Anders Boeck Jensen

Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance

Transposon inactivation of Arabidopsis MAP kinase 4 produced the mpk4 mutant exhibiting constitutive systemic acquired resistance (SAR) including elevated salicylic acid (SA) levels, increased resistance to virulent pathogens, and constitutive pathogenesis-related gene expression shown by Northern and microarray hybridizations. MPK4 kinase activity is required to repress SAR, as an inactive MPK4 form failed to complement mpk4. Analysis of mpk4 expressing the SA hydroxylase NahG and of mpk4/npr1 double mutants indicated that SAR expression in mpk4 is dependent upon elevated SA levels but is independent of NPR1. PDF1.2 and THI2.1 gene induction by jasmonate was blocked in mpk4 expressing NahG, suggesting that MPK4 is required for jasmonic acid-responsive gene expression.

Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

A key prerequisite for precision medicine is the estimation of disease progression from the current patient state. Disease correlations and temporal disease progression (trajectories) have mainly been analysed with focus on a small number of diseases or using large-scale approaches without time consideration, exceeding a few years. So far, no large-scale studies have focused on defining a comprehensive set of disease trajectories. Here we present a discovery-driven analysis of temporal disease progression patterns using data from an electronic health registry covering the whole population of Denmark. We use the entire spectrum of diseases and convert 14.9 years of registry data on 6.2 million patients into 1,171 significant trajectories. We group these into patterns centred on a small number of key diagnoses such as chronic obstructive pulmonary disease (COPD) and gout, which are central to disease progression and hence important to diagnose early to mitigate the risk of adverse outcomes. We suggest such trajectory analyses may be useful for predicting and preventing future diseases of individual patients.

Drought signal transduction in plants

Water deficit is one of the most common environmental limitations of crop productivity by affecting growth through alterations in metabolism and gene expression. The mechanisms involved in drought perception and signal transduction pathways are poorly understood. The participation of the plant hormone abscisic acid (ABA) has been well established. ABA levels increase when there are changes in the environment that result in cellular dehydration. Different approaches have been taken to understanding the molecular responses to desiccation and how ABA regulates gene expression. Recent efforts have identified particular topics of importance in the dissection of the signal transduction pathway which are summarized as follows: physiological approaches: identification of signalling molecules. Genetic approaches: the use of mutants, and Molecular approaches: promoter analysis.

Molecular characterization of L2 lipoxygenase from maize embryos.

We investigated the expression and accumulation pattern of lipoxygenaseisoforms throughout the maize plant life. Two forms of lipoxygenase L1and L2 have been identified as acidic proteins of 100 kDa (pI 6.4) and90 kDa (pI 5.5-5.7) which accumulate in dry embryos and in variousorgans of maize seedlings. In young embryos, only the L2 form wasdetected and accumulation of L2 mRNA decreased during embryodevelopment. Identification of lipoxygenases from in vivo and in vitro synthesized proteins indicates that similar levels of both L1and L2 forms accumulated during treatment with abscisic acid, (ABA)gibberellic acid (GA3) and jasmonic acid (JA). However,differences in the activity of both enzymes were detected. By using anantiserum directed against purified L2 we isolated and characterized apartial cDNA clone of maize embryos encoding a lipoxygenase. The deducedamino acid sequence of L2 cDNA shares 78% identity with the rice L2protein, and 51-56% identity with lipoxygenases from thedicotyledonous plants soybean and Arabidopsis/. DNA blotanalysis indicated that maize contains a family of lipoxygenase geneswhich are presently being characterized.

Diagnosis trajectories of prior multi-morbidity predict sepsis mortality

Sepsis affects millions of people every year, many of whom will die. In contrast to current survival prediction models for sepsis patients that primarily are based on data from within-admission clinical measurements (e.g. vital parameters and blood values), we aim for using the full disease history to predict sepsis mortality. We benefit from data in electronic medical records covering all hospital encounters in Denmark from 1996 to 2014. This data set included 6.6 million patients of whom almost 120,000 were diagnosed with the ICD-10 code: A41 ‘Other sepsis’. Interestingly, patients following recurrent trajectories of time-ordered co-morbidities had significantly increased sepsis mortality compared to those who did not follow a trajectory. We identified trajectories which significantly altered sepsis mortality, and found three major starting points in a combined temporal sepsis network: Alcohol abuse, Diabetes and Cardio-vascular diagnoses. Many cancers also increased sepsis mortality. Using the trajectory based stratification model we explain contradictory reports in relation to diabetes that recently have appeared in the literature. Finally, we compared the predictive power using 18.5 years of disease history to scoring based on within-admission clinical measurements emphasizing the value of long term data in novel patient scores that combine the two types of data.

Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity

Abstract Klinefelter syndrome (KS) (47,XXY) is the most common male sex chromosome aneuploidy. Diagnosis and clinical supervision remain a challenge due to varying phenotypic presentation and insufficient characterization of the syndrome. Here we combine health data-driven epidemiology and molecular level systems biology to improve the understanding of KS and the molecular interplay influencing its comorbidities. In total, 78 overrepresented KS comorbidities were identified using in- and out-patient registry data from the entire Danish population covering 6.8 million individuals. The comorbidities extracted included both clinically well-known (e.g. infertility and osteoporosis) and still less established KS comorbidities (e.g. pituitary gland hypofunction and dental caries). Several systems biology approaches were applied to identify key molecular players underlying KS comorbidities: Identification of co-expressed modules as well as central hubs and gene dosage perturbed protein complexes in a KS comorbidity network build from known disease proteins and their protein–protein interactions. The systems biology approaches together pointed to novel aspects of KS disease phenotypes including perturbed Jak-STAT pathway, dysregulated genes important for disturbed immune system (IL4), energy balance (POMC and LEP) and erythropoietin signalling in KS. We present an extended epidemiological study that links KS comorbidities to the molecular level and identify potential causal players in the disease biology underlying the identified comorbidities.

How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease.

Background: Congenital heart disease (CHD) occurs in approximately 1% of all live births, and 3% to 8% of these have until now been considered familial cases, defined as the occurrence of two or more affected individuals in a family. The validity of CHD diagnoses in Danish administrative registry data has only been studied previously in highly selected patient populations. These studies identified high positive predictive values (PPVs) and recurrence risk ratios (RRRs—ratio between probabilities of CHD given family history of CHD and no family history). However, the RRR can be distorted if registry data are used indiscriminately. Here, we investigated the consequences of misclassifications for the RRR using validated diagnoses on Danish patients with familial CHD. Methods: Danish citizens are assigned a civil registration number (CPR number) at birth or immigration, which acts as a unique identifier in the Danish registries, thus enabling connection of information from several registries. Utilizing the CPR number, we identified Danish patients with familial CHD and reviewed each patient’s file. We compared diagnoses from the registries with those manually assigned, which enabled calculation of the PPVs of diagnoses in the Danish registries, and from this, we deduced the false discovery rate (FDR). To measure the consequences on the RRR, the FDR was applied to a simulated data set with true RRR values of 2 and 10. Results: We validated diagnoses of 2,442 patients from 1,593 families. Of these, 874 patients were misclassified corresponding to an FDR of 36%. Applying this FDR on the simulated data sets, we found that the RRR decreased from 2 and 10 to 1.4 and 5.1, respectively. Lastly, we estimated that 11% of all cases with CHD were familial. Conclusion: We found that approximately one of nine of all cases with CHD are familial, and we also found that 36% of individuals with CHD in administrative medical registries are misclassified, which distort the RRR in simulated scenarios.

MicroRNAs, Regulatory Networks, and Comorbidities: Decoding Complex Systems

MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of messenger RNAs (mRNAs). Each miRNA targets a specific set of mRNAs. Upon binding the miRNA inhibits mRNA translation or facilitate mRNA degradation. miRNAs are frequently deregulated in several pathologies including cancer and cardiovascular diseases. Since miRNAs have a crucial role in fine-tuning the expression of their targets, they have been proposed as biomarkers of disease progression and prognostication.In this chapter we discuss different approaches for computational predictions of miRNA targets based on sequence complementarity and integration of expression data. In the last section of the chapter we discuss new opportunities in the study of miRNA regulatory networks in the context of temporal disease progression and comorbidities.

Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014

Objectives The hypothesis of the study was that if the gut microbiota is involved in the development of atherosclerotic cardiovascular and cerebrovascular diseases (CVDs), total colectomy may reduce the long-term risk of CVDs. The aim was therefore to investigate the risk of CVD in patients after a total colectomy compared with patients undergoing other types of surgery, which are not expected to alter the gut microbiota or the CVD risk. Setting The Danish National Patient Register including all hospital discharges in Denmark from 1996 to 2014. Participants Patients (n=1530) aged 45 years and above and surviving 1000 days after total colectomy without CVDs were selected and matched with five control patients who were also free of CVD 1000 days after other types of surgery. The five control patients were randomly selected from each of the three surgical groups: orthopaedic surgery, surgery in the gastrointestinal tract leaving it intact and other surgeries not related to the gastrointestinal tract or CVD (n=22 950). Primary and secondary outcome measures The primary outcome was the first occurring CVD event in any of the seven diagnostic domains (hypertensive disorders, acute ischaemic heart diseases, chronic ischaemic heart disease, cardiac arrhythmias, heart failure, cerebrovascular diseases and other arterial diseases) and the secondary outcomes were the first occurring event within each of these domains. Results Estimated by Cox proportional hazard models, the HRs of the composite CVD end point for patients with colectomy compared with the control patients were not significantly reduced (HR=0.94, 95% confidence limits 0.85 to 1.04). Among the seven CVD domains, only the risk of hypertensive disorders was significantly reduced (HR=0.85, 0.73 to 0.98). Conclusions Colectomy did not reduce the general risk of CVD, but reduced the risk of hypertensive disorders, most likely due to salt and water depletion induced by colectomy. These results encourage a reappraisal of the associations between gut microbiota and CVD.

Expression of the Maize rabl7 Gene in Response to Abscisic Acid and Osmotic Stress

Expression of the maize abscisic acid (ABA)-responsive gene rab17, was studied in seeds and vegetative tissues. RNA gel blot analysis of rabl7 mRNA accumulation in response to desiccation and exogenous applied ABA, detected expression in all tissues tested. NaCl, in concentrations higher than 50 mM activated accumulation of rab17 mRNA expression in leaf tissue of maize, whereas a weak accumulation was observed in root tissue. Barley aleurone layers also responded to NaCl by an increase in rab mRNA levels. Moreover, an inhibitor of ABA biosynthesis, fluridone, completely prevented rab gene induction in response to 250 mM NaCl in aleurone layers. In the corresponding protoplasts, which can not synthesize ABA, no accumulation of endogenous gene products was detected and transiently transformed homologous rice and maize gene promoters did not respond to increased osmotic levels. These results suggest that accumulation of rab17 mRNA in response to desiccation and high salt concentrations are dependent on increased levels of ABA.