Diseases articles within Nature Communications

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  • Article
    | Open Access

    The circadian clock affects immune responses, but its role in influenza infection is not well understood. Here, Sengupta et al. show that time of infection and the circadian clock have no effect on lung virus titers, but affect inflammation, morbidity and mortality.

    • Shaon Sengupta
    • , Soon Y. Tang
    •  & Garret A. FitzGerald

  • Article
    | Open Access

    Antibiotic therapy is usually not effective for salmonellosis. Here, the authors present an approach that may be useful for the treatment of salmonellosis, consisting of hydrogen sulfide (H2S)-responsive glycovesicles that release antibiotics in the presence of Salmonella in the gut.

    • Haibo Mu
    • , Hu Bai
    •  & Jinyou Duan

  • Article
    | Open Access

    While many pleiotropic genetic loci have been identified, how they contribute to phenotypes across traits and diseases is unclear. Here, the authors propose decomposition of genetic associations (DeGAs), which uses singular value decomposition, to characterize the underlying latent structure of genetic associations of 2,138 phenotypes.

    • Yosuke Tanigawa
    • , Jiehan Li
    •  & Manuel A. Rivas

  • Article
    | Open Access

    A variety of biological differences exist between strains and phylogenetic lineages in the Mycobacterium tuberculosis complex (MTBC). Here, the authors perform RNAseq and methylome analysis of the main clades of the MTBC and show variation in transcriptional profiles is mainly due to mutations in transcriptional start sites.

    • Álvaro Chiner-Oms
    • , Michael Berney
    •  & Iñaki Comas

  • Article
    | Open Access

    Noise due to genetic heterogeneity potentially impacts the the discovery of genes that contribute to diseases such as schizophrenia (SCZ). In this study, authors minimize the disease-irrelevant noise between SCZ and healthy individuals by profiling transcriptional signatures among discordant monozygotic twin pairs, and demonstrate that although sexes share many of the final common pathways, the underlying primary pathophysiology of SCZ differs between males and females.

    • Jari Tiihonen
    • , Marja Koskuvi
    •  & Jari Koistinaho

  • Article
    | Open Access

    Investigating malaria transmission at three sites in Uganda, the authors identify super-spreaders and show that super-spreading is more prominent at low-intensity transmission, and that seasonality and environmental stochasticity have a greater influence on super-spreading.

    • Laura Cooper
    • , Su Yun Kang
    •  & David L. Smith

  • Article
    | Open Access

    Innate immune responses are essential in the control of flavivirus infection. Here, the authors provide evidence that the unfolded protein response and the pattern recognition receptor pathways synergize to orchestrate innate antiviral responses and cell intrinsic inhibition of viral replication, a process mediated by IRF3.

    • Tea Carletti
    • , Mohammad Khalid Zakaria
    •  & Alessandro Marcello

  • Article
    | Open Access

    Antibody cross-reactivity can help to prevent escape mutations from enabling viral escape, but underlying mechanisms are unclear. Here the authors identify influenza hemagglutinin epitopes that are exposed during viral replication and which result in the generation of a class of protective cross-reactive antibodies.

    • Yu Adachi
    • , Keisuke Tonouchi
    •  & Yoshimasa Takahashi

  • Article
    | Open Access

    Persistently low levels of estimated glomerular filtration rate (eGFR) are a biomarker of chronic kidney disease. Here, the authors reinterpret the genetic architecture of kidney function across ancestries, to identify not only genes, but the tissue and anatomical contexts of renal homeostasis.

    • Jacklyn N. Hellwege
    • , Digna R. Velez Edwards
    •  & Adriana M. Hung

  • Article
    | Open Access

    Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne virus with no specific treatment or vaccine available. Here, the authors develop a DNA vaccine for SFTSV that is protective against lethal challenge in ferrets and show that anti-envelope antibodies are important for protection.

    • Jeong-Eun Kwak
    • , Young-Il Kim
    •  & Su-Hyung Park

  • Article
    | Open Access

    Here, the authors show that reticulocytes derived from immortalized erythroblasts support invasion and development of Plasmodium falciparum and use CRISPR-mediated gene knockout and complementation of an invasion receptor to demonstrate utility of this model system for research in malaria invasion.

    • Timothy J. Satchwell
    • , Katherine E. Wright
    •  & Jake Baum

  • Article
    | Open Access

    Promyelocytic leukemia protein (PML) is the scaffolding protein that organizes PML nuclear bodies. Here the authors determine the crystal structure of a PML B1-box multimer and characterise the oligomerisation behaviour of the PML RBCC construct and show that disrupting B1-B1 interactions precludes promyelocytic leukemia leukemogenesis in transgenic mice.

    • Yuwen Li
    • , Xiaodan Ma
    •  & Guoyu Meng

  • Article
    | Open Access

    Tuberculosis meningitis (TBM) is a severe form of TB with limited treatment options. Here, the authors perform RNA sequencing on whole blood and on ventricular and lumbar cerebrospinal fluid (CSF) samples from pediatric patients treated for TBM to characterize the immune response and tissue damage.

    • Ursula K. Rohlwink
    • , Anthony Figaji
    •  & Rachel P. J. Lai

  • Article
    | Open Access

    Between 5 and 15% of latent Mycobacterium tuberculosis infections develop into active tuberculosis (TB). Here, Luo et al. report a genome-wide association study for early TB progression in a total of 4002 active TB cases and their household contacts in Peru and they identify a locus on 3q23 in which ATP1B3 is mapped as the likely causal gene.

    • Yang Luo
    • , Sara Suliman
    •  & Soumya Raychaudhuri

  • Article
    | Open Access

    Detection of viral biomarkers is important for disease treatment and prevention. Here, the authors report on a system that uses an electrical pulse-induced electrochemical sensor for the detection of hepatitis E virus, and demonstrate potential application of the device.

    • Ankan Dutta Chowdhury
    • , Kenshin Takemura
    •  & Enoch Y. Park

  • Article
    | Open Access

    Genome-wide association studies have only revealed a handful of genetic loci for longevity. Here, in a case–control design based on phenotype definitions of individuals surviving at or beyond the age corresponding to the 90th and 99th survival percentile, the authors report two additional loci located in the APOE locus and near GPR78.

    • Joris Deelen
    • , Daniel S. Evans
    •  & Joanne M. Murabito

  • Article
    | Open Access

    Topoisomerases are required to release topological stress on DNA during replication and transcription. Here, Broderick et al. report genetic variants in TOP2B that cause a syndromic B cell immunodeficiency associated with reduced TOP2B function, defects in B cell development and B cell activation.

    • Lori Broderick
    • , Shawn Yost
    •  & Hal M. Hoffman

  • Article
    | Open Access

    The studies showing health benefits of flavonoids and their impact on cancer mortality are incomplete. Here, the authors perform a prospective cohort study in Danish participants and demonstrate an inverse association between regular flavonoid intake and both cardiovascular and cancer related mortality.

    • Nicola P. Bondonno
    • , Frederik Dalgaard
    •  & Jonathan M. Hodgson

  • Article
    | Open Access

    RIG-I- like receptors (RLRs) play an important role in immune defense against West Nile virus (WNV). Here, using a systems biology approach, the authors show that macrophage polarization to a proinflammatory M1 phenotype via RIG-I and MDA5 signaling is critical for innate immune control in WNV-infected mouse tissues.

    • Amy E. L. Stone
    • , Richard Green
    •  & Michael Gale Jr.

  • Article
    | Open Access

    Present understanding of Plasmodium vivax biology is hampered by its inability to grow in vitro. Here, the authors developed an in vitro culture of its simian counterpart, P. cynomolgi, which shares morphological and phenotypic similarities with P. vivax, initiating a new phase in vivax research.

    • Adeline C. Y. Chua
    • , Jessica Jie Ying Ong
    •  & Pablo Bifani

  • Article
    | Open Access

    PIK3CA mutations and ARID1A loss co-exist in endometrial neoplasms. Here, the authors show that these co-mutations drive gene expression profiles correlated with differential chromatin accessibility and ARID1A binding in the endometrial epithelium, resulting in partial EMT and myometrial invasion.

    • Mike R. Wilson
    • , Jake J. Reske
    •  & Ronald L. Chandler

  • Article
    | Open Access

    Cystic fibrosis is caused by mutations in the CFTR chloride channel. Here, the authors develop a gene therapy approach using the programmable nuclease AsCas12a to correct a splicing mutation in CFTR, and show efficient repair of the mutation and recovery of CFTR function in patient-derived organoids and airway epithelial cells.

    • Giulia Maule
    • , Antonio Casini
    •  & Anna Cereseto

  • Article
    | Open Access

    The NDM-1 metallo-β-lactamase confers resistance to β-lactam antibiotics. Here, the authors show that the antimicrobial peptide thanatin is active against NDM-1-producing bacteria through a dual mechanism of action consisting of disruption of outer membrane integrity and inhibition of the NDM-1 enzymatic activity.

    • Bo Ma
    • , Chao Fang
    •  & Zheng Hou

  • Article
    | Open Access

    There are few studies of structural changes in ascending and descending sensorimotor pathways after stroke, beyond the corticospinal tract, in the brain. Here the authors identify changes in white matter structure in brainstem and spinal cord following stroke, and show its relationship to motor impairment.

    • Haleh Karbasforoushan
    • , Julien Cohen-Adad
    •  & Julius P. A. Dewald

  • Article
    | Open Access

    People with a genetic deletion of the 15q11.2 locus are at increased risk for psychiatric disorders and white matter disturbances, but the gene(s) responsible are unclear. Here, the authors show that low dosage of CYFIP1, present in the human 15q11.2 region, alters white matter structure and cognition in rats.

    • Ana I. Silva
    • , Josephine E. Haddon
    •  & Lawrence S. Wilkinson

  • Article
    | Open Access

    Identification of host factors associated with severe influenza infection could provide insights into treatment options. Here, the authors provide transcriptomic analyses of blood from >100 influenza infected patients and show that changes in circulating neutrophils are associated with severe influenza infection.

    • Benjamin M. Tang
    • , Maryam Shojaei
    •  & Klaus Schughart

  • Article
    | Open Access

    Mitochondria of alveolar type 2 epithelial cells (AEC2) in the lung have been suggested to play a role in the development of idiopathic pulmonary fibrosis (IPF). Here the authors show that loss of mitofusin1 and mitofusin2 in murine AEC2 cells leads to the development of lung fibrosis through the regulation of surfactant lipids.

    • Kuei-Pin Chung
    • , Chia-Lang Hsu
    •  & Augustine M. K. Choi

  • Perspective
    | Open Access

    No effective therapies exist for dry age-related macular degeneration. In this perspective, the authors propose that research should emphasize system biology approaches that integrate various ‘omics’ data into mathematical models to establish pathogenic mechanisms on which to design novel treatments, and identify biomarkers that predict disease progression and therapeutic response.

    • James T. Handa
    • , Cathy Bowes Rickman
    •  & Lindsay A. Farrer

  • Article
    | Open Access

    The repertoire of adaptive immune receptor is generated by V(D)J recombination, somatic rearrangements of V, D and J gene segments, in the respective loci. Here the authors show that the deficiency of Setd2, a histone methyl transfer, impairs V(D)J recombination and induces severe developmental blocks in both T and B lineages.

    • Zhongzhong Ji
    • , Yaru Sheng
    •  & Helen He Zhu

  • Article
    | Open Access

    In patients with sporadic Alzheimer’s disease part of the Asp23 residues are isomerized to L-isoaspartate (L-isoAsp23). Here the authors present the MicroED structures of wild-type and L-isoAsp23 Aβ 20–34 amyloid fibrils that both form tightly packed cores and self-associate through two distinct interfaces with one of these interfaces being strengthened by the isoaspartyl modification.

    • Rebeccah A. Warmack
    • , David R. Boyer
    •  & Steven G. Clarke

  • Article
    | Open Access

    The depolarizing funny current contributing to cardiac pacemaking is upregulated in the myocardium of  failing and infarcted hearts, but whether the current is implied in disease mechanisms is unclear. Here the authors generate HCN4 transgenic mice and show that upregulation of funny current to the levels observed in human heart failure alters calcium homeostasis leading to cardiac remodelling and arrhythmia.

    • Pessah Yampolsky
    • , Michael Koenen
    •  & Patrick A. Schweizer

  • Article
    | Open Access

    Syphilis is caused by the bacterium Treponema pallidum subspecies pallidum (TPA), and incidence has risen recently in many countries. Here, Beale et al. provide whole-genome TPA sequences from 73 clinical samples and show how antimicrobial resistance emerged independently in circulating lineages.

    • Mathew A. Beale
    • , Michael Marks
    •  & Nicholas R. Thomson

  • Article
    | Open Access

    Primaquine (PQ) is a widely used anti-malaria drug, but its mechanism of action is unclear. Here, Camarda et al. show that PQ’s activity against liver and sexual Plasmodium stages depends on generation of hydroxylated-PQ metabolites (OH-PQm), which, undergoing further reactions, results in production of H2O2.

    • Grazia Camarda
    • , Piyaporn Jirawatcharadech
    •  & Giancarlo A. Biagini

  • Article
    | Open Access

    Altered iron homeostasis resulting in excessive oxidative stress has been implicated in smoke-induced lung diseases. Here the authors show that ferroptosis of lung epithelial cells, potentially resulting from excessive ferritinophagy, is involved in the pathogenesis of COPD.

    • Masahiro Yoshida
    • , Shunsuke Minagawa
    •  & Kazuyoshi Kuwano

  • Article
    | Open Access

    Defective CFTR protein, responsible for Cystic Fibrosis (CF), is highly expressed in pancreatic ductal epithelial cells (PDECs) but their impact on insulin secreting pancreatic islets is not fully understood. Here the authors develop a non-CF and CF patient derived pancreas-on-a-chip model to study how CF affects insulin secretion.

    • Kyu Shik Mun
    • , Kavisha Arora
    •  & Anjaparavanda P. Naren

  • Article
    | Open Access

    Streptococcus pneumoniae is a common coloniser of the human nasopharynx, but it also causes severe diseases. Here, Weight et al. use an experimental human pneumococcal carriage model to show that bacterial colonisation is associated with invasion of the epithelium and enhancement of immune responses.

    • Caroline M. Weight
    • , Cristina Venturini
    •  & Robert S. Heyderman

  • Comment
    | Open Access

    Infectious disease modeling has played a prominent role in recent outbreaks, yet integrating these analyses into public health decision-making has been challenging. We recommend establishing ‘outbreak science’ as an inter-disciplinary field to improve applied epidemic modeling.

    • Caitlin Rivers
    • , Jean-Paul Chretien
    •  & Simon Pollett

  • Article
    | Open Access

    CTLA-4 is critical for balancing protective immunity with self-tolerance. Here the authors identify homozygous DEF6 mutations in patients with severe autoimmunity, one of which received and responds to CTLA-4-Ig, and show that DEF6 is crucial for CTLA-4 cell surface trafficking and immune regulatory function.

    • Nina K. Serwas
    • , Birgit Hoeger
    •  & Kaan Boztug

  • Article
    | Open Access

    Epigenetic differences in nasal epithelium have been proposed as a biomarker for lower airway disease and asthma. Here, in epigenome-wide association studies for asthma and other airway traits using nasal swabs, the authors identify differentially methylated CpGs that highlight genes involved in TH2 response.

    • Andres Cardenas
    • , Joanne E. Sordillo
    •  & Diane R. Gold

  • Article
    | Open Access

    Dimethyl fumarate (DMF) is an established treatment for relapsing multiple sclerosis with unclear mechanism of action. Here the authors distinguish DMF responders by monocyte counts and redox gene signature in a prospective longitudinal cohort at 3 month of therapy, and associate NOX3 genetic variants with outcome.

    • Karl E. Carlström
    • , Ewoud Ewing
    •  & Fredrik Piehl

  • Article
    | Open Access

    Advanced paternal age associates with increased risk for psychiatric and developmental disorders in offspring. Here, Taylor et al. utilize parent-child trio exome sequencing data sets to estimate the contribution of paternal age-related de novo mutations to multiple disorders, including heart disease and schizophrenia.

    • Jacob L. Taylor
    • , Jean-Christophe P. G. Debost
    •  & Elise B. Robinson

  • Article
    | Open Access

    Various host factors may impact within-host pathogen evolution. Here, the authors develop a Bayesian approach for identifying host-pathogen interactions using large data sets of pathogen diversity, and apply it to investigate HLA-induced selection in the HIV-1 genome.

    • Duncan S. Palmer
    • , Isaac Turner
    •  & Gil McVean

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