Biomarkers articles within Nature Communications

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  • Article
    | Open Access

    The response to respiratory virus exposure can currently not be predicted by pre- or early post-exposure molecular signatures. Here, the authors conduct a community-based analysis of blood gene expression from healthy individuals exposed to respiratory viruses and provide predictive models and biological insight into the physiological response.

    • Slim Fourati
    • , Aarthi Talla
    •  & Solveig K. Sieberts

  • Article
    | Open Access

    Patients with myotonic dystrophy need to undergo invasive muscle biopsies to monitor disease progression and response to therapy. Here, the authors show that extracellular RNAs in human urine can be used as biomarkers to differentiate patients from unaffected controls, and to monitor exon skipping in patients with Duchenne muscular dystrophy taking the drug eteplirsen.

    • Layal Antoury
    • , Ningyan Hu
    •  & Thurman M. Wheeler

  • Article
    | Open Access

    Brain function alterations in schizophrenia and other psychotic disorders remain poorly understood. Here, the authors discover that increased neural connectivity in the cerebello-thalamo-cortical circuitry predicts psychosis in those at high risk, and is present in people with schizophrenia.

    • Hengyi Cao
    • , Oliver Y. Chén
    •  & Tyrone D. Cannon

  • Article
    | Open Access

    People vary in the extent to which they feel better after taking an inert, placebo, treatment, but the basis for individual placebo response is unclear. Here, the authors show how brain structural and functional variables, as well as personality traits, predict placebo response in those with chronic back pain.

    • Etienne Vachon-Presseau
    • , Sara E. Berger
    •  & A. Vania Apkarian

  • Article
    | Open Access

    Upstream pathways regulating Brg1 stability and their role in carcinogenesis are unknown. Here they show Brg1 to be phosphorylated by CK1δ to promote its ubiquitination by SCFFBW7 (FBW7), Brg1 stabilization to promote gastric cancer metastasis, and suggest targeting Brg1 in FBW7 compromised gastric cancer.

    • Li-Yu Huang
    • , Junjie Zhao
    •  & Wenyi Wei

  • Article
    | Open Access

    Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, the authors use phosphoproteomics to define kinases with distinct activity profiles in TNBC, demonstrating their prognostic value as well as their utility for simplifying TNBC classification and designing drug regimens.

    • Ivana Zagorac
    • , Sara Fernandez-Gaitero
    •  & Miguel Quintela-Fandino

  • Article
    | Open Access

    Little is known about the contribution of germline genetic variants to cancer drug sensitivity. Here, the authors devise an approach for joint analysis of germline variants and somatic mutations, identifying substantial germline contributions to variation in drug sensitivity.

    • Michael P. Menden
    • , Francesco Paolo Casale
    •  & Oliver Stegle

  • Article
    | Open Access

    Synthetic lethality (SL) offers a new precision oncology approach, which is based on targeting cancer-specific vulnerabilities across the whole genome, going beyond cancer drivers. The authors develop an approach termed ISLE to identify clinically relevant SL interactions and use them for patient stratification and novel target identification.

    • Joo Sang Lee
    • , Avinash Das
    •  & Eytan Ruppin

  • Article
    | Open Access

    Rhinovirus (RV) infections can trigger acute exacerbations of respiratory diseases. Here, Niespodziana et al. develop a PreDicta chip that identifies the culprit RV strain from small blood samples and show that RV-A and RV-C strains are associated with most severe symptoms.

    • Katarzyna Niespodziana
    • , Katarina Stenberg-Hammar
    •  & Rudolf Valenta

  • Article
    | Open Access

    FOS has been linked to bone tumour pathogenesis, and viral homologue v-fos causes osteosarcoma in mice. Here, the authors report rearrangement of FOS and its paralogue FOSB in osteoblastoma and osteoid osteoma, revealing human bone tumours that are defined by mutations of FOS and FOSB.

    • Matthew W. Fittall
    • , William Mifsud
    •  & Sam Behjati

  • Article
    | Open Access

    High frequency oscillations (HFO) are a promising biomarker for identifying epileptogenic zones without the need to monitor spontaneous seizure episodes. Here the authors report that there is much variability in the location of HFOs offering a note of caution toward using HFO locations from short recordings as a guide for surgery.

    • Stephen V. Gliske
    • , Zachary T. Irwin
    •  & William C. Stacey

  • Article
    | Open Access

    Previous studies showed that children with autism spectrum disorder (ASD) have atypicalities in the pupillary light reflex (PLR). This study uses longitudinal monitoring of infants at risk for ASD to show that PLR magnitude at 10 months of age is associated with later ASD diagnosis and symptom severity.

    • Pär Nyström
    • , Teodora Gliga
    •  & Terje Falck-Ytter

  • Review Article
    | Open Access

    This review summarizes how predictive modeling, a method that uses brain features to predict individual differences in behavior, is used to understand developmental periods. Rosenberg et al focus specifically on adolescence and examples of characteristic adolescent behaviors such as risk-taking.

    • Monica D. Rosenberg
    • , B. J. Casey
    •  & Avram J. Holmes

  • Article
    | Open Access

    Sepsis is characterized by deregulated host response to infection. Efficient therapies are still needed but a limitation for sepsis treatment is the heterogeneity in patients. Here Sweeney et al. generate prognostic models based on gene expression to improve risk stratification classification and prediction for 30-day mortality of patients.

    • Timothy E. Sweeney
    • , Thanneer M. Perumal
    •  & Raymond J. Langley

  • Article
    | Open Access

    Biomarkers of the tipping point before metastasis in hepatocellular carcinoma (HCC) could help stratify patient treatment. Here, the authors study dynamic network biomarkers to identify CALM3 as a potential suppressor of metastasis, the level of which can predict overall survival and relapse-free survival in postoperative HCC.

    • Biwei Yang
    • , Meiyi Li
    •  & Jinglin Xia

  • Article
    | Open Access

    Naturally acquired antibodies may inhibit Plasmodium survival in mosquitoes, alter malaria transmission dynamics, and form the basis for transmission-blocking vaccines. Here, using sera from malaria-exposed individuals, Stone et al. reveal novel antibody correlates of transmission-reducing activity.

    • Will J. R. Stone
    • , Joseph J. Campo
    •  & Matthijs M. Jore

  • Article
    | Open Access

    The extracellular matrix is under variable strain, but we lack the tools to detect differences in strain. Here the authors develop a probe based on a bacterial fibronectin-binding peptide that binds to relaxed fibronectin fibrils and detects relaxed matrix in cell culture, tissue slices and in vivo.

    • Simon Arnoldini
    • , Alessandra Moscaroli
    •  & Viola Vogel

  • Article
    | Open Access

    The authors use an integrative clustering approach to identify two laryngeal cancer clusters with distinct prognosis and show that mutations damaging the NSD1 and NSD2 methyltransferases segregate to the cluster with favorable prognosis, and independently predict longer survival in patients with laryngeal, but not other head and neck cancers.

    • Suraj Peri
    • , Evgeny Izumchenko
    •  & Erica A. Golemis

  • Article
    | Open Access

    The current FDA-approved whole blood stabilization method for circulating tumor cell (CTC) isolation suffers from RNA degradation. Here the authors combine hypothermic preservation and antiplatelet strategies to stabilize whole blood up to 72 h without compromising CTC yield and RNA integrity.

    • Keith H. K. Wong
    • , Shannon N. Tessier
    •  & Mehmet Toner

  • Article
    | Open Access

    CD4+ T cells secreting interleukin-17 (TH17) have diverse functions in modulating autoimmune diseases. Here the authors show via transcriptome analyses that a subset of human TH 17 co-expressing interferon-γ (TH1/17) has a molecular signature similar to “pathogenic” mouse TH 17 but distinct from “non-pathogenic” mouse TH 17.

    • Dan Hu
    • , Samuele Notarbartolo
    •  & Howard L. Weiner

  • Article
    | Open Access

    Abnormal levels of Aβ42 in the cerebrospinal fluid occur prior to a positive amyloid PET scan in the brain of individuals with Alzheimer’s disease and here the authors use this temporal pattern to identify individuals with very early stage AD. They show that Aβ fibrils start to accumulate in some of the regions of the default mode network and affect brain connectivity before neurodegeneration occurs.

    • Sebastian Palmqvist
    • , Michael Schöll
    •  & Oskar Hansson

  • Article
    | Open Access

    Liver mitochondrial metabolism plays an important role for glucose and lipid homeostasis and its alterations contribute to metabolic disorders, including fatty liver and diabetes. Here Perry et al. develop a method for the measurement of hepatic fluxes by using lactate and glucose tracers in combination with NMR spectroscopy.

    • Rachel J. Perry
    • , Liang Peng
    •  & Gerald I. Shulman

  • Article
    | Open Access

    In prostate cancer, the role of mutations in the maternally-inherited mitochondrial genome are not well known. Here, the authors demonstrate frequent, age-dependent mitochondrial mutation in prostate cancer. Strong links between mitochondrial and nuclear mutational profiles are associated with clinical aggressivity.

    • Julia F. Hopkins
    • , Veronica Y. Sabelnykova
    •  & Paul C. Boutros

  • Article
    | Open Access

    Caloric restriction has been shown to increase lifespan in mammals. Here, the authors provide evidence that age-related methylation drift correlates with lifespan and that caloric restriction in mice and rhesus monkeys results in attenuation of age-related methylation drift.

    • Shinji Maegawa
    • , Yue Lu
    •  & Jean-Pierre J. Issa

  • Article
    | Open Access

    Real-time monitoring of phosphate metabolism and distribution in the live body without ionizing radiation is highly desirable. Here, the authors show dissolution-dynamic nuclear polarization technology can enable nuclear magnetic resonance detection of hyperpolarized 31P of important biological phosphates in aqueous solutions.

    • Atara Nardi-Schreiber
    • , Ayelet Gamliel
    •  & Rachel Katz-Brull

  • Article
    | Open Access

    Early detection of gum inflammation caused by dental implants helps prevent tissue damage. Here, the authors present a peptide sensor that generates a bitter taste when cleaved by proteases present in peri-implant disease, embed it in a chewing gum, and compare the probe to existing sensors using patient saliva.

    • J. Ritzer
    • , T. Lühmann
    •  & L. Meinel

  • Article
    | Open Access

    Preparation of samples for diagnosis can affect the detection of biomarkers and metabolites. Here, the authors use a silver nanoparticle plasmonics approach for the detection of biomarkers in patients as well as investigate the distribution of drugs in serum and cerebral spinal fluid.

    • Lin Huang
    • , Jingjing Wan
    •  & Kun Qian

  • Article
    | Open Access

    Predicting the hepatotoxic effects of new drugs is still a challenge. Using toxicogenomics data, the authors here define a predictive toxicogenomic space (PTGS), the component gene space capturing dose-dependent cytotoxicity, and demonstrate that it can be used to accurately predict drug-induced liver pathology, including human drug-induced liver injury fromin vitrodata.

    • Pekka Kohonen
    • , Juuso A. Parkkinen
    •  & Roland C. Grafström

  • Article
    | Open Access

    Sleep patterns vary and are associated with health and disease. Here Purcellet alcharacterize sleep spindle activity in 11,630 individuals and describe age-related changes, genetic influences, and possible confounding effects, serving as a resource for further understanding the physiology of sleep.

    • S. M. Purcell
    • , D. S. Manoach
    •  & R. Stickgold

  • Article
    | Open Access

    Cancer cells adapt to the changing microenvironment by activating different pathways through multiple mechanisms. Here the authors identify long noncoding RNAMIR31HGas a HIF-1α co-activator required for the induction of the hypoxic response and show its oncogenic role in oral carcinogenesis.

    • Jing-Wen Shih
    • , Wei-Fan Chiang
    •  & Hsing-Jien Kung

  • Article
    | Open Access

    Some cancers with DNA mismatch repair deficiency display microsatellite instability. Here the authors analyse twenty three cancer types at the exome and whole-genome level, and identify loci with recurrent microsatellite instability that could be used to identify patients who would benefit from immunotherapy.

    • Isidro Cortes-Ciriano
    • , Sejoon Lee
    •  & Peter J. Park

  • Article
    | Open Access

    Antidepressant drugs are the most common treatment for depressive episodes but only a fraction of patients experience adequate response. Here the authors find dysregulation of miRNAs in peripheral blood samples from depressed patients after antidepressant treatment, and show that the miRNAs are regulators of psychiatrically relevant signalling pathways.

    • Juan Pablo Lopez
    • , Laura M. Fiori
    •  & Gustavo Turecki

  • Article
    | Open Access

    DNA methylation is modulated by environmental factors and has a role in many complex diseases. Here, the authors find that methylation at specific DNA sites is associated with all-cause mortality, and a methylation-based risk score may be informative for risk assessment and stratification.

    • Yan Zhang
    • , Rory Wilson
    •  & Hermann Brenner

  • Article
    | Open Access

    Some adolescents seek novelty, but it is unknown whether the brain circuits underlying this behaviour can be used to predict later, problematic behaviour. Here, authors show that diminished ventral striatal and prefrontal activity in response to anticipated rewards at age 14 in these individuals predicts problematic drug use at age 16.

    • Christian Büchel
    • , Jan Peters
    •  & Veronika Ziesch

  • Article
    | Open Access

    Pain is affected by cerebral processes in addition to afferent nociceptive input. Here the authors develop an fMRI-based signature that predicts pain independent of the intensity of nociceptive signals and mediates the pain-modulating effects of several cognitive interventions.

    • Choong-Wan Woo
    • , Liane Schmidt
    •  & Tor D. Wager

  • Article
    | Open Access

    The heterogeneity of colorectal cancer has important clinical and therapeutic implications. Here the authors analysed the responses of a large biobank of organoids and xenografts derived from colorectal patients to a panel of clinically relevant therapeutic agents to identify genes signatures associated with drug response.

    • Moritz Schütte
    • , Thomas Risch
    •  & Marie-Laure Yaspo

  • Article
    | Open Access

    The rat is a widely-used model for human biology, but we must be aware of metabolic differences. Here, the authors reconstruct the genome-scale metabolic network of the rat, and after reconciling it with an improved human metabolic model, demonstrate the power of the models to integrate toxicogenomics data, providing species-specific biomarker predictions in response to a panel of drugs.

    • Edik M. Blais
    • , Kristopher D. Rawls
    •  & Jason A. Papin

  • Article
    | Open Access

    ATM is a tumor suppressor often mutated in lung adenocarcinoma. In this study, the authors starting from a synthetic lethal screen, demonstrate that tumor cells with mutations in ATM exhibit increased sensitivity to MEK1/2 inhibition through the modulation of the AKT/mTOR pathway.

    • Michal Smida
    • , Ferran Fece de la Cruz
    •  & Sebastian M. B. Nijman

  • Article
    | Open Access

    Whether Alzheimer’s disease originates in basal forebrain or entorhinal cortex remains highly debated. Here the authors use structural magnetic resonance data from a longitudinal sample of participants stratified by cerebrospinal biomarker and clinical diagnosis to show that tissue volume changes appear earlier in the basal forebrain than in the entorhinal cortex.

    • Taylor W. Schmitz
    • , R. Nathan Spreng
    •  & Ansgar J. Furst

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