The transition from genomics to phenomics in personalized population health.

Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.

Every life has equal value.

The 2013 Lasker∼Bloomberg Public Service Award will be given to Bill and Melinda Gates "for leading an historic transformation in the way we view the globe's most pressing health concerns and improving the lives of millions of the world's most vulnerable."

Impella percutaneous left ventricular assist device as mechanical circulatory support for cardiogenic shock: A retrospective analysis from a tertiary academic medical center.

OBJECTIVES: To describe hemodynamic efficacy and clinical outcomes of Impella percutaneous left ventricular assist device (pLVAD) in patients with cardiogenic shock (CS). BACKGROUND: Percutaneous LVADs are increasingly used in CS management. However, device-related outcomes and optimal utilization remain active areas of investigation. METHODS: All CS patients receiving pLVAD as mechanical circulatory support (MCS) between 2011 and 2017 were identified. Clinical characteristics and outcomes were analyzed. A multivariable logistic regression model was created to predict MCS escalation despite pLVAD. Outcomes were compared between early and late implantation. RESULTS: A total of 115 CS patients (mean age 63.6 ± 13.8 years; 69.6% male) receiving pLVAD as MCS were identified, the majority with CS secondary to acute myocardial infarction (AMI; 67.0%). Patients experienced significant cardiac output improvement (median 3.39 L/min to 3.90 L/min, p = .002) and pharmacological support reduction (median vasoactive-inotropic score [VIS] 25.4 to 16.4, p = .049). Placement of extracorporeal membrane oxygenation (ECMO) occurred in 48 (41.7%) of patients. Higher pre-pLVAD VIS was associated with subsequent MCS escalation in the entire cohort and AMI subgroup (OR 1.27 [95% CI 1.02-1.58], p = .034 and OR 1.72 [95% CI 1.04-2.86], p = .035, respectively). Complications were predominantly access site related (bleeding [9.6%], vascular injury [5.2%], and limb ischemia [2.6%]). In-hospital mortality was 57.4%, numerically greater survival was noted with earlier device implantation. CONCLUSIONS: Treatment with pLVAD for CS improved hemodynamic status but did not uniformly obviate MCS escalation. Mortality in CS remains high, though earlier device placement for appropriately selected patients may be beneficial.

Improving Fluid Output Monitoring in the Intensive Care Unit.

PURPOSE: To assess the potential clinical impact of an automated urine output (UOP) monitoring system in the intensive care unit. METHODS: Frequency of UOP documentation during a 20-month period was assessed in records of inpatients on the medicine floor, cardiac intensive care (CCU), and cardiothoracic-intensive care units (CTICU). Documentation timeliness (time between expected and observed UOP recording) was assessed over a 3-month period. A novel reusable device that monitors UOP based on continuous analysis of the weight of a urine collection container was tested in the CCU/CTICU. RESULTS: A total of 165,363 UOP measurements were recorded for 2,039 CCU/CTICU admissions. Sixty percent of CCU/CTICU admissions had UOP recorded in the electronic medical record (EMR) less than every 2 hours. One-third of CCU/CTICU measurements were documented more than 2 hours late, and only 10% were recorded less than 20 minutes late. Half of these patients had fewer than 2 measurements recorded per nursing shift and recordings were documented an average of 85 minutes late. There was no significant difference between daytime and nighttime shifts. UOP values obtained by the novel electronic monitoring device were within 27 ml (-224 ml, +228 ml) of nurses documented values, across 74 patients over a 24-hour period. CONCLUSIONS: Automating UOP monitoring using a reusable weight-based device is feasible and can improve timeliness of documentation and reduce nursing workload without compromising accuracy.

Disorders of Consciousness in Hospitalized Patients with COVID-19: The Role of the Systemic Inflammatory Response Syndrome.

BACKGROUND: Prevalence and etiology of unconsciousness are uncertain in hospitalized patients with coronavirus disease 2019 (COVID-19). We tested the hypothesis that increased inflammation in COVID-19 precedes coma, independent of medications, hypotension, and hypoxia. METHODS: We retrospectively assessed 3203 hospitalized patients with COVID-19 from March 2 through July 30, 2020, in New York City with the Glasgow Coma Scale and systemic inflammatory response syndrome (SIRS) scores. We applied hazard ratio (HR) modeling and mediation analysis to determine the risk of SIRS score elevation to precede coma, accounting for confounders. RESULTS: We obtained behavioral assessments in 3203 of 10,797 patients admitted to the hospital who tested positive for SARS-CoV-2. Of those patients, 1054 (32.9%) were comatose, which first developed on median hospital day 2 (interquartile range [IQR] 1-9). During their hospital stay, 1538 (48%) had a SIRS score of 2 or above at least once, and the median maximum SIRS score was 2 (IQR 1-2). A fivefold increased risk of coma (HR 5.05, 95% confidence interval 4.27-5.98) was seen for each day that patients with COVID-19 had elevated SIRS scores, independent of medication effects, hypotension, and hypoxia. The overall mortality in this population was 13.8% (n = 441). Coma was associated with death (odds ratio 7.77, 95% confidence interval 6.29-9.65) and increased length of stay (13 days [IQR 11.9-14.1] vs. 11 [IQR 9.6-12.4]), accounting for demographics. CONCLUSIONS: Disorders of consciousness are common in hospitalized patients with severe COVID-19 and are associated with increased mortality and length of hospitalization. The underlying etiology of disorders of consciousness in this population is uncertain but, in addition to medication effects, may in part be linked to systemic inflammation.

[Human and animal health]. / Santé humaine et santé animale.

The concept of "one health" applies perfectly to human health and animal health because many diseases are zoonoses. There are many historical examples of effective collaboration between veterinary medicine and human medicine in the development of the first vaccines used in the world (smallpox, rabies, tetanus, diphtheria, tuberculosis, etc.). But when a new disease appears in animals, the risk of possible transmission to humans is difficult to estimate. In the latter case, the loss of consumer confidence in the face of scientific uncertainties can cause a health crisis (examples of bovine spongiform encephalopathy and H5N1 avian plague). But the most serious crisis that we have known since early 2020 is Covid-19 pandemic, which confirms that the modification of the ecosystems of certain wild species such as the horseshoe bats can have significant consequences for the public health. Animals infected with Covid-19 have been contaminated by humans but we cannot currently exclude an animal reservoir risk for SARS-CoV-2 which has circulated around the world.

Epidemiology, clinical course, and outcomes of critically ill adults with COVID-19 in New York City: a prospective cohort study.

BACKGROUND: Over 40 000 patients with COVID-19 have been hospitalised in New York City (NY, USA) as of April 28, 2020. Data on the epidemiology, clinical course, and outcomes of critically ill patients with COVID-19 in this setting are needed. METHODS: This prospective observational cohort study took place at two NewYork-Presbyterian hospitals affiliated with Columbia University Irving Medical Center in northern Manhattan. We prospectively identified adult patients (aged ≥18 years) admitted to both hospitals from March 2 to April 1, 2020, who were diagnosed with laboratory-confirmed COVID-19 and were critically ill with acute hypoxaemic respiratory failure, and collected clinical, biomarker, and treatment data. The primary outcome was the rate of in-hospital death. Secondary outcomes included frequency and duration of invasive mechanical ventilation, frequency of vasopressor use and renal replacement therapy, and time to in-hospital clinical deterioration following admission. The relation between clinical risk factors, biomarkers, and in-hospital mortality was modelled using Cox proportional hazards regression. Follow-up time was right-censored on April 28, 2020 so that each patient had at least 28 days of observation. FINDINGS: Between March 2 and April 1, 2020, 1150 adults were admitted to both hospitals with laboratory-confirmed COVID-19, of which 257 (22%) were critically ill. The median age of patients was 62 years (IQR 51-72), 171 (67%) were men. 212 (82%) patients had at least one chronic illness, the most common of which were hypertension (162 [63%]) and diabetes (92 [36%]). 119 (46%) patients had obesity. As of April 28, 2020, 101 (39%) patients had died and 94 (37%) remained hospitalised. 203 (79%) patients received invasive mechanical ventilation for a median of 18 days (IQR 9-28), 170 (66%) of 257 patients received vasopressors and 79 (31%) received renal replacement therapy. The median time to in-hospital deterioration was 3 days (IQR 1-6). In the multivariable Cox model, older age (adjusted hazard ratio [aHR] 1·31 [1·09-1·57] per 10-year increase), chronic cardiac disease (aHR 1·76 [1·08-2·86]), chronic pulmonary disease (aHR 2·94 [1·48-5·84]), higher concentrations of interleukin-6 (aHR 1·11 [95%CI 1·02-1·20] per decile increase), and higher concentrations of D-dimer (aHR 1·10 [1·01-1·19] per decile increase) were independently associated with in-hospital mortality. INTERPRETATION: Critical illness among patients hospitalised with COVID-19 in New York City is common and associated with a high frequency of invasive mechanical ventilation, extrapulmonary organ dysfunction, and substantial in-hospital mortality. FUNDING: National Institute of Allergy and Infectious Diseases and the National Center for Advancing Translational Sciences, National Institutes of Health, and the Columbia University Irving Institute for Clinical and Translational Research.

[Covid-19 and the animal world, from a still mysterious origin towards an always unpredictable future]. / Rapport 21-11. Covid-19 et monde animal, d'une origine encore mystérieuse vers un futur toujours incertain.

Although the emergence of Covid-19 in China has not been clearly elucidated, the hypothesis of an animal origin remains the most likely. It is supported by the presence of the horseshoe bat suspected to be the progenitor of SARS-CoV-2 and by the scarcity of pork, due to African swine fever, diverting consumers to exotic animals of breeding sold in the markets. During this pandemic, several animal species were affected by SARS-CoV-2. Sporadic cases were first reported in pets (dogs and cats) infected by their owners, then in large feline species and apes infected in zoos by their nurses. The most significant human-to-animal transmission has occurred in mink farms, especially in the Netherlands and Denmark, requiring the euthanasia of several million animals, with mink in turn having contaminated men and stray or nomadic cats. The study of natural or experimental transmissions of SARS-CoV-2 has made it possible to identify the most receptive animal species: American minks and raccoon dogs, and to a lesser extent stray or nomadic cats, which could become an animal reservoir due to their sensitivity to this virus and their extending prolificacy. The European Commission decided on May 17, 2021 to strengthen the surveillance of SARS-CoV-2 infections in minks and other mustelids, as well as in raccoon dogs, highlighting stressing that the epidemiological assessment of the risk presented by the he appearance of SARS-CoV-2 in these susceptible species was a public health priority.

The cardiac intensive care unit and the cardiac intensivist during the COVID-19 surge in New York City.

Critical care cardiology has been impacted by the coronavirus disease-2019 (COVID-19) pandemic. COVID-19 causes severe acute respiratory distress syndrome, acute kidney injury, as well as several cardiovascular complications including myocarditis, venous thromboembolic disease, cardiogenic shock, and cardiac arrest. The cardiac intensive care unit is rapidly evolving as the need for critical care beds increases. Herein, we describe the changes to the cardiac intensive care unit and the evolving role of critical care cardiologists and other clinicians in the care of these complex patients affected by the COVID-19 pandemic. These include practical recommendations regarding structural and organizational changes to facilitate care of patients with COVID-19; staffing and personnel changes; and health and safety of personnel. We draw upon our own experiences at NewYork-Presbyterian Columbia University Irving Medical Center to offer insights into the unique challenges facing critical care clinicians and provide recommendations of how to address these challenges during this unprecedented time.

Taking Systems Medicine to Heart.

Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine.

High resolution time-course mapping of early transcriptomic, molecular and cellular phenotypes in Huntington's disease CAG knock-in mice across multiple genetic backgrounds.

Huntington's disease is a dominantly inherited neurodegenerative disease caused by the expansion of a CAG repeat in the HTT gene. In addition to the length of the CAG expansion, factors such as genetic background have been shown to contribute to the age at onset of neurological symptoms. A central challenge in understanding the disease progression that leads from the HD mutation to massive cell death in the striatum is the ability to characterize the subtle and early functional consequences of the CAG expansion longitudinally. We used dense time course sampling between 4 and 20 postnatal weeks to characterize early transcriptomic, molecular and cellular phenotypes in the striatum of six distinct knock-in mouse models of the HD mutation. We studied the effects of the HttQ111 allele on the C57BL/6J, CD-1, FVB/NCr1, and 129S2/SvPasCrl genetic backgrounds, and of two additional alleles, HttQ92 and HttQ50, on the C57BL/6J background. We describe the emergence of a transcriptomic signature in HttQ111/+ mice involving hundreds of differentially expressed genes and changes in diverse molecular pathways. We also show that this time course spanned the onset of mutant huntingtin nuclear localization phenotypes and somatic CAG-length instability in the striatum. Genetic background strongly influenced the magnitude and age at onset of these effects. This work provides a foundation for understanding the earliest transcriptional and molecular changes contributing to HD pathogenesis.

Transcriptional regulatory networks underlying gene expression changes in Huntington's disease.

Transcriptional changes occur presymptomatically and throughout Huntington's disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD We reconstructed a genome-scale model for the target genes of 718 transcription factors (TFs) in the mouse striatum by integrating a model of genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and CAG repeat length-dependent gene expression changes in Htt CAG knock-in mouse striatum and replicated many of these associations in independent transcriptomic and proteomic datasets. Thirteen of 48 of these predicted TF-target gene modules were also differentially expressed in striatal tissue from human disease. We experimentally validated a specific model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found CAG repeat length-dependent changes in the genomic occupancy of SMAD3 and confirmed our model's prediction that many SMAD3 target genes are downregulated early in HD.

La Jument lighthouse: a real-scale laboratory for the study of giant waves and their loading on marine structures.

This paper presents results from an experiment designed to improve the understanding of the relationship between extreme breaking waves and their mechanical loading on heritage offshore lighthouses. The experiment, conducted at La Jument, an iconic French offshore lighthouse, featured several records of wave, current and structure accelerations acquired during severe storm conditions, with individual waves as high as 24 m. Data analysis focuses on a storm event marked by a strong peak in the horizontal accelerations measured inside La Jument. Thanks to stereo-video wave measurements synchronized to the acceleration record we were able to identify and describe the breaking wave responsible for this intense loading. Our observations suggest that this giant wave (19 m high) had a crest elevation high enough to directly hit the lighthouse tower, above the substructure. This paper reveals the potential for conducting ambitious field experiments from offshore lighthouses in order to collect valuable storm waves and wave loading observations. This offers a possible second service life for these heritage structures as in situ laboratories dedicated to the study of the coastal hydrodynamics and its interaction with marine structures. This article is part of the theme issue 'Environmental loading of heritage structures'.

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories.

Laboratory-acquired infections due to a variety of bacteria, viruses, parasites, and fungi have been described over the last century, and laboratory workers are at risk of exposure to these infectious agents. However, reporting laboratory-associated infections has been largely voluntary, and there is no way to determine the real number of people involved or to know the precise risks for workers. In this study, an international survey based on volunteering was conducted in biosafety level 3 and 4 laboratories to determine the number of laboratory-acquired infections and the possible underlying causes of these contaminations. The analysis of the survey reveals that laboratory-acquired infections have been infrequent and even rare in recent years, and human errors represent a very high percentage of the cases. Today, most risks from biological hazards can be reduced through the use of appropriate procedures and techniques, containment devices and facilities, and the training of personnel.

Characterization and phylogenetic analysis of new bat astroviruses detected in Gabon, Central Africa.

Astroviruses are emerging RNA viruses that cause enteropathogenic infections in humans and in other mammals. The identification of astroviruses in a wide range of animals highlights the zoonotic importance of these viruses. Bats can harbor many different viruses, among which some are highly pathogenic for humans (for instance, Nipah, Ebola and SARS coronavirus), and also several astroviruses. As some RNA viruses can be directly transmitted from bats to humans, it is crucial to collect data about their frequency, genetic diversity and phylogenetic characterization. In this study, we report the molecular identification of 44 new astroviruses (with a detection rate of 4.5%) in 962 apparently healthy bats that belong to five different species and that were captured in different caves in North-East Gabon, Central Africa. Our results show that bat astroviruses form a group that is genetically distinct from astroviruses infecting other mammals. Moreover, these astroviruses showed an important genetic diversity and low host restriction in bat species.

Disrupted SOX10 function causes spongiform neurodegeneration in gray tremor mice.

Mice homozygous for the gray tremor (gt) mutation have a pleiotropic phenotype that includes pigmentation defects, megacolon, whole body tremors, sporadic seizures, hypo- and dys-myelination of the central nervous system (CNS) and peripheral nervous system, vacuolation of the CNS, and early death. Vacuolation similar to that caused by prions was originally reported to be transmissible, but subsequent studies showed the inherited disease was not infectious. The gt mutation mapped to distal mouse chromosome 15, to the same region as Sox10, which encodes a transcription factor with essential roles in neural crest survival and differentiation. As dominant mutations in mouse or human SOX10 cause white spotting and intestinal aganglionosis, we screened the Sox10 coding region for mutations in gt/gt DNA. An adenosine to guanine transversion was identified in exon 2 that changes a highly conserved glutamic acid residue in the SOX10 DNA binding domain to glycine. This mutant allele was not seen in wildtype mice, including the related GT/Le strain, and failed to complement a Sox10 null allele. Gene expression analysis revealed significant down-regulation of genes involved in myelin lipid biosynthesis pathways in gt/gt brains. Knockout mice for some of these genes develop CNS vacuolation and/or myelination defects, suggesting that their down-regulation may contribute to these phenotypes in gt mutants and could underlie the neurological phenotypes associated with peripheral demyelinating neuropathy-central dysmyelinating leukodystrophy-Waardenburg syndrome-Hirschsprung disease, caused by mutations in human SOX10.

Prevalence and anatomical features of acute longitudinal stent deformation: An intravascular ultrasound study.

OBJECTIVES: We report the prevalence and anatomical features of longitudinal stent deformation as detected by intravascular ultrasound (IVUS) BACKGROUND: Angiographic studies have recently reported longitudinal stent deformation as a mechanical complication occurring during percutaneous coronary intervention; however, there are no IVUS studies on this phenomenon METHODS: We retrospectively analyzed 1,489 consecutive stent-treated lesions in 1,057 patients who underwent IVUS post-stent implantation RESULTS: Seventeen longitudinal stent deformations in 17 lesions (1.1% per lesion) in 17 patients (1.6% per patient) were identified by IVUS. Of the 17 IVUS-detected deformations, only three deformations (17.6%) were detectable by angiography. By IVUS, there were three patterns of longitudinal stent deformation: (1) Deformation with intra-stent wrinkling and overlapping of the proximal and distal stent fragments within a single stent (n = 14), (2) deformation with elongation (n = 2), and (3) deformation with shortening (n = 1). Most of the deformations were located near to the proximal stent edge (88%), consistent with the finding that they were observed in 11 ostial (65%) and eight left main lesions (47%), and 8.3% of 96 left main stented lesions had evidence of deformation CONCLUSIONS: By IVUS, longitudinal stent deformation during percutaneous coronary intervention was seen more frequently than in previous studies; however, it is still uncommon (1.1%) except in the left main location. The most frequent pattern was intrastent wrinkling and overlapping of the proximal and distal stent fragments.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Next-generation sequencing (NGS) technologies-based transcriptomic profiling method often called RNA-seq has been widely used to study global gene expression, alternative exon usage, new exon discovery, novel transcriptional isoforms and genomic sequence variations. However, this technique also poses many biological and informatics challenges to extracting meaningful biological information. The RNA-seq data analysis is built on the foundation of high quality initial genome localization and alignment information for RNA-seq sequences. Toward this goal, we have developed RNASEQR to accurately and effectively map millions of RNA-seq sequences. We have systematically compared RNASEQR with four of the most widely used tools using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. Our results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs). RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers.

A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations.

Cancer cells are heterogeneous and, it has been proposed, fall into at least two classes: the tumor-initiating cancer stem cells (CSC) and the more differentiated tumor cells. The transmembrane protein CD133 has been widely used to isolate putative CSC populations in several cancer types, but its validity as a CSC marker and hence its clinical ramifications remain controversial. Here, we conducted transcriptomic profiling of sorted CD133(+) and CD133(-) cells from human glioblastoma multiforme (GBM) and, by subtractive analysis, established a CD133 gene expression signature composed of 214 differentially expressed genes. Extensive computational comparisons with a compendium of published gene expression profiles reveal that the CD133 gene signature transcriptionally resembles human ES cells and in vitro cultured GBM stem cells, and this signature successfully distinguishes GBM from lower-grade gliomas. More importantly, the CD133 gene signature identifies an aggressive subtype of GBM seen in younger patients with shorter survival who bear excessive genomic mutations as surveyed through the Cancer Genome Atlas Network GBM mutation spectrum. Furthermore, the CD133 gene signature distinguishes higher-grade breast and bladder cancers from their lower-grade counterparts. Our systematic analysis provides molecular and genetic support for the stem cell-like nature of CD133(+) cells and an objective means for evaluating cancer aggressiveness.