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Supplemental Figure 1. Sets of variants identified with sign test and respective controls in network enrichment analysis. Supplemental Figure 2 - Genes and networks identified in the Network enrichment analysis. Supplemental Table 1 - Exome sequencing results Supplemental Table 2 A-F - Top SNVs for each bioinformatic strategy Supplemental Table 3. Genes selected from a priori knowledge of gemcitabine and carboplatin mechanism of action, transport, and metabolism. Supplemental Table 4. Summary of Ingenuity top pathways Supplemental Table 5. Patient characteristics in the validation set Supplemental Table 6. Genetic variants included in the validation

Purpose: Chemotherapies are associated with significant interindividual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients is basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression.Experimental Design: We exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3 or 4 after first chemotherapy cycle) or were virtually unaffected (grade 0 or 1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: (i) whole-exome nonsynonymous single-nucleotide variants association analysis, (ii) deviation from Hardy–Weinberg equilibrium, (iii) analysis of genes selected by a priori biologic knowledge, (iv) analysis of genes selected from gene expression meta-analysis of toxicity datasets, (v) Ingenuity Pathway Analysis, and (vi) FunCoup network enrichment analysis.Results: A total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (P = 0.0008; OR, 5.2; 95% CI, 1.8–18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (P = 0.0015; OR, 0.36; 95% CI, 0.17–0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia.Conclusions: We have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy. Clin Cancer Res; 22(2); 366–73. ©2015 AACR.

We thank N. Terzi and co-workers for taking an interest in our work and for their valuable comments. Although there are many studies on the coordination of breathing and swallowing, there is still much to investigate and learn about swallowing function in stable and acute COPD. In fact, few published studies have investigated swallowing function in patients hospitalised due to an acute illness other than stroke [1] and this is true for COPD patients with an acute exacerbation [2–4]. There is also much to learn regarding patient-reported outcomes, which was one focus of our study., Swallowing dysfunction is common in COPD patients with severe exacerbations but this kind of dysfunction is potentially correctable, at least in some patients. Further interventional studies on this topic are urgently needed. https://bit.ly/3mFKNq1

In the present work, the determination of omeprazole (OME) enantiomers in oral fluid and plasma samples was carried out utilizing microextraction by packed sorbent (MEPS) and liquid chromatography-tandem mass spectrometry. A chiral column with cellulose-SB phase was used for the first time for enantiomeric separation of OME with an isocratic elution system using 0.2% ammonium hydroxide in hexane-ethanol mixture (70 : 30, v/v) as the mobile phase. OME enantiomers were determined utilizing a triple quadrupole tandem mass spectrometer in positive ion mode (ESI+) monitoring mass transitions: m/z 346.3 ⟶ 198.0 for OME and m/z 369.98 ⟶ 252.0 for internal standard. The limits of detection and quantification of the present method for both enantiomers were 0.1 and 0.4 ng/mL, respectively. The method validation provided good accuracy and precision. The matrix effect factor was less than 5%, and no interfering peaks were observed. The interday precision values ranged from 2.2 to 7.5 (%RSD), and the accuracy of determinations varied from −9.9% to 8.3%. In addition, the pharmacokinetics (PK) of omeprazole enantiomers in healthy subjects after a single oral dose was investigated. (S)-Enantiomers showed higher levels than (R)-enantiomers throughout 24 h. It was found that the mean maximum concentrations of (R)- and (S)-omeprazole in plasma samples were about two times higher than in oral fluid.

Gemcitabine/carboplatin-induced myelosuppressive adverse drug reactions (ADRs) are clinical problems leading to patient suffering and dose alterations. There is a need for personalised medicine to improve treatment effects and patients well-being. We tested four genetic variants, rs11141915, rs1901440, rs12046844 and rs11719165, previously suggested as potential biomarkers for gemcitabine-induced leukopenia/neutropenia in Japanese patients, in 213 Swedish gemcitabine/carboplatin-treated non-small cell lung cancer (NSCLC) patients. DNA was genotyped using TaqMan probes and real-time PCR. The relationships between the risk alleles and low toxicity (non-ADR: Common Terminology Criteria for Adverse Events [CTCAE] grades 0) or high toxicity (ADR: CTCAE grades 3-4) of platelets, leukocytes and neutrophils were evaluated using Fishers exact test. The risk alleles did not correlate with myelosuppression, and the strongest borderline significance (not withstanding adjustment for multiple testing) was for rs1901440 (neutropenia, p = 0.043) and rs11719165 (leukopenia, p = 0.049) where the risk alleles trended towards lower toxicity, contrasting with previous study findings. Risk alleles and higher risk scores were more common among our patients. We conclude that the genetic variants do not apply to Swedish patients treated with gemcitabine/carboplatin. However, they can still be important in other populations and cohorts, especially in a gemcitabine monotherapy setting, where the causal genetic variation might influence myelosuppressive ADRs. Funding Agencies|Swedish Cancer SocietySwedish Cancer Society; Swedish Research CouncilSwedish Research CouncilEuropean Commission; Linkoping University; ALF grants Region ostergotland; Funds of Radiumhemmet; Marcus Borgstroms stiftelse

BACKGROUND: Endobronchial lung volume reduction (EBVR) with one-way valves introduced into the most diseased lobe of the lung is a non-invasive method to improve lung function in patients with severe heterogenous emphysema. The problem is to select the right patients for the procedure. Furthermore, the long-term effects have not been reported in most studies. METHODS: EBVR was performed in 35 patients with severely handicapping emphysema and with one radiologically clearly enlarged (at least 125%) target lung lobe and clearly visible and complete interlobar fissures on CT. Most of the successful survivors have then been followed for five years. RESULTS: Five (14%) were primary failures (defined as less than 15% increase of FEV(1sec)) and 10 (28%) were secondary failures (the valves were coughed up or removed for some reason). In the 21 successful l patients, the improvement of FEV(1sec) was in the mean 59%. Over the years, FEV(1sec) gradually decreased but was still higher 5 years later than initially. Of the successful group, 76% were still alive after 5 years, while only 50% were in the refused or failed groups. CONCLUSIONS: With careful selection of patients remarkably good results in lung function can be achieved, and these improvements will last for years though slowly decrease. In addition, the results indicate an improvement in survival with successful EBVR procedure.

Introduction: Infiltration of T and B/plasma cells has been linked to NSCLC prognosis, but this has not been thoroughly investigated in relation to the expression of programmed death ligand 1 (PD-L1). Here, we determine the association of lymphocytes and PD-L1 with overall survival (OS) in two retrospective cohorts of operated NSCLC patients who were not treated with checkpoint inhibitors targeting the programmed death 1/PD-L1 axis. Moreover, we evaluate how PD-L1 positivity and clinicopathologic factors affect the prognostic association of lymphocytes. Methods: Cluster of differentiation (CD) 3 (CD3)-, CD8-, CD4-, forkhead box P3 (FOXP3)-, CD20-, CD79A-, and immunoglobulin kappa constant (IGKC)-positive immune cells, and tumor PD-L1 positivity, were determined by immunohistochemistry on tissue microarrays (n = 705). Affymetrix data was analyzed for a patient subset, and supplemented with publicly available transcriptomics data (N = 1724). Associations with OS were assessed by Kaplan-Meier plots and uni- and multivariate Cox regression. Results: Higher levels of T and B plasma cells were associated with longer OS (p = 0.004 and p < 0.001, for CD8 and IGKC, respectively). Highly proliferative tumors with few lymphocytes had the worst outcome. No association of PD-L1 positivity with OS was observed in a nonstratified patient population; however, a significant association with shorter OS was observed in never-smokers (p = 0.009 and p = 0.002, 5% and 50% cutoff). Lymphocyte infiltration was not associated with OS in PD-L1–positive tumors (50% cutoff). The prognostic association of lymphocyte infiltration also depended on the patients’ smoking history and histologic subtype. Conclusions: Proliferation, PD-L1 status, smoking history, and histology should be considered if lymphocyte infiltration is to be used as a prognostic biomarker.

Disease recurrence in surgically treated lung adenocarcinoma (AC) remains high. New approaches for risk stratification beyond tumor stage are needed. Gene expression‐based AC subtypes such as the Cancer Genome Atlas Network (TCGA) terminal‐respiratory unit (TRU), proximal‐inflammatory (PI) and proximal‐proliferative (PP) subtypes have been associated with prognosis, but show methodological limitations for robust clinical use. We aimed to derive a platform independent single sample predictor (SSP) for molecular subtype assignment and risk stratification that could function in a clinical setting. Two‐class (TRU/nonTRU=SSP2) and three‐class (TRU/PP/PI=SSP3) SSPs using the AIMS algorithm were trained in 1655 ACs (n = 9659 genes) from public repositories vs TCGA centroid subtypes. Validation and survival analysis were performed in 977 patients using overall survival (OS) and distant metastasis‐free survival (DMFS) as endpoints. In the validation cohort, SSP2 and SSP3 showed accuracies of 0.85 and 0.81, respectively. SSPs captured relevant biology previously associated with the TCGA subtypes and were associated with prognosis. In survival analysis, OS and DMFS for cases discordantly classified between TCGA and SSP2 favored the SSP2 classification. In resected Stage I patients, SSP2 identified TRU‐cases with better OS (hazard ratio [HR] = 0.30; 95% confidence interval [CI] = 0.18‐0.49) and DMFS (TRU HR = 0.52; 95% CI = 0.33‐0.83) independent of age, Stage IA/IB and gender. SSP2 was transformed into a NanoString nCounter assay and tested in 44 Stage I patients using RNA from formalin‐fixed tissue, providing prognostic stratification (relapse‐free interval, HR = 3.2; 95% CI = 1.2‐8.8). In conclusion, gene expression‐based SSPs can provide molecular subtype and independent prognostic information in early‐stage lung ACs. SSPs may overcome critical limitations in the applicability of gene signatures in lung cancer., What's new? New tools are needed in order to improve risk stratification and therapy selection in early‐stage lung adenocarcinoma. Inherent differences in gene expression between adenocarcinoma subtypes could facilitate the development of such tools. The authors of this study derived platform‐independent, single‐sample predictors (SSP) of adenocarcinoma subtypes, based on gene expression. Derived SSPs successfully provided prognostic information in surgically treated stage I lung adenocarcinoma patients. The single‐sample classifier was readily translated into assays applicable to archival tissue, indicating clinical utility. The findings highlight the clinical relevance of transcriptional signatures and gene expression predictors in lung adenocarcinoma, warranting their further investigation and development.

Publisher's version (útgefin grein), Objectives: Gemcitabine/carboplatin treatment is known to cause severe adverse drug reactions which can lead to the need for reduction or cessation of chemotherapy. It would be beneficial to identify patients at risk of severe hematological toxicity in advance before treatment start. This study aims to identify genetic markers for gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients. Material and methods: Whole-exome sequencing was performed on 215 patients. Association analysis was performed on single-nucleotide variants (SNVs) and genes, and the validation was based on an independent genome-wide association study (GWAS). Based on the association and validation analyses the genetic variants were then selected for and used in weighted genetic risk score (wGRS) prediction models for leukopenia and neutropenia. Results: Association analysis identified 50 and 111 SNVs, and 12 and 20 genes, for leukopenia and neutropenia, respectively. Of these SNVS 20 and 19 were partially validated for leukopenia and neutropenia, respectively. The genes SVIL (p = 2.48E-06) and EFCAB2 (p = 4.63E-06) were significantly associated with leukopenia contain the partially validated SNVs rs3740003, rs10160013, rs1547169, rs10927386 and rs10927387. The wGRS prediction models showed significantly different risk scores for high and low toxicity patients. Conclusion: We have identified and partially validated genetic biomarkers in SNVs and genes correlated to gemcitabine/carboplatin-induced leukopenia and neutropenia and created wGRS models for predicting the risk of chemotherapy-induced hematological toxicity. These results provide a strong foundation for further studies of chemotherapy-induced toxicity., This work was supported by grants from the Swedish Cancer Society [Grant CAN 2016/602 ], the Swedish Research Council, Linköping University, ALF grants Region Östergötland, the Funds of Radiumhemmet , Marcus Borgströms stiftelse and the Spanish Ministry of Economy and Competitiveness ( SAF2015-64850-R ).

Gemcitabine/carboplatin chemotherapy commonly induces myelosuppression, including neutropenia, leukopenia, and thrombocytopenia. Predicting patients at risk of these adverse drug reactions (ADRs) and adjusting treatments accordingly is a long-term goal of personalized medicine. This study used whole-genome sequencing (WGS) of blood samples from 96 gemcitabine/carboplatin-treated non-small cell lung cancer (NSCLC) patients and gene network modules for predicting myelosuppression. Association of genetic variants in PLINK found 4594, 5019, and 5066 autosomal SNVs/INDELs with p ≤ 1 × 10−3 for neutropenia, leukopenia, and thrombocytopenia, respectively. Based on the SNVs/INDELs we identified the toxicity module, consisting of 215 unique overlapping genes inferred from MCODE-generated gene network modules of 350, 345, and 313 genes, respectively. These module genes showed enrichment for differentially expressed genes in rat bone marrow, human bone marrow, and human cell lines exposed to carboplatin and gemcitabine (p Funding agencies: Swedish Cancer Society, the Swedish Research Council, Linköping University, ALF grants Region Östergötland, the Funds of Radiumhemmet, Marcus Borgströms stiftelse, Stiftelsen Assar Gabrielssons Fond

Chemotherapy-induced myelosuppression, including thrombocytopenia, is a recurrent problem during cancer treatments that may require dose alterations or cessations that could affect the antitumor effect of the treatment. To identify genetic markers associated with treatment-induced thrombocytopenia, we whole-exome sequenced 215 non-small cell lung cancer patients homogeneously treated with gemcitabine/carboplatin. The decrease in platelets (defined as nadir/baseline) was used to assess treatment-induced thrombocytopenia. Association between germline genetic variants and thrombocytopenia was analyzed at single-nucleotide variant (SNV) (based on the optimal false discovery rate, the severity of predicted consequence, and effect), gene, and pathway levels. These analyses identified 130 SNVs/INDELs and 25 genes associated with thrombocytopenia (P-value Funding agencies: Swedish Cancer SocietySwedish Cancer Society; Swedish Research CouncilSwedish Research Council; ALF grants Region ostergotland; Radiumhemmet; Marcus Borgstroms stiftelse; Spanish Ministry of Economy and Competitiveness [SAF2015-64850-R]; Science for Life

Aim Accurate classification of lung carcinomas is crucial for selecting appropriate and adequate chemotherapy treatment. In this study, glandular (adenocarcinoma), and squamous cell differentiation were examined in non-small cell lung carcinoma (NSCLC) without obvious light-microscopic signs of squamous and glandular differentiation. Materials and methods All lung tumours diagnosed as NSCLC (n=61), without obvious squamous or glandular features, were obtained by bronchial biopsy or core biopsy supported by computed tomography. They were diagnosed during 1996-2009, at the Department of Pathology, Gavle Hospital, Sweden. The tumours were examined immunohistochemically with antibodies against CK5/6, p63 (squamous cell markers) and carcinoembryonic antigen (CEA) (adenocarcinoma cell marker). Double immunostaining (p63/CEA) was also performed on individual tumours. Results The tumours originated from 36 males and 25 females, aged 54-83 years. Pure squamous cell differentiation (CK5/6 positive only) occurred in 34.4% (n=21) tumours and pure adenocarcinoma cell differentiation (CEA positive only) was present in 14.9% (n=9). Tumours with both squamous and adenocarcinoma features (CK5/6 and CEA positive) were most prevalent (47.5%, n=29). Two tumours (3.3%) were negative with both stains (and also synaptophysin negative). Double immunostaining (p63/CEA) revealed that squamous and adenocarcinoma markers were co-localised in cells in certain tumours. Conclusion Co-localisation of squamous and adenocarcinoma markers in the same tumour cell suggests that additional analyses for novel biomarkers of specific lung cancer types may subsequently lead to a refined treatment choice for patients with the goal of improving clinical outcomes.

Tumor-associated macrophages (TAMs) are attractive targets for immunotherapy. Recently, studies in animal models showed that treatment with an anti-TAM antibody directed against the scavenger receptor MARCO resulted in suppression of tumor growth and metastatic dissemination. Here we investigated the expression of MARCO in relation to other macrophage markers and immune pathways in a non-small cell lung cancer (NSCLC) cohort (n = 352). MARCO, CD68, CD163, MSR1 and programmed death ligand-1 (PD-L1) were analyzed by immunohistochemistry and immunofluorescence, and associations to other immune cells and regulatory pathways were studied in a subset of cases (n = 199) with available RNA-seq data. We observed a large variation in macrophage density between cases and a strong correlation between CD68 and CD163, suggesting that the majority of TAMs present in NSCLC exhibit a protumor phenotype. Correlation to clinical data only showed a weak trend toward worse survival for patients with high macrophage infiltration. Interestingly, MARCO was expressed on a distinct subpopulation of TAMs, which tended to aggregate in close proximity to tumor cell nests. On the transcriptomic level, we found a positive association between MARCO gene expression and general immune response pathways including strong links to immunosuppressive TAMs, T-cell infiltration and immune checkpoint molecules. Indeed, a higher macrophage infiltration was seen in tumors expressing PD-L1, and macrophages residing within tumor cell nests co-expressed MARCO and PD-L1. Thus, MARCO is a potential new immune target for anti-TAM treatment in a subset of NSCLC patients, possibly in combination with available immune checkpoint inhibitors.

Objective To examine the incidence and epidemiology of malignant mesothelioma in immigrants from Karain where there is an extraordinarily high incidence of mesothelioma, Cappadocia, Turkey, to Stockholm, Sweden, and their children over 20 years of age born in Stockholm, i.e. two genetically similar populations with and without erionite exposure. Methods This survey was conducted as a retrospective cohort study. Standardized average annual mesothelioma incidence rates (AAMIRs) and mesothelioma standardized incidence ratio (mSIR) were calculated. Cox regression analysis was used to determine the importance of different factors related to mesothelioma risk. Results The cohort consisted of 337 people, 203 of whom were born and/or lived in Karain before immigrating to Sweden (erionite-exposed), and 134 who were born in Stockholm (erionite-unexposed). There were 69 deaths, 42 (61%) due to mesothelioma, and two patients with the disease who were still alive. Of these 44 patients, 22 were men. All mesothelioma patients were in the erionite-exposed group. In the age group 30–49 years, mesothelioma developed in 11 of 38 (29%) with erionite exposure, while there were no cases among 86 persons in the non-exposed group. For men, the AAMIR was 253.9 per 100,000 persons in the whole cohort, and for women, it was 350.9. The mSIR was 71.9 for men and 393.1 for women. Exposure to erionite exceeding 20 years and age over 40 years were associated with increased mesothelioma risk. Conclusion Exposure to erionite is the leading cause of mesothelioma in Karain villagers, and genetic factors are probably of minor importance.

Introduction: We review the current knowledge of CT screening for lung cancer and present an expert-based, joint protocol for the proper implementation of screening in the Nordic countries.Materials and methods: Experts representing all the Nordic countries performed literature review and concensus for a joint protocol for lung cancer screening.Results and discussion: Areas of concern and caution are presented and discussed. We suggest to perform CT screening pilot studies in the Nordic countries in order to gain experience and develop specific and safe protocols for the implementation of such a program.

Margareta Gonzalez Lindh,1,2 Monica Blom Johansson,1 Margareta Jennische,1 Hirsh Koyi2,3 1Department of Neuroscience, Speech and Language Pathology, Uppsala University, Uppsala, Sweden; 2Centre for Research and Development (CFUG), Uppsala University, County Council of Gävleborg, Gävle, Sweden; 3Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden Background: COPD is a common problem associated with morbidity and mortality. COPD may also affect the dynamics and coordination of functions such as swallowing. A misdirected swallow may, in turn, result in the bolus entering the airway. A growing body of evidence suggests that a subgroup of people with COPD is prone to oropharyngeal dysphagia. The aim of this study was to evaluate swallowing dysfunction in patients with stable COPD and to determine the relation between signs and symptoms of swallowing dysfunction and lung function (forced expiratory volume in 1 second percent predicted).Methods: Fifty-one patients with COPD in a stable phase participated in a questionnaire survey, swallowing tests, and spirometry. A post-bronchodilator ratio of the forced expiratory volume in 1second/best of forced vital capacity and vital capacity

BACKGROUND/AIM Globally, an increasing proportion of cancer patients are aged >65 years and many are aged >70 years. Treatment of the elderly with lung cancer has, therefore, become an important issue. We performed a retrospective study of our patients to demonstrate how octogenarians with non-small cell lung cancer (NSCLC) are treated in real-life clinical practice. PATIENTS AND METHODS This was a retrospective observational study of all elderly (≥80 years) patients with NSCLC referred to the Department of Respiratory Medicine and Allergy, Karolinska Hospital, Sweden, 2003-2010, and followed until June, 2016. RESULTS In total, 452 patients, 216 (47.8%) men and 236 (52.2%) women, were included. The mean and median age was 83 years; 28 (6.2%) were aged 90 years or more. Current or former smokers constituted 91.1%, with men having smoked more (p

Background: The effect of inhaled therapy is dependent on the patient´s ability to use the inhaler devices correctly. The aim of this study was to evaluate inhaler technique and critical handling errors of the inhalers used by patients with chronic obstructive pulmonary disease (COPD). Methods: COPD patients (59% female, mean±SD age 69±8 years, FEV1 54±17% predicted) were included in the prospective multicentre TIE-study in Sweden. Patients´ inhaler handling with single-dose dry-powder (sDPI), multi-dose dry-powder (mDPI), soft-mist (SMI) and pressurized metered dose (pMDI) inhalers were examined at the study visit based on a list of predefined critical errors: preparing the inhaler device, positioning the inhaler, preparing/loading the dose and exhalation into the mouthpiece. Results: Out of 689 observed inhalation episodes (190 sDPIs, 435 mDPIs, 52 SMIs and 12 pMDIs) in 372 patients, a total of 234 critical errors were observed. The percentage of patients performing at least one critical error was 48%. The most common error was incorrect positioning of the inhaler, observed in 131 (35%) patients. Other errors were incorrect preparing/loading of the dose in 73 (20%) patients, exhalation into the mouthpiece in 22 (6%) patients and incorrect preparing of the inhaler device (2%). Of the patients with mDPI, 46% demonstrated at least one critical error. The corresponding numbers were 15% for SMI, 13% for sDPI and 8% for pMDI. Conclusions: Almost half of the COPD patients performed at least one critical error. Incorrect positioning of the inhaler device was the most common type of critical error. The highest frequency of critical errors were observed among mDPI users.

Objectives This study aimed to investigate the prevalence of subjective (i.e. self-reported) swallowing symptoms in a large cohort of patients with stable chronic obstructive pulmonary disease (COPD) and to identify potential related risk factors. Methods A total of 571 patients with COPD, investigated in a stable phase, participated in this multicentre study (335 females, 236 males; mean age: 68.6 years (sd 7.7)). Data were derived from spirometry, a questionnaire and a 30-metre walking test. Results In total, 33% (n=186) patients reported at least some degree of swallowing problem. The most frequently reported symptom was food lodging in the throat (23%). A significant relationship was found between swallowing symptoms and dyspnoea, assessed as modified Medical Research Council (mMRC) ≥2 compared with 0.28). Conclusion Subjective swallowing symptoms seem to be a common problem in patients with stable COPD. This problem is seen in all stages of the disease, but is more common in symptomatic patients and in patients with lower physical capacity., Patients with #COPD can experience problems swallowing food and liquid efficiently and safely, according to new research from Margareta Gonzalez Lindh and colleagues at @UU_University http://bit.ly/2Kmxyqx

With an estimated number of 1.8 million new cases every year, lung cancer accounts for about 13% of the global cancer burden [1]. Lung cancer is the leading cause of cancer death among males, where...

Lung cancer (LC) is the leading cause of cancer-related death worldwide, including Sweden. Several studies have shown that socioeconomic status affects the risk, treatment, and survival of LC. Due to immigration after Second World War, foreign-born people constitute 12.5% of the Swedish population. We wanted to investigate if there were any differences in LC management, treatment and survival among the foreign-born Swedes (FBS) compared to the native Swedish population (NatS) in Stockholm.A retrospective analysis of all patients diagnosed with non-small cell lung cancer (NSCLC) at the Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Solna from 1 January 2003 to 31 December 2008 was made. In all, 2041 cases of LC were diagnosed, thereof 1803 with NSCLC. Of these, 211 (11.7%) were FBS.The mean age of NatS and FBS patients was 69.9 years, median 70 (range 26-96) and 66.0 years, median 66 (range 38-94), respectively (p 0.001). In all, 89.8% of NatS and 90.0% of FBS were either smokers or former smokers. Adenocarcinoma was the most common subtype in both groups (NatS 54.7%, FBS 48.3%). In 140 (8.8%) of the NatS and 17 (8.1%) of the FBS the diagnosis was clinical only. There were no significant differences in stage at diagnosis, nor in performance status (PS) or different therapies between the groups. The median overall survival time for the NatS was 272 days and for FBS 328 days, again no significant difference. However, the median overall survival time for female NatS was 318 days and for female FBS 681 days (p = 0.002).FBS patients were significantly younger than NatS at diagnosis, and female FBS lived longer than female NatS, but otherwise there were no significant differences between NatS and FBS patients with LC regarding diagnosis, treatment, and survival.

Purpose: Chemotherapies are associated with significant interindividual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients is basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression. Experimental Design: We exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3 or 4 after first chemotherapy cycle) or were virtually unaffected (grade 0 or 1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: (i) whole-exome nonsynonymous single-nucleotide variants association analysis, (ii) deviation from Hardy–Weinberg equilibrium, (iii) analysis of genes selected by a priori biologic knowledge, (iv) analysis of genes selected from gene expression meta-analysis of toxicity datasets, (v) Ingenuity Pathway Analysis, and (vi) FunCoup network enrichment analysis. Results: A total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (P = 0.0008; OR, 5.2; 95% CI, 1.8–18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (P = 0.0015; OR, 0.36; 95% CI, 0.17–0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia. Conclusions: We have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy. Clin Cancer Res; 22(2); 366–73. ©2015 AACR.

An Online post-column solvent-assisted ionization (OPSAI) method was developed for enhancing the ionization of the beta-blocker propranolol utilizing normal phase LC-MS/MS. Solvent-assisted electrospray ionization (SAESI) was studied by the introduction of the assistant solvents A: 0.5% Formic acid in Isopropanolol, B: 0.5% Formic acid in Isopropanolol-Water (1:1), and C: 0.5% Formic acid in water into the electrospray ionization chamber using a spray needle. Analyte molecules can be directly ionized by the aid of the assistant solvent spray. Both methods were applied to the chiral separation of propranolol enantiomers using normal phase analysis on cellulose-based chiral column. Interestingly, both methods are easy to handle and offer a wide range of assistant solvents that can be used in order to gain the optimum ionization of the analyte molecules. The both methods considerably improved the analyte signal and the peak area greatly increased. The propranolol average signal-to-noise (S/N) ratio was enhanced from 26±1 and 42±1 to 2341±61 and 1725±29 for R-propranolol and S-propranolol, respectively, when the post-column solvent method (OPSAI) was used with isopropanol-assistant solvent (A). While in case of solvent-assisted electrospray ionization method (SAESI) signal was enhanced from 26±1 and 42±1 to 2223±72 and 2155±58 for R-propranolol and S-propranolol, respectively, with water as an assistant solvent. The limit of detection was 10ng/mL and the method was linear in the range 50-2000ng/mL. The NPLC-MS method was applied for the determination of propranolol enantiomers in human plasma after microextraction by packed C18 sorbent.

Non-small cell lung cancer (NSCLC) is a heterogeneous disease with unique combinations of somatic molecular alterations in individual patients, as well as significant differences in populations across the world with regard to mutation spectra and mutation frequencies. Here we aim to describe mutational patterns and linked clinical parameters in a population-based NSCLC cohort.Using targeted resequencing the mutational status of 82 genes was evaluated in a consecutive Swedish surgical NSCLC cohort, consisting of 352 patient samples from either fresh frozen or formalin fixed paraffin embedded (FFPE) tissues. The panel covers all exons of the 82 genes and utilizes reduced target fragment length and two-strand capture making it compatible with degraded FFPE samples.We obtained a uniform sequencing coverage and mutation load across the fresh frozen and FFPE samples by adaption of sequencing depth and bioinformatic pipeline, thereby avoiding a technical bias between these two sample types. At large, the mutation frequencies resembled the frequencies seen in other western populations, except for a high frequency of KRAS hotspot mutations (43%) in adenocarcinoma patients. Worse overall survival was observed for adenocarcinoma patients with a mutation in either TP53, STK11 or SMARCA4. In the adenocarcinoma KRAS-mutated group poor survival appeared to be linked to concomitant TP53 or STK11 mutations, and not to KRAS mutation as a single aberration. Similar results were seen in the analysis of publicly available data from the cBioPortal. In squamous cell carcinoma a worse prognosis could be observed for patients with MLL2 mutations, while CSMD3 mutations were linked to a better prognosis.Here we have evaluated the mutational status of a NSCLC cohort. We could not confirm any survival impact of isolated driver mutations. Instead, concurrent mutations in TP53 and STK11 were shown to confer poor survival in the KRAS-positive adenocarcinoma subgroup.

99 Background: For patients with NSCLC clinical stages I and II disease with no medical contraindications, surgery is treatment of choice showing 5-year survival rates of about 60–80% for stage I and 40–50% for stage II, respectively. However, for patients who are medically or technically unfit for surgery and for patients refusing surgery, SBRT is an alternative with local control rates > 90% at 3 years. Methods: Medical journals in all patients with stage I or II NSCLC who were underwent surgery and treated with SBRT at the Department of oncology or thoracic surgery, Karolinska University Hospital, Sweden from 2003 to 2010 were retrospectively reviewed. Results: In all, 267 (74.8%) underwent surgery and 90 (25.2%) were treated with SBRT. Mean, median and range of age among the surgery group was 69.2, 70.0 and 41-85 years, while in the SBRT group, these figures were 77.6, 79.0 and 52-90 years. The difference in age between the groups was significant (p < 0.001).There were significantly more comorbidites in the SBRT group. Among the surgery group, 90.2% were smokers or former smokers. The figures for SBRT group was 91.1%. The difference in smoking habits between the groups was not significant (p < 0.713). There was a significant difference in performance status (PS) between the groups (p < 0.001) with with PS 0-1 in 99.3% in the surgery group compared with 66.7% in the SBRT group. There was a significant difference in lung function with median FEV1 2.11 liter in surgery group compared to 1.3 in the SBRT group. The figures for median FEV1% was 85.0% respectively 57.0%. The median overall survival was 7.7 years for the surgery group and 3.72 years for the SBRT group (p < 0.001). Five years survival was 65.5% in the surgery group and 31.6% in the SBRT group (p < 0.001). Conclusions: The much worse median overall survival in the SBRT group can be explained by the selection of patients, but still, a median survival for nearly 4 years in an elderly group with so many comorbidities and a poor PS indicates that SBRT has been of value.

Aims Erlotinib is a tyrosine kinase inhibitor used in the treatment of non-small cell lung cancer highly metabolized by the cytochrome P450 (CYP) 3A. Hence, CYP3A4 activity might be a useful predictor of erlotinib pharmacokinetics in personalized medicine. The effect of erlotinib on CYP3A activity was therefore studied in non-small cell lung cancer patients. Methods The study included 32 patients scheduled for erlotinib monotherapy. CYP3A activity was assessed using quinine as a probe before and during erlotinib treatment. Plasma from blood samples drawn 16 hours post quinine administration were analysed using HPLC with fluorescence detection to determine the quinine/3-OH-quinine ratio. Results Matched samples, available from 13 patients, showed an induction of CYP3A activity (P = 0.003, Wilcoxons signed rank test) after 2 months of treatment. The quinine/3-OH-quinine ratio decreased from 20.2 (+/- 13.4) at baseline to 11.0 (+/- 4.34). Single-point samples, available from 19 patients, supported the decrease in ratio (P = 0.007, Mann-Whitney U-test). Generally, females had a higher CYP3A activity both at baseline and after two months of treatment. Statistical analysis by gender also showed significant increase in CYP3A activity (males, n = 10, P = 0.001, and females, n = 22, P = 0.001). Conclusions An induction of CYP3A activity was observed after 2 months of erlotinib treatment which was also seen when subdividing based on gender. It could be important to take this into consideration for patients co-administering other CYP3A-metabolizing drugs during erlotinib treatment and also makes it difficult to use baseline CYP3A activity to predict erlotinib pharmacokinetics. Funding Agencies|Cancerfonden [CAN 2016/602]; Forskningsradet i Sydostra Sverige [760411]; Swedish Research Council; Linkoping University

Hypothesis The inherent challenges associated with tissue biopsies from lung have spurred an interest in the use of liquid biopsies. Pleural effusions are one source of liquid biopsy. Recently, extracellular vesicles of endocytic origin, exosomes, have attracted interest as liquid biopsy of tumors as they are thought to be a mirror of their tumor of origin. Here, we aimed to analyze if RNA profiling of exosomes isolated from pleural effusions could differentiate patients with lung adenocarcinoma from patients with benign inflammatory processes. Methods Exosomes were isolated from 36 pleural effusions from patients with adenocarcinoma (n = 18) and patients with benign inflammatory processes (n = 18). The two groups were balanced with respect to age and smoking history but with a gender bias towards males in the benign group. Profiling was conducted using RT-qPCR arrays covering 754 microRNAs and 624 mRNAs followed by statistical ranking of differentially regulated transcripts between the two patient cohorts. Results RNA profiling revealed differential expression of 17 microRNAs and 71 mRNAs in pleural effusions collected from patients with lung adenocarcinoma compared to pleural effusions from benign lung disease. Overall, top differentially expressed microRNAs, including miR-200 family microRNAs, provided a stronger diagnostic power compared to top differentially expressed mRNAs. However, the mRNA transcript encoding Lipocalin-2 (LCN2) displayed the strongest diagnostic power of all analyzed transcripts (AUC: 0.9916). Conclusions Our study demonstrates that exosomal RNA profiling from pleural effusions can be used to identify patients with lung adenocarcinoma from individuals with benign processes and further proposes miR-200 microRNAs and LCN2 as diagnostic markers in lung cancer liquid biopsies.

Introduction Atrial fibrillation (AF) causes ischaemic stroke and based on risk factor evaluation warrants anticoagulation therapy. In stroke survivors, AF is typically detected with short-term ECG monitoring in the stroke unit. Prolonged continuous ECG monitoring requires substantial resources while insertable cardiac monitors are invasive and costly. Chest and thumb ECG could provide an alternative for AF detection poststroke. The primary objective of our study is to assess the incidence of newly diagnosed AF during 28 days of chest and thumb ECG monitoring in cryptogenic stroke. Secondary objectives are to assess health-related quality of life (HRQoL) using short-form health survey (SF-36) and the feasibility of the Coala Heart Monitor in patients who had a stroke. Methods Stroke survivors in Region Gavleborg, Sweden, will be eligible for the study from October 2017. Patients with a history of ischaemic stroke without documented AF before or during ECG evaluation in the stroke unit will be evaluated by the chest and thumb ECG system Coala Heart Monitor. The monitoring system is connected to a smartphone application which allows for remote monitoring and prompt advice on clinical management. Over a period of 28 days, patients will be monitored two times a day and may activate the ECG recording at symptoms. On completion, the system is returned by mail. This system offers a possibility to evaluate the presence of AF poststroke, but the feasibility of this system in patients who recently suffered from a stroke is unknown. In addition, HRQoL using SF-36 in comparison to Swedish population norms will be assessed. The feasibility of the Coala Heart Monitor will be assessed by a self-developed questionnaire. Ethics and dissemination The study was approved by The Regional Ethical Committee in Uppsala (2017/321). The database will be closed after the last follow-up, followed by statistical analyses, interpretation of results and dissemination to a scientific journal. Trial registration number NCT03301662; Pre-results.

Background: Smoking is by far the most important cause of lung cancer. However, lung cancer among never-smokers is common and increasing [1]. A smoking-independent subgroup of lung adenocarcinoma w ...

Background: The aim of this study was to evaluate implantable loop recorders (ILRs) in an unselected cohort in order to determine diagnostic yield, time to pacemaker/implantable cardioverter-defibrillator (ICD) implantation, predictors thereof, safety issues, and syncope management including usage of preceding diagnostic tools. Methods: Patients who underwent ILR evaluation in any of three centers in Region Gavleborg, Swe­den, between April 2007 and April 2013 were included and their medical records retrieved. Logistic regression was used to evaluate predictors of pacemaker/ICD outcome expressed as odds ratios (ORs) and Kaplan-Meier estimates for time-dependent analysis. Results: A total of 173 patients (52.6% females) with a mean age of 56.2 years received an ILR dur­ing a mean follow-up of 605 days. In the 146 patients evaluated for syncope/presyncope, 28.1% received a pacemaker (n = 39) or ICD (n = 2). The cumulative incidence at 6, 12, and 18 months were 8.8%, 21.3%, and 26.7%, respectively. Age > 75 years was the only significant predictor for outcome (p = 0.010) and the following variables showed a tendency toward significance: abnormal elevation of the biomarker B-type natriuretic peptide (OR 2.05, p = 0.100), a history of trauma (OR 1.71, p = 0.179), and patho­logic electrocardiogram (OR 1.68, p = 0.231). A computerized tomography of the skull was performed in 52.1% of the syncope cases. Conclusions: In syncope evaluation in an unselected cohort, 28.1% were diagnosed with an arrhyth­mia necessitating a pacemaker/ICD. The only significant predictor was advanced age. Time to diag­nosis is unpredictable and prolonged ILR monitoring is warranted in addition to optimal use of other diagnostic tools.

Background: Core biopsies are valuable in obtaining sufficient tissue to ensure diagnosis of diseases in the thorax. Objective: To evaluate the complication rate and the diagnostic yield in computer tomography (CT)-guided core biopsies performed in a county hospital in Sweden. Methods: Medical journals, spirometry results, pathology reports and CT scans were reviewed in 463 consecutive cases, where a transthoracic core biopsy was performed between January 2005 and December 2010. Of these 380 (82%) were lung lesions, 48 (10%) were mediastinal lesions and 35 (8%) were pleural lesions. Results: All patients underwent a chest X-ray 4 hours post-biopsy and pneumothorax was seen in 156/463 (34%) patients: 137 after lung biopsy and 17 after mediastinal biopsy. Chest tube insertion was required for 27 (17%) of these patients (6% of all core biopsies). Small intraparenchymal hemorrhages and hemoptysis were observed with subjective difficulty in one case. The diagnostic yield for the 463 patients was 212 (46%) cases of lung cancer, 188 (41%) benign lesions and 39 (8%) pulmonary metastases. Conclusions: A transthoracic core biopsy ensures diagnosis with a low complication rate and is suitable as an outpatient procedure. An increased risk for pneumothorax was observed when the biopsied lesion was small or when emphysema was in the path of the biopsy needle. Reduced lung function pre-biopsy or emphysema in the path of the biopsy needle increased the need for chest tube treatment of pneumothorax. A CT-guided core biopsy is safe and applicable in a county hospital.

Numerous protein biomarkers have been analyzed to improve prognostication in non-small cell lung cancer, but have not yet demonstrated sufficient value to be introduced into clinical practice. Here, we aimed to develop and validate a prognostic model for surgically resected non-small cell lung cancer. A biomarker panel was selected based on (1) prognostic association in published literature, (2) prognostic association in gene expression data sets, (3) availability of reliable antibodies, and (4) representation of diverse biological processes. The five selected proteins (MKI67, EZH2, SLC2A1, CADM1, and NKX2-1 alias TTF1) were analyzed by immunohistochemistry on tissue microarrays including tissue from 326 non-small cell lung cancer patients. One score was obtained for each tumor and each protein. The scores were combined, with or without the inclusion of clinical parameters, and the best prognostic model was defined according to the corresponding concordance index (C-index). The best-performing model was subsequently validated in an independent cohort consisting of tissue from 345 non-small cell lung cancer patients. The model based only on protein expression did not perform better compared to clinicopathological parameters, whereas combining protein expression with clinicopathological data resulted in a slightly better prognostic performance (C-index: all non-small cell lung cancer 0.63 vs 0.64; adenocarcinoma: 0.66 vs 0.70, squamous cell carcinoma: 0.57 vs 0.56). However, this modest effect did not translate into a significantly improved accuracy of survival prediction. The combination of a prognostic biomarker panel with clinicopathological parameters did not improve survival prediction in non-small cell lung cancer, questioning the potential of immunohistochemistry-based assessment of protein biomarkers for prognostication in clinical practice.

Background: For effective drug delivery it is essential to ensure that patients can use their inhaler devices. Patients9 inhaler technique should be monitored at each visit according to guidelines.The TIE-study is a prospective multi-centre study in primary and secondary care in Sweden to identify predictors of exacerbations in chronic obstructive pulmonary disease (COPD). Aim: To evaluate inhaler technique in COPD patients and to find out how many have received information about correct technique or had their inhaler technique checked. Methods: Patients from two study centres were observed for their inhaler technique. A correct and an incorrect inhaler technique were defined as having no errors respective ≥1 error in any of the four critical steps. Specific questions were asked whether they had received information about correct inhaler technique and whether the technique had been checked during the past year. Results: A total of 253 patients (56% female, median age 70 years, FEV 1 53±18% of predicted) were investigated. Incorrect inhaler technique for at least one of the patient´s inhaler devices was displayed by 126 patients (50%). The most common errors were holding the inhaler in incorrect position (71%) and inability to load the device (34%). The number of patients who reported that they had received information about correct technique for all their devices and who had their technique checked during the last year was 70 (28%) and 64 (25%), respectively. Conclusions: Half of the patients had a poor inhaler technique. Surprisingly few patients reported that they had received information about correct inhaler technique or had their inhaler technique checked by a health caregiver during the last year.

Background: Increased blood eosinophils (B-Eos) are common in asthma and correlate with asthma attacks. The role of blood eosinophilia in COPD and its relation to acute exacerbations of COPD (AECOPD) have been less studied. Method: Subjects from the TIE-study with spirometry-verified COPD and CRP levels Results: A total of 301 COPD patients (56% females) with a mean ± SD age of 69 ± 8 years and FEV 1 of 55.6 ± 18.3% predicted were recruited. Thirty percent experienced an AECOPD during the preceding year, and these subjects had higher B-Neu (geometric mean (95% CI)) and lower B-Eos than subjects without AECOPD: 4954 (4623-5309) cells/mm 3 vs 4444 (4258-4637), p = 0.007 and 151 (128-178) vs 180 (165-197), p = 0.046. Higher B-Neu related to poorer FEV 1 (% predicted): rho = -0.20, p 1 : rho = 0.12, p = 0.03. Higher B-Neu independently related (p = 0.02) to a history of AECOPD, after adjustments for gender, age and FEV 1 . Conclusions: Increased neutrophils and decreased eosinophils in blood related to poorer FEV 1 and a history of COPD exacerbations. The prospective value of these markers remains to be studied.

Background Identification of targetable EML4-ALK fusion proteins has revolutionized the treatment of a minor subgroup of non-small cell lung cancer (NSCLC) patients. Although fluorescence in situ hybridization (FISH) is regarded as the gold standard for detection of ALK rearrangements, ALK immunohistochemistry (IHC) is often used as screening tool in clinical practice. In order to unbiasedly analyze the diagnostic impact of such a screening strategy, we compared ALK IHC with ALK FISH in three large representative Swedish NSCLC cohorts incorporating clinical parameters and gene expression data. Methods ALK rearrangements were detected using FISH on tissue microarrays (TMAs), including tissue from 851 NSCLC patients. In parallel, ALK protein expression was detected using IHC, applying the antibody clone D5F3 with two different protocols (the FDA approved Ventana CDx assay and our in house Dako IHC protocol). Gene expression microarray data (Affymetrix) was available for 194 patients. Results ALK rearrangements were detected in 1.7 % in the complete cohort and 2.0 % in the non-squamous cell carcinoma subgroup. ALK protein expression was observed in 1.8 and 1.4 % when applying the Ventana assay or the in house Dako protocol, respectively. The specificity and accuracy of IHC was high (> 98 %), while the sensitivity was between 69 % (Ventana) and 62 % (in house Dako protocol). Furthermore, only 67 % of the ALK IHC positive cases were positive with both IHC assays. Gene expression analysis revealed that 6/194 (3 %) tumors showed high ALK gene expression (≥ 6 AU) and of them only three were positive by either FISH or IHC. Conclusion The overall frequency of ALK rearrangements based on FISH was lower than previously reported. The sensitivity of both IHC assays was low, and the concordance between the FISH and the IHC assays poor, questioning current strategies to screen with IHC prior to FISH or completely replace FISH by IHC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2646-x) contains supplementary material, which is available to authorized users.

Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small-cell lung cancer (NSCLC), we compared RNAseq data from 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the Caner Testis Database (CTdatabase), 96 were confirmed in NSCLC. To obtain an unbiased CTA profile of NSCLC, we applied stringent criteria on our RNAseq data set and defined 90 genes as CTAs, of which 55 genes were not annotated in the CTdatabase, thus representing potential new CTAs. Cluster analysis revealed that CTA expression is histology dependent and concurrent expression is common. IHC confirmed tissue-specific protein expression of selected new CTAs (TKTL1, TGIF2LX, VCX, and CXORF67). Furthermore, methylation was identified as a regulatory mechanism of CTA expression based on independent data from The Cancer Genome Atlas. The proposed prognostic impact of CTAs in lung cancer was not confirmed, neither in our RNAseq cohort nor in an independent meta-analysis of 1,117 NSCLC cases. In summary, we defined a set of 90 reliable CTAs, including information on protein expression, methylation, and survival association. The detailed RNAseq catalog can guide biomarker studies and efforts to identify targets for immunotherapeutic strategies.