FEV1Q: a race-neutral approach to assessing lung function.

BACKGROUND: Forced expiratory volume in 1 s quotient (FEV1Q) is a simple approach to spirometry interpretation that compares measured lung function to a lower boundary. This study evaluated how well FEV1Q predicts survival compared with current interpretation methods and whether race impacts FEV1Q. METHODS: White and Black adults with complete spirometry and mortality data from the National Health and Nutrition Examination Survey (NHANES) III and the United Network for Organ Sharing (UNOS) database for lung transplant referrals were included. FEV1Q was calculated as FEV1 divided by 0.4 L for females or 0.5 L for males. Cumulative distributions of FEV1 were compared across races. Cox proportional hazards models tested mortality risk from FEV1Q adjusting for age, sex, height, smoking, income and among UNOS individuals, referral diagnosis. Harrell's C-statistics were compared between absolute FEV1, FEV1Q, FEV1/height2, FEV1 z-scores and FEV1 % predicted. Analyses were stratified by race. RESULTS: Among 7182 individuals from NHANES III and 7149 from UNOS, 1907 (27%) and 991 (14%), respectively, were Black. The lower boundary FEV1 values did not differ between Black and White individuals in either population (FEV1 first percentile difference ≤0.01 L; p>0.05). Decreasing FEV1Q was associated with increasing hazard ratio (HR) for mortality (NHANES III HR 1.33 (95% CI 1.28-1.39) and UNOS HR 1.18 (95% CI 1.12-1.23)). The associations were not confounded nor modified by race. Discriminative power was highest for FEV1Q compared with alternative FEV1 approaches in both Black and White individuals. CONCLUSIONS: FEV1Q is an intuitive and simple race-neutral approach to interpreting FEV1 that predicts survival better than current alternative methods.

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer.

Although immunotherapy with PD-(L)1 blockade is routine for lung cancer, little is known about acquired resistance. Among 1,201 patients with non-small cell lung cancer (NSCLC) treated with PD-(L)1 blockade, acquired resistance is common, occurring in >60% of initial responders. Acquired resistance shows differential expression of inflammation and interferon (IFN) signaling. Relapsed tumors can be separated by upregulated or stable expression of IFNγ response genes. Upregulation of IFNγ response genes is associated with putative routes of resistance characterized by signatures of persistent IFN signaling, immune dysfunction, and mutations in antigen presentation genes which can be recapitulated in multiple murine models of acquired resistance to PD-(L)1 blockade after in vitro IFNγ treatment. Acquired resistance to PD-(L)1 blockade in NSCLC is associated with an ongoing, but altered IFN response. The persistently inflamed, rather than excluded or deserted, tumor microenvironment of acquired resistance may inform therapeutic strategies to effectively reprogram and reverse acquired resistance.

Ovarian tumors orchestrate distinct cellular compositions.

The determinants of T cell infiltration in tumors remain largely unknown. In a recent issue of Cancer Cell, Hornburg et al. use single-cell RNA sequencing to characterize the cellular compartments of the ovarian cancer microenvironment and shed light on how tumor, immune, and stromal cells interact and shape T cell infiltration.

Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer.

Somatic DNA copy number variations (CNVs) are prevalent in cancer and can drive cancer progression, albeit with often uncharacterized roles in altering cell signaling states. Here, we integrate genomic and proteomic data for 5,598 tumor samples to identify CNVs leading to aberrant signal transduction. The resulting associations recapitulate known kinase-substrate relationships, and further network analysis prioritizes likely causal genes. Of the 303 significant associations we identify from the pan-tumor analysis, 43% are replicated in cancer cell lines, including 44 robust gene-phosphosite associations identified across multiple tumor types. Several predicted regulators of hippo signaling are experimentally validated. Using RNAi, CRISPR, and drug screening data, we find evidence of kinase addiction in cancer cell lines, identifying inhibitors for targeting of kinase-dependent cell lines. We propose copy number status of genes as a useful predictor of differential impact of kinase inhibition, a strategy that may be of use in the future for anticancer therapies.

Promises and challenges of adoptive T-cell therapies for solid tumours.

Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, many patients with advanced-stage- or high-risk cancers still die, owing to metastatic disease. Adoptive T-cell therapy, involving the autologous or allogeneic transplant of tumour-infiltrating lymphocytes or genetically modified T cells expressing novel T-cell receptors or chimeric antigen receptors, has shown promise in the treatment of cancer patients, leading to durable responses and, in some cases, cure. Technological advances in genomics, computational biology, immunology and cell manufacturing have brought the aspiration of individualised therapies for cancer patients closer to reality. This new era of cell-based individualised therapeutics challenges the traditional standards of therapeutic interventions and provides opportunities for a paradigm shift in our approach to cancer therapy. Invited speakers at a 2020 symposium discussed three areas-cancer genomics, cancer immunology and cell-therapy manufacturing-that are essential to the effective translation of T-cell therapies in the treatment of solid malignancies. Key advances have been made in understanding genetic intratumour heterogeneity, and strategies to accurately identify neoantigens, overcome T-cell exhaustion and circumvent tumour immunosuppression after cell-therapy infusion are being developed. Advances are being made in cell-manufacturing approaches that have the potential to establish cell-therapies as credible therapeutic options. T-cell therapies face many challenges but hold great promise for improving clinical outcomes for patients with solid tumours.

Integrated Multi-Tumor Radio-Genomic Marker of Outcomes in Patients with High Serous Ovarian Carcinoma.

Purpose: Develop an integrated intra-site and inter-site radiomics-clinical-genomic marker of high grade serous ovarian cancer (HGSOC) outcomes and explore the biological basis of radiomics with respect to molecular signaling pathways and the tumor microenvironment (TME). Method: Seventy-five stage III-IV HGSOC patients from internal (N = 40) and external factors via the Cancer Imaging Archive (TCGA) (N = 35) with pre-operative contrast enhanced CT, attempted primary cytoreduction, at least two disease sites, and molecular analysis performed within TCGA were retrospectively analyzed. An intra-site and inter-site radiomics (cluDiss) measure was combined with clinical-genomic variables (iRCG) and compared against conventional (volume and number of sites) and average radiomics (N = 75) for prognosticating progression-free survival (PFS) and platinum resistance. Correlation with molecular signaling and TME derived using a single sample gene set enrichment that was measured. Results: The iRCG model had the best platinum resistance classification accuracy (AUROC of 0.78 [95% CI 0.77 to 0.80]). CluDiss was associated with PFS (HR 1.03 [95% CI: 1.01 to 1.05], p = 0.002), negatively correlated with Wnt signaling, and positively to immune TME. Conclusions: CluDiss and the iRCG prognosticated HGSOC outcomes better than conventional and average radiomic measures and could better stratify patient outcomes if validated on larger multi-center trials.

Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases.

Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment naïve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.

CO2 laser ablative fractional resurfacing photodynamic therapy for actinic keratosis and nonmelanoma skin cancer: a randomized split-side study.

Aminolevulinic acid (ALA) photodynamic therapy (PDT) is a preferred method for treatment of multiple actinic keratoses (AKs) in broad skin areas (referred to as field cancerization). Pretreatment with CO2 laser ablative fractional resurfacing (AFR) may increase the efficacy of PDT. This study compared the effect and durability of CO2 laser AFR-assisted ALA-PDT vs ALA-PDT alone in the treatment of AKs and nonmelanoma skin cancers (NMSCs) at various body locations. In this randomized, split-side study, 19 patients had 1 side pretreated with AFR before treatment of both sides with ALA-PDT. Results indicated that pretreatment with AFR provided superior clearance of AKs and thin NMSCs at 6 months compared to ALA-PDT alone.

Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy.

In metastatic cancer, the degree of heterogeneity of the tumor microenvironment (TME) and its molecular underpinnings remain largely unstudied. To characterize the tumor-immune interface at baseline and during neoadjuvant chemotherapy (NACT) in high-grade serous ovarian cancer (HGSOC), we performed immunogenomic analysis of treatment-naive and paired samples from before and after treatment with chemotherapy. In treatment-naive HGSOC, we found that immune-cell-excluded and inflammatory microenvironments coexist within the same individuals and within the same tumor sites, indicating ubiquitous variability in immune cell infiltration. Analysis of TME cell composition, DNA copy number, mutations and gene expression showed that immune cell exclusion was associated with amplification of Myc target genes and increased expression of canonical Wnt signaling in treatment-naive HGSOC. Following NACT, increased natural killer (NK) cell infiltration and oligoclonal expansion of T cells were detected. We demonstrate that the tumor-immune microenvironment of advanced HGSOC is intrinsically heterogeneous and that chemotherapy induces local immune activation, suggesting that chemotherapy can potentiate the immunogenicity of immune-excluded HGSOC tumors.

Lack of detectable neoantigen depletion signals in the untreated cancer genome.

Somatic mutations can result in the formation of neoantigens, immunogenic peptides that are presented on the tumor cell surface by HLA molecules. These mutations are expected to be under negative selection pressure, but the extent of the resulting neoantigen depletion remains unclear. On the basis of HLA affinity predictions, we annotated the human genome for its translatability to HLA binding peptides and screened for reduced single nucleotide substitution rates in large genomic data sets from untreated cancers. Apparent neoantigen depletion signals become negligible when taking into consideration trinucleotide-based mutational signatures, owing to lack of power or to efficient immune evasion mechanisms that are active early during tumor evolution.

Comprehensive Benchmarking and Integration of Tumor Microenvironment Cell Estimation Methods.

Various computational approaches have been developed for estimating the relative abundance of different cell types in the tumor microenvironment (TME) using bulk tumor RNA data. However, a comprehensive comparison across diverse datasets that objectively evaluates the performance of these approaches has not been conducted. Here, we benchmarked seven widely used tools and gene sets and introduced ConsensusTME, a method that integrates gene sets from all the other methods for relative TME cell estimation of 18 cell types. We collected a comprehensive benchmark dataset consisting of pan-cancer data (DNA-derived purity, leukocyte methylation, and hematoxylin and eosin-derived lymphocyte counts) and cell-specific benchmark datasets (peripheral blood cells and tumor tissues). Although none of the methods outperformed others in every benchmark, ConsensusTME ranked top three in all cancer-related benchmarks and was the best performing tool overall. We provide a Web resource to interactively explore the benchmark results and an objective evaluation to help researchers select the most robust and accurate method to further investigate the role of the TME in cancer (www.consensusTME.org). SIGNIFICANCE: This work shows an independent and comprehensive benchmarking of recently developed and widely used tumor microenvironment cell estimation methods based on bulk expression data and integrates the tools into a consensus approach.

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma.

Although clonal neo-antigen burden is associated with improved response to immune therapy, the functional basis for this remains unclear. Here we study this question in a novel controlled mouse melanoma model that enables us to explore the effects of intra-tumor heterogeneity (ITH) on tumor aggressiveness and immunity independent of tumor mutational burden. Induction of UVB-derived mutations yields highly aggressive tumors with decreased anti-tumor activity. However, single-cell-derived tumors with reduced ITH are swiftly rejected. Their rejection is accompanied by increased T cell reactivity and a less suppressive microenvironment. Using phylogenetic analyses and mixing experiments of single-cell clones, we dissect two characteristics of ITH: the number of clones forming the tumor and their clonal diversity. Our analysis of melanoma patient tumor data recapitulates our results in terms of overall survival and response to immune checkpoint therapy. These findings highlight the importance of clonal mutations in robust immune surveillance and the need to quantify patient ITH to determine the response to checkpoint blockade.

Model-based evaluation of the long-term cost-effectiveness of systematic case-finding for COPD in primary care.

INTRODUCTION: 'One-off' systematic case-finding for COPD using a respiratory screening questionnaire is more effective and cost-effective than routine care at identifying new cases. However, it is not known whether early diagnosis and treatment is beneficial in the longer term. We estimated the long-term cost-effectiveness of a regular case-finding programme in primary care. METHODS: A Markov decision analytic model was developed to compare the cost-effectiveness of a 3-yearly systematic case-finding programme targeted to ever smokers aged ≥50 years with the current routine diagnostic process in UK primary care. Patient-level data on case-finding pathways was obtained from a large randomised controlled trial. Information on the natural history of COPD and treatment effects was obtained from a linked COPD cohort, UK primary care database and published literature. The discounted lifetime cost per quality-adjusted life-year (QALY) gained was calculated from a health service perspective. RESULTS: The incremental cost-effectiveness ratio of systematic case-finding versus current care was £16 596 per additional QALY gained, with a 78% probability of cost-effectiveness at a £20 000 per QALY willingness-to-pay threshold. The base case result was robust to multiple one-way sensitivity analyses. The main drivers were response rate to the initial screening questionnaire and attendance rate for the confirmatory spirometry test. DISCUSSION: Regular systematic case-finding for COPD using a screening questionnaire in primary care is likely to be cost-effective in the long-term despite uncertainties in treatment effectiveness. Further knowledge of the natural history of case-found patients and the effectiveness of their management will improve confidence to implement such an approach.

Self-reported intake of fruit and vegetables and risk of chronic obstructive pulmonary disease: A nation-wide twin study.

BACKGROUND: Although smoking is the major risk factor for chronic obstructive pulmonary disease (COPD) many patients with obstructive lung function suggesting COPD are never-smokers. Therefore, other lifestyle factors have been suggested as risk factors. AIMS: i) To examine the association between self-reported intake of fruit and vegetables and risk of COPD and ii) to examine whether the association between these traits are due to underlying genetic factors. METHODS: 12,449 twins, aged 40-80, from the Danish Twin Registry were recruited. The participants completed a questionnaire on medical history and lifestyle factors and participated in clinical examination. COPD was defined according to ATS/ERS recommendations. Multivariate logistic regressions were used to estimate the risk of COPD in individuals with a low intake of fruit and vegetables. Co-twin control analyses were performed to examine whether the association between fruit and vegetables and COPD is explained by genetic factors. Self-reported physician-diagnosed asthmatic individuals were excluded. RESULTS: Of the 11,458 individuals were included in the analyses, 48% of the participants were males. Mean age was 58.9 (years)±SD 9.6, mean BMI (kg/m2)26.6 ±â€¯SD 4.4. A multivariate logistic regression, including sex, age and BMI showed that both smoking, no and heavy drinking and physical inactivity were independent predictors of COPD. There was a significant frequency-pendent association between intake of fruit and vegetables and increased risk of COPD. Conditional logistic regression analyses showed that the association might be controlled by genetic factors. CONCLUSIONS: This study shows that low intake of fruit and vegetables is associated with an increased risk of COPD and the association might be under influence of genetic factors.

New-onset COPD and Decline in Lung Function Among Wood Dust-Exposed Workers: Re-analysis of a 6-year Follow-up Study.

Objectives: There is a lack of longitudinal studies exploring the association between organic wood dust exposure and new-onset chronic obstructive pulmonary disease (COPD) and change in lung function. We have re-investigated these associations in a 6-year follow-up cohort of furniture workers exposed to wood dust using improved outcome measures and methods. Methods: A large follow-up study of 1112 woodworkers (63%) from the Danish furniture industry and 235 controls (57%) was conducted between 1998 and 2004. Forced expiratory volume in the first second (FEV1), forced vital capacity (FVC), and the ratio (FEV1/FVC) standardized for age, height, and sex using the Global Lung Function Initiative 2012 equations were assessed at baseline and follow-up. Questionnaires on respiratory symptoms, wood dust exposure, and smoking habits were collected. Exposure was assessed as exposure level at baseline and as cumulative exposure in the follow-up period from quantitative task specific job exposure matrix available at both baseline and follow-up based on personal dust sampling using passive dust monitors. The association between exposure to wood dust and new-onset COPD was assessed with logistic regression, whereas the association between wood dust and the longitudinal change in z-score for lung function was assessed with linear regression. Results: Similar associations were seen for different exposure metrics. An exposure-response relation was seen for new-onset COPD for female smokers with an odds ratio (OR) (95% confidence interval [CI]) of 8.47 (0.9-82.4) in the highest exposed group compared to controls, and a significant test for trend P = 0.049. No such association was seen among males for whom only smoking was strongly associated to new-onset COPD. For change in lung function, a significant exposure-response was seen for females, confirming previous findings, with increasing levels of wood dust exposure showing larger decline in lung function (ß [95% CI]: -0.32 ΔzFEV1 (-0.56 to -0.08, P = 0.009) for third quartile exposure compared to controls, test for trend, P = 0.005, equivalent to an excess loss of 125 ml in the 6 years of follow-up). An opposite association was seen for men. Conclusion: In conclusion, we found that female woodworkers have a dose-dependent increased OR of new-onset COPD and an excess decline in lung function suggesting that female woodworkers may be more susceptible to wood dust exposure than male woodworkers. Among male woodworkers, only smoking and asthma were significant predictors for new-onset COPD and excess decline in lung function. These results emphasize that reduction in both smoking and wood dust exposure should continuously be an effort to prevent adverse pulmonary health effects.

Mutational Analysis Identifies Therapeutic Biomarkers in Inflammatory Bowel Disease-Associated Colorectal Cancers.

Purpose: Inflammatory bowel disease-associated colorectal cancers (IBD-CRC) are associated with a higher mortality than sporadic colorectal cancers. The poorly defined molecular pathogenesis of IBD-CRCs limits development of effective prevention, detection, and treatment strategies. We aimed to identify biomarkers using whole-exome sequencing of IBD-CRCs to guide individualized management.Experimental Design: Whole-exome sequencing was performed on 34 formalin-fixed paraffin-embedded primary IBD-CRCs and 31 matched normal lymph nodes. Computational methods were used to identify somatic point mutations, small insertions and deletions, mutational signatures, and somatic copy number alterations. Mismatch repair status was examined.Results: Hypermutation was observed in 27% of IBD-CRCs. All hypermutated cancers were from the proximal colon; all but one of the cancers with hypermutation had defective mismatch repair or somatic mutations in the proofreading domain of DNA POLE Hypermutated IBD-CRCs had increased numbers of predicted neo-epitopes, which could be exploited using immunotherapy. We identified six distinct mutation signatures in IBD-CRCs, three of which corresponded to known mechanisms of mutagenesis. Driver genes were also identified.Conclusions: IBD-CRCs should be evaluated for hypermutation and defective mismatch repair to identify patients with a higher neo-epitope load who may benefit from immunotherapies. Prospective trials are required to determine whether IHC to detect loss of MLH1 expression in dysplastic colonic tissue could identify patients at increased risk of developing IBD-CRC. We identified mutations in genes in IBD-CRCs with hypermutation that might be targeted therapeutically. These approaches would complement and individualize surveillance and treatment programs. Clin Cancer Res; 24(20); 5133-42. ©2018 AACR.

The protein kinase SIK downregulates the polarity protein Par3.

The multifunctional cytokine transforming growth factor ß (TGFß) controls homeostasis and disease during embryonic and adult life. TGFß alters epithelial cell differentiation by inducing epithelial-mesenchymal transition (EMT), which involves downregulation of several cell-cell junctional constituents. Little is understood about the mechanism of tight junction disassembly by TGFß. We found that one of the newly identified gene targets of TGFß, encoding the serine/threonine kinase salt-inducible kinase 1 (SIK), controls tight junction dynamics. We provide bioinformatic and biochemical evidence that SIK can potentially phosphorylate the polarity complex protein Par3, an established regulator of tight junction assembly. SIK associates with Par3, and induces degradation of Par3 that can be prevented by proteasomal and lysosomal inhibition or by mutation of Ser885, a putative phosphorylation site on Par3. Functionally, this mechanism impacts on tight junction downregulation. Furthermore, SIK contributes to the loss of epithelial polarity and examination of advanced and invasive human cancers of diverse origin displayed high levels of SIK expression and a corresponding low expression of Par3 protein. High SIK mRNA expression also correlates with lower chance for survival in various carcinomas. In specific human breast cancer samples, aneuploidy of tumor cells best correlated with cytoplasmic SIK distribution, and SIK expression correlated with TGFß/Smad signaling activity and low or undetectable expression of Par3. Our model suggests that SIK can act directly on the polarity protein Par3 to regulate tight junction assembly.

The impact of different spirometric definitions on the prevalence of airway obstruction and their association with respiratory symptoms.

The fixed ratio criterion of forced expiratory volume in 1 s/forced vital capacity <0.70 for diagnosing airway obstruction may overdiagnose the condition, particularly in the elderly, so the lower limit of normal (LLN) is recommended as the most appropriate criterion. Our aim was to compare LLN versus fixed ratio on the prevalence of chronic obstructive pulmonary disease (COPD) and examine the association between respiratory symptoms and airway obstruction defined by LLN and fixed ratio. 12 449 twins aged 40-80 years participated in a nationwide survey using the Danish Twin Registry. They completed a questionnaire, underwent clinical examination and recorded prebronchodilator spirometry. Individuals with self-reported asthma were excluded. Clinical COPD was defined by respiratory symptoms together with airway obstruction. 10 329 individuals were included, with a mean±sd age of 58.4±9.6 years and mean body mass index of 26.6±4.4 kg·m-2; 20% were current smokers, 37% former smokers and 43% never-smokers; and 48% were male. The prevalence of LLN airway obstruction (LLN-AO) and fixed ratio airway obstruction (FR-AO) was 5.6% and 18.0%, respectively (p<0.001). Overall, 26% reported current respiratory symptoms, but 50% of those with LLN-AO had respiratory symptoms compared to 39% with FR-AO, p<0.001. The prevalence of clinical LLN-COPD and fixed ratio COPD was 2.6% and 6.3%, respectively (p<0.001). Individuals with LLN-AO had a significantly higher probability of reporting respiratory symptoms compared with both healthy individuals and FR-AO when adjusted for sex, age and ever-smoking. The use of fixed ratio more than doubled the prevalence of clinical COPD compared with LLN, this being more pronounced with increased age, and identified subjects with a lower prevalence of respiratory symptoms than LLN-AO.

Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient.

We present an exceptional case of a patient with high-grade serous ovarian cancer, treated with multiple chemotherapy regimens, who exhibited regression of some metastatic lesions with concomitant progression of other lesions during a treatment-free period. Using immunogenomic approaches, we found that progressing metastases were characterized by immune cell exclusion, whereas regressing and stable metastases were infiltrated by CD8+ and CD4+ T cells and exhibited oligoclonal expansion of specific T cell subsets. We also detected CD8+ T cell reactivity against predicted neoepitopes after isolation of cells from a blood sample taken almost 3 years after the tumors were resected. These findings suggest that multiple distinct tumor immune microenvironments co-exist within a single individual and may explain in part the heterogeneous fates of metastatic lesions often observed in the clinic post-therapy. VIDEO ABSTRACT.