Pan-cancer analyses of the associations between 109 pre-existing conditions and cancer treatment patterns across 19 adult cancers

Comorbidities present considerable challenges to cancer treatment and care. However, little is known about the effect of comorbidity on cancer treatment decisions across a wide range of cancer types and treatment modalities. Harnessing a cohort of 280,543 patients spanning 19 site-specific cancers, we explored pan-cancer frequencies of 109 comorbidities. Multinomial logistic regression was used to analyse the relationship between comorbidities and cancer treatment types, while binomial logistic regression examined the association between comorbidities and chemotherapy drug types, adjusting for demographic and clinical factors. Patients with comorbidity exhibited lower odds of receiving chemotherapy and multimodality treatment. End-stage renal disease was significantly associated with a decreased odds of receiving chemotherapy and surgery. Patients with prostate cancer who have comorbid non-acute cystitis, obstructive and reflux uropathy, urolithiasis, or hypertension were less likely to receive chemotherapy. Among patients with breast cancer, dementia, left bundle branch block, peripheral arterial disease, epilepsy, Barrett's oesophagus, ischaemic stroke, unstable angina and asthma were associated with lower odds of receiving multimodal chemotherapy, radiotherapy and surgery. Comorbidity is also consistently associated with the lower odds of receiving chemotherapy when comparing across 10 drug classes. Patients with comorbid dementia, intracerebral haemorrhage, subarachnoid haemorrhage, oesophageal varices, liver fibrosis sclerosis and cirrhosis and secondary pulmonary hypertension were less likely to receive antimetabolites. Comorbidity can influence the effectiveness and tolerability of cancer treatment and ultimately, prognosis. Multi-specialty collaborative care is essential for the management of comorbidity during cancer treatment, including prophylactic measures to manage toxicities.

Injury primes mutation-bearing astrocytes for dedifferentiation in later life

Despite their latent neurogenic potential, most normal parenchymal astrocytes fail to dedifferentiate to neural stem cells in response to injury. In contrast, aberrant lineage plasticity is a hallmark of gliomas, and this suggests that tumor suppressors may constrain astrocyte dedifferentiation. Here, we show that p53, one of the most commonly inactivated tumor suppressors in glioma, is a gatekeeper of astrocyte fate. In the context of stab-wound injury, p53 loss destabilized the identity of astrocytes, priming them to dedifferentiate in later life. This resulted from persistent and age-exacerbated neuroinflammation at the injury site and EGFR activation in periwound astrocytes. Mechanistically, dedifferentiation was driven by the synergistic upregulation of mTOR signaling downstream of p53 loss and EGFR, which reinstates stemness programs via increased translation of neurodevelopmental transcription factors. Thus, our findings suggest that first-hit mutations remove the barriers to injury-induced dedifferentiation by sensitizing somatic cells to inflammatory signals, with implications for tumorigenesis.

Cumulative burden of 144 conditions, critical care hospitalisation and premature mortality across 26 adult cancers

A comprehensive evaluation of the total burden of morbidity endured by cancer survivors remains unavailable. This study quantified the burden of 144 health conditions and critical care admissions across 26 adult cancers and treatment modalities in 243,767 adults. By age 60, top conditions ranked by fold difference (cumulative burden in survivors divided by cumulative burden in controls) were haematology, immunology/infection and pulmonary conditions. Patients who had all three forms of treatment (chemotherapy, radiotherapy and surgery) experienced a high cumulative burden of late morbidities compared with patients who received radiotherapy alone. The top five cancers with the highest cumulative burden of critical care admissions by age 60 were bone (12.4 events per 100 individuals [CI: 11.6-13.1]), brain (9.0 [7.5-10.5]), spinal cord and nervous system (7.2 [6.7-7.8]), testis (6.7 [4.9-8.4]) and Hodgkin lymphoma (4.4 [3.6-5.1]). Conditions that were associated with high excess years-of-life-lost were haematological conditions (9.6 years), pulmonary conditions (8.6 years) and immunological conditions or infections (7.8 years). As the population of cancer survivors continues to grow, our results indicate that it is important to tackle long-term health consequences through enacting data-driven policies.

Comparing clinical trial population representativeness to real-world populations: an external validity analysis encompassing 43 895 trials and 5 685 738 individuals across 989 unique drugs and 286 conditions in England

BACKGROUND

Randomised controlled trials (RCTs) inform prescription guidelines, but stringent eligibility criteria exclude individuals with vulnerable characteristics, which we define as comorbidities, concomitant medication use, and vulnerabilities due to age. Poor external validity can result in inadequate treatment decision information. Our first aim was to quantify the extent of exclusion of individuals with vulnerable characteristics from RCTs for all prescription drugs. Our second aim was to quantify the prevalence of individuals with vulnerable characteristics from population electronic health records who are actively prescribed such drugs. In tandem, these two aims will allow us to assess the representativeness between RCT and real-world populations and identify vulnerable populations potentially at risk of inadequate treatment decision information. When a vulnerable population is highly excluded from RCTs but has a high prevalence of individuals actively being prescribed the same medication, there is likely to be a gap in treatment decision information. Our third aim was to investigate the use of real-world evidence in contributing towards quantifying missing treatment risk or benefit through an observational study.

METHODS

We extracted RCTs from ClinicalTrials.gov from its inception to April 28, 2021, and primary care records from the Clinical Practice Research Datalink Gold database from Jan 1, 1998, to Dec 31, 2020. We referred to the British National Formulary to classify prescription drugs into drug categories. We conducted descriptive analyses and quantified RCT exclusion and prevalence of individuals with vulnerable characteristics for comparison to identify populations without treatment decision information. Exclusion and prevalence were assessed separately for different age groups, individual clinical specialities, and for quantities of concomitant conditions by clinical specialities, where multimorbidity was defined as having two or more clinical specialties, and medications prescribed, where polypharmacy was defined as having five or more medications prescribed. Population trends of individuals with multimorbidity or polypharmacy were assessed separately by age group. We conducted an observational cohort study to validate the use of real-world evidence in contributing towards quantifying treatment risk or benefit for patients with dementia on anti-dementia drugs with and without a contraindicated clinical speciality. To do so, we identified the clinical specialities that anti-dementia drug RCTs highly excluded yet had corresponding high prevalence in the real-world population, forming the groups with highest risk of having scarce treatment decision information. Cox regression was used to assess if the risk of mortality outcomes differs between both groups.

FINDINGS

43 895 RCTs from ClinicalTrials.gov and 5 685 738 million individuals from primary care records were used. We considered 989 unique drugs and 286 conditions across 13 drug-category cohorts. For the descriptive analyses, the median RCT exclusion proportion across 13 drug categories was 81·5% (IQR 76·7-85·5) for adolescents (aged <18 years), 26·3% (IQR 21·0-29·5) for individuals older than 60 years, 40·5% (IQR 33·7-43·0) for individuals older than 70 years, and 52·9% (IQR 47·1-56·0) for individuals older than 80 years. Multimorbidity had a median exclusion proportion of 91·1% (IQR 88·9-91·8) and median prevalence of 41·0% (IQR 34·9-46·0). Concomitant medication use had a median exclusion proportion of 52·5% (IQR 50·0-53·7) and a median prevalence of 94·3% (IQR 84·3-97·2), and polypharmacy had a median prevalence of 47·7% (IQR 38·0-56·1). Population trends show increasing multimorbidity with age and consistently high polypharmacy across age groups. Populations with cardiovascular or otorhinolaryngological comorbidities had the highest risk of having scarce treatment decision information. For the observational study, populations with cardiovascular or psychiatric comorbidities had highest risk of having scarce treatment decision information. Patients with dementia with an anti-dementia prescription and contraindicated cardiovascular condition had a higher risk of mortality (hazard ratio [HR] 1·20 [95% CI 1·13-1·28 ; p<0·0001]) compared with patients with dementia without a contraindicated cardiovascular condition. Patients with dementia with comorbid delirium (HR 1·25 [95% CI 1·06-1·48]; p<0·0088), intellectual disability (HR 2·72 [95% CI 1·53-4·81]; p=0·0006), and schizophrenia and schizotypal delusional disorders (HR 1·36 [95% CI 1·02-1·82]; p=0·036) had a higher risk of mortality compared with patients with dementia without these conditions.

INTERPRETATION

Overly stringent RCT exclusion criteria do not appropriately account for the heterogeneity of vulnerable characteristics observed in real-world populations. Treatment decision information is scarce for such individuals, which might affect health outcomes. We discuss the challenges facing the inclusivity of such individuals and highlight the strength of real-world evidence as an integrative solution in complementing RCTs and increasing the completeness of evidence-based medicine assessments in evaluating the effectiveness of treatment decisions.

FUNDING

Wellcome Trust, National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Academy of Medical Sciences, and the University College London Overseas Research Scholarship.

Multimorbidity patterns and risk of hospitalisation in children: A population cohort study of 3.6 million children in England, with illustrative examples from childhood cancer survivors

Background

Population-level estimates of hospitalisation risk in children are currently limited. The study aims to characterise morbidity patterns in all children, focusing on childhood cancer survivors versus children without cancer.

Methods

Employing hospital records of children aged <19 years between 1997 to 2018 in England, we characterised morbidity patterns in childhood cancer survivors compared with children without cancer. The follow-up began on the 5^th anniversary of the index hospitalisation and the primary outcome was the incidence of comorbidities.

Findings

We identified 3,559,439 eligible participants having 12,740,666 hospital admissions, with a mean age at study entry of 11.2 years. We identified 32,221 patients who survived for at least 5 years since their initial cancer diagnosis. During the follow-up period and within the whole population of 3.6 million children, the leading conditions for admission were (i) metabolic, endocrine, digestive renal and genitourinary conditions (84,749, 2.5%), (ii) neurological (35,833, 1.0%) and (iii) musculoskeletal or skin conditions (23,574, 0.7%), fever, acute respiratory and sepsis (22,604, 0.7%). Stratified analyses revealed that females and children from socioeconomically deprived areas had a higher cumulative incidence for morbidities requiring hospitalisation (p < 0.001). At baseline (5 years after the initial cancer diagnosis or initial hospitalisation for survivors and population comparisons, respectively), cancer survivors experienced a higher prevalence of individual conditions and multimorbidity (≥ 2 morbidities) compared with children without cancer. Cox regression analyses showed that survivors had at least a 4-fold increase in the risk of hospitalisation for conditions such as chronic eye conditions (hazard ration (HR):4.0, 95% confidence interval (CI): 3.5-4.7), fever requiring hospitalisation (HR: 4.4, 95% CI: 3.8-5.0), subsequent neoplasms (HR: 5.7, 95% CI:5.0-6.5), immunological disorders (HR: 6.5, 95% CI:4.5-9.3) and metabolic conditions (HR: 7.1, 95% CI:5.9-8.5).

Interpretation

The overall morbidity burden among children was low in general; however, childhood cancer survivors experienced a higher prevalence and subsequent risk of hospitalisation for a range of morbidities. Targeted policies may be required to promote awareness on health vulnerabilities and gender disparity and to improve advocacy for healthcare in deprived communities.

Funding

Wellcome Trust, National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre and Academy of Medical Sciences. The funders of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report.

Depression, anxiety, substance misuse and self-harm in children and young people with rare chronic liver disease

The burden of mental illness in young people with chronic liver disease is not known. In this population cohort study in England, we identified 358 individuals (aged ≤25 years) diagnosed with autoimmune hepatitis or liver disease related to cystic fibrosis and 1541 propensity-score-matched controls. By the first year of follow-up, the cumulative burden of psychiatric events in participants with liver disease was high compared with controls: anxiety disorder (6.87 per 100 individuals [95% CI 4.00-9.73] v. 2.22 [95% CI 1.37-3.07]), depression (5.10 [95% CI 2.83-7.37] v. 0.86 [95% CI 0.53-1.19]), substance misuse (10.61 [95% CI 9.50-11.73] v. 1.23 [95% CI 0.71-1.75]) and self-harm (3.09 [95% CI 1.12-5.05] v. 0.20 [95% CI 0.07-0.33]). Participants with liver disease had a 2-fold increase (OR = 1.94, 95% CI 1.45-2.58), a 2.5-fold increase (OR = 2.59, 95% CI 1.91-3.50) and 4.4-fold increase (OR = 4.44; 95% CI 3.46-5.71) in the risk of anxiety, depression and substance misuse, respectively. These findings highlight the need for effective intervention in psychiatric disorders in young people with rare liver disease.

Cumulative burden of psychiatric disorders and self-harm across 26 adult cancers

Cancer is a life-altering event causing considerable psychological distress. However, information on the total burden of psychiatric disorders across all common adult cancers and therapy exposures has remained scarce. Here, we estimated the risk of self-harm after incident psychiatric disorder diagnosis in patients with cancer and the risk of unnatural deaths after self-harm in 459,542 individuals. Depression was the most common psychiatric disorder in patients with cancer. Patients who received chemotherapy, radiotherapy and surgery had the highest cumulative burden of psychiatric disorders. Patients treated with alkylating agent chemotherapeutics had the highest burden of psychiatric disorders, whereas those treated with kinase inhibitors had the lowest burden. All mental illnesses were associated with an increased risk of subsequent self-harm, where the highest risk was observed within 12 months of the mental illness diagnosis. Patients who harmed themselves were 6.8 times more likely to die of unnatural causes of death compared with controls within 12 months of self-harm (hazard ratio (HR), 6.8; 95% confidence interval (CI), 4.3-10.7). The risk of unnatural death after 12 months was markedly lower (HR, 2.0; 95% CI, 1.5-2.7). We provide an extensive knowledge base to help inform collaborative cancer-psychiatric care initiatives by prioritizing patients who are most at risk.

Increased burden of cardiovascular disease in people with liver disease: unequal geographical variations, risk factors and excess years of life lost

Background

People with liver disease are at increased risk of developing cardiovascular disease (CVD), however, there has yet been an investigation of incidence burden, risk, and premature mortality across a wide range of liver conditions and cardiovascular outcomes.

Methods

We employed population-wide electronic health records (EHRs; from 1998 to 2020) consisting of almost 4 million adults to assess regional variations in disease burden of five liver conditions, alcoholic liver disease (ALD), autoimmune liver disease, chronic hepatitis B infection (HBV), chronic hepatitis C infection (HCV) and NAFLD, in England. We analysed regional differences in incidence rates for 17 manifestations of CVD in people with or without liver disease. The associations between biomarkers and comorbidities and risk of CVD in patients with liver disease were estimated using Cox models. For each liver condition, we estimated excess years of life lost (YLL) attributable to CVD (i.e., difference in YLL between people with or without CVD).

Results

The age-standardised incidence rate for any liver disease was 114.5 per 100,000 person years. The highest incidence was observed in NAFLD (85.5), followed by ALD (24.7), HCV (6.0), HBV (4.1) and autoimmune liver disease (3.7). Regionally, the North West and North East regions consistently exhibited high incidence burden. Age-specific incidence rate analyses revealed that the peak incidence for liver disease of non-viral aetiology is reached in individuals aged 50–59 years. Patients with liver disease had a two-fold higher incidence burden of CVD (2634.6 per 100,000 persons) compared to individuals without liver disease (1339.7 per 100,000 persons). When comparing across liver diseases, atrial fibrillation was the most common initial CVD presentation while hypertrophic cardiomyopathy was the least common. We noted strong positive associations between body mass index and current smoking and risk of CVD. Patients who also had diabetes, hypertension, proteinuric kidney disease, chronic kidney disease, diverticular disease and gastro-oesophageal reflex disorders had a higher risk of CVD, as do patients with low albumin, raised C-reactive protein and raised International Normalized Ratio levels. All types of CVD were associated with shorter life expectancies. When evaluating excess YLLs by age of CVD onset and by liver disease type, differences in YLLs, when comparing across CVD types, were more pronounced at younger ages.

Conclusions

We developed a public online app (https://lailab.shinyapps.io/cvd_in_liver_disease/) to showcase results interactively. We provide a blueprint that revealed previously underappreciated clinical factors related to the risk of CVD, which differed in the magnitude of effects across liver diseases. We found significant geographical variations in the burden of liver disease and CVD, highlighting the need to devise local solutions. Targeted policies and regional initiatives addressing underserved communities might help improve equity of access to CVD screening and treatment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-03210-9.

Late effects of cancer in children, teenagers and young adults: Population-based study on the burden of 183 conditions, in-patient and critical care admissions and years of life lost

BACKGROUND

Children, teenagers and young adults who survived cancer are prone to developing late effects. The burden of late effects across a large number of conditions, in-patient hospitalisation and critical care admissions have not been described using a population-based dataset. We aim to systematically quantify the cumulative burden of late effects across all cancer subtypes, treatment modalities and chemotherapy drug classes.

METHODS

We employed primary care records linked to hospitals, the death registry and cancer registry from 1998-2020. CTYA survivors were 25 years or younger at the time of cancer diagnosis had survived ≥5 years post-diagnosis. Year-of-birth and sex-matched community controls were used for comparison. We considered nine treatment types, nine chemotherapy classes and 183 physical and mental health late effects. Cumulative burden was estimated using mean cumulative count, which considers recurring events. Multivariable logistic regression was used to investigate the association between treatment exposures and late effects. Excess years of life lost (YLL) attributable to late effects were estimated.

FINDINGS

Among 4,063 patients diagnosed with cancer, 3,466 survived ≥ 5 years (85%); 13,517 matched controls were identified. The cumulative burden of late effects at age 35 was the highest in survivors of leukaemia (23.52 per individual [95% CI:19.85-29.33]) and lowest in survivors of germ cell tumours (CI:6.04 [5.32-6.91]). In controls, the cumulative burden was 3.99 (CI:3.93-4.08) at age 35 years. When survivors reach age 45, the cumulative burden for immunological conditions and infections was the highest (3.27 [CI:3.01-3.58]), followed by cardiovascular conditions (3.08 [CI:1.98-3.29]). Survivors who received chemotherapy and radiotherapy had the highest disease burden compared to those who received surgery only. These patients also had the highest burden of hospitalisation (by age 45: 10.43 [CI:8.27-11.95]). Survivors who received antimetabolite chemotherapy had the highest disease and hospitalisation burden, while the lowest burden is observed in those receiving antitumour antibiotics. Regression analyses revealed that survivors who received only surgery had lower odds of developing cardiovascular (adjusted odds ratio 0.73 [CI:0.56-0.94]), haematological (aOR 0.51 [CI:0.37-0.70]), immunology and infection (aOR 0.84 [CI:0.71-0.99]) and renal (aOR 0.51 [CI:0.39-0.66]) late effects. By contrast, the opposite trend was observed in survivors who received chemo-radiotherapy. High antimetabolite chemotherapy cumulative dose was associated with increased risks of subsequent cancer (aOR 2.32 [CI:1.06-4.84]), metastatic cancer (aOR 4.44 [CI:1.29-11.66]) and renal (aOR 3.48 [CI:1.36-7.86]) conditions. Patients who received radiation dose of ≥50 Gy experienced higher risks of developing metastatic cancer (aOR 5.51 [CI:2.21-11.86]), cancer (aOR 3.77 [CI:2.22-6.34]), haematological (aOR 3.43 [CI:1.54-6.83]) and neurological (aOR 3.24 [CI:1.78-5.66]) conditions. Similar trends were observed in survivors who received more than three teletherapy fields. Cumulative burden analyses on 183 conditions separately revealed varying dominance of different late effects across cancer types, socioeconomic deprivation and treatment modalities. Late effects are associated with excess YLL (i.e., the difference in YLL between survivors with or without late effects), which was the most pronounced among survivors with haematological comorbidities.

INTERPRETATION

To our knowledge, this is the first study to dissect and quantify the importance of late morbidities on subsequent survival using linked electronic health records from multiple settings. The burden of late effects is heterogeneous, as is the risk of premature mortality associated with late effects. We provide an extensive knowledgebase to help inform treatment decisions at the point of diagnosis, future interventional trials and late-effects screening centred on the holistic needs of this vulnerable population.

Antithrombotic therapy in patients with liver disease: population-based insights on variations in prescribing trends, adherence, persistence and impact on stroke and bleeding

BACKGROUND

Patients with liver disease have complex haemostasis and due to such contraindications, landmark randomised controlled trials investigating antithrombotic medicines have often excluded these patients. As a result, there has been limited consensus on the safety, efficacy and monitoring practices of anticoagulant and antiplatelet therapy in patients with liver disease. This study aims to investigate prescribing prevalence, adherence, persistence and impact of adherence on bleeding and stroke risk in people with and without liver disease taking anticoagulants and antiplatelets.

METHODS

We employed a population-based cohort consisting of person-level linked records from primary care, secondary care and the death registry. The cohort consisted of 3,929,596 adults aged ≥ 30 years during the study period of 1998 to 2020 and registered with an NHS general practitioner in England. The primary outcome was prescribing prevalence, adherence to and persistence with anticoagulant and antiplatelet therapy comparing patients with and without liver disease. Risk factors for non-adherence and non-persistence were analysed using multivariable logistic regression and Cox regression. Impact of adherence on bleeding and ischaemic stroke was assessed.

FINDINGS

Among patients with any of the six liver diseases (ALD, autoimmune liver disease, cirrhosis, HBV, HCV and NAFLD), we identified 4,237 individuals with incident atrial fibrillation (indication for anticoagulants) and 4,929 individuals with incident myocardial infarction, transient ischaemic attack, unstable angina or peripheral arterial disease (indication for antiplatelets). Among patients without liver disease, 321,510 and 386,643 individuals were identified as having indications for anticoagulant and antiplatelet therapy, respectively. Among drug-naïve individuals, prescribing prevalence was lower in patients with liver disease compared with individuals without liver disease: anticoagulants (20.6% [806/3,921] vs. 33.5% [103,222/307,877]) and antiplatelets (56.2% [2,207/3,927] vs. 71.1% [249,258/350,803]). Primary non-adherence rates (stopping after one prescription) were higher in patients with liver disease, compared with those without liver disease: anticoagulants (7.9% [64/806] vs. 4.7% [4,841/103,222]) and antiplatelets (6.2% [137/2,207] vs. 4.4% [10,993/249,258]). Among individuals who were not primary non-adherent and had at least 12 months of follow-up, patients with liver disease however had a higher one-year adherence rate: anticoagulants (33.1% [208/628] vs. 29.4% [26,615/90,569]) and antiplatelets (40.9% [743/1,818] vs. 34.4% [76,834/223,154]). Likelihood of non-adherence was lower in apixaban and rivaroxaban (relative to warfarin) and lower in clopidogrel (relative to aspirin). Increased comorbidity burden (by CHA₂DS₂VASc score) was associated with decreased risk of non-adherence and non-persistence with anticoagulants. Overall rates of 'non-adherent, non-persistent' were highest in warfarin (compared with apixaban and rivaroxaban) and aspirin (compared with clopidogrel or dipyridamole) in patients with and without liver disease. Among patients without liver disease, not taking antithrombotic medications for >3 months was associated with a higher risk of stroke, however, adherence to these medications was also associated with a small increase in risk of bleeding. Patients with liver disease (when compared with those without liver disease) had higher risks of stroke, especially when they stopped taking antiplatelets for >3 months. Patients with liver disease who were adherent to antiplatelets, however, had a higher risk of bleeding compared with patients without liver disease.

INTERPRETATION

Use of antithrombotic medicines in patients with and without liver disease is suboptimal with heterogeneity across medicines. As patients with liver disease are excluded from major randomised trials for these drugs, our results provide real-world evidence that may inform medicine optimisation strategies. We outline challenges and opportunities for tackling non-adherence, which begins with understanding patients' views of medicines to help them make informed decisions about appropriate use.

FUNDING

AGL is supported by funding from the Wellcome Trust (204841/Z/16/Z), National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre (BRC714/HI/RW/101440), NIHR Great Ormond Street Hospital Biomedical Research Centre (19RX02), the Health Data Research UK Better Care Catalyst Award (CFC0125) and the Academy of Medical Sciences (SBF006\1084). The funders have no role in the writing of the manuscript or the decision to submit it for publication.

An informatics consult approach for generating clinical evidence for treatment decisions

BACKGROUND

An Informatics Consult has been proposed in which clinicians request novel evidence from large scale health data resources, tailored to the treatment of a specific patient. However, the availability of such consultations is lacking. We seek to provide an Informatics Consult for a situation where a treatment indication and contraindication coexist in the same patient, i.e., anti-coagulation use for stroke prevention in a patient with both atrial fibrillation (AF) and liver cirrhosis.

METHODS

We examined four sources of evidence for the effect of warfarin on stroke risk or all-cause mortality from: (1) randomised controlled trials (RCTs), (2) meta-analysis of prior observational studies, (3) trial emulation (using population electronic health records (N = 3,854,710) and (4) genetic evidence (Mendelian randomisation). We developed prototype forms to request an Informatics Consult and return of results in electronic health record systems.

RESULTS

We found 0 RCT reports and 0 trials recruiting for patients with AF and cirrhosis. We found broad concordance across the three new sources of evidence we generated. Meta-analysis of prior observational studies showed that warfarin use was associated with lower stroke risk (hazard ratio [HR] = 0.71, CI 0.39-1.29). In a target trial emulation, warfarin was associated with lower all-cause mortality (HR = 0.61, CI 0.49-0.76) and ischaemic stroke (HR = 0.27, CI 0.08-0.91). Mendelian randomisation served as a drug target validation where we found that lower levels of vitamin K1 (warfarin is a vitamin K1 antagonist) are associated with lower stroke risk. A pilot survey with an independent sample of 34 clinicians revealed that 85% of clinicians found information on prognosis useful and that 79% thought that they should have access to the Informatics Consult as a service within their healthcare systems. We identified candidate steps for automation to scale evidence generation and to accelerate the return of results.

CONCLUSION

We performed a proof-of-concept Informatics Consult for evidence generation, which may inform treatment decisions in situations where there is dearth of randomised trials. Patients are surprised to know that their clinicians are currently not able to learn in clinic from data on 'patients like me'. We identify the key challenges in offering such an Informatics Consult as a service.

Application of ensemble clustering and survival tree analysis for identifying prognostic clinicogenomic features in patients with colorectal cancer from the 100,000 Genomes Project

OBJECTIVE

The objective of this study was to employ ensemble clustering and tree-based risk model approaches to identify interactions between clinicogenomic features for colorectal cancer using the 100,000 Genomes Project.

RESULTS

Among the 2211 patients with colorectal cancer (mean age of diagnosis: 67.7; 59.7% male), 16.3%, 36.3%, 39.0% and 8.4% had stage 1, 2, 3 and 4 cancers, respectively. Almost every patient had surgery (99.7%), 47.4% had chemotherapy, 7.6% had radiotherapy and 1.4% had immunotherapy. On average, tumour mutational burden (TMB) was 18 mutations/Mb and 34.4%, 31.3% and 25.7% of patients had structural or copy number mutations in KRAS, BRAF and NRAS, respectively. In the fully adjusted Cox model, patients with advanced cancer [stage 3 hazard ratio (HR)  =  3.2; p  <  0.001; stage 4 HR  =  10.2; p  <  0.001] and those who had immunotherapy (HR  =  1.8; p  <  0.04) or radiotherapy (HR  =  1.5; p  <  0.02) treatment had a higher risk of dying. The ensemble clustering approach generated four distinct clusters where patients in cluster 2 had the best survival outcomes (1-year: 98.7%; 2-year: 96.7%; 3-year: 93.0%) while patients in cluster 3 (1-year: 87.9; 2-year: 70.0%; 3-year: 53.1%) had the worst outcomes. Kaplan-Meier analysis and log rank test revealed that the clusters were separated into distinct prognostic groups (p  <  0.0001). Survival tree or recursive partitioning analyses were performed to further explore risk groups within each cluster. Among patients in cluster 2, for example, interactions between cancer stage, grade, radiotherapy, TMB, BRAF mutation status were identified. Patients with stage 4 cancer and TMB  ≥  1.6 mutations/Mb had 4 times higher risk of dying relative to the baseline hazard in that cluster.

Estimated impact of the COVID-19 pandemic on cancer services and excess 1-year mortality in people with cancer and multimorbidity: near real-time data on cancer care, cancer deaths and a population-based cohort study

OBJECTIVES

To estimate the impact of the COVID-19 pandemic on cancer care services and overall (direct and indirect) excess deaths in people with cancer.

METHODS

We employed near real-time weekly data on cancer care to determine the adverse effect of the pandemic on cancer services. We also used these data, together with national death registrations until June 2020 to model deaths, in excess of background (pre-COVID-19) mortality, in people with cancer. Background mortality risks for 24 cancers with and without COVID-19-relevant comorbidities were obtained from population-based primary care cohort (Clinical Practice Research Datalink) on 3 862 012 adults in England.

RESULTS

Declines in urgent referrals (median=-70.4%) and chemotherapy attendances (median=-41.5%) to a nadir (lowest point) in the pandemic were observed. By 31 May, these declines have only partially recovered; urgent referrals (median=-44.5%) and chemotherapy attendances (median=-31.2%). There were short-term excess death registrations for cancer (without COVID-19), with peak relative risk (RR) of 1.17 at week ending on 3 April. The peak RR for all-cause deaths was 2.1 from week ending on 17 April. Based on these findings and recent literature, we modelled 40% and 80% of cancer patients being affected by the pandemic in the long-term. At 40% affected, we estimated 1-year total (direct and indirect) excess deaths in people with cancer as between 7165 and 17 910, using RRs of 1.2 and 1.5, respectively, where 78% of excess deaths occured in patients with ≥1 comorbidity.

CONCLUSIONS

Dramatic reductions were detected in the demand for, and supply of, cancer services which have not fully recovered with lockdown easing. These may contribute, over a 1-year time horizon, to substantial excess mortality among people with cancer and multimorbidity. It is urgent to understand how the recovery of general practitioner, oncology and other hospital services might best mitigate these long-term excess mortality risks.

Differential early predictive factors for upper and lower extremity motor recovery after ischaemic stroke

BACKGROUND AND PURPOSE

Various clinical and neuroimaging predictive factors have been identified for the recovery of upper extremity (UE) motor function after stroke. However, few studies have addressed factors related to the recovery of lower extremity (LE) motor function after stroke or performed direct comparisons of UE and LE motor recovery in the same set of patients. In this study, predictive factors for UE and LE motor recovery after stroke were investigated using clinical and neuroimaging characteristics.

METHODS

Forty-two subacute ischaemic stroke patients underwent structural and functional magnetic resonance imaging data acquisition and cognitive/behavioral assessments using the Fugl-Meyer assessment, the National Institutes of Health Stroke Scale (NIHSS) and the Mini-Mental State Examination (MMSE) 2 weeks after stroke onset. Neuroimaging factors, including corticospinal tract (CST) fractional anisotropy, lesion volume, CST lesion load and interhemispheric homotopic functional connectivity, were extracted. The outcome of motor function was assessed by Fugl-Meyer assessment scores 3 months after onset.

RESULTS

Early clinical and neuroimaging factors for predicting motor recovery were noticeably different for UE and LE. UE motor function recovery was related to age, NIHSS, MMSE, CST lesion load, lesion volume, ipsilesional CST integrity and interhemispheric homotopic functional connectivity. In contrast, LE motor recovery was related to ipsilesional and contralesional CST integrity and MMSE. Specifically, LE recovery showed a strong relationship to the preservation of cognitive function compared with motor impairment.

CONCLUSIONS

Our results indicate that different mechanisms underlie UE and LE motor recovery after stroke. LE motor recovery seems to be more intensively modulated by cognitive functions than UE.

An integrative pan-cancer investigation reveals common genetic and transcriptional alterations of AMPK pathway genes as important predictors of clinical outcomes across major cancer types

BACKGROUND

The AMP-activated protein kinase (AMPK) is an evolutionarily conserved regulator of cellular energy homeostasis. As a nexus for transducing metabolic signals, AMPK cooperates with other energy-sensing pathways to modulate cellular responses to metabolic stressors. With metabolic reprogramming being a hallmark of cancer, the utility of agents targeting AMPK has received continued scrutiny and results have demonstrated conflicting effects of AMPK activation in tumorigenesis. Harnessing multi-omics datasets from human tumors, we seek to evaluate the seemingly pleiotropic, tissue-specific dependencies of AMPK signaling dysregulation.

METHODS

We interrogated copy number variation and differential transcript expression of 92 AMPK pathway genes across 21 diverse cancers involving over 18,000 patients. Cox proportional hazards regression and receiver operating characteristic analyses were used to evaluate the prognostic significance of AMPK dysregulation on patient outcomes.

RESULTS

A total of 24 and seven AMPK pathway genes were identified as having loss- or gain-of-function features. These genes exhibited tissue-type dependencies, where survival outcomes in glioma patients were most influenced by AMPK inactivation. Cox regression and log-rank tests revealed that the 24-AMPK-gene set could successfully stratify patients into high- and low-risk groups in glioma, sarcoma, breast and stomach cancers. The 24-AMPK-gene set could not only discriminate tumor from non-tumor samples, as confirmed by multidimensional scaling analyses, but is also independent of tumor, node and metastasis staging. AMPK inactivation is accompanied by the activation of multiple oncogenic pathways associated with cell adhesion, calcium signaling and extracellular matrix organization. Anomalous AMPK signaling converged on similar groups of transcriptional targets where a common set of transcription factors were identified to regulate these targets. We also demonstrated crosstalk between pro-catabolic AMPK signaling and two pro-anabolic pathways, mammalian target of rapamycin and peroxisome proliferator-activated receptors, where they act synergistically to influence tumor progression significantly.

CONCLUSION

Genetic and transcriptional aberrations in AMPK signaling have tissue-dependent pro- or anti-tumor impacts. Pan-cancer investigations on molecular changes of this pathway could uncover novel therapeutic targets and support risk stratification of patients in prospective trials.

Utilizing online stochastic optimization on scheduling of intensity-modulate radiotherapy therapy (IMRT)

According to Ministry of Health and Welfare of Taiwan, cancer has been one of the major causes of death in Taiwan since 1982. The Intensive-Modulated Radiation Therapy (IMRT) is one of the most important radiotherapies of cancers, especially for Nasopharyngeal cancers, Digestive system cancers and Cervical cancers. For patients, if they can receive the treatment at the earliest possibility while diagnosed with cancers, their survival rate increases. However, the discussion of effective patient scheduling models of IMRT to reduce patients' waiting time is still limited in literature. This study proposed a mathematical model to improve the efficiency of patient scheduling. The research was composed of two stages. In the first stage, the online stochastic algorithm was proposed to improve the performance of present scheduling system. In the second stage the impact of future treatment to reduce patients' waiting time was considered. A genetic algorithm (GA) was then proposed to solve the online stochastic scheduling problem. This research collected data from a practical medical institute and the proposed model was validated with real data. It contributes to both theory and practice by proposing a practical model to assist the medical institute in implementing patient scheduling in a more efficient manner.

The hypoxic tumour microenvironment: A safe haven for immunosuppressive cells and a therapeutic barrier to overcome

Dating back to the seminal work of Paul Ehrlich, the idea of harnessing our immune system to eliminate cancerous cells is now over a century old. In the presence of a functional immune system that so efficiently guards the host against developing neoplasms, tumour cells must evolve sophisticated strategies to escape immune destruction in order to give rise to clinically detectable cancers. A new way of treating cancer would thus be to target the immune system itself rather than the tumour, and extensive studies in randomised trials have cemented the possibility of using immunotherapy for treating advanced-stage cancers. Immunotherapy, however, is only tolerated in a minority of patients and in many cases, patients suffer from adverse immune-related reactions when the immune system goes into overdrive. A primary barrier thwarting the development of effective immunotherapy seems to coalesce into the peculiarities of the tumour microenvironment for which hypoxia is a key feature. Here, we review emerging themes on how hypoxia contributes to immune suppression and obstructs anti-tumour effector cell functions. We discuss the challenges and opportunities relating to the potential for dually targeting hypoxia and the immune system to promote durable and favourable responses in cancer patients.

An immunoevasive strategy through clinically-relevant pan-cancer genomic and transcriptomic alterations of JAK-STAT signaling components

BACKGROUND

Since its discovery almost three decades ago, the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway has paved the road for understanding inflammatory and immunity processes related to a wide range of human pathologies including cancer. Several studies have demonstrated the importance of JAK-STAT pathway components in regulating tumor initiation and metastatic progression, yet, the extent of how genetic alterations influence patient outcome is far from being understood.

METHODS

Focusing on 133 genes involved in JAK-STAT signaling, we investigated genomic, transcriptomic and clinical profiles of over 18,000 patients representing 21 diverse cancer types. We identified a core set of 28 putative gain- or loss-of-function JAK-STAT genes that correlated with survival outcomes using Cox proportional hazards regression and Kaplan-Meier analyses. Differential expression analyses between high- and low-expressing patient groups were performed to evaluate the consequences of JAK-STAT misexpression.

RESULTS

We found that copy number alterations underpinning transcriptional dysregulation of JAK-STAT pathway genes differ within and between cancer types. Integrated analyses uniting genomic and transcriptomic datasets revealed a core set of JAK-STAT pathway genes that correlated with survival outcomes in brain, renal, lung and endometrial cancers. High JAK-STAT scores were associated with increased mortality rates in brain and renal cancers, but not in lung and endometrial cancers where hyperactive JAK-STAT signaling is a positive prognostic factor. Patients with aberrant JAK-STAT signaling demonstrated pan-cancer molecular features associated with misexpression of genes in other oncogenic pathways (Wnt, MAPK, TGF-β, PPAR and VEGF). Brain and renal tumors with hyperactive JAK-STAT signaling had increased regulatory T cell gene (Treg) expression. A combined model uniting JAK-STAT and Tregs allowed further delineation of risk groups where patients with high JAK-STAT and Treg scores consistently performed the worst.

CONCLUSION

Providing a pan-cancer perspective of clinically-relevant JAK-STAT alterations, this study could serve as a framework for future research investigating anti-tumor immunity using combination therapy involving JAK-STAT and immune checkpoint inhibitors.

Aberrations in Notch-Hedgehog signalling reveal cancer stem cells harbouring conserved oncogenic properties associated with hypoxia and immunoevasion

Background

Cancer stem cells (CSCs) have innate abilities to resist even the harshest of therapies. To eradicate CSCs, parallels can be drawn from signalling modules that orchestrate pluripotency. Notch-Hedgehog hyperactivation are seen in CSCs, yet, not much is known about their conserved roles in tumour progression across cancers.

Methods

Employing a comparative approach involving 21 cancers, we uncovered clinically-relevant, pan-cancer drivers of Notch and Hedgehog. GISTIC datasets were used to evaluate copy number alterations. Receiver operating characteristic and Cox regression were employed for survival analyses.

Results

We identified a Notch-Hedgehog signature of 13 genes exhibiting high frequencies of somatic amplifications leading to transcript overexpression. The signature successfully predicted patients at risk of death in five cancers (n = 2278): glioma (P < 0.0001), clear cell renal cell (P = 0.0022), papillary renal cell (P = 0.00099), liver (P = 0.014) and stomach (P = 0.011). The signature was independent of other clinicopathological parameters and offered an additional resolution to stratify similarly-staged tumours. High-risk patients exhibited features of stemness and had more hypoxic tumours, suggesting that hypoxia may influence CSC behaviour. Notch-Hedgehog⁺ CSCs had an immune privileged phenotype associated with increased regulatory T cell function.

Conclusion

This study will set the stage for exploring adjuvant therapy targeting the Notch-Hedgehog axis to help optimise therapeutic regimes leading to successful CSC elimination.

Pan-cancer genomic amplifications underlie a WNT hyperactivation phenotype associated with stem cell-like features leading to poor prognosis

Cancer stem cells pose significant obstacles to curative treatment contributing to tumor relapse and poor prognosis. They share many signaling pathways with normal stem cells that control cell proliferation, self-renewal, and cell fate determination. One of these pathways known as Wnt is frequently implicated in carcinogenesis where Wnt hyperactivation is seen in cancer stem cells. Yet, the role of conserved genomic alterations in Wnt genes driving tumor progression across multiple cancer types remains to be elucidated. In an integrated pan-cancer study involving 21 cancers and 18,484 patients, we identified a core Wnt signature of 16 genes that showed a high frequency of somatic amplifications linked to increased transcript expression. The signature successfully predicted overall survival rates in 6 cancer cohorts (n = 3050): bladder (P = 0.011), colon (P = 0.013), head and neck (P = 0.026), pan-kidney (P < 0.0001), clear cell renal cell (P < 0.0001), and stomach (P = 0.032). Receiver operating characteristic analyses revealed that the performance of the 16-Wnt-gene signature was superior to tumor staging benchmarks in all 6 cohorts and multivariate Cox regression analyses confirmed that the signature was an independent predictor of overall survival. In bladder and renal cancer, high-risk patients as predicted by the Wnt signature had more hypoxic tumors and a combined model uniting tumor hypoxia and Wnt hyperactivation resulted in further increased death risks. Patients with hyperactive Wnt signaling had molecular features associated with stemness and epithelial-to-mesenchymal transition. Our study confirmed that genomic amplification underpinning pan-cancer Wnt hyperactivation and transcriptional changes associated with molecular footprints of cancer stem cells lead to increased death risks.

Dual prognostic role of 2-oxoglutarate-dependent oxygenases in ten cancer types: implications for cell cycle regulation and cell adhesion maintenance

Background

Tumor hypoxia is associated with metastasis and resistance to chemotherapy and radiotherapy. Genes involved in oxygen-sensing are clinically relevant and have significant implications for prognosis. In this study, we examined the pan-cancer prognostic significance of oxygen-sensing genes from the 2-oxoglutarate-dependent oxygenase family.

Methods

A multi-cohort, retrospective study of transcriptional profiles of 20,752 samples of 25 types of cancer was performed to identify pan-cancer prognostic signatures of 2-oxoglutarate-dependent oxygenase gene family (a family of oxygen-dependent enzymes consisting of 61 genes). We defined minimal prognostic gene sets using three independent pancreatic cancer cohorts (n = 681). We identified two signatures, each consisting of 5 genes. The ability of the signatures in predicting survival was tested using Cox regression and receiver operating characteristic (ROC) curve analyses.

Results

Signature 1 (KDM8, KDM6B, P4HTM, ALKBH4, ALKBH7) and signature 2 (KDM3A, P4HA1, ASPH, PLOD1, PLOD2) were associated with good and poor prognosis. Signature 1 was prognostic in 8 cohorts representing 6 cancer types (n = 2627): bladder urothelial carcinoma (P = 0.039), renal papillary cell carcinoma (P = 0.013), liver cancer (P = 0.033 and P = 0.025), lung adenocarcinoma (P = 0.014), pancreatic adenocarcinoma (P < 0.001 and P = 0.040), and uterine corpus endometrial carcinoma (P < 0.001). Signature 2 was prognostic in 12 cohorts representing 9 cancer types (n = 4134): bladder urothelial carcinoma (P = 0.039), cervical squamous cell carcinoma and endocervical adenocarcinoma (P = 0.035), head and neck squamous cell carcinoma (P = 0.038), renal clear cell carcinoma (P = 0.012), renal papillary cell carcinoma (P = 0.002), liver cancer (P < 0.001, P < 0.001), lung adenocarcinoma (P = 0.011), pancreatic adenocarcinoma (P = 0.002, P = 0.018, P < 0.001), and gastric adenocarcinoma (P = 0.004). Multivariate Cox regression confirmed independent clinical relevance of the signatures in these cancers. ROC curve analyses confirmed superior performance of the signatures to current tumor staging benchmarks. KDM8 was a potential tumor suppressor down-regulated in liver and pancreatic cancers and an independent prognostic factor. KDM8 expression was negatively correlated with that of cell cycle regulators. Low KDM8 expression in tumors was associated with loss of cell adhesion phenotype through HNF4A signaling.

Conclusion

Two pan-cancer prognostic signatures of oxygen-sensing genes were identified. These genes can be used for risk stratification in ten diverse cancer types to reveal aggressive tumor subtypes.

Electronic supplementary material

The online version of this article (10.1186/s40880-019-0369-5) contains supplementary material, which is available to authorized users.

Transcriptional landscape of DNA repair genes underpins a pan-cancer prognostic signature associated with cell cycle dysregulation and tumor hypoxia

Overactive DNA repair contributes to therapeutic resistance in cancer. However, pan-cancer comparative studies investigating the contribution of all DNA repair genes in cancer progression employing an integrated approach have remained limited. We performed a multi-cohort retrospective analysis to determine the prognostic significance of 138 DNA repair genes in 16 cancer types (n = 16,225). Cox proportional hazards analyses revealed a significant variation in the number of prognostic genes between cancers; 81 genes were prognostic in clear cell renal cell carcinoma while only two genes were prognostic in glioblastoma. We reasoned that genes that were commonly prognostic in highly correlated cancers revealed by Spearman's correlation analysis could be harnessed as a molecular signature for risk assessment. A 10-gene signature, uniting prognostic genes that were common in highly correlated cancers, was significantly associated with overall survival in patients with clear cell renal cell (P < 0.0001), papillary renal cell (P = 0.0007), liver (P = 0.002), lung (P = 0.028), pancreas (P = 0.00013) or endometrial (P = 0.00063) cancers. Receiver operating characteristic analyses revealed that a combined model of the 10-gene signature and tumor staging outperformed either classifier when considered alone. Multivariate Cox regression models incorporating additional clinicopathological features showed that the signature was an independent predictor of overall survival. Tumor hypoxia is associated with adverse outcomes. Consistent across all six cancers, patients with high 10-gene and high hypoxia scores had significantly higher mortality rates compared to those with low 10-gene and low hypoxia scores. Functional enrichment analyses revealed that high mortality rates in patients with high 10-gene scores were attributable to an overproliferation phenotype. Death risk in these patients was further exacerbated by concurrent mutations of a cell cycle checkpoint protein, TP53. The 10-gene signature identified tumors with heightened DNA repair ability. This information has the potential to radically change prognosis through the use of adjuvant DNA repair inhibitors with chemotherapeutic drugs.

Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

BACKGROUND

The circadian clock governs a large variety of fundamentally important physiological processes in all three domains of life. Consequently, asynchrony in timekeeping mechanisms could give rise to cellular dysfunction underpinning many disease pathologies including human neoplasms. Yet, detailed pan-cancer evidence supporting this notion has been limited.

METHODS

In an integrated approach uniting genomic, transcriptomic and clinical data of 21 cancer types (n = 18,484), we interrogated copy number and transcript profiles of 32 circadian clock genes to identify putative loss-of-function (ClockLoss) and gain-of-function (ClockGain) players. Kaplan-Meier, Cox regression and receiver operating characteristic analyses were employed to evaluate the prognostic significance of both gene sets.

RESULTS

ClockLoss and ClockGain were associated with tumour-suppressing and tumour-promoting roles respectively. Downregulation of ClockLoss genes resulted in significantly higher mortality rates in five cancer cohorts (n = 2914): bladder (P = 0.027), glioma (P < 0.0001), pan-kidney (P = 0.011), clear cell renal cell (P < 0.0001) and stomach (P = 0.0007). In contrast, patients with high expression of oncogenic ClockGain genes had poorer survival outcomes (n = 2784): glioma (P < 0.0001), pan-kidney (P = 0.0034), clear cell renal cell (P = 0.014), lung (P = 0.046) and pancreas (P = 0.0059). Both gene sets were independent of other clinicopathological features to permit further delineation of tumours within the same stage. Circadian reprogramming of tumour genomes resulted in activation of numerous oncogenic pathways including those associated with cancer stem cells, suggesting that the circadian clock may influence self-renewal mechanisms. Within the hypoxic tumour microenvironment, circadian dysregulation is exacerbated by tumour hypoxia in glioma, renal, lung and pancreatic cancers, resulting in additional death risks. Tumour suppressive ClockLoss genes were negatively correlated with hypoxia inducible factor-1A targets in glioma patients, providing a novel framework for investigating the hypoxia-clock signalling axis.

CONCLUSIONS

Loss of timekeeping fidelity promotes tumour progression and influences clinical outcomes. ClockLoss and ClockGain may offer novel druggable targets for improving patient prognosis. Both gene sets can be used for patient stratification in adjuvant chronotherapy treatment. Emerging interactions between the circadian clock and hypoxia may be harnessed to achieve therapeutic advantage using hypoxia-modifying compounds in combination with first-line treatments.

The circadian clock components BMAL1 and REV-ERBα regulate flavivirus replication

The circadian clock regulates immune responses to microbes and affects pathogen replication, but the underlying molecular mechanisms are not well understood. Here we demonstrate that the circadian components BMAL1 and REV-ERBα influence several steps in the hepatitis C virus (HCV) life cycle, including particle entry into hepatocytes and RNA genome replication. Genetic knock out of Bmal1 and over-expression or activation of REV-ERB with synthetic agonists inhibits the replication of HCV and the related flaviruses dengue and Zika via perturbation of lipid signaling pathways. This study highlights a role for the circadian clock component REV-ERBα in regulating flavivirus replication.

A novel signature derived from immunoregulatory and hypoxia genes predicts prognosis in liver and five other cancers

Background

Despite much progress in cancer research, its incidence and mortality continue to rise. A robust biomarker that would predict tumor behavior is highly desirable and could improve patient treatment and prognosis.

Methods

In a retrospective bioinformatics analysis involving patients with liver cancer (n = 839), we developed a prognostic signature consisting of 45 genes associated with tumor-infiltrating lymphocytes and cellular responses to hypoxia. From this gene set, we were able to identify a second prognostic signature comprised of 8 genes. Its performance was further validated in five other cancers: head and neck (n = 520), renal papillary cell (n = 290), lung (n = 515), pancreas (n = 178) and endometrial (n = 370).

Results

The 45-gene signature predicted overall survival in three liver cancer cohorts: hazard ratio (HR) = 1.82, P = 0.006; HR = 1.84, P = 0.008 and HR = 2.67, P = 0.003. Additionally, the reduced 8-gene signature was sufficient and effective in predicting survival in liver and five other cancers: liver (HR = 2.36, P = 0.0003; HR = 2.43, P = 0.0002 and HR = 3.45, P = 0.0007), head and neck (HR = 1.64, P = 0.004), renal papillary cell (HR = 2.31, P = 0.04), lung (HR = 1.45, P = 0.03), pancreas (HR = 1.96, P = 0.006) and endometrial (HR = 2.33, P = 0.003). Receiver operating characteristic analyses demonstrated both signatures superior performance over current tumor staging parameters. Multivariate Cox regression analyses revealed that both 45-gene and 8-gene signatures were independent of other clinicopathological features in these cancers. Combining the gene signatures with somatic mutation profiles increased their prognostic ability.

Conclusions

This study, to our knowledge, is the first to identify a gene signature uniting both tumor hypoxia and lymphocytic infiltration as a prognostic determinant in six cancer types (n = 2712). The 8-gene signature can be used for patient risk stratification by incorporating hypoxia information to aid clinical decision making.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1775-9) contains supplementary material, which is available to authorized users.

Glucose and glutamine availability regulate HepG2 transcriptional responses to low oxygen

Background: Little is known about the impact of nutrients on cellular transcriptional responses, especially in face of environmental stressors such as oxygen deprivation. Hypoxia-inducible factors (HIF) coordinate the expression of genes essential for adaptation to oxygen-deprived environments. A second family of oxygen-sensing genes known as the alpha-ketoglutarate-dependent dioxygenases are also implicated in oxygen homeostasis and epigenetic regulation. The relationship between nutritional status and cellular response to hypoxia is understudied. In vitro cell culture systems frequently propagate cells in media that contains excess nutrients, and this may directly influence transcriptional response in hypoxia. Methods: We studied the effect of glucose and glutamine concentration on HepG2 hepatoma transcriptional response to low oxygen and expression of hypoxia inducible factor-1α (HIF-1α). Mass spectrometry confirmed low oxygen perturbation of dioxygenase transcripts resulted in changes in DNA methylation. Results: Under normoxic conditions, we observed a significant upregulation of both HIF-target genes and oxygen-dependent dioxygenases in HepG2 cells cultured with physiological levels of glucose or glutamine relative to regular DMEM media, demonstrating that excess glutamine/glucose can mask changes in gene expression. Under hypoxic conditions, CA9 was the most upregulated gene in physiological glutamine media while TETs and FTO dioxygenases were downregulated in physiological glucose. Hypoxic regulation of these transcripts did not associate with changes in HIF-1α protein expression. Downregulation of TETs suggests a potential for epigenetic modulation. Mass-spectrometry quantification of modified DNA bases confirmed our transcript data. Hypoxia resulted in decreased DNA hydroxymethylation, which correlated with TETs downregulation. Additionally, we observed that TET2 expression was significantly downregulated in patients with hepatocellular carcinoma, suggesting that tumour hypoxia may deregulate TET2 expression resulting in global changes in DNA hydroxymethylation.   Conclusion: Given the dramatic effects of nutrient availability on gene expression, future in vitro experiments should be aware of how excess levels of glutamine and glucose may perturb transcriptional responses.

Mixed evolutionary origins of endogenous biomass-depolymerizing enzymes in animals

Background

Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated.

Results

We perform an exhaustive search for glycoside hydrolase (GH) genes from 21 genomes representing major bilaterian (Ecdysozoa, Spiralia, Echinodermata and Chordata) and basal metazoan (Porifera and Cnidaria) lineages. We also assessed the genome of a unicellular relative of Metazoa, Capsaspora owczarzaki and together with comparative analyses on 126 crustacean transcriptomes, we found that animals are living bioreactors at a microscale as they encode enzymatic suites for biomass decomposition. We identified a total of 16,723 GH homologs (2373 genes from animal genomes and 14,350 genes from crustacean transcriptomes) that are further classified into 60 GH families. Strikingly, through phylogenetic analyses, we observed that animal lignocellulosic enzymes have multiple origins, either inherited vertically over millions of years from a common ancestor or acquired more recently from non-animal organisms.

Conclusion

We have conducted a systematic and comprehensive survey of GH genes across major animal lineages. The ability of biomass decay appears to be determined by animals’ dietary strategies. Detritivores have genes that accomplish broad enzymatic functions while the number of GH families is reduced in animals that have evolved specialized diets. Animal GH candidates identified in this study will not only facilitate future functional genomics research but also provide an analysis platform to identify enzyme candidates with industrial potential.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4861-0) contains supplementary material, which is available to authorized users.

[Risk factors related to HIV new infections among men who have sex with men in a cohort study]

Objectives: To analyze and understand the risk factors related to HIV new infections among men who have sex with men (MSM). Methods: A longitudinal observational study among MSM was conducted to collect information on HIV related behaviors and sero-conversion. Univariate and multivariate generalized estimating equations (GEE) were used to discuss the risk factors for HIV new infection. Results: A total number of 4 305 MSM were followed during 2013-2015. Among those self-reported MSM who are seeking partners on the Interner tended to have higher proportion on receptive anal intercourse and consistent condom use during anal intercourse than the subgroups seeking their partners in gay bars or bathrooms. HIV incidence among followed MSM during the study period appeared as 4.3/100 person years, with adjusted RR (aRR) of HIV infection for receptive anal intercourse as group 2.20 (95% CI: 1.49-3.24) times than that of insertion anal intercourse group. Those who used rush-poppers (aRR=1.55, 95% CI: 1.10-2.17), unprotected anal intercourse (aRR=2.24, 95%CI: 1.62-3.08), and those with syphilis infection (aRR=2.95, 95%CI: 2.00-4.35) were also risk factors for HIV new infections. After controlling other factors, the relationship between the ways of seeking partners and HIV new infection was not statistical significant. Conclusion: Risk factors for HIV new infection among MSM appeared complex and interactive, suggesting that further studies are needed to generate tailored strategies for the prevention of HIV epidemic among MSM population.

Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

The basic helix-loop-helix (bHLH) proteins represent a key group of transcription factors implicated in numerous eukaryotic developmental and signal transduction processes. Characterization of bHLHs from model species such as humans, fruit flies, nematodes and plants have yielded important information on their functions and evolutionary origin. However, relatively little is known about bHLHs in non-model organisms despite the availability of a vast number of high-throughput sequencing datasets, enabling previously intractable genome-wide and cross-species analyses to be now performed. We extensively searched for bHLHs in 126 crustacean species represented across major Crustacea taxa and identified 3777 putative bHLH orthologues. We have also included seven whole-genome datasets representative of major arthropod lineages to obtain a more accurate prediction of the full bHLH gene complement. With focus on important food crop species from Decapoda, we further defined higher-order groupings and have successfully recapitulated previous observations in other animals. Importantly, we also observed evidence for lineage-specific bHLH expansions in two basal crustaceans (branchiopod and copepod), suggesting a mode of evolution through gene duplication as an adaptation to changing environments. In-depth analysis on bHLH-PAS members confirms the phenomenon coined as 'modular evolution' (independently evolved domains) typically seen in multidomain proteins. With the amphipod Parhyale hawaiensis as the exception, our analyses have focused on crustacean transcriptome datasets. Hence, there is a clear requirement for future analyses on whole-genome sequences to overcome potential limitations associated with transcriptome mining. Nonetheless, the present work will serve as a key resource for future mechanistic and biochemical studies on bHLHs in economically important crustacean food crop species.

Comparative genomic analysis of crustacean hyperglycemic hormone (CHH) neuropeptide genes across diverse crustacean species

Background: Recent studies on bioactive peptides have shed light on the importance of these compounds in regulating a multitude of physiological, behavioral and biological processes in animals. Specifically, the neuropeptides of the crustacean hyperglycemic hormone (CHH) superfamily is known to control a number of important functions ranging from energy metabolism, molting, osmoregulation to reproduction. Methods: Given the importance of this peptide family, we employed a conservative approach utilizing extant transcriptome datasets from 112 crustacean species, which not only include important food crop species from the order Decapoda, but also from other lower order crustaceans (Branchiopoda and Copepoda), to identify putative CHH-like sequences. Results and conclusions: Here we describe 413 genes that represent a collection of CHH-like peptides in Crustacea, providing an important staging point that will now facilitate the next stages of neuroendocrine research across the wider community.

A TALE of shrimps: Genome-wide survey of homeobox genes in 120 species from diverse crustacean taxa

The homeodomain-containing proteins are an important group of transcription factors found in most eukaryotes including animals, plants and fungi. Homeobox genes are responsible for a wide range of critical developmental and physiological processes, ranging from embryonic development, innate immune homeostasis to whole-body regeneration. With continued fascination on this key class of proteins by developmental and evolutionary biologists, multiple efforts have thus far focused on the identification and characterization of homeobox orthologs from key model organisms in attempts to infer their evolutionary origin and how this underpins the evolution of complex body plans. Despite their importance, the genetic complement of homeobox genes has yet been described in one of the most valuable groups of animals representing economically important food crops. With crustacean aquaculture being a growing industry worldwide, it is clear that systematic and cross-species identification of crustacean homeobox orthologs is necessary in order to harness this genetic circuitry for the improvement of aquaculture sustainability. Using publicly available transcriptome data sets, we identified a total of 4183 putative homeobox genes from 120 crustacean species that include food crop species, such as lobsters, shrimps, crayfish and crabs. Additionally, we identified 717 homeobox orthologs from 6 other non-crustacean arthropods, which include the scorpion, deer tick, mosquitoes and centipede. This high confidence set of homeobox genes will now serve as a key resource to the broader community for future functional and comparative genomics studies.

Effects of flavones of sea buckthorn fruits on growth performance, carcass quality, fat deposition and lipometabolism for broilers

The objective of this study was to evaluate the effects of different levels of flavones of sea buckthorn fruits (FSBF) on growth performance, carcass quality, fat deposition, and lipometabolism for broilers. 240 one-day-old Arbor Acres male broilers were randomly allotted to 4 dietary treatments (0, 0.05%, 0.10%, and 0.15% FSBF) with 6 replicates of 10 birds. Broilers were reared for 42 d. Results showed FSBF quadratically improved average daily feed intake (ADFI), average daily gain (ADG), and final body weight (BW) (P = 0.002, P = 0.019 and P = 0.018, respectively). The abdominal fat percentage in 0.05%, 0.10%, and 0.15% FSBF supplementation groups was decreased by 21.08%, 19.12%, and 19.61% with respect to the control group, respectively (P < 0.05). The intramuscular fat (IMF) content in the breast muscle of the broilers was increased by 7.21%, 23.42% and 6.30% in 0.05%, 0.10% and 0.15% FSBF groups, and that in the thigh meat was raised by 4.43%, 24.63% and 12.32%, compared with the control group, respectively (P < 0.05). FSBF had a quadratic effect on the abdominal fat percentage and IMF in the breast muscle (P < 0.05). Dietary FSBF also modified fatty acids of muscular tissues, resulting in a higher ratio of unsaturated to saturated fatty acids (P < 0.05). Supplementing FSBF in the diet greatly decreased the levels of triglyceride, cholesterol, and low-density lipoprotein cholesterol (P < 0.05). Moreover, the quadratic responses were also observed in the levels of insulin and adiponectin in serum (P = 0.020 and P = 0.037, respectively). Abdominal fat percentage was correlated negatively with insulin and positively with adiponectin (P < 0.05). IMF content in the breast and thigh muscles were correlated positively with insulin, and negatively with adiponectin (P < 0.05). A positive correlation existed between breast muscle, IMF, and leptin (P < 0.05). In conclusion, adding FSBF into the diets affected growth performance and fat deposition of broilers by regulating lipometabolism. Fat deposition and distribution of broilers were closely associated with concentrations of insulin and adiponectin. The optimal level of FSBF supplemented in diet was 0.05 to 0.10% in this study.

The brain-derived neurotrophic factor Val66Met polymorphism and degeneration of the corticospinal tract after stroke: a diffusion tensor imaging study

BACKGROUND AND PURPOSE

A common single nucleotide polymorphism, Val66Met, in the human brain-derived neurotrophic factor (BDNF) gene has a potential role in the pathogenesis and treatment of stroke. The relevance of the BDNF Val66Met polymorphism to long-term stroke outcomes was examined, specifically with respect to changes in corticospinal integrity.

METHODS

Thirty-five stroke patients with unilateral motor weakness were genotyped within 2 weeks after onset (T1), and changes in the integrity of the ipsilesional corticospinal tract (CST) as well as alterations in motor function at 1 month (T2) and 3 months after onset (T3) were tracked.

RESULTS

On the basis of the Fugl-Meyer assessment upper extremity score, carriers of the Met allele (Val/Met and Met/Met) showed poorer motor outcomes at T2 and T3 compared to carriers of only the Val allele (Val/Val). For both BDNF allele types, patients exhibited characteristic degeneration of the CST compared to healthy controls. There were no differences between the two genotypes with respect to time-dependent changes in diffusion-tensor-imaging-derived parameters of the CST. However, the two groups showed different relationships between motor outcomes and directional diffusivities according to the elapsed time after onset. Poorer motor function was associated with lower axial diffusivity values for the Val/Val genotype group in the sub-acute phase (T1 and T2) but with higher radial diffusivity values for the Val/Met and Met/Met genotype group in the early chronic phase (T3).

CONCLUSIONS

Motor recovery in stroke patients may be affected by the BDNF Val66Met polymorphism, possibly through its effects on distinct pathological processes underlying corticospinal degeneration.

Designer germanium quantum dot phototransistor for near infrared optical detection and amplification

We demonstrated a unique CMOS approach for the production of a high-performance germanium (Ge) quantum dot (QD) metal-oxide-semiconductor phototransistor. In the darkness, low off-state leakage (Ioff ∼ 0.27 pA μm(-2)), a high on-off current ratio (Ion/Ioff ∼ 10(6)), and good switching behaviors (subthreshold swing of 175 mV/dec) were measured on our Ge-QD phototransistor at 300 K, indicating good hetero-interfacial quality of the Ge-on-Si. Illumination makes a significant enhancement in the drain current of Ge QD phototransistors when biased at both the on- and off-states, which is a great benefit from Ge QD-mediated photoconductive and photovoltaic effects. The measured photocurrent-to-dark-current ratio (Iphoto/Idark) and the photoresponsivities from the Ge QD phototransistor are as high as 4.1 × 10(6) and 1.7 A W(-1), respectively, under an incident power of 0.9 mW at 850 nm illumination. A superior external quantum efficiency of 240% and a very fast temporal response time of 1.4 ns suggest that our Ge QD MOS phototransistor offers great promise as optical switches and transducers for Si-based optical interconnects.

Attempts to increase inosinic acid in broiler meat by using feed additives

To explore regulation of inosinic acid content in chicken meat as a result of feed additives, 576 one-day-old male Arbor Acres broilers were randomly allotted into 8 dietary treatments including control, purine nucleotide (P), betaine (B), soybean isoflavone (S), purine nucleotide + betaine (PB), purine nucleotide + soybean isoflavone (PS), betaine +soybean isoflavone (BS), and purine nucleotide + betaine + soybean isoflavone (PBS) by a 2 × 2 × 2 factorial arrangement. At d 42 of age, broilers were slaughtered, and growth performance, carcass characteristics, inosinic acid content, and activities of enzyme closely related to inosinic acid metabolism of broilers were measured. The results revealed that these feed additives did not affect ADG and ADFI of the broilers (P > 0.05). However, supplementing purine nucleotides lowered feed/gain of broilers in PS and PBS groups (P < 0.05). There was a significant interaction on feed/gain of broilers between purine nucleotides and soybean isoflavone (P < 0.05). The abdominal fat percentages in groups B, S, BS, and PBS were lower than the control group, respectively (P < 0.05). The thigh muscle percentages of groups P and B were higher than that of group PB (P < 0.05). There were certain interactions on the percentage of thigh muscle (P = 0.05) and abdominal fat (P < 0.05) between P, B, and S groups. Compared with the control group, inosinic acid content in broiler breast meat was improved by using feed additives (P < 0.05). Supplementing purine nucleotides, betaine, soybean isoflavone, and their combinations increased alkaline phosphatase activity in breast meat of broilers (P < 0.05). Purine nucleotides improved the activity of adenosine deaminase, but decreased the activity of 5'-nucleotidase. Soybean isoflavone lowered the activity of alkaline phosphatase. There were no significant interactions on activities of creatine kinase, adenosine deaminase, alkaline phosphatase, and 5'-nucleotidase between these additives (P > 0.05). The umami rating of broiler breast meat increased in conjunction with supplementing these additives. In conclusion, supplementing standard feed with the additives investigated in this study could improve inosinic acid content in chicken meat by increasing synthase activity or inhibiting degradation enzyme activity without inferior growth performance and carcass quality.

P300 waveform and dopamine transporter availability: a controlled EEG and SPECT study in medication-naive patients with schizophrenia and a meta-analysis

BACKGROUND

Reduced P300 event-related potential (ERP) amplitude and latency prolongation have been reported in patients with schizophrenia compared to healthy controls. However, the influence of antipsychotics (and dopamine) on ERP measures are poorly understood and medication confounding remains a possibility.

METHOD

We explored ERP differences between 36 drug-naive patients with schizophrenia and 138 healthy controls and examined whether P300 performance was related to dopamine transporter (DAT) availability, both without the confounding effects of medication. We also conducted a random effects meta-analysis of the available literature, synthesizing the results of three comparable published articles and our local study.

RESULTS

No overall significant difference was found in mean P300 ERP between patients and controls in latency or in amplitude. There was a significant gender effect, with females showing greater P300 amplitude than males. A difference between patients and controls in P300 latency was evident with ageing, with latency increasing faster in patients. No effect of DAT availability on P300 latency or amplitude was detected. The meta-analysis computed the latency pooled standardized effect size (PSES; Cohen's d) of -0.13 and the amplitude PSES (Cohen's d) of 0.48, with patients showing a significant reduction in amplitude.

CONCLUSIONS

Our findings suggest the P300 ERP is not altered in the early stages of schizophrenia before medication is introduced, and the DAT availability does not influence the P300 ERP amplitude or latency. P300 ERP amplitude reduction could be an indicator of the progression of illness and chronicity.

Distance dependence of energy transfer from InGaN quantum wells to graphene oxide

We report the distance-dependent energy transfer from an InGaN quantum well to graphene oxide (GO) by time-resolved photoluminescence (PL). A pronounced shortening of the PL decay time in the InGaN quantum well was observed when interacting with GO. The nature of the energy-transfer process has been analyzed, and we find the energy-transfer efficiency depends on the 1/d² separation distance, which is dominated by the layer-to-layer dipole coupling.

Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies

The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20 microsatellites. Consequently, the VNN populations exhibited a higher diversity than did CNO populations in terms of number of alleles but showed a slightly lower observed heterozygosity. The VNN populations showed in total seven private alleles, whereas no CNO private alleles were found. The expected heterozygosity of 0.576 in the VNN populations was higher than the observed heterozygosity of 0.490, leading to heterozygote deficiency within populations. This issue could be partly explained by the Wahlund effect due to fragmentation of several populations between chicken flocks. Molecular analysis of variance showed that most of genetic variation was found within VNN populations. The Bayesian clustering analysis showed that VNN and CNO chickens were separated into two distinct groups with little evidence for gene flow between them. Among the 24 populations, 13 were successfully assigned to their own cluster, whereas the structuring was not clear for the remaining 11 chicken populations. The contributions of 24 populations to the total genetic diversity were mostly consistent across two approaches, taking into account the within- and between-populations genetic diversity and allelic richness. The black H'mong, Lien Minh, Luong Phuong and Red Jungle Fowl were ranked with the highest priorities for conservation according to Caballero and Toro's and Petit's approaches. In conclusion, a national strategy needs to be set up for Vietnamese chicken populations, with three main components: conservation of high-priority breeds, within-breed management with animal exchanges between flocks to avoid Wahlund effect and monitoring of inbreeding rate.

Comparing thermal welding instrument-assisted laparoscopic radical hysterectomy versus conventional radical hysterectomy in the management of FIGO IB1 squamous cell cervical carcinoma

PURPOSE OF INVESTIGATION

The authors sought to evaluate the feasibility and acceptability of using the thermal welding technique with thermal ligating shear (TWT-TLS)-assisted laparoscopic radical hysterectomy (LRH) and systemic pelvic lymphadenectomy (SPL) in the management of Stage IB1 squamous cell carcinoma of the cervix.

MATERIALS AND METHODS

The authors compared operating time, blood loss, and other intra- and postoperative parameters and outcomes in 53 patients between May 2003 and April 2007.

RESULTS

Twenty-three patients were treated with TWT-TLS-assisted LRH and SPL (TWT-TLS group) and 30 patients with abdominal radical hysterectomy (ARH) and SPL (ARH group). The surgical time of the TWT-TLS group was significantly shorter than that of the ARH group (221.4 vs 264.6 min, p < 0.05). The blood loss of the TWT-TLS group was less than that of the ARH group (195.7 vs 1,214.7 ml, p < 0.001). The immediate postoperative recovery seemed to be rapid in the TWT-TLS group compared with the ARH group (1.4 vs 3.5 days for full diet, p < 0.001; 8.32 vs 12.14 days for hospital stay, p < 0.001). The recurrence rate between the two groups was similar during the median four-year follow-up (8.7% vs 13.3%).

CONCLUSIONS

TWT-TLS is a safe and efficient method for laparoscopic RH and SPL with reduction of morbidity for early-stage cervical cancer. A further study is needed to confirm the above observation.

A multiobjective hybrid genetic algorithm for the capacitated multipoint network design problem

The capacitated multipoint network design problem (CMNDP) is NP-complete. In this paper, a hybrid genetic algorithm for CMNDP is proposed. The multiobjective hybrid genetic algorithm (MOHGA) differs from other genetic algorithms (GAs) mainly in its selection procedure. The concept of subpopulation is used in MOHGA. Four subpopulations are generated according to the elitism reservation strategy, the shifting Prufer vector, the stochastic universal sampling, and the complete random method, respectively. Mixing these four subpopulations produces the next generation population. The MOHGA can effectively search the feasible solution space due to population diversity. The MOHGA has been applied to CMNDP. By examining computational and analytical results, we notice that the MOHGA can find most nondominated solutions and is much more effective and efficient than other multiobjective GAs.

Energy transfer from InGaN quantum wells to Au nanoclusters via optical waveguiding

We present the first observation of resonance energy transfer from InGaN quantum wells to Au nanoclusters via optical waveguiding. Steady-state and time-resolved photoluminescence measurements provide conclusive evidence of resonance energy transfer and obtain an optimum transfer efficiency of ~72%. A set of rate equations is successfully used to model the kinetics of resonance energy transfer.

Childhood obesity in ambulatory children and adolescents with spastic cerebral palsy in Korea

OBJECTIVE

Childhood obesity is an emerging health issue in Korea. We investigated the prevalence of obesity and its trend over time in ambulatory Korean children with CP.

METHODS

We retrospectively reviewed the medical records of 1,397 children with CP between 1995 and 2008. The data were grouped into 4 time periods (1995-1997, 1998-2002, 2003-2004 and 2005-2008). The prevalence of obesity over each period and its relationship to gender, birth weight, age, and gross motor function classification system were investigated.

RESULTS

The percentage of obese children was 5.8%, overweight children 11.2%, and underweight children 10.4%. The prevalence of obesity significantly increased from the first time period to the third time period. The prevalence of obesity found in our study was significantly lower than the report from the U.S.A. during same time period between 1994 and 2004 (p<0.05). The prevalence of obesity significantly decreased with age as well.

CONCLUSIONS

The prevalence of obesity in our subjects significantly increased and has reached a plateau in recent years. Compared to the prevalence of childhood obesity in ambulatory individuals with CP in the U.S.A. study, the prevalence in our study was significantly lower.

Assessment of post-stroke extrapersonal neglect using a three-dimensional immersive virtual street crossing program

OBJECTIVE

To investigate the potential of our newly developed three-dimensional immersive virtual reality (VR) program modeled on a real street crossing as an assessment tool for extrapersonal neglect in stroke patients.

METHODS

Thirty-two patients with right-hemispheric stroke (neglect group, 16; non-neglect group, 16) were enrolled. The deviation angle, reaction time, left-to-right reaction time ratio, visual and auditory cue rates, and failure rate were evaluated during missions to keep a virtual avatar safe from a traffic accident in the VR program. The line bisection test and letter cancellation test were also evaluated.

RESULTS

The deviation angle, left-to-right reaction time ratio, left visual and auditory cue rates and left failure rate in the VR program showed significant differences between the two groups (P < 0.05). Depending on the direction of approach of the virtual car, the left parameters were significantly higher than the right parameters in the neglect group (P < 0.05). In the neglect group, the line bisection test correlated significantly with the deviation angle (P < 0.05). None of the other virtual reality parameters significantly correlated with the paper and pencil tests.

CONCLUSION

Post-stroke neglect in the extrapersonal space can be easily and safely detected and measured using our three-dimensional immersive virtual street crossing program.

Detection of focal cerebral injury using diffusion tensor magnetic resonance imaging in a boy with becker muscular dystrophy

Here, we report on a boy affected by both cerebral palsy and Becker muscular dystrophy (BMD). He had infrequently used his right hand since birth. But brain magnetic resonance imaging (MRI) taken at the age of 15 months showed no specific finding. Approximately 1 month later, muscle enzymes of his older brother were incidentally found to be elevated. The patient and his brother were diagnosed with progressive muscular dystrophy by gene analysis. At the age of 6 years, he underwent orthopedic surgery due to a right equinovarus deformity and BMD was confirmed by concomitant muscle biopsy. During the post-operative rehabilitation, clumsiness of the right hand was also observed. A follow-up brain MRI with diffusion tensor imaging (DTI) was taken. Although no responsible lesion was found on conventional MRI, DTI and fiber tractography revealed a decrease in the quantity of fibers in the left corticospinal tract. He was additionally diagnosed as having cerebral palsy.