Translating the potential of the urine steroid metabolome to stage NAFLD (TrUSt-NAFLD): study protocol for a multicentre, prospective validation study.

INTRODUCTION: Non-alcoholic fatty liver disease (NAFLD) affects approximately one in four individuals and its prevalence continues to rise. The advanced stages of NAFLD with significant liver fibrosis are associated with adverse morbidity and mortality outcomes. Currently, liver biopsy remains the 'gold-standard' approach to stage NAFLD severity. Although generally well tolerated, liver biopsies are associated with significant complications, are resource intensive, costly, and sample only a very small area of the liver as well as requiring day case admission to a secondary care setting. As a result, there is a significant unmet need to develop non-invasive biomarkers that can accurately stage NAFLD and limit the need for liver biopsy. The aim of this study is to validate the use of the urine steroid metabolome as a strategy to stage NAFLD severity and to compare its performance against other non-invasive NAFLD biomarkers. METHODS AND ANALYSIS: The TrUSt-NAFLD study is a multicentre prospective test validation study aiming to recruit 310 patients with biopsy-proven and staged NAFLD across eight centres within the UK. 150 appropriately matched control patients without liver disease will be recruited through the Oxford Biobank. Blood and urine samples, alongside clinical data, will be collected from all participants. Urine samples will be analysed by liquid chromatography-tandem mass spectroscopy to quantify a panel of predefined steroid metabolites. A machine learning-based classifier, for example, Generalized Matrix Relevance Learning Vector Quantization that was trained on retrospective samples, will be applied to the prospective steroid metabolite data to determine its ability to identify those patients with advanced, as opposed to mild-moderate, liver fibrosis as a consequence of NAFLD. ETHICS AND DISSEMINATION: Research ethical approval was granted by West Midlands, Black Country Research Ethics Committee (REC reference: 21/WM/0177). A substantial amendment (TrUSt-NAFLD-SA1) was approved on 26 November 2021. TRIAL REGISTRATION NUMBER: ISRCTN19370855.

Type 2 Diabetes risk alleles in Peptidyl-glycine Alpha-amidating Monooxygenase influence GLP-1 levels and response to GLP-1 Receptor Agonists.

Patients with type 2 diabetes vary in their response to currently available therapeutic agents (including GLP-1 receptor agonists) leading to suboptimal glycemic control and increased risk of complications. We show that human carriers of hypomorphic T2D-risk alleles in the gene encoding peptidyl-glycine alpha-amidating monooxygenase (PAM), as well as Pam-knockout mice, display increased resistance to GLP-1 in vivo. Pam inactivation in mice leads to reduced gastric GLP-1R expression and faster gastric emptying: this persists during GLP-1R agonist treatment and is rescued when GLP-1R activity is antagonized, indicating resistance to GLP-1's gastric slowing properties. Meta-analysis of human data from studies examining GLP-1R agonist response (including RCTs) reveals a relative loss of 44% and 20% of glucose lowering (measured by glycated hemoglobin) in individuals with hypomorphic PAM alleles p.S539W and p.D536G treated with GLP-1R agonist. Genetic variation in PAM has effects on incretin signaling that alters response to medication used commonly for treatment of T2D.

Risk of severe COVID-19 outcomes associated with rheumatoid arthritis and phenotypic subgroups: a retrospective, comparative, multicentre cohort study.

Background: Rheumatoid arthritis has been associated with severe COVID-19, but few studies have investigated how phenotypes of rheumatoid arthritis affect these associations. We aimed to investigate the associations between rheumatoid arthritis and phenotypes of interstitial lung disease, serostatus, and bone erosions with COVID-19 severity. Methods: We did a retrospective, comparative, multicentre cohort study at two large health-care systems (Mayo Clinic [19 hospitals and affiliated outpatient centres] and Mass General Brigham [14 hospitals and affiliated outpatient centres]) in the USA. Consecutive patients with rheumatoid arthritis meeting the 2010 American College of Rheumatology/European League Against Rheumatism classification criteria and who had COVID-19 between March 1, 2020, and June 6, 2021, were matched 1:5 on age, sex, and calendar date with patients without rheumatoid arthritis (comparators). Data were received from electronic health records from Mayo Clinic and Mass General Brigham. We examined subgroups of patients with rheumatoid arthritis by phenotypic features: rheumatoid arthritis-associated interstitial lung disease, seropositivity (for anti-cyclic citrullinated peptide, rheumatoid factor, or both), and bone erosions. Severe COVID-19 was a composite of hospitalisation or death. We used Cox regression to estimate hazard ratios (HR) for severe COVID-19, comparing rheumatoid arthritis and subgroups to the comparator group. Findings: We identified 582 patients with rheumatoid arthritis and 2875 matched comparators, all of whom had COVID-19 within the study dates. The mean age of those with rheumatoid arthritis was 62 [SD 14] years, 421 (72%) of 582 were women and 161 (28%) were men, 457 (79%) were White, 65 (11%) were Hispanic or Latino, and 41 (7%) were Black. Among patients with rheumatoid arthritis, 50 (9%) of 582 had interstitial lung disease, 388 (68%) of 568 were seropositive, and 159 (27%) of 582 had bone erosions. Severe COVID-19 occurred in 126 (22%) of 582 patients with rheumatoid arthritis versus 363 (13%) 2875 in the comparator group. Patients with rheumatoid arthritis had an HR of 1·75 (95% CI 1·45-2·10) for severe COVID-19 versus the comparator group. Patients with rheumatoid arthritis-associated interstitial lung disease had an HR of 2·50 (1·66-3·77) versus the comparator group for severe COVID-19. The risk for severe COVID-19 was also higher in patients with rheumatoid arthritis who were seropositive (HR 1·97 [95% CI 1·58-2·46]) or had erosive disease (1·93 [1·41-2·63]) than for those in the comparator group. Interpretation: Patients with rheumatoid arthritis have an increased risk of severe COVID-19 across phenotypic subgroups, especially among patients with interstitial lung disease. These findings suggest that rheumatoid arthritis with interstitial lung disease, or its treatment, might be a substantial contributor to severe COVID-19 outcomes for patients with rheumatoid arthritis. Funding: None.

Clonal diversification and histogenesis of malignant germ cell tumours.

Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.

TCF7L2 plays a complex role in human adipose progenitor biology, which might contribute to genetic susceptibility to type 2 diabetes.

INTRODUCTION: Non-coding genetic variation at TCF7L2 is the strongest genetic determinant of type 2 diabetes (T2D) risk in humans. TCF7L2 encodes a transcription factor mediating the nuclear effects of WNT signaling in adipose tissue (AT). In vivo studies in transgenic mice have highlighted important roles for TCF7L2 in adipose tissue biology and systemic metabolism. OBJECTIVE: To map the expression of TCF7L2 in human AT, examine its role in human adipose cell biology in vitro, and investigate the effects of the fine-mapped T2D-risk allele at rs7903146 on AT morphology and TCF7L2 expression. METHODS: Ex vivo gene expression studies of TCF7L2 in whole and fractionated human AT. In vitro TCF7L2 gain- and/or loss-of-function studies in primary and immortalized human adipose progenitor cells (APCs) and mature adipocytes (mADs). AT phenotyping of rs7903146 T2D-risk variant carriers and matched controls. RESULTS: Adipose progenitors (APs) exhibited the highest TCF7L2 mRNA abundance compared to mature adipocytes and adipose-derived endothelial cells. Obesity was associated with reduced TCF7L2 transcript levels in whole subcutaneous abdominal AT but paradoxically increased expression in APs. In functional studies, TCF7L2 knockdown (KD) in abdominal APs led to dose-dependent activation of WNT/ß-catenin signaling, impaired proliferation and dose-dependent effects on adipogenesis. Whilst partial KD enhanced adipocyte differentiation, near-total KD impaired lipid accumulation and adipogenic gene expression. Over-expression of TCF7L2 accelerated adipogenesis. In contrast, TCF7L2-KD in gluteal APs dose-dependently enhanced lipid accumulation. Transcriptome-wide profiling revealed that TCF7L2 might modulate multiple aspects of AP biology including extracellular matrix secretion, immune signaling and apoptosis. The T2D-risk allele at rs7903146 was associated with reduced AP TCF7L2 expression and enhanced AT insulin sensitivity. CONCLUSIONS: TCF7L2 plays a complex role in AP biology and has both dose- and depot-dependent effects on adipogenesis. In addition to regulating pancreatic insulin secretion, genetic variation at TCF7L2 might also influence T2D risk by modulating AP function.

Genetic and chemotherapeutic influences on germline hypermutation.

Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome1,2. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.

Clinical and laboratory profiles of the SARS-CoV-2 Delta variant compared with pre-Delta variants.

OBJECTIVES: The emergence of SARS-CoV-2 variants of concern has led to significant phenotypical changes in transmissibility, virulence, and public health measures. Our study used clinical data to compare characteristics between a Delta variant wave and a pre-Delta variant wave of hospitalized patients. METHODS: This single-center retrospective study defined a wave as an increasing number of COVID-19 hospitalizations, which peaked and later decreased. Data from the United States Department of Health and Human Services were used to identify the waves' primary variant. Wave 1 (August 8, 2020-April 1, 2021) was characterized by heterogeneous variants, whereas Wave 2 (June 26, 2021-October 18, 2021) was predominantly the Delta variant. Descriptive statistics, regression techniques, and machine learning approaches supported the comparisons between waves. RESULTS: From the cohort (N = 1318), Wave 2 patients (n = 665) were more likely to be younger, have fewer comorbidities, require more care in the intensive care unit, and show an inflammatory profile with higher C-reactive protein, lactate dehydrogenase, ferritin, fibrinogen, prothrombin time, activated thromboplastin time, and international normalized ratio compared with Wave 1 patients (n = 653). The gradient boosting model showed an area under the receiver operating characteristic curve of 0.854 (sensitivity 86.4%; specificity 61.5%; positive predictive value 73.8%; negative predictive value 78.3%). CONCLUSION: Clinical and laboratory characteristics can be used to estimate the COVID-19 variant regardless of genomic testing availability. This finding has implications for variant-driven treatment protocols and further research.

Reduced reproductive success is associated with selective constraint on human genes.

Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants1. Although genes under the strongest selective constraint are highly enriched for associations with Mendelian disorders, most of these genes are not associated with disease and therefore the nature of the selection acting on them is not known2. Here we show that genetic variants that damage these genes are associated with markedly reduced reproductive success, primarily owing to increased childlessness, with a stronger effect in males than in females. We present evidence that increased childlessness is probably mediated by genetically associated cognitive and behavioural traits, which may mean that male carriers are less likely to find reproductive partners. This reduction in reproductive success may account for 20% of purifying selection against heterozygous variants that ablate protein-coding genes. Although this genetic association may only account for a very minor fraction of the overall likelihood of being childless (less than 1%), especially when compared to more influential sociodemographic factors, it may influence how genes evolve over time.

Low antispike antibody levels correlate with poor outcomes in COVID-19 breakthrough hospitalizations.

BACKGROUND: While COVID-19 immunization programs attempted to reach targeted rates, cases rose significantly since the emergence of the delta variant. This retrospective cohort study describes the correlation between antispike antibodies and outcomes of hospitalized, breakthrough cases during the delta variant surge. METHODS: All patients with positive SARS-CoV-2 polymerase chain reaction hospitalized at Mayo Clinic Florida from 19 June 2021 to 11 November 2021 were considered for analysis. Cases were analyzed by vaccination status. Breakthrough cases were then analyzed by low and high antibody titers against SARS-CoV-2 spike protein, with a cut-off value of ≥132 U/ml. Outcomes included hospital length of stay (LOS), need for intensive care unit (ICU), mechanical ventilation, and mortality. We used 1:1 nearest neighbor propensity score matching without replacement to assess for confounders. RESULTS: Among 627 hospitalized patients with COVID-19, vaccine breakthrough cases were older with more comorbidities compared to unvaccinated. After propensity score matching, the unvaccinated patients had higher mortality (27 [28.4%] vs. 12 [12.6%], p = 0.002) and LOS (7 [1.0-57.0] vs. 5 [1.0-31.0] days, p = 0.011). In breakthrough cases, low-titer patients were more likely to be solid organ transplant recipients (16 [34.0%] vs. 9 [12.3%], p = 0.006), with higher need for ICU care (24 [51.1%] vs. 22 [11.0%], p = 0.034), longer hospital LOS (median 6 vs. 5 days, p = 0.013), and higher mortality (10 [21.3%] vs. 5 [6.8%], p = 0.025) than high-titer patients. CONCLUSIONS: Hospitalized breakthrough cases were more likely to have underlying risk factors than unvaccinated patients. Low-spike antibody titers may serve as an indicator for poor prognosis in breakthrough cases admitted to the hospital.

Clinical outcomes of first- and second-generation hydrogel coils compared with bare platinum coils: a systematic literature review.

Endovascular coiling has revolutionized intracranial aneurysm treatment; however, recurrence continues to represent a major limitation. The hydrogel coil was developed to increase packing density and improve neck healing and therefore decrease recurrence rates. In this paper, we review treatment outcomes of first- (1HCs) and second-generation (2HCs) hydrogel coils and compare them to those of bare platinum coils (BPC). A query of multiple databases was performed. Articles with at least 10 aneurysms treated with either 1HC or 2HC were selected for analysis. Collected data included aneurysm size, rupture status, initial occlusion, initial residual neck/aneurysm, packing density, mortality, morbidity, recurrence, and retreatment rates. The primary endpoint was recurrence at final follow-up. Secondary endpoints included residual neck and dome rates as well as procedure-related complications and functional dependence at final follow-up. Studies that compared 1HC to BPC showed significant lower recurrence (24% vs. 30.8%, p = 0.02) and higher packing density (58.5% vs. 24.1%, p < 0.001) in 1HC but no significant difference in initial occlusion rate (p = 0.08). Studies that compared 2HC to BPC showed lower recurrence (6.3% vs. 14.3%, p = 0.007) and retreatment rates (3.4% vs. 7.7%, p = 0.010) as well as higher packing density (36.4% vs. 29.2%, p = 0.002) in 2HC, with similar initial occlusion rate (p = 0.86). The rate of complications was not statistically different between HC (25.5%) and BPC (22.6%, p = 0.06). Based on our review, the 1HC and 2HC achieved higher packing density and lower recurrence rates compared to BPC. The safety profile was similar between both groups.

Postoperative Opioid Utilization and Patient Satisfaction in General Surgery Procedures: A Prospective Observational Study.

BACKGROUND: Wide variation of opioid prescribing persists despite attempts to quantify number of opioids utilized postoperatively. We aim to prospectively determine number of opioids used after common surgery procedures to guide future prescribing. METHODS: A prospective observational trial was performed of opioids prescribed and used postoperatively. Patients filled out pre- and postoperative surveys, and number of opioids utilized was captured at postoperative visit. RESULTS: One-hundred-and-thirteen patients met inclusion. Median opioids prescribed exceeded number of opioids taken for all procedures. Median number of opioids taken postoperatively was fewer than 10 for all categories of procedures: simple skin/soft tissue 2 (IQR 1-4), complex skin/soft tissue 1.5 (IQR 0-14), simple laparoscopy 1 (IQR 0-20) and complex laparoscopy 4 (IQR 0-20), laparotomy 0 (IQR 0-26), and open inguinal hernia 2 (IQR 0-2). Nearly 80% of patients had leftover opioids, and 31% planned to keep them. There was little difference between preoperative and postoperative level of satisfaction with a pain control regimen. DISCUSSION: Postoperatively, patients utilize opioids less frequently than prescribed and often keep leftover pills. Patient pain control satisfaction is unrelated to number of opioids prescribed and taken postoperatively.

Coronavirus Disease 2019 Vaccine-Breakthrough Infections Requiring Hospitalization in Mayo Clinic Florida Through August 2021.

We characterized coronavirus disease 2019 (COVID-19) breakthrough cases admitted to a single center in Florida. With the emergence of delta variant, an increased number of hospitalizations was seen due to breakthrough infections. These patients were older and more likely to have comorbidities. Preventive measures should be maintained even after vaccination.

The mutational landscape of human somatic and germline cells.

Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.

Extensive phylogenies of human development inferred from somatic mutations.

Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.

Quantifying the Importance of COVID-19 Vaccination to Our Future Outlook.

Predictive models have played a critical role in local, national, and international response to the COVID-19 pandemic. In the United States, health care systems and governmental agencies have relied on several models, such as the Institute for Health Metrics and Evaluation, Youyang Gu (YYG), Massachusetts Institute of Technology, and Centers for Disease Control and Prevention ensemble, to predict short- and long-term trends in disease activity. The Mayo Clinic Bayesian SIR model, recently made publicly available, has informed Mayo Clinic practice leadership at all sites across the United States and has been shared with Minnesota governmental leadership to help inform critical decisions during the past year. One key to the accuracy of the Mayo Clinic model is its ability to adapt to the constantly changing dynamics of the pandemic and uncertainties of human behavior, such as changes in the rate of contact among the population over time and by geographic location and now new virus variants. The Mayo Clinic model can also be used to forecast COVID-19 trends in different hypothetical worlds in which no vaccine is available, vaccinations are no longer being accepted from this point forward, and 75% of the population is already vaccinated. Surveys indicate that half of American adults are hesitant to receive a COVID-19 vaccine, and lack of understanding of the benefits of vaccination is an important barrier to use. The focus of this paper is to illustrate the stark contrast between these 3 scenarios and to demonstrate, mathematically, the benefit of high vaccine uptake on the future course of the pandemic.

Providing safe care for patients in the coronavirus disease 2019 (COVID-19) era: A case series evaluating risk for hospital-associated COVID-19.

OBJECTIVE: We evaluated the risk of patients contracting coronavirus disease 2019 (COVID-19) during their hospital stay to inform the safety of hospitalization for a non-COVID-19 indication during this pandemic. METHODS: A case series of adult patients hospitalized for 2 or more nights from May 15 to June 15, 2020 at large tertiary-care hospital in the midwestern United States was reviewed. All patients were screened at admission with the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) polymerase chain reaction (PCR) test. Selected adult patients were also tested by IgG serology. After dismissal, patients with negative serology and PCR at admission were asked to undergo repeat serologic testing at 14-21 days after discharge. The primary outcome was healthcare-associated COVID-19 defined as a new positive SARS-CoV-2 PCR test on or after day 4 of hospital stay or within 7 days of hospital dismissal, or seroconversion in patients previously established as seronegative. RESULTS: Of the 2,068 eligible adult patients, 1,778 (86.0%) completed admission PCR testing, while 1,339 (64.7%) also completed admission serology testing. Of the 1,310 (97.8%) who were both PCR and seronegative, 445 (34.0%) repeated postdischarge serology testing. No healthcare-associated COVID-19 cases were detected during the study period. Of 1,310 eligible PCR and seronegative adults, no patients tested PCR positive during hospital admission (95% confidence interval [CI], 0.0%-0.3%). Of the 445 (34.0%) who completed postdischarge serology testing, no patients seroconverted (0.0%; 95% CI, 0.0%-0.9%). CONCLUSION: We found low likelihood of hospital-associated COVID-19 with strict adherence to universal masking, physical distancing, and hand hygiene along with limited visitors and screening of admissions with PCR.

A haemagglutination test for rapid detection of antibodies to SARS-CoV-2.

Serological detection of antibodies to SARS-CoV-2 is essential for establishing rates of seroconversion in populations, and for seeking evidence for a level of antibody that may be protective against COVID-19 disease. Several high-performance commercial tests have been described, but these require centralised laboratory facilities that are comparatively expensive, and therefore not available universally. Red cell agglutination tests do not require special equipment, are read by eye, have short development times, low cost and can be applied at the Point of Care. Here we describe a quantitative Haemagglutination test (HAT) for the detection of antibodies to the receptor binding domain of the SARS-CoV-2 spike protein. The HAT has a sensitivity of 90% and specificity of 99% for detection of antibodies after a PCR diagnosed infection. We will supply aliquots of the test reagent sufficient for ten thousand test wells free of charge to qualified research groups anywhere in the world.

Deployment of an Interdisciplinary Predictive Analytics Task Force to Inform Hospital Operational Decision-Making During the COVID-19 Pandemic.

In March 2020, our institution developed an interdisciplinary predictive analytics task force to provide coronavirus disease 2019 (COVID-19) hospital census forecasting to help clinical leaders understand the potential impacts on hospital operations. As the situation unfolded into a pandemic, our task force provided predictive insights through a structured set of visualizations and key messages that have helped the practice to anticipate and react to changing operational needs and opportunities. The framework shared here for the deployment of a COVID-19 predictive analytics task force could be adapted for effective implementation at other institutions to provide evidence-based messaging for operational decision-making. For hospitals without such a structure, immediate consideration may be warranted in light of the devastating COVID-19 third-wave which has arrived for winter 2020-2021.