, with PvSRA potentially changing HSF cell function to participate in immune evasion of P. vivax.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Yue A. Qi, Tapan K. Maity, Shaojian Gao, Tao Gong, Meriam Bahta, Abhilash Venugopalan, Xu Zhang, Udayan Guha
Summary: By studying the proteomics of EGFR TKI-resistant lung adenocarcinoma cells, we have identified a reduction in the HLA class I-presented immunopeptidome, downregulation of antigen presentation core complex and immunoproteasome, as well as differential alterations in certain components of the autophagy pathway. These findings reveal potential immune evasion mechanisms in osimertinib-resistant lung adenocarcinoma.
Review
Biochemistry & Molecular Biology
Katrin Pansy, Barbara Uhl, Jelena Krstic, Marta Szmyra, Karoline Fechter, Ana Santiso, Lea Thueminger, Hildegard Greinix, Julia Kargl, Katharina Prochazka, Julia Feichtinger, Alexander JA. Deutsch
Summary: The TME plays a crucial role in regulating tumor growth and metastasis, with immune escape enabling tumor cells to maintain their proliferation. Novel immunotherapies have been successfully developed based on intensive study of the mechanisms involved in immune evasion, such as membrane-bound and soluble factors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Miroslawa Panasiuk, Milena Chraniuk, Karolina Zimmer, Lilit Hovhannisyan, Vasil Krapchev, Grazyna Peszynska-Sularz, Magdalena Narajczyk, Jan Weslawski, Agnieszka Konopacka, Beata Gromadzka
Summary: Chimeric virus-like particles (cVLPs) have the potential to improve public health as safe and effective vaccine candidates. Capsid proteins of caliciviruses can be genetically modified to present foreign epitopes on the surface of cVLPs, enhancing the immune response to low immunogenic antigens. The impact of epitope localization in different structural loops of the VP1 protein of norovirus (NoV) on immunogenicity was investigated using insect cells to produce cVLPs presenting influenza virus-conserved epitopes. The study compared the specific reaction to influenza epitopes in vaccinated mice to determine the impact of epitope localization on immunogenicity.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Genetics & Heredity
Jeziel D. Damasceno, Catarina A. Marques, Jennifer Black, Emma Briggs, Richard McCulloch
Summary: Genomes are read and copied during growth and development, purposely altered to adapt cellular behavior and drive evolution. Kinetoplastids demonstrate a wide range of genome activities that affect their adaptability and biology.
TRENDS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Ann-Kathrin Mehnert, Marco Prorocic, Annick Dujeancourt-Henry, Sebastian Hutchinson, Richard McCulloch, Lucy Glover
Summary: In Trypanosoma brucei, RAD50 and MRE11 are essential for RAD51-dependent homologous recombination and phosphorylation of histone H2A following a DNA double strand break. RAD50 suppresses DSB repair using short stretches of homology at a subtelomeric locus, while MRE11 directs DSB resection at the same locus. Loss of either MRE11 or RAD50 leads to increased diversity of expressed VSG variants following DSB repair, suggesting that MRN promotes stringent homologous recombination at subtelomeric loci and restrains antigenic variation.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Parasitology
Emma M. Briggs, Felix S. L. Warren, Keith R. Matthews, Richard McCulloch, Thomas D. Otto
Summary: Single-cell transcriptomics can help researchers overcome challenges in studying kinetoplastid parasites, discover key genes in the life cycle, and analyze host-parasite interactions in depth.
Article
Multidisciplinary Sciences
Emma M. Briggs, Federico Rojas, Richard McCulloch, Keith R. Matthews, Thomas D. Otto
Summary: This study models the developmental steps of Trypanosoma brucei using oligopeptide-induced differentiation in vitro, capturing the transcriptomes of parasites through single cell transcriptomics. It details the relative order of biological events during asynchronous development, profiles dynamic gene expression patterns, identifies putative regulators, and provides a paradigm for dissecting differentiation events in parasites.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Pieter C. Steketee, Emily A. Dickie, James Iremonger, Kathryn Crouch, Edith Paxton, Siddharth Jayaraman, Omar A. Alfituri, Georgina Awuah-Mensah, Ryan Ritchie, Achim Schnaufer, Tim Rowan, Harry P. de Koning, Catarina Gadelha, Bill Wickstead, Michael P. Barrett, Liam J. Morrison
Summary: This study comprehensively analyzed the core metabolism of Trypanosoma congolense, a parasite responsible for Animal African Trypanosomiasis, revealing significant differences in metabolic pathways compared to T. brucei. The findings suggest that T. congolense is less sensitive to metabolic inhibitors, especially those targeting fatty acid synthesis, highlighting key metabolic distinctions between the two species.
Article
Cell Biology
Nicolas Rabas, Sarah Palmer, Louise Mitchell, Shehab Ismail, Andrea Gohlke, Joel S. Riley, Stephen W. G. Tait, Payam Gammage, Leandro Lemgruber Soares, Iain R. Macpherson, Jim C. Norman
Summary: This study reveals that breast cancer cells activate Rab27-dependent release of EVs through mGluR3, containing mtDNA that promotes intercellular transfer of invasive behavior via Toll-like receptor 9, highlighting the role of altered cellular metabolism in generating and disseminating pro-invasive microenvironments during mammary carcinoma progression.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y. Basenko, Wojciech Bazant, Robert Belnap, Ann S. Blevins, Ulrike Bohme, John Brestelli, Brian P. Brunk, Mark Caddick, Danielle Callan, Lahcen Campbell, Mikkel B. Christensen, George K. Christophides, Kathryn Crouch, Kristina Davis, Jeremy DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria Giraldo-Calderon, Omar S. Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J. Hickman, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S. Roos, Samuel S. C. Rund, Stephanie Wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J. Stoeckert, Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Lin Xu, Jie Zheng
Summary: VEuPathDB project is a bioinformatics resource center funded by the National Institutes of Health, supporting over 500 organisms including invertebrate vectors, eukaryotic pathogens, and hosts. It integrates over 1700 pre-analyzed datasets, providing advanced search capabilities, visualizations, and analysis tools, with standardized workflows for researchers to access Omics data and bioinformatic analyses.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Stevie A. Bain, Heleen Plaisier, Felicity Anderson, Nicola Cook, Kathryn Crouch, Thomas R. Meagher, Michael G. Ritchie, Edward W. J. Wallace, Daniel Barker
Summary: The nature of life sciences research has changed, creating a demand for a workforce with computational skills. However, bioinformatics education has not kept up with research advancements. The 4273pi Bioinformatics at School project aims to address this issue by providing hands-on bioinformatics workshops for secondary school students and has reached over 180 schools in Scotland.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Infectious Diseases
Pieter C. Steketee, Federica Giordani, Isabel M. Vincent, Kathryn Crouch, Fiona Achcar, Nicholas J. Dickens, Liam J. Morrison, Annette Macleod, Michael P. Barrett
Summary: Acoziborole, a newly developed benzoxaborole, shows promise in treating Human African Trypanosomiasis and potentially reducing drug resistance.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Multidisciplinary Sciences
Juan F. Quintana, Praveena Chandrasegaran, Matthew C. Sinton, Emma M. Briggs, Thomas D. Otto, Rhiannon Heslop, Calum Bentley-Abbot, Colin Loney, Luis de Lecea, Neil A. Mabbott, Annette MacLeod
Summary: By studying single-cell and spatial transcriptomics of the mouse brain, we found that glial cell responses triggered by African trypanosome infection could be detected near circumventricular organs, which coincided with the spatial localization of the parasite. Additionally, we discovered an unknown interaction between homeostatic microglia and plasma cells. This study provides important insights into the molecular and cellular responses in the brain during infection with African trypanosomes.
NATURE COMMUNICATIONS
(2022)
Article
Infectious Diseases
Achchuthan Shanmugasundram, David C. Starns, Ulrike Bohme, Beatrice S. Amos, Paul A. Wilkinson, Omar S. R. Harb, Susanne Warrenfeltz, Jessica C. Kissinger, Mary Ann McDowell, David S. Roos, Kathryn Crouch, Andrew Jones
Summary: Parasitic diseases caused by kinetoplastid parasites are a global public health burden, particularly in tropical and subtropical regions. TriTrypDB is an online resource that allows users to access genomic and functional data from these parasites. It offers a user-friendly interface, a genome browser, and bioinformatics tools for custom experiments. TriTrypDB also integrates various types of data, including transcriptomic, proteomic, and epigenomic information.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Microbiology
Wojtek Bazant, Ann S. S. Blevins, Kathryn Crouch, Daniel P. P. Beiting
Summary: The study presents a tool called CORRAL for identifying eukaryotes in shotgun metagenomic data. It utilizes eukaryote-specific marker genes and Markov clustering to automate the detection of eukaryotes, even those not represented in the reference marker gene set, such as novel strains.
Article
Microbiology
Jennifer A. Black, Christen M. Klinger, Leandro Lemgruber, Joel B. Dacks, Jeremy C. Mottram, Richard McCulloch
Summary: Cargo selection and internalization during clathrin-mediated endocytosis rely on adaptor protein complexes, such as AP-2. African trypanosomes lack most components of the AP-2 complex, but possess two orthologues of the AP-2-associated protein kinase 1 (AAK1), AAK1L1 and AAK1L2. While AAK1L2 is absent in salivarian trypanosomes, AAK1L1 is found in various trypanosomes but lacks important kinase-specific residues. In Trypanosoma brucei, the absence of AAK1L1 results in slowed proliferation, morphological abnormalities, and altered cargo uptake, suggesting an unconventional role for this putative pseudokinase in endocytosis and vesicular trafficking.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mark J. Girasol, Emma M. Briggs, Catarina A. Marques, Jose M. Batista, Dario Beraldi, Richard Burchmore, Leandro Lemgruber, Richard McCulloch
Summary: This study identifies and characterizes proteins that interact with RNA-DNA hybrids in the African trypanosome, revealing their diverse and important roles in host immune evasion and eukaryotic genome function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
William Haese-Hill, Kathryn Crouch, Thomas D. Otto
Summary: In this study, peaks2utr, an easy-to-use Python command line tool, is presented to accurately annotate 30 UTRs for a given canonical annotation using UTR enrichment of single-cell technologies, such as 10x Chromium. This addresses the open problem of annotation of nonmodel organisms.