Current State-of-the-Art Therapy for Malignant Pleural Mesothelioma and Future Options Centered on Immunotherapy

Malignant pleural mesothelioma (MPM) is a locally aggressive disease related to asbestos exposure with a median survival for untreated patients of 4-8 months. The combination of chemotherapy based on platinum and antifolate is the standard treatment, and the addition of bevacizumab adds two months to median survival. Recently, in first-line treatment, immunotherapy combining nivolumab with ipilimumab has been shown to be superior to chemotherapy in the CheckMate-743 study in terms of overall survival (18.1 months), leading to its approval by the FDA and EMA. The positive results of this study represent a new standard of treatment for patients with MPM; however, not all patients will benefit from immunotherapy treatment. In an effort to improve the selection of patient candidates for immunotherapy for different tumors, biomarkers that have been associated with a greater possibility of response to treatment have been described. MPM is a type of tumor with low mutational load and neo-antigens, making it a relatively non-immunogenic tumor for T cells and possibly less susceptible to responding to immunotherapy. Different retrospective studies have shown that PD-L1 expression occurs in 20-40% of patients and is associated with a poor prognosis; however, the predictive value of PD-L1 in response to immunotherapy has not been confirmed. The purpose of this work is to review the state of the art of MPM treatment in the year 2023, focusing on the efficacy results of first-line or subsequent immunotherapy studies on patients with MPM and possible chemo-immunotherapy combination strategies. Additionally, potential biomarkers of response to immunotherapy will be reviewed, such as histology, PD-L1, lymphocyte populations, and TMB.

Expression of TILs and Patterns of Gene Expression from Paired Samples of Malignant Pleural Mesothelioma (MPM) Patients

MPM is an aggressive disease with an immunosuppressive tumor microenvironment, and interest in exploring immunotherapy in this disease has been increasing. In the first line of treatment, the combination of nivolumab and ipilimumab demonstrated an improvement in survival over chemotherapy. The presence of TILs has been recognized as a marker of antitumor immune response to chemotherapy in solid tumors. The aim of our study is to identify the effect of treatment on immune cells and the immune gene profile in MPM. We investigated the changes in expression of TILs in 10 human MPM paired tumor tissues using immunohistochemistry and gene expression analysis from paired untreated and treated samples. In this small series, we demonstrated that during the evolution of disease without any treatment there was an increase in the inflammatory component in tumor samples. After systemic treatment there was a decrease in the number of TILs. We observed that after systemic treatment or disease progression immune gene signatures were suppressed. Our integrated analysis of paired samples with immune profile and genomic changes on MPM suggested that during the evolution of the disease the immune system tends to switch, turning off with treatment.

Dynamic changes in circulating tumor DNA assessed by shallow whole-genome sequencing associate with clinical efficacy of checkpoint inhibitors in NSCLC

Immune checkpoint inhibitors (ICIs) targeting the PD-1/PD-L1 axis are the main therapeutic option for patients with advanced non-small cell lung cancer (NSCLC) without a druggable oncogenic alteration. Nevertheless, only a portion of patients benefit from this type of treatment. Here, we assessed the value of shallow whole-genome sequencing (sWGS) on plasma samples to monitor ICI benefit. We applied sWGS on cell-free DNA (cfDNA) extracted from plasma samples of 45 patients with metastatic NSCLC treated with ICIs. Over 150 samples were obtained before ICI treatment initiation and at several time points throughout treatment. From sWGS data, we computed the tumor fraction (TFx) and somatic copy number alteration (SCNA) burden and associated them with ICI benefit and clinical features. TFx at baseline correlated with metastatic lesions at the bone and the liver, and high TFx (≥ 10%) associated with ICI benefit. Moreover, its assessment in on-treatment samples was able to better predict clinical efficacy, regardless of the TFx levels at baseline. Finally, for a subset of patients for whom SCNA burden could be computed, increased burden correlated with diminished benefit following ICI treatment. Thus, our data indicate that the analysis of cfDNA by sWGS enables the monitoring of two potential biomarkers-TFx and SCNA burden-of ICI benefit in a cost-effective manner, facilitating multiple serial-sample analyses. Larger cohorts will be needed to establish its clinical potential.

Connection between Weather Types and Air Pollution Levels: A 19-Year Study in Nine EMEP Stations in Spain

This study focuses on the analysis of the distribution, both spatial and temporal, of the PM10 (particulate matter with a diameter of 10 µm or less) concentrations recorded in nine EMEP (European Monitoring and Evaluation Programme) background stations distributed throughout mainland Spain between 2001 and 2019. A study of hierarchical clusters was used to classify the stations into three main groups with similarities in yearly concentrations: GC (coastal location), GNC (north-central location), and GSE (southeastern location). The highest PM10 concentrations were registered in summer. Annual evolution showed statistically significant decreasing trends in PM10 concentration in all the stations covering a range from -0.21 to -0.50 µg m-3/year for Barcarrota and Víznar, respectively. Through the Lamb classification, the weather types were defined during the study period, and those associated with high levels of pollution were identified. Finally, the values exceeding the limits established by the legislation were analyzed for every station assessed in the study.

T-cell infiltration in matched samples from malignant pleural mesothelioma (MPM) during evolution of disease

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Background: MPM is an aggressive cancer associated with asbestos exposure. Chemotherapy has been a mainstay of therapy and recently immunotherapy has been associated with survival improvements. Chemotherapy and immunotherapy influence the tumor microenvironment and some reports have shown increased of TIL after chemotherapy in MPM. The purpose of this study was to determine dynamic changes in the tumor immune environment during mesothelioma evolution and after systemic therapies in paired samples. Methods: We examined 20 matched formalin-fixed paraffin embedded tissue samples from 10 patients (p) with MPM taken at diagnosis and at disease progression (follow-up), including untreated and treated with chemotherapy or immunotherapy. Tissue densities (number of cells/mm2) of key immune effector cells such as total lymphocytes (CD3), cytotoxic T cells (CD8), regulatory T cells (FOXP3) and monocytes/macrophages (CD163) were quantified by image analysis using multiplexed immunohistochemistry (IHC). PD-L1 expression in both tumor cells and immune cells was analysed by singleplex IHC and quantified using the CPS score. Results: Median age was 62 years (range 53-84), 7 p were male and all p presented epithelioid histology. Three matched samples belong to patients that did not receive any systemic treatment between biopsies and the other 7 pair of samples belong to patients treated with chemotherapy +/- immunotherapy. The median interval between paired biopsies was 12 m (3-33 m). Median overall survival was 27.8 months (1 m-NR). Median densities of T cells and macrophages in diagnostic and matched follow-up samples were: CD3+:982 vs 712; CD8+:422 vs 334, FOXP3+: 22 vs 25 and CD163+: 2086 vs 1706. Median PD-L1 CPS was 2.5 and 4 in diagnostic and follow-up samples, respectively. In p receiving treatment between sample pairs, the median densities in diagnostic and follow-up matched samples were: CD3+:979 vs 407; CD8+:467 vs 225, FOXP3+: 25 vs 15, CD163+: 1583 vs 1508, and PD-L1: 2 and 1. In p without any systemic treatment between sample pairs, the median densities were CD3+:1645 vs 2397; CD8+:376 vs 1605, FOXP3+: 19 vs 121, CD163+: 2102 vs 2377, and PD-L1: 3 vs 25. Conclusions: In our small series with paired samples from MPM p, we observed immune cells infiltration changes during MPM evolution with a trend towards a decrease after systemic therapy. Further investigation in tumor microenvironment in MPM to define the most appropriate time for immunotherapy is needed.

Overview of Checkpoint Inhibitors Mechanism of Action: Role of Immune-Related Adverse Events and Their Treatment on Progression of Underlying Cancer

In recent years, immunotherapy-based regimens have been included into the treatment's algorithm of several cancer types. Programmed death-1 (PD-1) and cytotoxic T lymphocyte antigen-4 (CTLA-4) interact with their ligands found on the surface of antigen presenting cells (APC) or tumor cells (PD-L1/2 and CD80/86). Through these interactions, stimulatory or inhibitory signals are established. Immune checkpoint inhibitors (ICIs), block these interactions, and when administered not only as monotherapy but also as part of combination regimens, have shown to improve survival results in multiple advanced cancers leading to an increasing number of patients treated with ICI and, as a consequence, a rise in the number of patients developing immune-related adverse events (irAEs). Presence of irAEs has been associated with greater benefit from treatment, especially when blocking PD-L1. Recent data suggests that treatment benefit persists after discontinuation of ICIs due to a treatment related adverse event, regardless of the grade. Patients experiencing grade 3-4 irAEs are at risk of toxicity recurrence after reintroducing immunotherapy and therefore, the decision to resume the treatment is challenging. In these cases, a multidisciplinary approach is always needed and several factors should be considered. Management of severe toxicities may require systemic corticosteroids which can impact on T-cell function. Due to their immunosuppressive properties, it is necessary to deeper determine how corticosteroids influence responses. In terms of overall survival (OS), the use of steroids as therapy for irAEs seems not to reduce OS and several studies have reported durable responses in patients experiencing autoimmune toxicities treated with corticosteroids.

Trend analysis and outlier distribution of CO2 and CH4: A case study at a rural site in northern Spain

CO₂ and CH₄ outliers may have a noticeable impact on the trend of both gases. Nine years of measurements since 2010 recorded at a rural site in northern Spain were used to investigate these outliers. Their influence on the trend was presented and two limits were established. No more than 23.5% of outliers should be excluded from the measurement series in order to obtain representative trends, which were 2.349 ± 0.012 ppm year^-1 for CO₂ and 0.00879 ± 0.00004 ppm year^-1 for CH₄. Two types of outliers were distinguished. Those above the trend line and the rest below the trend line. Outliers were described by skewed distributions where the Weibull distribution figures prominently in most cases. A qualitative procedure was presented to exclude the worst fits, although five statistics were considered to select the best fit. In this case, the modified Nash-Sutcliffe efficiency is prominent. Finally, three symmetrical distributions were added to fit the observations when outliers are excluded, with the Gaussian and beta distributions providing the best fits. As a result, certain skewed functions, such as the lognormal distribution, whose use is frequent for air pollutants, could be questioned in certain applications.

High levels of chromosomal aberrations negatively associate with benefit to checkpoint inhibition in NSCLC

BACKGROUND

Immune checkpoint inhibitors (ICIs) targeting the programmed cell death 1/programmed death-ligand 1 axis have transformed the management of advanced non-small cell lung cancer (NSCLC). However, many patients do not benefit from this type of treatment, and thus several molecular biomarkers of benefit have been explored. The value of somatic copy number alterations (SCNAs) burden remains elusive.

PATIENTS AND METHODS

We assembled a cohort of 109 patients with NSCLC treated with ICIs and available tumor samples. We performed shallow whole-genome sequencing on 89 patients to determine genome-wide SCNAs and targeted gene expression analysis on 63 patients to study immune infiltration. We analyzed SCNAs burden in different ways (ie, the fraction of the genome altered or number of events) and studied their association with ICIs benefit based on survival analysis. We correlated SCNAs burden and immune infiltration on 35 patients of our cohort and on patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA).

RESULTS

High SCNAs burden, computed in diverse ways, is negatively associated with ICIs progression-free survival (PFS), with the fraction of the genome altered (FGA) by arm and chromosome events showing the strongest association with PFS (p=0.002) (n=77). Nevertheless, we found differences in SCNAs across some clinicopathological features (sample site origin). A multivariate analysis adjusted for relevant characteristics showed that the FGA of arm and chromosome alterations was strongly associated with PFS (HR=2.21, p=3.3 x 10^-5). Finally, we confirmed that SCNAs burden negatively correlates with tumor immune infiltration (n=35), although this correlation was not found for the males studied. Similar results were observed in the TCGA cohort.

CONCLUSIONS

SCNAs burden is a potential biomarker of benefit to ICIs in patients with NSCLC, although there appear to be some nuances worth consideration. Further studies will be needed to establish its role as a biomarker of benefit to ICIs.

Hepatic Rupture as the Initial Presentation of an EGFR-Mutated Lung Adenocarcinoma: A Case Report

Hepatic rupture is a rare complication of solid tumor malignancies, notably in lung adenocarcinomas, and carries an extremely poor overall prognosis. Epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma predict benefit with tyrosine kinase inhibitors (TKIs). This case report describes a female patient who presented with a metastatic hepatic rupture and was subsequently diagnosed with EGFR-mutated lung adenocarcinoma. The tumor had an impressive response to TKI inhibitor treatment, reversing her extremely poor, short-term prognosis. We believe this unique case sheds light on the treatment management of hepatic ruptures and supports the high response rate seen with TKIs in EGFR-mutated lung cancers, regardless of the patient’s performance status.

Efficacy of chemotherapy for malignant pleural mesothelioma according to histology in a real-world cohort

CheckMate 743 trial demonstrated survival benefit of immunotherapy in first line in MPM with some differences in the efficacy of chemotherapy according to histology. The objective of this study is to characterize the impact of chemotherapy according to histology in patients diagnosed with MPM at our institution. Clinical records of all MPM patients diagnosed at Vall d'Hebron University Hospital between November 2002 and April 2020 were reviewed. Associations between clinical variables and outcomes were assessed with Cox regression models. Survival data were calculated by the Kaplan-Meier method. 189 patients were included with 76% of tumors classified as epithelioid subtype. First line chemotherapy was offered to 85% of patients. Median survival in overall population was 21.3 months (95% CI 17.2-24.3). We found that patients with epithelioid tumors had better overall survival (OS) and progression free survival (PFS). Median OS of epithelioid patients treated with first line chemotherapy was 26.7 months versus 15.0 months in non-epithelioid patients (HR 2.25 CI 95% 1.4-3.4; p < 0.001). Median PFS for patients with epithelioid tumors treated with chemotherapy was 4.8 months versus 3.6 months in non-epithelioid (HR 1.5 CI 95% 1.0-2.3; p = 0.03). The improvement of outcomes in patients with epithelioid histology was detected in patients treated with cisplatin or carboplatin. Histology was not a predictive factor for the platinum agent sensitivity (p of interaction PFS = 0.09, p of interaction OS = 0.65). In our series, patients with non-epithelioid tumors presented worse prognosis. Although epithelioid tumors exposed to cisplatin had higher PFS, histology was not a clear predictor of chemotherapy efficacy.

Genetic evolution to tyrosine kinase inhibitory therapy in patients with EGFR-mutated non-small-cell lung cancer

BACKGROUND

Tumour heterogeneity impacts the efficacy of metastatic cancer treatment even if actionable mutations are identified. Clinicians need to understand if assessing one lesion provides reliable information to drive a therapeutic decision in non-small-cell lung cancer (NSCLC) patients.

METHODS

We analysed inter-tumour heterogeneity from five autopsied individuals with NSCLC-harbouring mutations in the epidermal growth factor receptor (EGFR), treated with EGFR tyrosine kinase inhibitors (TKIs). Through a comprehensive next-generation sequencing (NGS) oncopanel, and an EGFR panel for digital droplet PCR (ddPCR), we compared metastases within individuals, longitudinal biopsies from the same lesions and, whenever possible, the primary naive tumour.

RESULTS

Analysis of 22 necropsies from five patients revealed homogeneity in pathogenic mutations and TKI-resistance mechanisms within each patient in four of them. In-depth analysis by whole-exome sequencing from patient 1 confirmed homogeneity in clonal mutations, but heterogeneity in passenger subclonal alterations. Different resistance mechanisms were detected depending on the patient and line of treatment. Three patients treated with a c-MET inhibitor in combination with TKI lost MET amplification upon progression.

CONCLUSION

At a given point and under selective TKI pressure, a single metastasis biopsy in disseminated tumours from EGFR-mutated NSCLC patients could provide a reasonable assessment of actionable alterations useful for therapeutic decisions.

Direct introgression of untapped diversity into elite wheat lines

The effective utilization of natural variation has become essential in addressing the challenges that climate change and population growth pose to global food security. Currently adopted protracted approaches to introgress exotic alleles into elite cultivars need substantial transformation. Here, through a strategic three-way crossing scheme among diverse exotics and the best historical elites (exotic/elite1//elite2), 2,867 pre-breeding lines were developed, genotyped and screened for multiple agronomic traits in four mega-environments. A meta-genome-wide association study, selective sweeps and haplotype-block-based analyses unveiled selection footprints in the genomes of pre-breeding lines as well as exotic-specific associations with agronomic traits. A simulation with a neutrality assumption demonstrated that many pre-breeding lines had significant exotic contributions despite substantial selection bias towards elite genomes. National breeding programmes worldwide have adopted 95 lines for germplasm enhancement, and 7 additional lines are being advanced in varietal release trials. This study presents a great leap forwards in the mobilization of GenBank variation to the breeding pipelines.

Interrelations between Patients' Clinicopathological Characteristics and Their Association with Response to Immunotherapy in a Real-World Cohort of NSCLC Patients

Immune checkpoint inhibitors (ICIs) have transformed non-small cell lung cancer (NSCLC) treatment. Unfortunately, only some patients benefit from these therapies. Thus, certain clinicopathological characteristics of the patients have been proposed as biomarkers of ICIs response. We assembled a retrospective cohort of 262 NSCLC patients treated with ICIs, compiled relevant clinicopathological characteristics, and studied their associations with treatment outcome using Cox proportional-hazards survival models. Additionally, we investigated the interrelations between clinicopathological features and devised a method to create a compendium associated with ICIs response by selecting those that provide non-redundant information. In multivariate analyses, ECOG performance status (hazard ratio (HR) 1.37 (95% CI 1.11 to 1.68), p < 0.005), LDH (HR 1.24 (95% CI 1.03 to 1.48), p = 0.02)) and PD-L1 negativity were associated with decreased PFS (HR 1.92 (95% CI 1.03 to 3.58), p < 0.04), whereas presentation of immune-related adverse events (irAEs) (HR 0.35 (95% CI 0.22 to 0.55, p < 0.005) or females (HR 0.52 (95% CI 0.33 to 0.80, p < 0.005) had longer progression-free survival. Additionally, numerous clinicopathological indicators were found to be interrelated. Thus, we searched for features that provide non-redundant information, and found the combination of LDH levels, irAEs, and gender to have a better association with ICIs treatment response (cross-validated c-index = 0.66). We concluded that several clinicopathological features showed prognostic value in our real-world cohort. However, some are interrelated, and compendiums of features should therefore consider these interactions. Joint assessment of LDH, irAEs, and gender may be a good prognostic compendium.

Spatial analysis and evolution of four air pollutants in England and Wales

Pollution control is based on an exhaustive knowledge of concentration distributions. This study analyses a detailed database of NO₂, O₃, PM₁₀ and PM_2.5 in England and Wales over the period 2007-2011. Daily and annual means were considered in a 1-km spatial resolution. Histograms revealed a shape like a sawtooth. The interval was wide for NO₂ and O₃, although with a gap, whilst the particulate matter range was narrow. Spring provided the peak for the O₃ annual cycle, whereas minima for the other pollutants were reached in summer. A trend for the annual medians of particulate matter was observed, with a minimum in the period analysed. However, the pattern was uniform for NO₂ and O₃. Cities appeared as NO₂ hot spots and O₃ cold spots. Wales stood out as an NO₂ clean country, although with high O₃ levels. Sources or sinks of particulate matter were not observed, suggesting that more detailed analysis is required. Two NO₂ pollution axes were sometimes seen, one in the south from London to Bristol, and the second in the north, from Liverpool to Kingston Upon Hull. No annual spatial pattern was seen for the remaining pollutants beyond the contrast between cities and country sites for O₃. Consequently, spatial analysis allows the real impact of pollutant sources be known, although it must be performed with a detailed temporal resolution in order to investigate the extension, quantity, and length of the concentrations calculated.

Analysis of chemotherapy efficacy according to histology in malignant pleural mesothelioma (MPM) patients (p)

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Background: MPM is a highly aggressive pleural tumor associated with asbestos exposure and with limited survival despite systemic therapy. Histology is a prognostic factor and recently CheckMate 743 trial demonstrated survival benefit of immunotherapy in first line with some differences in the efficacy of chemotherapy according to histology. However, randomized trials who led to the approval of antifolate in mesothelioma did not include analysis of outcomes by histology. The objective of this study is to characterize the impact of chemotherapy according to histology in p with MPM at our institution. Methods: We review 189 MPM p diagnosed at Vall d´Hebron University Hospital between November 2002 and April 2020. Associations between clinical variables and outcome were assessed with Cox regression models and survival data were calculated by the Kaplan-Meier method. Results: Patient’s characteristics: median age 68 years (y) (45-88 y), males: 70%, performance status (PS)1: 69%, asbestos exposure: 75%, epithelioid subtype: 76%. First line chemotherapy was offered to 85% of p (66% cisplatin-pemetrexed and 27% carboplatin-pemetrexed). Median overall survival (OS) in overall population was 21.3 m (95%CI17.2-24.3). Epithelioid histology, PS 0, neutrophil-lymphocyte ratio <5 and treatment with cisplatin vs carboplatin were associated with significant improvements in OS (p<0.001). When we analyzed the survival of patients who received first line chemotherapy according to histology, we found that patients with epithelioid tumors had better PFS and OS. Median PFS for p with epithelioid tumors treated with chemotherapy in first line was 4.8 m versus 3.6 months non-epithelioid (HR1.5 CI95% 1.1-2.3; p=0.03). OS of epithelioid p treated with first line chemotherapy was 26.7 m versus 15.0 m non-epithelioid patients (HR2.25 CI95% 1.4-3.4; p<0.001). We analyzed if the differences in survival according to histology were due to type of systemic treatment received (Table). Conclusions: In our series, p with non-epithelioid tumors presented worse prognosis. We confirmed histology is a prognostic factor with better OS for p with epithelioid tumors. Moreover, we demonstrated better efficacy of chemotherapy in epithelioid tumors, although histology is not a predictive factor for the platinum agent sensitivity (p of interaction PFS=0.09, p of interaction OS= 0.65).[Table: see text]

Molecular profiling of long-term responders to immune checkpoint inhibitors in advanced non-small cell lung cancer

Immunotherapy has transformed advanced non-small cell lung cancer (NSCLC) treatment strategies and has led to unprecedented long-lasting responses in some patients. However, the molecular determinants driving these long-term responses remain elusive. To address this issue, we performed an integrative analysis of genomic and transcriptomic features of long-term immune checkpoint inhibitors (ICIs)-associated responders. We assembled a cohort of 47 patients with NSCLC receiving ICIs that was enriched in long-term responders [>18 months of progression-free survival (PFS)]. We performed whole-exome sequencing from tumor samples, estimated the tumor mutational burden (TMB), and inferred the somatic copy number alterations (SCNAs). We also obtained gene transcription data for a subset of patients using Nanostring, which we used to assess the tumor immune infiltration status and PD-L1 expression. Our results indicate that there is an association between TMB and benefit to ICIs, which is driven by those patients with long-term response. Additionally, high SCNAs burden is associated with poor response and negatively correlates with the presence of several immune cell types (B cells, natural killers, regulatory T cells or effector CD8 T cells). Also, CD274 (PD-L1) expression is increased in patients with benefit, mainly in those with long-term response. In our cohort, combined assessment of TMB and SCNAs burden enabled identification of long-term responders (considering PFS and overall survival). Notably, the association between TMB, SCNAs burden, and PD-L1 expression with the outcomes of ICIs treatment was validated in two public datasets of ICI-treated patients with NSCLC. Thus, our data indicate that TMB is associated with long-term benefit following ICIs treatment in NSCLC and that TMB, SCNAs burden, and PD-L1 are complementary determinants of response to ICIs.

Analysis of mismatch repair (MMR) proteins expression in a series of malignant pleural mesothelioma (MPM) patients

BACKGROUND

Promising results have been reported with immune checkpoint inhibitors (ICI) in a small proportion of MPM patients. MMR deficiency (dMMR) has been well described in several malignancies and was approved as a biomarker for anti-PD-1 inhibitors. Next generation sequencing (NGS) data demonstrated that 2% of MPM harbor microsatellite instability. The aim of this study is to characterize MMR by immunohistochemistry (IHC) in a series of MPM including a subset of patients treated with immunotherapy.

METHODS

Tumors of 159 MPM p diagnosed between 2002 and 2017 were reviewed. Formalin-fixed, paraffin-embedded tissue was stained for MLH1, MSH2, MSH6 and PMS2 and tumors were classified as dMMR (MMR protein expression negative) and MMR intact (all MMR proteins positively expressed). We retrospectively collected clinical outcomes under standard chemotherapy and experimental immunotherapy in the entire cohort.

RESULTS

MMR protein expression was analyzed in 158 samples with enough tissue and was positive in all of the cases. Twenty two patients received ICI with anti-CTLA4 or anti-PD-1 blockade in clinical trials, 58% had a response or stable disease for more than 6 m, with median progression-free survival (PFS) of 5.7 m (2.1-26.1 m). The median overall survival (mOS) in all population was 15 months (m) (13.5-18.8 m). In a multivariable model factors associated to improved mOS were PS 0, neutrophil-lymphocyte ratio (NLR) < 5 and epithelioid histology (p < 0.001).

CONCLUSIONS

In our series we were unable to identify any MPM patient with dMMR by IHC. Further studies are needed to elucidate potential predictive biomarkers of ICI benefit in MPM.

CO2 spatio-temporal analysis in the Iberian Peninsula

A comparison between monthly CO₂ values calculated in the Iberian Peninsula and those measured during six years commencing on October 2010 in the centre of its upper plateau is presented. Gaussian and Epanechnikov kernels are used to calculate CO₂ concentration and its growth rate in the study region from values at certain grid points. Slight spatial differences are obtained, revealing that both concentration and growth rate are nearly uniform in the region. However, some intervals were proposed that were represented by bands (strips), distributed meridionally for concentration and zonally for growth rate. Band borders were smoother for the Gaussian kernel than for the Epanechnikov kernel. In addition, the probability distribution function of concentration and growth rate were obtained with both kernels. Temporal analysis is carried out adding a linear evolution for growth rate and a sinusoidal function for the annual cycle. This revealed similar patterns for the region and at the grid point nearest to the measurement site, given by a sinusoidal function with nearly constant amplitude, providing satisfactory agreement. However, measurements showed great dispersion, with the concentration being around 7 ppm higher than for the region. Temporal evolution is characterised by a growth rate of 2.39 ppm yr^-1 and a sinusoidal function with an amplitude decrease of 0.25 ppm yr^-1.

Activity of HSP90 Inhibiton in a Metastatic Lung Cancer Patient With a Germline BRCA1 Mutation

Heat shock proteins (HSPs) are molecular chaperones that maintain proteins in their correct conformation to ensure stability and protect carcinoma cells from apoptosis. HSP90 inhibitors (HSP90i) block multiple targets simultaneously, and despite responses in a selected population, no HSP90i have yet been approved. We present a patient with a lung tumor with an exceptional response to cisplatin/gemcitabine in combination with HSP90i, which nowadays continues with HSP90i maintenance after three years. Whole-exome sequencing of the lung tumor unveiled a BRCA1/2 deficiency mutational signature, and mutation analysis confirmed a germline BRCA1 mutation. The striking efficacy of HSP90i plus chemotherapy vs chemotherapy alone was reproduced in a patient-derived xenograft (PDX) model from a breast cancer patient with a BRCA1 mutation (mean tumor volume [SD], No. of tumors: vehicle 8.38 [7.07] mm³, n = 3; HSP90i 4.18 [1.93] mm³, n = 5; cisplatin plus gemcitabine 3.31 [1.95] mm³, n = 5; cisplatin plus gemcitabine plus HSP90i 0.065 [0.076] mm³, n = 6). This case and the PDX demonstrate the efficacy for therapeutic inhibition of HSP90 in a BRCA-mutated patient, opening a new potential avenue for better identifying patients who might benefit most from HSP90i.

Whole exome sequencing (WES) of non-small cell lung cancer (NSCLC) for tumor mutational burden (TMB) analysis and long-term benefit to immune checkpoint inhibitors (ICIs)

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Background: ICIs have significantly changed the therapeutic landscape of advanced NSCLC. As such, characterizing predictive markers of long-term clinical benefit is a critical objective. TMB quantification using targeted gene panels associates with long-term response to ICIs in NSCLC patients (Rizvi H ASCO 18). Although TMB quantified by targeted NGS correlates with that of WES, caution may be needed when using smaller panels. Methods: Here we analyzed WES of tumors and matched normal tissue from 67 NSCLC patients including 42 treated with ICIs. We correlated TMB with clinico-pathological features and outcomes. TMB was categorized as high vs. low according to the upper quartile of cohort distribution. Results: The median TMB was 2.68 non-synonymous variants (nSNVs)/Mb, ranging from 0 to 15.6 nSNVs/Mb, with upper quartile at 5.42 nSNVs/Mb. TMB was higher for smoker/current smoker (median 3.51) compared to never smokers (median 0.94, p = 0.0048) but no differences were seen in elderly ( > 70 years) vs. young patients or across histologies (squamous, adeno and other) and stages at diagnosis. In patients treated with ICIs, median TMB was 5.44 for those achieving complete response, 3.87 for patients with partial response and 2.42 for patients with progressive disease (PD) (p = 0.04). Moreover, improved clinical outcomes were associated with higher TMB (Table). In patients treated with ICIs, TMB as continuous variable had an impact on progression free survival (PFS) (p = 0.03). Median PFS was 22.3 months (mo) (14-not reached) for those with high TMB and 6.4 mo (3-16) for those with low TMB (HR 0.34, 0.13-0.9, p = 0.03). Median overall survival was not reached for those patients with high TMB and 32 mo (22-43) for those with low TMB (HR 0.29, 0.1-0.86, p = 0.02). Conclusions: High TMB correlates with long-term ICI benefit in NSCLC patients. Mutations in individual genes potentially linked to long-term benefit or resistance to ICIs will be presented. [Table: see text]

Analysis of mismatch repair (MMR) proteins expression in a series of malignant pleural mesothelioma (MPM) patients

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Background: The increasing incidence and poor outcome associated with MPM demand identification of effective treatment options. Promising results have been reported with immunotherapy (IO) in a small proportion of MPM patients (p). MMR deficiency (dMMR) has been well described in several malignancies and was recently approved as a tumor biomarker for IO with anti-PD-1 checkpoint inhibitor. Next generation sequencing (NGS) data demonstrated that 2% of MPM harbor microsatellite instability. The aim of this study is to characterize MMR by immunohistochemistry (IHC) in a series of MPM p. Methods: Tumors of 159 MPM p from Vall d´Hebron University Hospital and October 12th University Hospital diagnosed between 2002 and 2017 were reviewed. Formalin-fixed, paraffin-embedded tissue was stained for MLH1, MSH2, MSH6 and PMS2 and tumors were classified as dMMR when any MMR protein expression was negative and MMR intact when all MMR proteins were positively expressed. Associations between clinical variables and outcome were assessed with Cox regression models and survival data were calculated by the Kaplan-Meier method. Results: P characteristics: median age: 69 years (29-88 years), males: 71%, performance status (PS) 1:69%, asbestos exposure: 52%, stage III at diagnosis: 42%, epithelial subtype: 65%, systemic treatment 81% (57% chemotherapy with cisplatin plus pemetrexed in first line), 50% received second line and 28% third line. MMR protein expression was analyzed in 158 samples with enough tissue and was positive in all of the cases. The median overall survival (mOS) in all population was 15 months (m) (13.5-18.8m). In a multivariate model factors associated to improved mOS were PS 0 vs PS2 (13 v 2 m, HR 12.8, p < 0.01), neutrophil-lymphocyte ratio (NLR) < 5 (18 v 9 m in NLR ≥5,HR 1.5, p < 0.05) and epitheliod vs sarcomatoid histology (18 vs 4 m HR 4.7, p < 0.01). Thirteen p received IO with anti-CTLA4 or anti-PD-1 blockade in clinical trials, 58% had a response or stable disease for more than 6 m, with median progression-free survival (PFS) of 5.7 m (2.1-26.1m). Conclusions: In our series we were unable to identify any MPM patient with dMMR by IHC. Further studies are needed to elucidate novel predictive biomarkers benefit from IO in MPM.

Genomic Profiling Identifies Outcome-Relevant Mechanisms of Innate and Acquired Resistance to Third-Generation Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Therapy in Lung Cancer

PURPOSE

Third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective in acquired resistance (AR) to early-generation EGFR TKIs in EGFR-mutant lung cancer. However, efficacy is marked by interindividual heterogeneity. We present the molecular profiles of pretreatment and post-treatment samples from patients treated with third-generation EGFR TKIs and their impact on treatment outcomes.

METHODS

Using the databases of two lung cancer networks and two lung cancer centers, we molecularly characterized 124 patients with EGFR p.T790M-positive AR to early-generation EGFR TKIs. In 56 patients, correlative analyses of third-generation EGFR TKI treatment outcomes and molecular characteristics were feasible. In addition, matched post-treatment biopsy samples were collected for 29 patients with progression to third-generation EGFR TKIs.

RESULTS

Co-occurring genetic aberrations were found in 74.4% of EGFR p.T790-positive samples (n = 124). Mutations in TP53 were the most frequent aberrations detected (44.5%; n = 53) and had no significant impact on third-generation EGFR TKI treatment. Mesenchymal-epithelial transition factor (MET) amplifications were found in 5% of samples (n = 6) and reduced efficacy of third-generation EGFR TKIs significantly (eg, median progression-free survival, 1.0 months; 95% CI, 0.37 to 1.72 v 8.2 months; 95% CI, 1.69 to 14.77 months; P ≤ .001). Genetic changes in the 29 samples with AR to third-generation EGFR TKIs were found in EGFR (eg, p.T790M loss, acquisition of p.C797S or p.G724S) or in other genes (eg, MET amplification, KRAS mutations).

CONCLUSION

Additional genetic aberrations are frequent in EGFR-mutant lung cancer and may mediate innate and AR to third-generation EGFR TKIs. MET amplification was strongly associated with primary treatment failure and was a common mechanism of AR to third-generation EGFR TKIs. Thus, combining EGFR inhibitors with TKIs targeting common mechanisms of resistance may delay AR.

Analysis of PM10 and PM2.5 Concentrations in an Urban Atmosphere in Northern Spain

This work analyses levels of particles PM10 and PM2.5 recorded at four air-quality monitoring stations located in the urban area of Valladolid (Spain) during 2015-2016. To achieve this, the evolution of particle concentrations at different time scales was determined. Average concentrations ranged from 15.3 to 17.6 µg m^-3 for PM10 and between 8.9 and 14.8 µg m^-3 for PM2.5. The highest monthly means were recorded in autumn and winter. The difference between mean concentrations at weekends and on weekdays for PM10 was around 3 µg m^-3 at most of the measuring stations and was 1 µg m^-3 for PM2.5. Two concentration peaks were found during the day, one in the morning and the other in the evening, which evidenced the influence of traffic and other anthropogenic activities on PM concentrations. Their mean values were approximately 21 and 17-21 µg m^-3, respectively, for PM10. Mean maximum values for PM2.5 were 12 µg m^-3, except at one of the measuring sites, with 17 µg m^-3 for the morning maximum and 1 µg m^-3 more for the nocturnal peak. In addition, the impact of long-distance transport of air masses in the study area was analysed by applying a HYSPLIT trajectory model, taking into account backward trajectories of European, African, and Atlantic origins as well as local conditions. In particular, high concentration events due to Saharan dust intrusions are presented. Finally, background levels of particle concentrations estimated at most sampling areas were around 15 and 7.7 µg m^-3 for the PM10 and PM2.5 particle fractions, respectively.

SCOPE model applied for rapeseed in Spain

The integrated SCOPE (Soil, Canopy Observation, Photochemistry and Energy balance) model, coupling radiative transfer theory and biochemistry, was applied to a biodiesel crop grown in a Spanish agricultural area. Energy fluxes and CO₂ exchange were simulated with this model for the period spanning January 2008 to October 2008. Results were compared to experimental measurements performed using eddy covariance and meteorological instrumentation. The reliability of the model was proven by simulating latent (LE) and sensible (H) heat fluxes, soil heat flux (G), and CO₂ exchanges (NEE and GPP). LAI data used as input in the model were retrieved from the MODIS and MERIS sensors. SCOPE was able to reproduce similar seasonal trends to those measured for NEE, GPP and LE. When considering H, the modelled values were underestimated for the period covering July 2008 to mid-September 2008. The modelled fluxes reproduced the observed seasonal evolution with determination coefficients of over 0.77 when LE and H were evaluated. The modelled results offered good agreement with observed data for NEE and GPP, regardless of whether LAI data belonged to MODIS or MERIS, showing slopes of 0.87 and 0.91 for NEE-MODIS and NEE-MERIS, and 0.91 and 0.94 for GPP-MODIS and GPP-MERIS, respectively. Moreover, SCOPE was able to reproduce similar seasonal behaviours to those observed for the experimental carbon fluxes, clearly showing the CO₂ sink/source behaviour for the whole period studied.

Dual MET and ERBB inhibition overcomes intratumor plasticity in osimertinib-resistant-advanced non-small-cell lung cancer (NSCLC)

Background

Third-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as osimertinib are the last line of targeted treatment of metastatic non-small-cell lung cancer (NSCLC) EGFR-mutant harboring T790M. Different mechanisms of acquired resistance to third-generation EGFR-TKIs have been proposed. It is therefore crucial to identify new and effective strategies to overcome successive acquired mechanisms of resistance.

Methods

For Amplicon-seq analysis, samples from the index patient (primary and metastasis lesions at different timepoints) as well as the patient-derived orthotopic xenograft tumors corresponding to the different treatment arms were used. All samples were formalin-fixed paraffin-embedded, selected and evaluated by a pathologist. For droplet digital PCR, 20 patients diagnosed with NSCLC at baseline or progression to different lines of TKI therapies were selected. Formalin-fixed paraffin-embedded blocks corresponding to either primary tumor or metastasis specimens were used for analysis. For single-cell analysis, orthotopically grown metastases were dissected from the brain of an athymic nu/nu mouse and cryopreserved at -80°C.

Results

In a brain metastasis lesion from a NSCLC patient presenting an EGFR T790M mutation, we detected MET gene amplification after prolonged treatment with osimertinib. Importantly, the combination of capmatinib (c-MET inhibitor) and afatinib (ErbB-1/2/4 inhibitor) completely suppressed tumor growth in mice orthotopically injected with cells derived from this brain metastasis. In those mice treated with capmatinib or afatinib as monotherapy, we observed the emergence of KRAS G12C clones. Single-cell gene expression analyses also revealed intratumor heterogeneity, indicating the presence of a KRAS-driven subclone. We also detected low-frequent KRAS G12C alleles in patients treated with various EGFR-TKIs.

Conclusion

Acquired resistance to subsequent EGFR-TKI treatment lines in EGFR-mutant lung cancer patients may induce genetic plasticity. We assess the biological insights of tumor heterogeneity in an osimertinib-resistant tumor with acquired MET-amplification and propose new treatment strategies in this situation.

The influence of meteorological variables on CO2 and CH4 trends recorded at a semi-natural station

CO₂ and CH₄ evolution is usually linked with sources, sinks and their changes. However, this study highlights the role of meteorological variables. It aims to quantify their contribution to the trend of these greenhouse gases and to determine which contribute most. Six years of measurements at a semi-natural site in northern Spain were considered. Three sections are established: the first focuses on monthly deciles, the second explores the relationship between pairs of meteorological variables, and the third investigates the relationship between meteorological variables and changes in CO₂ and CH₄. In the first section, monthly outliers were more marked for CO₂ than for CH₄. The evolution of monthly deciles was fitted to three simple expressions, linear, quadratic and exponential. The linear and exponential are similar, whereas the quadratic evolution is the most flexible since it provided a variable rate of concentration change and a better fit. With this last evolution, a decrease in the change rate was observed for low CO₂ deciles, whereas an increasing change rate prevailed for the rest and was more accentuated for CH₄. In the second section, meteorological variables were provided by a trajectory model. Backward trajectories from 1-day prior to reaching the measurement site were used to calculate distance and direction averages as well as the recirculation factor. Terciles of these variables were determined in order to establish three intervals with low, medium and high values. These intervals were used to classify the variables following their interval widths and skewnesses. The best correlation between pairs of meteorological variables was observed for the average distance, in particular with horizontal wind speed. Sinusoidal relationships with the average direction were obtained for average distance and for vertical wind speed. Finally, in the third section, the quadratic evolution was considered in each interval of all the meteorological variables. As regards the main result, the greatest increases were obtained for high potential temperature for both gases followed by low and medium boundary layer height for CO₂ and CH₄, respectively. Combining both meteorological variables provided increases of 22 ± 9 and 0.070 ± 0.019 ppm for CO₂ and CH₄, respectively, although the number of observations affected is small, around 7%.

Temporal patterns of CO2 and CH4 in a rural area in northern Spain described by a harmonic equation over 2010-2016

The present paper seeks to improve our knowledge concerning the evolution of CO₂ and CH₄ in terms of monthly trends, growth rate and seasonal variations in the lower atmosphere. Dry continuous measurements of CO₂ and the CH₄ mixing ratio were carried out over five and a half years (from 15 October 2010 to 29 February 2016) by multi-point sampling at 1.8, 3.7 and 8.3m, using a Picarro analyzer at a rural site in the Low Atmosphere Research Centre (CIBA), on the upper Spanish plateau. Data were divided into diurnal and nocturnal records. The mathematical equation proposed to analyze the overall data was a harmonic one, comprising a polynomial (trend) and a series of harmonics (seasonal cycle). Amplitude was considered as a constant and variable term over time. Quite different behaviour was found between day and night measurements in both climate forcing agents. CO₂ showed an accelerating trend in autumn, whereas CH₄ trends were higher during the winter. Increasing growth rates were reported for CO₂ and CH₄ over the whole study period. Nocturnal CO₂ amplitudes are higher than diurnal ones except in winter for both gases, and also in the autumn for CH₄.

Immune-Related Gene Expression Profiling After PD-1 Blockade in Non-Small Cell Lung Carcinoma, Head and Neck Squamous Cell Carcinoma, and Melanoma

Antibody targeting of the immune checkpoint receptor PD1 produces therapeutic activity in a variety of solid tumors, but most patients exhibit partial or complete resistance to treatment for reasons that are unclear. In this study, we evaluated tumor specimens from 65 patients with melanoma, lung nonsquamous, squamous cell lung or head and neck cancers who were treated with the approved PD1-targeting antibodies pembrolizumab or nivolumab. Tumor RNA before anti-PD1 therapy was analyzed on the nCounter system using the PanCancer 730-Immune Panel, and we identified 23 immune-related genes or signatures linked to response and progression-free survival (PFS). In addition, we evaluated intra- and interbiopsy variability of PD1, PD-L1, CD8A, and CD4 mRNAs and their relationship with tumor-infiltrating lymphocytes (TIL) and PD-L1 IHC expression. Among the biomarkers examined, PD1 gene expression along with 12 signatures tracking CD8 and CD4 T-cell activation, natural killer cells, and IFN activation associated significantly with nonprogressive disease and PFS. These associations were independent of sample timing, drug used, or cancer type. TIL correlated moderately (∼0.50) with PD1 and CD8A mRNA levels and weakly (∼0.35) with CD4 and PD-L1. IHC expression of PD-L1 correlated strongly with PD-L1 (0.90), moderately with CD4 and CD8A, and weakly with PD1. Reproducibility of gene expression in intra- and interbiopsy specimens was very high (total SD <3%). Overall, our results support the hypothesis that identification of a preexisting and stable adaptive immune response as defined by mRNA expression pattern is reproducible and sufficient to predict clinical outcome, regardless of the type of cancer or the PD1 therapeutic antibody administered to patients. Cancer Res; 77(13); 3540-50. ©2017 AACR.

Influence of atmospheric stability and transport on CH4 concentrations in northern Spain

Continuous methane (CH4) concentrations were measured in Northern Spain over two years (2011-2012) by multi-point sampling at 1.8, 3.7 and 8.3m using a Picarro analyser. The technique is based on cavity ring-down spectroscopy. The contrast in mean concentrations was about 1.2ppb, with 95th percentiles differing by 2.2ppb and mean minimum concentrations proving similar. Temporal variations of CH4 were also analysed, with a similar seasonal variability being found for the three heights. The highest CH4 concentrations were obtained in late autumn and winter and the lowest in summer, yielding a range of 52ppb. This variation may depend on the active photochemical reaction with OH radical during a period of intense solar radiation and changes in soil conditions together with variations in emissions. Peak concentration levels were recorded at night-time, between 5:00-7:00 GMT, with mean values ranging between 1920 and 1923ppb. The lowest value, around 1884ppb, was obtained at 16:00 GMT. This diurnal variation was mainly related to vertical mixing and photochemistry. Therefore, CH4 concentrations were also examined using the bulk Richardson number (RB) as a stability indicator. Four groups were distinguished: unstable cases, situations with pure shear flow, transitional stages and drainage flows. The highest contrast in mean CH4 concentrations between lower and upper heights was obtained for the transition and drainage cases, mainly associated to high concentrations from nearby sources. The impact of long range transport was analysed by means of 3-day isobaric backward air mass trajectories, which were calculated taking into account origins from Europe, Africa, the Atlantic Ocean and Local conditions. Assessment of the results showed the influence of S and SE wind sectors, especially with Local conditions associated with low winds. Finally, an estimation of the background CH4 concentration in the study period provided an average value of about 1892ppb.

An experimental relationship between airflow and carbon dioxide concentrations at a rural site

The influence of airflow on CO2 concentrations is considered. Two years of measurements recorded with a Picarro G1301 analyser during the night at a rural site were used. Three concentration groups were formed and were related to wind speed. Yearly, directional, and hourly evolution indicated that the isolated contribution of factors affecting CO2 concentrations proves hard to evaluate. Two approaches to airflow based on average wind and a rotating residual were considered. Around two thirds of observations corresponded to anticyclonic rotations. Firstly, circular hodographs of rotating residuals indicated that wavelengths were in the mesoscale range. The greatest concentrations were linked to the lowest wind speeds and no prevailing directions were revealed by the roundness calculation in a spatial analysis using hexagonal cells. Secondly, composite hodographs for anticyclonic turnings were calculated, the greatest concentrations being associated to hodographs with a pronounced curvature. Moreover, these were successfully parameterised using two models. A harmonic function was first used, which satisfactorily fitted hodographs linked to low and intermediate concentrations. The second model initially described the wind direction of residuals with the error function since its change was slow in early and late night-time. Residuals were later parameterised with a second order logarithmic spiral. This procedure successfully fitted the most curved hodographs of low and high concentrations.

Cluster analysis applied to CO₂ concentrations at a rural site

In rural environments, atmospheric CO2 is mainly controlled by natural processes such as respiration-photosynthesis or low atmosphere evolution. This paper considers atmospheric CO2 measurements obtained at a rural site during 2011 using the wavelength-scanned cavity ringdown spectroscopy technique and presents two clustering methods, the silhouette being calculated to evaluate procedure validity. In the first method, clusters were formed depending on the similarity of wind roses, with satisfactory silhouette values. An anticyclonic rotation of the wind direction was observed during the daily cycle and clusters were formed by consecutive directions following the mixing layer evolution. However, monthly roses revealed four quite different wind directions, mainly oriented in the E-W axis. Although CO2 was not used in this procedure, a successful link between clusters and CO2 was obtained. In the second procedure, clusters were formed by the similarity of CO2 histograms calculated in intervals of one or two ancillary variables, wind direction, time of day, or month. The influence of a nearby city, the daily evolution of the low atmosphere, and the growing season were highlighted. Finally, the usefulness of the method lies in its easy extension to other gases or variables.