Article
Medicine, Research & Experimental
Caishang Zheng, Yanjun Wei, Peng Zhang, Longyong Xu, Zhenzhen Zhang, Kangyu Lin, Jiakai Hou, Xiangdong Lv, Yao Ding, Yulun Chiu, Antrix Jain, Nelufa Islam, Anna Malovannaya, Yun Wu, Feng Ding, Han Xu, Ming Sun, Xi Chen, Yiwen Chen
Summary: Emerging evidence shows that cryptic translation within lncRNAs may produce new proteins with important functions. In this study, researchers found that estrogen receptor alpha-positive breast cancer depends on the cryptic ORFs encoded by upregulated lncRNA genes. They identified an unannotated protein, GT3-INCP, which promotes tumor growth and is associated with poor prognosis in luminal tumors. Mechanistically, GT3-INCP interacts with GATA3, a transcription factor important in mammary gland development and breast cancer cell proliferation, and regulates the expression of genes involved in estrogen response and cell proliferation.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Biochemistry & Molecular Biology
Bing Wang, Zhiwei Wang, Ni Pan, Jiangmei Huang, Cuihong Wan
Summary: A strategy combining top-down and de novo sequencing was proposed to improve SEP identification and sequence coverage, leading to the discovery of new coding sORFs and highly accurate sequences of their SEPs. The use of different sequencing methods revealed important insights into the characteristics of SEPs and their encoding sORFs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Lei Chen, Yuanliang Zhang, Ying Yang, Yang Yang, Huihui Li, Xuan Dong, Hongwei Wang, Zhi Xie, Qian Zhao
Summary: By implementing complementary bioinformatic strategies, this study improved the identification of noncanonical MHC-I peptides, leading to the discovery of 308 noncanonical peptides with vigorous validation. This approach not only benefits research in immunology, but also sheds light on potential implications for cancer immunotherapies.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Xinyu Miao, Yinyan Yin, Yulian Chen, Wenhui Bi, Yuncong Yin, Sujuan Chen, Daxin Peng, Lizeng Gao, Tao Qin, Xiufan Liu
Summary: A novel multi-antiviral metastable iron sulfides (mFeS) has been developed to target various influenza A/B subtype viruses. mFeS induces high levels of lipid peroxidation and center dot OH free radicals in the viral envelope, leading to viral ferroptosis and the loss of viral infectibility and pathogenicity. The decoction of mFeS inhibits intracellular viral replication by correcting virus-induced reprogrammed sulfur metabolism. mFeS represents a broad-spectrum antiviral alternative with potential therapeutic effect against influenza virus.
Article
Immunology
Stav Kozlovski, Ofer Regev, Anita Sapoznikov, Marina Kizner, Hagit Achdout, Ekaterina Petrovich-Kopitman, Jacob Elkahal, Yoseph Addadi, Fernanda Vargas E. Silva Castanheira, Sara W. Feigelson, Paul Kubes, Noam Erez, Natalio Garbi, Ronen Alon
Summary: In this study, the role of ICAM-1 and ICAM-2 in immune responses to influenza infection was investigated in mice. The results showed that lung capillary ICAMs were not essential for the entry of NK and neutrophils into virus-infected lungs. Additionally, ICAM-1 and ICAM-2 had little effect on the recruitment of naive T cells and B lymphocytes in mediastinal lymph nodes, but were critical for humoral immunity and the differentiation of CD8(+) T cells.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Virology
Lehao Ren, Wanju Zhang, Jing Zhang, Jiaxiang Zhang, Huiying Zhang, Yong Zhu, Xiaoxiao Meng, Zhigang Yi, Ruilan Wang
Summary: In this study, it was observed that the influenza A virus induces glycolysis in host cells, promoting viral replication. Inhibiting or enhancing the glycolytic pathway affects H1N1 replication, independent of interferon signaling. These findings suggest that metabolic inhibitors targeting glycolysis could potentially be used to treat influenza A virus infection in the future.
Article
Microbiology
Fadi G. Alnaji, William K. Reiser, Joel Rivera-Cardona, Aartjan J. W. te Velthuis, Christopher B. Brooke
Summary: Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection, influenced by specific molecular mechanisms such as direct sequence repeats and base enrichment. DelVGs face a significant bottleneck during genome packaging, with larger DelVGs showing signs of enrichment in packaged virions, suggesting size as an important determinant of packaging efficiency.
Article
Biology
Yansheng Li, Mingkai Xu, Yongqiang Li, Wu Gu, Gulinare Halimu, Yuqi Li, Zhichun Zhang, Libao Zhou, Hui Liao, Songyuan Yao, Huiwen Zhang, Chenggang Zhang
Summary: The study developed a recombinant protein named NMHC that induced both cross-protective antibody responses and T cell reactions, effectively protecting mice from multiple influenza virus infections. This vaccine holds promise as a candidate universal broad-spectrum vaccine for the prevention and treatment of multiple influenza viruses.
Article
Biochemistry & Molecular Biology
Chorong Jang, Scott W. Blume, Hyoung Soo Choi
Summary: This study confirmed the expression and intracellular location of MYCN uORF-encoded proteins MNOP and MYCNOT in neuroblastoma and medulloblastoma cells and tissues. The findings suggest that these proteins may play a role in regulating the expression of MYCN oncogene. Further research is needed to understand the physiological and pathological roles of these uORF-encoded proteins and their potential as targets for modulating MYC-family oncogenes.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Maximilian P. Kohl, Maria Kompatscher, Nina Clementi, Lena Holl, Matthias D. Erlacher
Summary: This study investigates the important factors in start codon recognition during translation initiation and discovers the existence of an ambiguous translation initiation mechanism, which may lead to the identification of unrecognized ORFs and translation products in bacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Virology
Rebecca Penn, John S. Tregoning, Katie E. Flight, Laury Baillon, Rebecca Frise, Daniel H. Goldhill, Cecilia Johansson, Wendy S. Barclay
Summary: Infections with highly pathogenic avian influenza viruses can cause severe disease due to excessive production of proinflammatory cytokines. Defective viral genomes (DVGs), which are generated during viral replication, can stimulate the immune response and alter the outcome of infection. This study found that the timing and levels of immunostimulatory DVGs are important factors in the pathogenesis of H5N1. Different levels of DVGs in virus stocks led to diverse outcomes in a mouse model, with high-DVG stocks causing mild disease and low-DVG stocks with accumulation of DVGs causing severe disease.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Xing Li, Zhiping Ye, Ewan P. Plant
Summary: By analyzing clinical and cultured samples using the same bioinformatic pipeline, it was found that 5' copyback DVGs are prevalent in human clinical samples but not in cultured samples. Furthermore, there are differences in DVG production and composition between in vivo and in vitro infections.
Article
Multidisciplinary Sciences
Katherine Kaugars, Joseph Dardick, Anna Paula de Oliveira, Kayla A. Weiss, Regy Lukose, John Kim, Lawrence Leung, Saranathan Rajagopalan, Sydney Wolin, Leor Akabas, David M. Knipe, Goran Bajic, William R. Jacobs Jr
Summary: Despite annual vaccination efforts, influenza continues to cause significant morbidity and mortality worldwide. To improve vaccine efficacy, researchers are exploring the use of antibodies that can activate immune cell effector functions, such as ADCC. Evidence suggests that ADCC is crucial for protection against influenza and other infectious diseases, leading to the development of innovative vaccine strategies such as using Delta gD-2 as a vector for a broadly protective influenza vaccine.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Zachary Ardern
Summary: Protein-coding DNA sequences can produce different amino acid sequences by shifting nucleotide triplets or translating codons from the opposite strand. These alternative reading frames contribute to the evolution of novel proteins. Recent studies have demonstrated this phenomenon in various organisms. These sequences provide more opportunities for the creation of new genes and have unique properties that may facilitate gene origin. The implications of these findings are significant in molecular biology, including genome annotation, structural biology, and evolutionary genomics.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Microbiology
Alexander M. Price, Robert T. Steinbock, Richard Lauman, Matthew Charman, Katharina E. Hayer, Namrata Kumar, Edwin Halko, Krystal K. Lum, Monica Wei, Angus C. Wilson, Benjamin A. Garcia, Daniel P. Depledge, Matthew D. Weitzman
Summary: In this study, the complexity of the adenoviral transcriptome was revealed using a combination of short-read and long-read direct RNA sequencing techniques. Several novel viral transcripts were identified, including those encoding for proteins that could alter protein functions through truncation or fusion of canonical open reading frames.
Article
Infectious Diseases
Glenn A. Marsh, Alexander J. McAuley, Sheree Brown, Elizabeth A. Pharo, Sandra Crameri, Gough G. Au, Michelle L. Baker, Jennifer A. Barr, Jemma Bergfeld, Matthew P. Bruce, Kathie Burkett, Peter A. Durr, Clare Holmes, Leonard Izzard, Rachel Layton, Suzanne Lowther, Matthew J. Neave, Timothy Poole, Sarah-Jane Riddell, Brenton Rowe, Elisha Soldani, Vittoria Stevens, Willy W. Suen, Vinod Sundaramoorthy, Mary Tachedjian, Shawn Todd, Lee Trinidad, Sinead M. Williams, Julian D. Druce, Trevor W. Drew, Seshadri S. Vasan
Summary: Researchers made efforts early in the SARS-CoV-2 outbreak to propagate and characterize an Australian isolate of the virus in vitro and in an ex vivo model of human airway epithelium, as well as to demonstrate the susceptibility of domestic ferrets to SARS-CoV-2 infection following intranasal challenge.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Virology
Leon C. W. Lin, Sarah N. Croft, Nathan P. Croft, Yik Chun Wong, Stewart A. Smith, Swee-Seong Tang, Anthony W. Purcell, David C. Tscharke
Summary: The study investigated the CD8(+) T cell priming pathways for Vaccinia virus (VACV) by engineering the virus to express inhibitors of antigen presentation. While the inhibitors had diverse impacts on CD8(+) T cell responses, unexpectedly, the direct priming of CD8(+) T cells by poxviruses was robust enough to withstand potent viral inhibitors of antigen presentation. This demonstrates the flexibility and robustness of immune processes in activating immune responses required to fight infection.
JOURNAL OF VIROLOGY
(2021)
Article
Immunology
Thi H. O. Nguyen, Louise C. Rowntree, Jan Petersen, Brendon Y. Chua, Luca Hensen, Lukasz Kedzierski, Carolien E. van de Sandt, Priyanka Chaurasia, Hyon-Xhi Tan, Jennifer R. Habel, Wuji Zhang, Lilith F. Allen, Linda Earnest, Kai Yan Mak, Jennifer A. Juno, Kathleen Wragg, Francesca L. Mordant, Fatima Amanat, Florian Krammer, Nicole A. Mifsud, Denise L. Doolan, Katie L. Flanagan, Sabrina Sonda, Jasveen Kaur, Linda M. Wakim, Glen P. Westall, Fiona James, Effie Mouhtouris, Claire L. Gordon, Natasha E. Holmes, Olivia C. Smibert, Jason A. Trubiano, Allen C. Cheng, Peter Harcourt, Patrick Clifton, Jeremy Chase Crawford, Paul G. Thomas, Adam K. Wheatley, Stephen J. Kent, Jamie Rossjohn, Joseph Torresi, Katherine Kedzierska
Summary: This study characterized CD8(+) T cells specific for SARS-CoV-2 epitopes in COVID-19 patients and unexposed individuals, revealing that CD8(+) T cells specific for the immunodominant B7/N-105 epitope were detected at high frequencies both before and during acute COVID-19 and convalescence. The research also showed high naive precursor frequency and TCR alpha beta diversity within immunodominant B7/N-105-specific CD8(+) T cells, shedding light on the origins and responses of SARS-CoV-2-specific T cells.
Article
Immunology
Katharina Hochheiser, Florian Wiede, Teagan Wagner, David Freestone, Matthias H. Enders, Moshe Olshansky, Brendan Russ, Simone Nussing, Emma Bawden, Asolina Braun, Annabell Bachem, Elise Gressier, Robyn McConville, Simone L. Park, Claerwen M. Jones, Gayle M. Davey, David E. Gyorki, David Tscharke, Ian A. Parish, Stephen Turner, Marco J. Herold, Tony Tiganis, Sammy Bedoui, Thomas Gebhardt
Summary: The deficiency of Ptpn2 affects the formation and function of TRM cells in the skin. The repression of KLRG1 is necessary for optimal TRM cell formation.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemical Research Methods
Chen Li, Jerico Revote, Sri H. Ramarathinam, Shan Zou Chung, Nathan P. Croft, Katherine E. Scull, Ziyi Huang, Rochelle Ayala, Asolina Braun, Nicole A. Mifsud, Patricia T. Illing, Pouya Faridi, Anthony W. Purcell
Summary: This study utilized tandem mass spectrometry and proteomic techniques to analyze a dataset of MS/MS spectra derived from synthetic peptides of SARS-CoV-2, creating an online knowledgebase called virusMS. The database provides detailed annotations of peptides, experimental information, and predicted peptide-HLA binding affinities, aiding in vaccination target identification and immune monitoring research. VirusMS offers a user-friendly interface for easy access to the database content.
Article
Immunology
Shivam K. Purohit, Carolyn Samer, Hamish E. G. McWilliam, Renee Traves, Megan Steain, Brian P. McSharry, Paul R. Kinchington, David C. Tscharke, Jose A. Villadangos, Jamie Rossjohn, Allison Abendroth, Barry Slobedman
Summary: This study demonstrates that varicella zoster virus suppresses the expression of antigen presentation molecule MR1, highlighting the intricate temporal relationship between infection and ligand availability. The study also suggests that VZV likely encodes multiple viral genes targeting MR1.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Editorial Material
Immunology
Patricia T. Illing, Nicole A. Mifsud, Michael R. Ardern-Jones, Jason Trubiano
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Jennifer Habel, Andrea Nguyen, Louise Rowntree, Christopher Szeto, Nicole Mifsud, E. Bridie Clemens, Liyen Loh, Weisan Chen, Steve Rockman, Jane W. Nelson, Jane Davies, Adrian Miller, Steven Y. C. T. Tong, Jamie Rossjohn, Stephanie M. Gras, Anthony Purcell, Luca M. Hensen, Katherine Kedzierska, Patricia M. Illing
Summary: HLA-A*11:01 is highly prevalent in East Asian and Oceanian populations and is associated with high risk of severe influenza disease. Using immunopeptidomics, researchers identified novel CD8(+) T cell targets for influenza A and influenza B viruses in HLA-A*11:01-expressing individuals. These findings have implications for the design of broadly cross-reactive influenza vaccines.
Article
Chemistry, Multidisciplinary
Deepu Ashok, Mahdiar Taheri, Puneet Garg, Daryl Webb, Pawan Parajuli, Yi Wang, Bronte Funnell, Bradley Taylor, David C. Tscharke, Takuya Tsuzuki, Naresh K. Verma, Antonio Tricoli, David R. Nisbet
Summary: This article reports on a sprayable coating that has the ability to resist the uptake and transmission of bacteria and viruses, while also providing bactericidal functionality and reducing viral contamination.
Review
Virology
A. K. M. Muraduzzaman, Patricia T. Illing, Nicole A. Mifsud, Anthony W. Purcell
Summary: Influenza A virus is a respiratory pathogen that causes significant damage to life and the economy. Current vaccines do not provide sufficient cross-protection, while vaccines that induce CD8(+) T cells have shown promise in providing cross-protection against different strains of the virus.
Article
Biochemistry & Molecular Biology
Xia Yang, Hailiang Sun, Zhening Zhang, Weixin Ou, Fengxiang Xu, Ling Luo, Yahong Liu, Weisan Chen, Jianxin Chen
Summary: Influenza A virus (IAV) infections pose a serious threat to public health and there is an urgent need for novel anti-IAV medications. This study reveals that ginsenoside rk1 (G-rk1) and G-rg5, derived from panax ginseng, exhibit significant antiviral effects against different IAV subtypes both in vitro and in vivo. G-rk1 specifically blocks IAV binding to sialic acid and interacts with HA1, making it a potential approach for preventing and treating IAV infections.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Allergy
Nicole A. A. Mifsud, Patricia T. T. Illing, Rebecca Ho, Johanna E. E. Tuomisto, Heidi Fettke, Kerry A. A. Mullan, James McCluskey, Jamie Rossjohn, Julian Vivian, Rangsima Reantragoon, Anthony W. W. Purcell
Summary: Allopurinol is a drug used in the treatment of gout but can cause severe and life-threatening hypersensitivity reactions. People carrying the HLA-B*58:01 allotype are at higher risk. The drug metabolite oxypurinol is responsible for T cell-mediated immunopathology, and the TCR repertoire usage of reactive T cells in ALP-induced hypersensitivity reactions has been limitedly studied. This research shows that oxypurinol drives CD8(+) T cell responses and that drug-exposed memory T cells exhibit a proinflammatory immunophenotype. The study also supports the concept of pharmacological interaction with immune receptors and highlights oligoclonal and private clonotypic profiles of OXP-induced TCRs.
Article
Pharmacology & Pharmacy
Xia Yang, Feixiang Long, Weixin Jia, Mingxin Zhang, Guanming Su, Ming Liao, Zhenling Zeng, Weisan Chen, Jianxin Chen
Summary: We demonstrated that artemisinin and its derivative artesunate (AS) have broad antiviral activity against H5N1, H1N1, H3N2, and oseltamivir-resistant influenza A virus in vitro. AS treatment significantly protected mice from lethal challenges with H1N1 and H5N1 IAV, and the combination of AS and peramivir showed improved survival outcomes compared to monotherapy. Mechanistically, AS inhibited PDE4, induced cAMP accumulation, reduced ERK phosphorylation, and blocked IAV vRNP export, thus suppressing IAV replication.
ANTIVIRAL RESEARCH
(2023)
Article
Immunology
Kimberly M. Edwards, Jurre Y. Siegers, Xiaoman Wei, Ammar Aziz, Yi-Mo Deng, Sokhoun Yann, Chan Bun, Seng Bunnary, Leonard Izzard, Makara Hak, Peter Thielen, Sothyra Tum, Frank Wong, Nicola S. Lewis, Joe James, Filip Claes, Ian G. Barr, Vijaykrishna Dhanasekaran, Erik A. Karlsson
Summary: Institute in Cambodia collaborated with FAO to monitor AI virus in bird markets and poultry storage in Cambodia. The surveillance showed high levels of AIV circulation, with approximately 30%-50% of ducks and 20%-40% of chickens testing positive for various subtypes. The predominant subtypes were H5N1 during 2005-2014 and H5N1 and H5N6 since 2014, with sporadic detection of other subtypes including novel H7Nx in late 2021. Some samples tested positive for HPAIV H5 HA but negative for neuraminidase PCR, and further analysis confirmed them as H5N8 subtype.
EMERGING INFECTIOUS DISEASES
(2023)