Fine mapping and analysis of a candidate gene controlling Phytophthora blight resistance in cucumber

Cucumber blight is a destructive disease. The best way to control this disease is resistance breeding. This study focuses on disease resistance gene mapping and molecular marker development. We used the resistant cucumber, JSH, and susceptible cucumber, B80, as parents to construct F2 populations. Bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) were used, from which we developed cleaved amplified polymorphic sequence (CAPs) markers to map the resistance gene. Resistance in F2 individuals showed a segregation ratio of resistance:susceptibility close to 3:1. The gene in JSH resistant cucumber was mapped to an interval of 9.25 kb, and sequencing results for the three genes in the mapped region revealed three mutations at base sites 225, 302, and 591 in the coding region of Csa5G139130 between JSH and B80, but no mutations in coding regions of Csa5G139140 and Csa5G139150. The mutations caused changes in amino acids 75 and 101 of the protein encoded by Csa5G139130, suggesting that Csa5G139130 is the most likely resistance candidate gene. We developed a molecular marker, CAPs-4, as a closely linked marker for the cucumber blight resistance gene. This is the first report on mapping of a cucumber blight resistance gene and will provideg a useful marker for molecular breeding of cucumber resistance to Phytophthora blight.

Prediction of toxicity outcomes following radiotherapy using deep learning-based models: A systematic review

PURPOSE

This study aims to perform a comprehensive systematic review of deep learning (DL) models in predicting RT-induced toxicity.

MATERIALS AND METHODS

A literature review was performed following the PRISMA guidelines. Systematic searches were performed in PubMed, Scopus, Cochrane and Embase databases from the earliest record up to September 2022. Related studies on deep learning models for radiotherapy toxicity prediction were selected based on predefined PICOS criteria.

RESULTS

Fourteen studies of radiotherapy-treated patients on different types of cancer [prostate (n=2), HNC (n=4), liver (n=2), lung (n=4), cervical (n=1), and oesophagus (n=1)] were eligible for inclusion in the systematic review. Information regarding patient characteristics and model development was summarized. Several approaches, such as ensemble learning, data augmentation, and transfer learning, that were utilized by selected studies were discussed.

CONCLUSION

Deep learning techniques are able to produce a consistent performance for toxicity prediction. Future research using large and diverse datasets and standardization of the study methodologies are required to improve the consistency of the research output.

'But what if you miss something …?': factors that influence medical student consideration of cost in decision making

CONTEXT

Cost-conscious care is critical for healthcare sustainability but evidence suggests that most doctors do not consider cost in their clinical decision making. A critical step in changing this is understanding the barriers to encouraging behaviours and attitudes related to cost-conscious care. We therefore conducted a qualitative study to address the research question: what factors influence consideration of cost in emergency medicine (ED) clinical decision making?

METHODS

This was a qualitative focus group study using patient vignettes to explore attitudes towards cost-conscious clinical decision making. Participants were Year 4 and Year 5 medical students from Singapore, a country with a fee-for-service healthcare system. After a data-driven initial data analysis, and to make sense of a multitude of factors impacting on cost conscious care, we selected Fishbein's integrative model of behavioural prediction to underpin secondary data analysis.

RESULTS

Via four focus groups with 21 participants, we identified five main themes relevant to the integrative model of behavioural prediction. These were: attitudes towards considering cost when managing a patient (e.g., "better safe than sorry"); normative beliefs (e.g., doing what others do, perceptions of patient wishes); efficacy beliefs (e.g., no authority to take decisions or challenge); skills and knowledge (e.g., little knowledge of costs), and environmental constraints (e.g., the nature of the healthcare system).

DISCUSSION

Medical students do not consider cost in their clinical decision making due to numerous factors, of which lack of knowledge of costs is but one. While some of the factors identified reflect those found in previous studies with residents and fully-trained staff, and in other contexts, theory driven analysis added value in that it facilitated a richer exploration of why students do not consider cost in clinical decision making. Our findings provide insight to inform how best to engage and empower educators and learners in teaching and learning about cost-conscious care.

Motivations and experiences of patients with advanced cancer participating in Phase 1 clinical trials: A qualitative study

BACKGROUND

Persons with advanced cancer may participate in Phase 1 clinical trials - first-in-human trials that are conducted with the main objectives of safety and dosing. The motivations for participation are not well understood and may include hope for cure.

AIM

To explore the perspectives of persons with advanced cancer in order to understand the motivations for participating in Phase 1 clinical trials, experiences while being on trial and views on palliative care provision.

DESIGN

Qualitative study with a constructivist stance, using thematic analysis based upon the grounded theory approach.

SETTING/PARTICIPANTS

20 persons with advanced cancer who were participating in a Phase 1 clinical trial.

RESULTS

Many participants described how Phase 1 clinical trial participation was their last hope, as they were cognisant of their advanced disease. Information-seeking needs differed - some needed comprehensive information while others relied on the doctor's recommendation. Participants experienced varied negative and positive physical and psycho-emotional concerns, and needed to draw on multiple sources of support such as family, friends and healthcare professionals. Some could list potential benefits of palliative care but felt they did not require it yet. The overarching theme was hope and positive thinking as a way of coping.

CONCLUSIONS

The concepts of hope as a way of coping and the supportive presence of healthcare professionals could be weaved into a future model of palliative care to improve the illness journey for patients considering Phase 1 clinical trial participation and other persons with advanced cancer.

Global burden of metabolic diseases: data from Global Burden of Disease 2000-2019. A cosortium of metabolic disease

Funding Acknowledgements

Type of funding sources: None.

Background

The growing prevalence of metabolic diseases is a major concern. We sought to examine the global trends and mortality of metabolic diseases using estimates from the Global Burden of Diseases, Injuries and Risk Factors Study (GBD) 2019.

Methods

Global estimates of prevalence, deaths, and disability-adjusted life year (DALYs) from 2000-2019 were examined for metabolic diseases (type 2 diabetes mellitus [T2DM], hypertension, and nonalcoholic fatty liver disease [NAFLD]). For metabolic risk factors (hyperlipidemia and obesity), estimates were limited to mortality and DALYs. Death rates was compared across sex, World Health Organisation regions and Socio-demographic Index (SDI) quintiles. Age-standardised prevalence and death rates were presented per 100,000 population with 95% uncertainty intervals (UI).

Findings

From 2000 to 2019, prevalence rates increased for all metabolic diseases, with the most pronounced increase in high SDI countries. In 2019, the mean (95%UI) age-standardised prevalence per 100,000 population was estimated to be 15,023 (13,493-16,764) for NAFLD, 5,283 (4,864–5,720) for T2DM and 234 (171-313) for hypertension. The highest age-standardised death rates were observed in obesity (62·59 [39·92-89·13]; males, 66·55 [39·76-97·21]; females. 58·14 [38·53-81·39]), followed by hyperlipidemia (56·51 [41·83-73·62]; males, 67·33 [50·78-86·43]; females, 46·50 [32·70-62·38]), T2DM (18·49 [17·18-19·66], males, 67·33 [50·78-86·43]; females, 46·50 [32·70-62·38]), hypertension (15·16 [11·20-16·75]; males, 14·95 [10·32-16·75]; females, 15·05 [11·51-17·09]) and NAFLD (2·09 [1·61-2·60]; males, 2·38 [1·82-3·02]; females, 1·82 [1·41-2·27]). Mortality rates decreased over time in hyperlipidemia (-154%), hypertension (-52%) and NAFLD (-52%), but not in T2DM and obesity. The highest mortality for metabolic diseases was found in Eastern Mediterranean, and low to low-middle SDI countries.

Conclusion

The global prevalence of metabolic diseases has risen over the past two decades regardless of SDI. Attention is needed to address the unchanging mortality rates attributed to metabolic disease and the regional, socioeconomic, and sex disparities in mortality from metabolic disease.

Expert consensus recommendations on biomarker testing in metastatic and non-metastatic non-small cell lung cancer in Asia

INTRODUCTION

Most published guidelines for genomic biomarker testing in NSCLC reflect the disease epidemiology and treatments readily available in Europe and North America. Nevertheless, 60% of annual global NSCLC cases occur in Asia, where patient characteristics, tumor molecular profiles, and treatments vary greatly from the Western world. For example, mutations in the EGFR occur at a higher prevalence in Asia than in other world regions. Although medical associations such as the International Association for the Study of Lung Cancer, European Society for Medical Oncology, and American Society of Clinical Oncology have described principles for tumor genomic biomarker testing in NSCLC, there is a need for recommendations specific for Asia.

METHODS

This report provides consensus recommendations for NSCLC biomarker testing from Asian lung cancer experts for clinicians working in Asia to improve patient care. Biomarker testing approaches for actionable genetic alterations in EGFR, ALK, ROS1, and others are discussed.

RESULTS

These recommendations are divided into nonmetastatic and metastatic forms of adenocarcinoma and squamous cell carcinoma. Owing to the higher prevalence of EGFR mutations in Asia, the experts emphasized the need for EGFR testing to include not just common mutations (exon 19 deletions and L858R substitutions) but also other uncommon EGFR mutations. In addition to the assessment of biomarkers in the tumor tissue, the role of assessing tumor biomarkers by liquid biopsy is discussed.

CONCLUSION

This consensus provides practical recommendations for biomarker testing in nonmetastatic and metastatic Asian NSCLC patients.

Reconstructed meta-analysis of percutaneous coronary intervention versus coronary artery bypass grafting for left main disease

Background

Randomized controlled trials (RCTs) comparing percutaneous coronary intervention (PCI) with drug-eluting stents and coronary artery bypass grafting (CABG) for patients with left main coronary artery disease (LMCAD) have reported conflicting results.

Objectives

We performed a systematic review from inception to 23 May 2021 and one-stage reconstructed individual-patient data meta-analysis (IPDMA) that included 10-year mortality outcomes.

Methods

The primary outcome was 10-year all-cause mortality. Secondary outcomes included myocardial infarction (MI), stroke and unplanned revascularization at 5 years. We did IPDMA using published Kaplan-Meier curves to provide individual data points in coordinates and numbers at risk were used to increase the calibration accuracy of the reconstructed data. Shared frailty model or, when proportionality assumptions were not met, a restricted mean survival time model were fitted to compare outcomes between treatment groups.

Results

Of 583 articles retrieved, 5 RCTs were included. A total of 4595 patients from these 5 RCTs were randomly assigned to PCI (N=2297) or CABG (N=2298). The cumulative 10-year all-cause mortality after PCI and CABG was 12.0% versus 10.6% respectively (HR 1.093, 95% CI: 0.925–1.292; p=0.296). PCI conferred similar time-to-MI (RMST ratio 1.006, 95% CI: 0.992–1.021, p=0.391) and stroke (RMST ratio 1.005, 95% CI: 0.998–1.013, p=0.133) at 5 years. Unplanned revascularization was more frequent following PCI compared with CABG (HR 1.807, 95% CI: 1.524–2.144, p<0.001) at 5 years.

Conclusion

This meta-analysis using reconstructed participant-level time-to-event data showed no statistically significant difference in cumulative 10-year all-cause mortality between PCI versus CABG in the treatment of LMCAD.

Funding Acknowledgement

Type of funding sources: None.

THIRD bedside ultrasound protocol for rapid diagnosis of undifferentiated shock: a prospective observational study

INTRODUCTION

It is clinically challenging to differentiate the pathophysiological types of shock in emergency situations. Here, we evaluated the ability of a novel bedside ultrasound protocol (Tamponade/tension pneumothorax, Heart, Inferior vena cava, Respiratory system, Deep venous thrombosis/aorta dissection [THIRD]) to predict types of shock in the emergency department.

METHODS

An emergency physician performed the THIRD protocol on all patients with shock who were admitted to the emergency department. All patients were closely followed to determine their final clinical diagnoses. The kappa index, sensitivity, specificity, positive predictive value, and negative predictive value were calculated for the initial diagnostic impression provided by the THIRD protocol, compared with each patient's final diagnosis.

RESULTS

In total, 112 patients were enrolled in this study. The kappa index between initial impression and final diagnosis was 0.81 (95% confidence interval=0.73-0.89; P<0.001). For hypovolaemic, cardiogenic, distributive, and obstructive types of shock, the sensitivities of the THIRD protocol were 100%, 100%, 93%, and 100%, respectively; the sensitivity for a 'mixed' shock aetiology was 86%. The negative predictive value of the THIRD protocol for all five types of shock was ≥96%.

CONCLUSION

Initial diagnostic judgements determined using the THIRD protocol showed favourable agreement with the final diagnosis in patients who presented with undifferentiated shock. The THIRD protocol has great potential for use as a bedside approach that can guide the rapid management of undifferentiated shock in emergency settings, particularly for patients with obstructive, hypovolaemic, or cardiogenic shock.

Functional assessment of military aircrew applicants in a hypobaric chamber

Background

Aircrew are exposed to environmental pressure changes. In the Republic of Singapore Air Force (RSAF), applicants assessed to be at intermediate risk of otic barotrauma undergo a hypobaric chamber assessment [“trial of chamber” (TOC)] to functionally evaluate their suitability for military aircrew vocations.

Aims

To identify factors associated with TOC failure among applicants with otorhinolaryngological conditions.

Methods

All applicants to RSAF aircrew vocations who were assessed to be at intermediate risk of otic barotrauma over a 3-yr period were identified using the RSAF Aeromedical Centre’s electronic database. Their medical records, as well as the TOC assessment records of the subset of applicants who underwent TOC, were reviewed for demographic data, clinical findings, and TOC outcomes.

Results

Of the 483 identified applicants, 374 (77%) had abnormal otoscopic findings, 103 (21%) had rhinitis symptoms, and 6 (1%) had previous ENT surgery. 123 (25%) underwent TOC, of which 20 (16%) failed. Holding other predictor variables constant, the odds of TOC failure increased by 0.79 per unit decrease in BMI (95% CI 0.63–0.99), and the odds of TOC failure increased by 0.93 per kg decrease in body weight (95% CI 0.87–1.00). An abnormal tympanogram was not a statistically significant predictor of TOC failure (OR 1.96, 95% CI 0.59–6.42). Of the 47 applicants who passed TOC and were eventually recruited, none subsequently developed otic barotrauma (mean follow-up, 3.3 yr ± 1.5 yr).

Conclusions

Applicants with lower weight and BMI are more likely to develop otic barotrauma with environmental pressure change. Tympanometry cannot be reliably used to identify applicants who would more likely pass TOC.

In-Bi Electrocatalyst for the Reduction of CO2 to Formate in a Wide Potential Window

The CO₂ atmospheric concentration level hit the record at more than 400 ppm and is predicted to keep increasing as the dependence on fossil fuels is inevitable. The CO₂ electrocatalytic conversion becomes an alternative due to its environmental and energy-friendly properties and benign operation condition. Lately, bimetallic materials have drawn significant interest as electrocatalysts due to their distinct properties, which the parents' metal cannot mimic. Herein, the indium-bismuth nanosphere (In₁₆Bi₈₄ NS) was fabricated via the facile liquid-polyol technique. The In₁₆Bi₈₄ NS exhibits exceptional performance for CO₂ reduction to formate, with the faradaic efficiency (FE) approaching ∼100% and a corresponding partial current density of 14.1 mA cm^-2 at -0.94 V [vs the reversible hydrogen electrode (RHE)]. Furthermore, the FE could be maintained above 90% in a wide potential window (-0.84 to -1.54 V vs the RHE). This superior performance is attributed to the tuned electronic properties induced by the synergistic interaction between In and Bi, enabling the intermediates to be stably adsorbed on the catalyst surface to generate more formate ions.

Abstract CT559: Capmatinib plus osimertinib vs platinum-pemetrexed doublet chemotherapy as second-line therapy in patients with stage IIIB/IIIC or IV EGFR-mutant, T790M-negative NSCLC harboring MET amplification

Background: MET amplification can arise as a bypass resistance mechanism to EGFR tyrosine kinase inhibitors (TKIs) and occurs in ~5-26% of EGFR TKI resistant EGFR-mutant non-small cell lung cancer (NSCLC). These patients (pts) have limited treatment options, particularly in the EGFR T790M negative (T790M−) setting. Capmatinib, a MET inhibitor, is approved in more than 10 countries for the treatment of metastatic MET exon 14 skipping NSCLC. In preliminary studies, capmatinib plus EGFR TKIs showed antitumor activity in the post-EGFR TKI, EGFR-mutant NSCLC setting. GEOMETRY-E (NCT04816214) is a randomized, controlled, open-label, multicenter, phase 3 study evaluating the efficacy and safety of capmatinib + osimertinib vs platinum-pemetrexed doublet chemotherapy as second line treatment in the advanced NSCLC setting.

Methods: This ongoing study began enrollment in September 2021 and is recruiting adult pts with stage IIIB/IIIC or IV EGFR-mutant, T790M−, MET-amplified NSCLC who had progressed on either 1st/2nd generation EGFR TKIs, osimertinib or other 3rd generation EGFR TKIs. Pts with neurologically unstable, symptomatic CNS metastases or those requiring increasing doses of steroids ≤2 weeks prior to study entry to manage CNS symptoms are ineligible. This is a 2-part study where Part 1 (initial run-in, ~10 pts) will confirm the recommended dose for the randomized Part 2 and evaluate the safety and tolerability of capmatinib + osimertinib. In Part 1, pts will receive oral capmatinib 400 mg twice daily + osimertinib 80 mg once daily in 21-day cycles. Part 2 will evaluate the efficacy and safety of capmatinib + osimertinib vs platinum (cisplatin/carboplatin)-pemetrexed. Part 2 will enroll ~225 pts, in 2:1 randomization, stratified by the presence of brain metastases (yes/no) and prior treatment with 3rd generation EGFR TKIs (yes/no). In Part 1, the primary endpoint is the incidence of dose limiting toxicities during the first 21 days of treatment. Secondary endpoints include safety; tolerability; pharmacokinetics (PK); investigator-assessed overall response rate (ORR), duration of response (DOR), time to response (TTR), disease control rate (DCR) and progression-free survival (PFS) per the Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST 1.1). In Part 2, the primary endpoint is blinded independent review committee (BIRC)-assessed PFS per RECIST 1.1. The key secondary endpoints are ORR by BIRC per RECIST 1.1 and overall intracranial response rate (OiRR) by BIRC per Response Assessment in Neuro-Oncology Brain Metastases (RANO-BM). Other secondary endpoints include DOR, TTR and DCR by BIRC; investigator-assessed PFS after next line of treatment; PK; safety; overall survival; patient-reported outcomes; intracranial DCR, duration of and time to intracranial response by BIRC per RANO-BM.

Citation Format: Yi-Long Wu, Ji-Youn Han, Terufumi Kato, Fabrice Barlesi, Edward B. Garon, Federico Cappuzzo, Yuji Shibata, Nathalie Smith, Sadhvi Khanna, Riccardo Belli, Alejandro Yovine, Daniel Tan. Capmatinib plus osimertinib vs platinum-pemetrexed doublet chemotherapy as second-line therapy in patients with stage IIIB/IIIC or IV EGFR-mutant, T790M-negative NSCLC harboring MET amplification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT559.

Finding the "Sweet Spot": Sharing the decision-making in ADHD treatment selection

BACKGROUND

Stimulants are often prescribed as first-line therapy for attention-deficit/hyperactivity disorder. Currently, there are many therapeutic options available for clinicians and families to consider when making the decision to use a medication. In practice, selection of a stimulant medication for ADHD is highly personalized and can be narrowed down to two major factors: finding the optimal duration of the medication effect, and then estimating a starting dose and subsequently "fine-tuning" the medication to the optimal dosage of the medication. With the possibility of titrating to an optimal stimulant dosage within one prescription of a liquid stimulant, prescribers can recruit the parent/caregiver to actively participate in managing the transition to medication, allowing for greater ownership and a sense of shared control over the process.

CASE PRESENTATION

The short case series offers a communication method by which clinicians can apply the principles of shared decision-making in helping the parent or caregiver of a newly diagnosed patient with ADHD make informed decisions about medication selection, and to obtain a greater sense of comfort with the new medication regimen.

CONCLUSIONS

Much has been published on the importance of clinicians and their patients fostering an environment of clear and unrestricted information-sharing. This short case series illustrates the effectiveness of this approach. Once parents are comfortable with the decision to start drug treatment for ADHD, it is incumbent upon the healthcare provider to ensure that an open channel of communication is maintained, and that parent/caregivers are encouraged to raise concerns as soon as possible.

INSIGHT 2: a phase II study of tepotinib plus osimertinib in MET-amplified NSCLC and first-line osimertinib resistance

MET amplification (METamp), a mechanism of acquired resistance to EGFR tyrosine kinase inhibitors, occurs in up to 30% of patients with non-small-cell lung cancer (NSCLC) progressing on first-line osimertinib. Combining osimertinib with a MET inhibitor, such as tepotinib, an oral, highly selective, potent MET tyrosine kinase inhibitor, may overcome METamp-driven resistance. INSIGHT 2 (NCT03940703), an international, open-label, multicenter phase II trial, assesses tepotinib plus osimertinib in patients with advanced/metastatic EGFR-mutant NSCLC and acquired resistance to first-line osimertinib and METamp, determined centrally by fluorescence in situ hybridization (gene copy number ≥5 and/or MET/CEP7 ≥2) at time of progression. Patients will receive tepotinib 500 mg (450 mg active moiety) plus osimertinib 80 mg once-a-day. The primary end point is objective response, and secondary end points include duration of response, progression-free survival, overall survival and safety. Trial registration number: NCT03940703 (clinicaltrials.gov).

Ten-year prediction model for post-bronchodilator airflow obstruction and early detection of COPD: development and validation in two middle-aged population-based cohorts

Background

Classifying individuals at high chronic obstructive pulmonary disease (COPD)-risk creates opportunities for early COPD detection and active intervention.

Objective

To develop and validate a statistical model to predict 10-year probabilities of COPD defined by post-bronchodilator airflow obstruction (post-BD-AO; forced expiratory volume in 1 s/forced vital capacity<5th percentile).

Setting

General Caucasian populations from Australia and Europe, 10 and 27 centres, respectively.

Participants

For the development cohort, questionnaire data on respiratory symptoms, smoking, asthma, occupation and participant sex were from the Tasmanian Longitudinal Health Study (TAHS) participants at age 41–45 years (n=5729) who did not have self-reported COPD/emphysema at baseline but had post-BD spirometry and smoking status at age 51–55 years (n=2407). The validation cohort comprised participants from the European Community Respiratory Health Survey (ECRHS) II and III (n=5970), restricted to those of age 40–49 and 50–59 with complete questionnaire and spirometry/smoking data, respectively (n=1407).

Statistical method

Risk-prediction models were developed using randomForest then externally validated.

Results

Area under the receiver operating characteristic curve (AUC_ROC) of the final model was 80.8% (95% CI 80.0% to 81.6%), sensitivity 80.3% (77.7% to 82.9%), specificity 69.1% (68.7% to 69.5%), positive predictive value (PPV) 11.1% (10.3% to 11.9%) and negative predictive value (NPV) 98.7% (98.5% to 98.9%). The external validation was fair (AUC_ROC 75.6%), with the PPV increasing to 17.9% and NPV still 97.5% for adults aged 40–49 years with ≥1 respiratory symptom. To illustrate the model output using hypothetical case scenarios, a 43-year-old female unskilled worker who smoked 20 cigarettes/day for 30 years had a 27% predicted probability for post-BD-AO at age 53 if she continued to smoke. The predicted risk was 42% if she had coexistent active asthma, but only 4.5% if she had quit after age 43.

Conclusion

This novel and validated risk-prediction model could identify adults aged in their 40s at high 10-year COPD-risk in the general population with potential to facilitate active monitoring/intervention in predicted ‘COPD cases’ at a much earlier age.

Liquid Biopsy for Advanced NSCLC: A Consensus Statement From the International Association for the Study of Lung Cancer

Although precision medicine has had a mixed impact on the clinical management of patients with advanced-stage cancer overall, for NSCLC, and more specifically for lung adenocarcinoma, the advances have been dramatic, largely owing to the genomic complexity and growing number of druggable oncogene drivers. Furthermore, although tumor tissue is historically the "accepted standard" biospecimen for these molecular analyses, there are considerable innate limitations. Thus, liquid biopsy represents a practical alternative source for investigating tumor-derived somatic alterations. Although data are most robust in NSCLC, patients with other cancer types may also benefit from this minimally invasive approach to facilitate selection of targeted therapies. The liquid biopsy approach includes a variety of methodologies for circulating analytes. From a clinical point of view, plasma circulating tumor DNA is the most extensively studied and widely adopted alternative to tissue tumor genotyping in solid tumors, including NSCLC, first entering clinical practice for detection of EGFR mutations in NSCLC. Since the publication of the first International Association for the Study of Lung Cancer (IASLC) liquid biopsy statement in 2018, several additional advances have been made in this field, leading to changes in the therapeutic decision-making algorithm for advanced NSCLC and prompting this 2021 update. In view of the novel and impressive technological advances made in the past few years, the growing clinical application of plasma-based, next-generation sequencing, and the recent Food and Drug and Administration approval in the United States of two different assays for circulating tumor DNA analysis, IASLC revisited the role of liquid biopsy in therapeutic decision-making in a recent workshop in October 2020 and the question of "plasma first" versus "tissue first" approach toward molecular testing for advanced NSCLC. Moreover, evidence-based recommendations from IASLC provide an international perspective on when to order which test and how to interpret the results. Here, we present updates and additional considerations to the previous statement article as a consensus from a multidisciplinary and international team of experts selected by IASLC.

Comprehensive molecular profiling of advanced cancers in a real-world setting using an ultrasensitive amplicon-based next-generation sequencing (NGS) liquid biopsy assay

3062

Background: Molecular profiling of circulating tumor DNA (ctDNA) by NGS has demonstrated the value of liquid biopsy in informing treatment decisions and monitoring disease progression in cancer patients. Here we report results from the real-world clinical application of an ultrasensitive amplicon-based NGS liquid biopsy assay for advanced cancers. Methods: Plasma cell-free DNA (cfDNA) from 1,338 consecutive samples (51.3% lung, 15.6% breast, 8.4% colorectal, 26.8% from 18 other cancer types; 86.3% of cancer samples were metastatic) underwent real-world testing in a Singapore-based, CAP-accredited, CLIA-certified laboratory from Jan 2018 – Nov 2020. Genomic alterations were analyzed using an amplicon-based NGS assay that detects alterations in 80 cancer-related genes, microsatellite instability (MSI) and cancer-causing viruses, with previously validated cfDNA detection limits of 0.1% variant allele frequency (VAF) for SNPs and indels, 5% tumor fraction, and 2 IU/mL plasma, respectively. Results: ctDNA was successfully detected in 70.0% of cancer samples (76.3% from metastatic and 24.7% from localized tumors) for a total of 977 unique variants. Across ctDNA-positive samples the median VAF was 1.4%, and 8.5% of all reported variants had VAFs between 0.01 – 0.09%. The most frequently altered genes were TP53 (48.8%), EGFR (36.9%), KRAS (17.4%), PIK3CA (15.3%), and APC (9.5%). In ctDNA-positive lung cancer, 74.6% of samples (66.5% EGFR+) harbored ≥1 actionable target, with 29.9% of patients treated with a first- or second-generation EGFR tyrosine kinase inhibitor harboring an EGFR T790M resistance mutation. Among breast cancers, ESR1 or PIK3CA alterations predicting drug resistance/response were detected in 44.2% of HR+ cases. In colorectal cancer, alterations implicated in anti-EGFR resistance ( NRAS, KRAS, BRAF, ERBB2) were found in 50.0% of samples. Profiling of cfDNA also enabled cancer monitoring, even among cancers with low genetic biomarker prevalence. 50% of nasopharyngeal cancer samples were Epstein-Barr virus-positive while 35.7% of liver cancer samples were Hepatitis B virus-positive, enabling an additional yield of 14.3% and 7.1% respectively, over ctDNA detection. cfDNA profiling of cancers of unknown primary origins informed potential tumor origins via the detection of tumor type-specific alterations such as mutations in AR, ESR1, GNAS, EGFR genes, viral biomarkers, and MSI. Conclusions: The use of a comprehensive pan-cancer liquid biopsy panel with rational inclusion of actionable and driver genes resulted in detection of ctDNA in the vast majority of clinical cases processed routinely. These findings support the utility of ultrasensitive amplicon-based NGS liquid biopsy assays in probing cancer drug sensitivity/resistance, tumor burden monitoring, and molecular characterization of tumors.

Cystatin 2 leads to a worse prognosis in patients with gastric cancer

Despite the amazing progress in the treatment of gastric cancer (GC), it is still the third leading cause of cancer death in the world. This study explored the key genes that are related to the prognosis and pathogenesis of GC. Data from the cancer genome atlas (TCGA) and Oncomine were applied to evaluate the expression of cystatin 2 (CST2) in GC samples. Kaplan-Meier plotter was carried out to detect the overall survival of GC patients with different expression levels of CST2. Gene Set Enrichment Analysis (GSEA) was carried out to investigate the functions and pathways connected with CST2 expression. Quantitative real-time polymerase chain reaction (qPCR) and Western blot assays were used to assess CST2 expression. The biological properties of GC cells were assessed with the support of cell proliferation and Transwell assays. Important proteins involved in the regulation of CST2 in GC cell behaviors were evaluated by Western blot. Through analysis of the database, we found that CST2 expression was significantly upregulated in GC samples and actively related to GC patients' poor outcomes. Importantly, the analysis of GSEA showed that GST2 expression was closely connected with the proliferation and migration of cells, as well as the TGF-β1 signaling pathway. In addition, biological assays illustrated that over-expression of CST2 strengthened the activity and metastasis of GC cells. After the upregulation of CST2, the expression of cyclin D1, N-cadherin, vimentin, TGF-β1, and Smad4 increased, and E-cadherin expression decreased. Our findings revealed that over-expression of CST2 enhanced the growth, migration, and invasion of GC cells through modulating the epithelial-mesenchymal transition (EMT) and TGF-β1 signaling pathway, affording a possible biomarker for the treatment of GC.

Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

BACKGROUND

80% of individuals with cancer will require a surgical procedure, yet little comparative data exist on early outcomes in low-income and middle-income countries (LMICs). We compared postoperative outcomes in breast, colorectal, and gastric cancer surgery in hospitals worldwide, focusing on the effect of disease stage and complications on postoperative mortality.

METHODS

This was a multicentre, international prospective cohort study of consecutive adult patients undergoing surgery for primary breast, colorectal, or gastric cancer requiring a skin incision done under general or neuraxial anaesthesia. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression determined relationships within three-level nested models of patients within hospitals and countries. Hospital-level infrastructure effects were explored with three-way mediation analyses. This study was registered with ClinicalTrials.gov, NCT03471494.

FINDINGS

Between April 1, 2018, and Jan 31, 2019, we enrolled 15 958 patients from 428 hospitals in 82 countries (high income 9106 patients, 31 countries; upper-middle income 2721 patients, 23 countries; or lower-middle income 4131 patients, 28 countries). Patients in LMICs presented with more advanced disease compared with patients in high-income countries. 30-day mortality was higher for gastric cancer in low-income or lower-middle-income countries (adjusted odds ratio 3·72, 95% CI 1·70-8·16) and for colorectal cancer in low-income or lower-middle-income countries (4·59, 2·39-8·80) and upper-middle-income countries (2·06, 1·11-3·83). No difference in 30-day mortality was seen in breast cancer. The proportion of patients who died after a major complication was greatest in low-income or lower-middle-income countries (6·15, 3·26-11·59) and upper-middle-income countries (3·89, 2·08-7·29). Postoperative death after complications was partly explained by patient factors (60%) and partly by hospital or country (40%). The absence of consistently available postoperative care facilities was associated with seven to 10 more deaths per 100 major complications in LMICs. Cancer stage alone explained little of the early variation in mortality or postoperative complications.

INTERPRETATION

Higher levels of mortality after cancer surgery in LMICs was not fully explained by later presentation of disease. The capacity to rescue patients from surgical complications is a tangible opportunity for meaningful intervention. Early death after cancer surgery might be reduced by policies focusing on strengthening perioperative care systems to detect and intervene in common complications.

FUNDING

National Institute for Health Research Global Health Research Unit.

Indeterminate pulmonary nodules are not associated with worse overall survival in Ewing Sarcoma

AIM

Lung metastases are a negative prognostic factor in Ewing sarcoma, however, the incidence and significance of sub-centimetre pulmonary nodules at diagnosis is unclear. The aims of this study were to (1): determine the incidence of indeterminate pulmonary nodules (IPNs) in patients diagnosed with Ewing sarcoma (2); establish the impact of IPNs on overall and metastasis-free survival and (3) identify patient, oncological and radiological factors that correlate with poorer prognosis in patients that present with IPNs on their staging chest CT.

MATERIALS & METHODS

Between 2008 and 2016, 173 patients with a first presentation of Ewing sarcoma of bone were retrospectively identified from an institutional database. Staging and follow-up chest CTs for all patients with IPN were reviewed by a senior radiologist. Clinical and radiologic course were examined to determine overall- and metastasis-free survival for IPN patients and to identify demographic, oncological or nodule-specific features that predict which IPN represent true lung metastases.

RESULTS

Following radiologic re-review, IPN were found in 8.7% of patients. Overall survival for IPN patients was comparable to those with a normal staging chest CT (2-year overall survival of 73.3% [95% CI 43.6-89] and 89.4% [95% CI 81.6-94], respectively; p = 0.34) and was significantly better than for patients with clear metastases (46.0% [95% CI 31.9-59]; p < 0.0001). Similarly, there was no difference in metastasis-free survival between 'No Metastases' and 'IPN' patients (p = 0.16). Lung metastases developed in 40% of IPN patients at a median 9.6 months. Reduction of nodule size on neoadjuvant chemotherapy was associated with worse overall survival in IPN patients (p = 0.0084).

CONCLUSION

IPN are not uncommon in patients diagnosed with Ewing sarcoma. In this study, we were unable to detect a difference in overall- or metastasis-free survival between patients with IPN at diagnosis and patients with normal staging chest CTs.

Trajectories of asthma and allergies from 7 years to 53 years and associations with lung function and extrapulmonary comorbidity profiles: a prospective cohort study

BACKGROUND

Longitudinal trajectories of asthma and allergies from childhood to adulthood might be differentially associated with lung function and chronic obstructive pulmonary disease (COPD), but associations with extrapulmonary comorbidities have not been well investigated. We aimed to assess these trajectories and examine their associations with lung function outcomes and profiles of comorbidities.

METHODS

In this prospective cohort study, data for asthma and related allergic conditions (ie, eczema, hay fever, and food allergy) were prospectively collected from the Tasmanian Longitudinal Health Study for participants aged 7-53 years originally recruited in Tasmania, Australia. All surviving individuals in the database with contact details were invited in the most recent follow-up (mean age 53 years). There were no exclusion criteria. With use of latent class analysis, we identified longitudinal trajectories of asthma and allergic conditions from 7-53 years, and profiles of self-reported extrapulmonary conditions recorded at 53 years. The associations between asthma and allergy trajectories and morbidity profiles and lung function at 53 years were investigated with regression models.

FINDINGS

Between Sept 3, 2012, and Nov 8, 2016, of 6128 individuals invited, 3609 (58·9%) individuals were enrolled. We identified five asthma and allergy trajectories: minimal and least asthma and allergies (n= 1767 [49·0%]); late-onset hay fever, no asthma (n=1065 [29·5%]); early-onset remitted asthma and allergies (n=236 [6·5%]); late-onset asthma and allergies (n=317 [8·8%]); and early-onset persistent asthma and allergies (n=224 [6·2%]); and four profiles of extrapulmonary morbidities: minimal or least disease (n=2206 [61·1%]); dominant mental health disorders (n=861 [23·9%]); dominant cardiovascular diseases or risks (n=424 [11·7%]); and multiple disorders (n=117 [3·2%]). The late-onset asthma and allergies trajectory was predominantly associated with the multiple disorders profile (relative risk ratio 3·3 [95% CI 1·9-5·9]), whereas the other asthma and allergy trajectories were associated only with the dominant mental health disorders profile. Both spirometrically defined and clinical COPD were most strongly associated with the early-onset persistent asthma and allergies trajectory (odds ratio [OR] 5·3 [95% CI 3·2-8·6]) and also with the late-onset asthma and allergies trajectory (OR 3·8 [2·4-6·1]).

INTERPRETATION

Distinct longitudinal trajectories of asthma and allergic disease from childhood to 53 years are associated with different profiles of extrapulmonary comorbidities and varying risk of COPD. These findings can inform a personalised approach in clinical guidelines and management focusing on treatable traits. Comorbidity profiles are a new target for early identification and intervention.

FUNDING

National Health and Medical Research Council of Australia, EU's Horizon 2020, The University of Melbourne, Clifford Craig Medical Research Trust of Tasmania, The Victorian, Queensland & Tasmanian Asthma Foundations, The Royal Hobart Hospital, Helen MacPherson Smith Trust, and GlaxoSmithKline.

Are adults with asthma less physically active? A systematic review and meta-analysis

OBJECTIVE

To systematically review the evidence on whether having current, ever asthma and asthma control is associated with levels of total, moderate and vigorous physical activity.

METHODS

We searched EMBASE, MEDLINE, and CINAHL databases, limiting searches to English language papers from inception until Oct 2019. We synthesized the evidence comparing levels of total, moderate and vigorous physical activity between adults with and without current asthma or ever asthma by random effects meta-analyses.

RESULTS

A total of 25 studies were included, with 18 of these included in meta-analyses. A meta-analysis of 4 case-control studies found that adults with current asthma were less active, with 942.12 steps fewer per day, than adults without current asthma (SMD = -0.39, 95%CI: -0.54, -0.24, I² = 0). Meta-analysis of four-high quality cross-sectional studies found that those with current or ever asthma were more likely to be inactive than those without asthma (binary OR _{current asthma} = 0.85, 95%CI: 0.82, 0.89, I² = 45.6%, and binary OR _{ever asthma} = 0.83, 0.75, 0.91, I² = 0, respectively). Meta-analysis, inclusive of all 10 cross-sectional studies with binary ORs, supported this finding. There was also some evidence that adults with current asthma and ever asthma (6 studies with categorical ORs) were less likely to exercise moderately and vigorously, but these meta-analyses were limited by high heterogeneity. No synthesis of the studies considering asthma control was possible.

CONCLUSION

Adults with current or ever asthma had lower levels of total, moderate and vigorous physical activity than those without asthma and may be missing out on the health benefits of being physically active. The association between asthma control and physical activity warrants further investigation.