Review
Microbiology
Alison A. McBride
Summary: HPVs are a diverse group of viruses that replicate in specific anatomical niches of the stratified epithelia. Most infections are asymptomatic, but some can cause benign proliferative lesions or even cancer. These viruses have evolved to evade the host immune system and manipulate cellular processes to ensure their survival and replication.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Medicine, Research & Experimental
Diane Bruyere, Patrick Roncarati, Alizee Lebeau, Thomas Lerho, Florian Poulain, Elodie Hendrick, Charlotte Pilard, Celia Reynders, Marie Ancion, Margaux Luyckx, Michael Renard, Yves Jacob, Jean-Claude Twizere, Raphael Peiffer, Olivier Peulen, Philippe Delvenne, Pascale Hubert, Alison McBride, Nicolas Gillet, Murielle Masson, Michael Herfs
Summary: HPV-positive cancers are usually associated with a favorable outcome due to high sensitivity to radiation therapy. However, the impact of viral E6/E7 oncoproteins on cellular radiosensitivity and host DNA repair is still largely speculative.
Review
Biochemistry & Molecular Biology
Alison A. McBride, Alix Warburton, Simran Khurana
Summary: HPV reproduces in stratified epithelia by establishing a reservoir of low-level infection in dividing basal cells and restricting viral particle production to terminally differentiated cells. The Brd4 protein plays a key role in multiple stages of the HPV infectious cycle.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Georgios N. Dimitrakopoulos, Maria I. Klapa, Nicholas K. Moschonas
Summary: After 15 years of research, it has been observed that the addition rate of protein-protein interactions (PPIs) has decreased, with most new PPIs determined by high-throughput experiments mainly involving existing protein nodes with low degrees. Exploring the full interactome topology can reveal protein neighborhoods associated with biological processes such as transcriptional regulation and cell signaling. A well-reconstructed human protein interactome is crucial for network biology and medical research, forming the basis for multi-omic and dynamic analyses.
Review
Biochemistry & Molecular Biology
Roxanne Evande, Anshul Rana, Esther E. Biswas-Fiss, Subhasis B. Biswas
Summary: Human papillomavirus (HPV) is a group of alpha papillomaviruses that cause various illnesses, including cancer. Numerous studies have revealed the genetic characteristics of high-risk HPV types, the roles of HPV-encoded proteins in HPV DNA replication, the regulation of transcription of E6 and E7 oncogenes, and the development of oncogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Geography
Jeremy Auerbach, Hyun Kim
Summary: This paper introduces a robustness measurement method applicable to multiline networks to uncover potential vulnerabilities of network components. The effectiveness and applicability of these new robustness measures are demonstrated through comparisons with traditional indexes.
ANNALS OF THE AMERICAN ASSOCIATION OF GEOGRAPHERS
(2022)
Article
Pharmacology & Pharmacy
Yiqun Li, Mingrui Yang, Yanan Nan, Jiaming Wang, Sanjiao Wang, Dongxiao Cui, Jiajian Guo, Pengfei He, Wenxin Dai, Shuqi Zhou, Yue Zhang, Wenfu Ma
Summary: This study identified the COPI sorting signal of SARS-CoV-2 and developed a potent S COPI sorting inhibitor that can promote viral surface exposure and facilitate infected cell clearance through antibody-dependent cellular cytotoxicity. The research also revealed the lower surface exposure of Omicron BA.1 S compared to prototypes, providing insights into the evolution mechanism of SARS-CoV-2.
ACTA PHARMACEUTICA SINICA B
(2023)
Article
Oncology
Karin Hoppe-Seyler, Anja L. Herrmann, Antonia Daeschle, Bianca J. Kuhn, Tobias D. Strobel, Claudia Lohrey, Julia Bulkescher, Jeroen Krijgsveld, Felix Hoppe-Seyler
Summary: The study reveals that Metformin can effectively suppress the expression of HPV oncogenes in HPV-positive cancer cells, leading to a reversible proliferative halt without inducing senescence completely.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Multidisciplinary Sciences
Lucas Moitinho-Silva, Frauke Degenhardt, Elke Rodriguez, Hila Emmert, Simonas Juzenas, Lena Mobus, Florian Uellendahl-Werth, Nicole Sander, Hansjorg Baurecht, Lukas Tittmann, Wolfgang Lieb, Christian Gieger, Annette Peters, David Ellinghaus, Corinna Bang, Andre Franke, Stephan Weidinger, Malte Christoph Ruehlemann
Summary: This study identified candidate genes related to innate immune signaling, environmental sensing, cell differentiation, proliferation, and fibroblast activity that influence the skin microbiota. It also found evidence of the impact of staphylococci on eczema/dermatitis and suggested the modulating effects of microbiota on other skin diseases.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Mari Toppinen, Antti Sajantila, Diogo Pratas, Klaus Hedman, Maria F. Perdomo
Summary: The study reveals that various viral DNA can be detected in human bone marrow, potentially impacting hematopoiesis and immune function. These viruses include herpesviruses, hepatitis B virus, among others, and further research is needed to investigate their reactivation and oncogenic potential.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Xin Li, Yinyin Zhang, Shoujing Zhao, Bairu Li, Luning Cai, Xinyue Pang
Summary: Trypsin significantly improved the storage quality of Hylocereus undatus by inducing antioxidant signal pathways, impeding lignin catabolic process, and regulating the biosynthesis of various proteins. This novel preservative also influenced the metabolic network to enhance the bioactive metabolites, ultimately improving the storage quality of the fruit.
Article
Biochemical Research Methods
Vandana Ravindran, Jessica Wagoner, Paschalis Athanasiadis, Andreas B. Den Hartigh, Julia M. Sidorova, Aleksandr Ianevski, Susan L. Fink, Arnoldo Frigessi, Judith White, Stephen J. Polyak, Tero Aittokallio
Summary: The COVID-19 pandemic has emphasized the importance of understanding the interactions between the virus and the host. Researchers have developed a network-based method to expand the protein interaction network between the SARS-CoV-2 virus and the host, and have identified host targets that can modulate viral infection. Experimental tests have shown that certain host proteins have antiviral functions. However, the antiviral effects vary across different cell lines, highlighting the need for further development of this method's accuracy and specificity in different cellular contexts.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Oncology
Luhan Zhang, Hong Yu, Tian Deng, Li Ling, Juan Wen, Mingfen Lv, Rongying Ou, Qiaozhi Wang, Yunsheng Xu
Summary: The study revealed that key genes involved in HPV-mediated cervical carcinogenesis include those related to DNA replication/repair and cell cycle, with significant metabolic shifts observed. FNDC3B and BPGM were identified as key genes in the transformation from normal epithelium to precancerous lesions and cervical cancer. Higher FNDC3B expression or lower BPGM expression were associated with shorter overall survival and disease-free survival in patients with cervical cancer.
FRONTIERS IN ONCOLOGY
(2021)
Article
Virology
Nathan R. Fons, Rhonda C. Kines, Cynthia D. Thompson, Patricia M. Day, Douglas R. Lowy, John T. Schiller
Summary: Heparan sulfate proteoglycans (HSPGs) have been identified as primary attachment factors for human papillomaviruses (HPVs) prior to infection. In vitro experiments show that HPV binding to HSPGs strongly depends on the surrounding experimental conditions, including the concentration of fetal bovine serum (FBS). High concentrations of FBS obstruct the cell surface HSPGs and consequently, HPV particles utilize 6O-sulfated chondroitin sulfate proteoglycans (CSPGs) as initial binding receptors. The findings also suggest a possible role for CSPGs in active wound healing environments. These unexpected findings indicate the significance of serum/platelet factors in HPV binding and identify CSPGs as alternative cell attachment receptors for HPV.
JOURNAL OF VIROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Andraz Dovnik, Mario Poljak
Summary: CIN2 is an intermediate stage between CIN1 and CIN3. Traditional treatment involved conization or ablative methods, but recent years have seen a shift towards conservative management for younger patients due to the possibility of spontaneous regression and adverse effects on future pregnancies. Research has focused on the role of host and HPV gene methylation to identify patients at higher risk of progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Correction
Multidisciplinary Sciences
Nikolaos Vakirlis, Omer Acar, Brian Hsu, Nelson Castilho Coelho, S. Branden Van Oss, Aaron Wacholder, Kate Medetgul-Ernar, Ray W. Bowman, Cameron P. Hines, John Iannotta, Saurin Bipin Parikh, Aoife McLysaght, Carlos J. Camacho, Allyson F. O'Donnell, Trey Ideker, Anne-Ruxandra Carvunis
NATURE COMMUNICATIONS
(2021)
Article
Biophysics
Yihan Huang, Bradley S. Harris, Shiaki A. Minami, Seongwon Jung, Priya S. Shah, Somen Nandi, Karen A. McDonald, Roland Faller
Summary: Highly detailed steered molecular dynamics simulations were conducted on differently glycosylated receptor binding domains of the SARS-CoV-2 spike protein. Glycosylation increased the binding strength and range, and a catch-slip behavior was observed during protein pulling, where new interactions replaced broken interactions. Hydrogen bonds were the dominant interaction mode, while Lennard-Jones and electrostatic interactions were also relevant.
BIOPHYSICAL JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, Nozomu Yachie
Summary: This study proposes a deep distributed computing framework, FRACTAL, for inferring large-scale cell lineages. The framework constructs lineages from a large number of input sequences through recursive iteration, significantly enhancing scalability, and demonstrates its utility in different experiments.
NATURE BIOTECHNOLOGY
(2022)
Article
Biology
Sabine Ottilie, Madeline R. Luth, Erich Hellemann, Gregory M. Goldgof, Eddy Vigil, Prianka Kumar, Andrea L. Cheung, Miranda Song, Karla P. Godinez-Macias, Krypton Carolino, Jennifer Yang, Gisel Lopez, Matthew Abraham, Maureen Tarsio, Emmanuelle LeBlanc, Luke Whitesell, Jake Schenken, Felicia Gunawan, Reysha Patel, Joshua Smith, Melissa S. Love, Roy M. Williams, Case W. McNamara, William H. Gerwick, Trey Ideker, Yo Suzuki, Dyann F. Wirth, Amanda K. Lukens, Patricia M. Kane, Leah E. Cowen, Jacob D. Durrant, Elizabeth A. Winzeler
Summary: Ottilie et al. used an experimental evolution approach to investigate the role of transcription factors in yeast chemical resistance. They found that most emergent mutations in resistant strains were enriched in transcription factor coding genes, highlighting their importance in drug resistance. Through in vitro evolution and whole genome analysis, they comprehensively identified the genetic determinants of chemical resistance in Saccharomyces cerevisiae. This work emphasizes the important role of transcription factors in the evolution of antifungal xenobiotic resistance and poses challenges to the development of effective antifungal treatments.
COMMUNICATIONS BIOLOGY
(2022)
Letter
Biotechnology & Applied Microbiology
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
Article
Biochemical Research Methods
Shiaki A. Minami, Seongwon Jung, Yihan Huang, Bradley S. Harris, Matthew W. Kenaston, Roland Faller, Somen Nandi, Karen A. McDonald, Priya S. Shah
Summary: The study shows that transient Spike expression in Chinese hamster ovary cells can significantly increase the titer, and the truncation variant T1 has higher expression levels than the Spike receptor-binding domain. T1 is a promising alternative to Spike for various applications.
BIOTECHNOLOGY JOURNAL
(2022)
Review
Medicine, General & Internal
Adam Li, Zane Koch, Trey Ideker
Summary: Numerous studies have shown that epigenetic age is associated with various factors and can be computed based on DNA methylation patterns. The focus of research needs to shift from accurate age prediction to understanding the links between the epigenome and aging mechanisms. Current research areas include epigenetic clocks and investigation of the epigenome to build a mechanistic theory of aging and inform clinical practice.
JOURNAL OF INTERNAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Amy D. Westerling-Bui, Eva Maria Fast, Thomas W. Soare, Srinivasan Venkatachalan, Michael DeRan, Alyssa B. Fanelli, Sergii Kyrychenko, Hien Hoang, Grinal M. Corriea, Wei Zhang, Maolin Yu, Matthew Daniels, Goran Malojcic, Xin-Ru Pan-Zhou, Mark W. Ledeboer, Jean-Christophe Harmange, Maheswarareddy Emani, Thomas T. Tibbitts, John F. Reilly, Peter Mundel
Summary: Pharmacodynamic (PD) studies are crucial in preclinical drug discovery, but current approaches limited to animal models lack translatability to humans. To overcome this challenge, researchers developed a novel method using transplanted human kidney organoids for PD studies. By orally administering investigational drug GFB-887 to athymic rats with transplanted organoids, significant protection of kidney filter cells was observed in both the organoids and host kidneys.
Article
Cell Biology
Nitin Sai Beesabathuni, Soyoon Park, Priya S. Shah
Summary: This study presents a theoretical and experimental framework to measure autophagic steps in the form of rates under non-steady-state conditions. It demonstrates the ability to quantify changes in autophagy rates in response to different modulators and conditions, providing valuable insights into the regulation and dynamics of autophagy.
Article
Multidisciplinary Sciences
Christine E. Peters, Ursula Schulze-Gahmen, Manon Eckhardt, Gwendolyn M. Jang, Jiewei Xu, Ernst H. Pulido, Melanie Ott, Or Gozani, Kliment A. Verba, Ruth Huettenhain, Jan E. Carette, Nevan J. Krogan
Summary: This study reports the structure of the interaction between Actin histidine methyltransferase SETD3 and the enterovirus CV-B3 2A protease, revealing the importance of the SET domain for virus replication. Mutations in key residues of the SET domain result in reduced binding to 2A and complete protection against enteroviral infection.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Matthew W. W. Kenaston, Oanh H. H. Pham, Marine J. J. Petit, Priya S. S. Shah
Summary: This study investigates the role of polymerase associated factor 1 complex (PAF1C) in innate immunity by analyzing gene expression patterns in PAF1 knockout cells exposed to various immune stimuli. The results confirm PAF1 as an activator of immune response pathways and provide insights into its potential regulatory functions. The findings highlight the importance of PAF1C in innate immunity and pave the way for further studies on its role as a regulator.
Article
Biochemical Research Methods
Zeynep Cakir, Samuel J. Lord, Yuan Zhou, Gwendolyn M. Jang, Benjamin J. Polacco, Manon Eckhardt, David Jimenez-Morales, Billy W. Newton, Adam L. Orr, Jeffrey R. Johnson, Alexandre da Cruz, R. Dyche Mullins, Nevan J. Krogan, Robert W. Mahley, Danielle L. Swaney
Summary: Apolipoprotein E4 is the major genetic risk factor for Alzheimer's disease. Neuronal expression of apoE4 increases in response to stress and it disrupts VASP interactions with actin cytoskeletal and microtubular proteins, leading to cytoskeletal defects. Blocking the phosphorylation of VASP can restore cytoskeletal defects caused by apoE4.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Virology
Andrew P. P. Kurland, Boris Bonaventure, Jeffrey R. R. Johnson
Summary: In this study, we identified kinases that regulate innate immune pathways by conducting a small-scale kinase inhibitor screen and quantitative proteomics analysis. We found that inhibitors of ATM, ATR, AMPK, and PLK1 reduced interferon-stimulated gene expression in response to poly(I:C)-induced activation of innate immune pathways. However, RNA interference experiments did not validate these findings, suggesting off-target effects of the inhibitors. Mapping the effects of kinase inhibitors on various stages of innate immune pathways may reveal novel mechanisms of pathway control.
Article
Biochemical Research Methods
Shiaki A. Minami, Shruthi S. Garimella, Priya S. Shah
Summary: This study investigates the size limitation for optogenetics in large mammalian bioreactors using computer simulations. The results show that there is a limitation to light penetration in maximal size bioreactors. However, this does not exclude the application of optogenetics since cells do not require continuous exposure to light.
BIOTECHNOLOGY JOURNAL
(2023)