Mutations In Critical Genes Research Articles

An Additional L451G452N453 in the RpoB Protein Suppressed the Synthetic Lethality in Escherichia coli at 37 Degrees Caused by Depletion of DnaK/J and Trigger Factor.

Escherichia coli depletion of chaperone trigger factor and DnaK/J were not viable at 37°C, but viable below 30°C. Among the engineered E. coli depleted of trigger factor and DnaK/J, one strain Z625, exhibited survival at 37°C, while another strain Z629 only survived below 30°C. Comparative analysis of fatty acid profiles of Z625 and Z629 revealed absence of numerous saturated fatty acids in Z625 as compared to the wild-type E. coli BW25113. In addition, increased unsaturated fatty acids were present in Z625, whereas the fatty acids profile of Z629 closely resembled that of BW25113. Whole genome sequencing revealed a 9-bp insertion in rpoB of Z625. Combined structural analysis of simulated RpoB protein bearing the amino acid sequence L451G452N453 insertion and susceptibility analysis to rifampicin suggested that the insertion did not disturb the individual RpoB structure as beta subunit of RNA polymerase. Comparative transcriptomic analysis of Z625 and Z629 suggested that this insertion impacted transcription of the overall RNA polymerase in Z625, leading to potential repression of some genes whose overexpression was toxic to E. coli. Additionally, Z625 exhibited distinctive metabolic adaptations, likely contributing to its survival at 37°C. In summary, our study elucidated one LGN insertion in rpoB that impacts transcriptional regulation in E. coli, thereby explaining the survival of E. coli depletion of trigger factor and DnaK/J at 37°C, and these founding suggested that some simple mutations in critical genes like rpoB might play an important role in driving adaptive evolution.

From single DNA adducts measurement to DNA adductomics in molecular epidemiology of cancer.

Environmental carcinogens exert their carcinogenic effects by forming DNA adducts. This type of DNA damage can also be formed endogenously as a result of, e.g., oxidative damage. Unrepaired DNA adducts may induce mutations in critical genes, leading to the initiation of chemical carcinogenesis. Therefore, detection, identification, and quantification of DNA adducts is essential for cancer risk assessment. Over the last 50 years, the major DNA adducts formed by different classes of environmental carcinogens were characterized. With the development of techniques such as 32P-postlabeling, their measurement was implemented into molecular epidemiology. Advances in liquid chromatography-tandem mass spectrometry (LC-MS ) made the measurement of adducts more precise and allowed to gain knowledge about their identity and structures. Therefore, opened the way to DNA adductomics, the "omics" approach investigating DNA adducts comprehensively, similarly to proteomics. This review presents the historical perspective of DNA adducts research and the emerging field of adductomics.

Building, Breaking, and Repairing Neuromuscular Synapses.

A coordinated and complex interplay of signals between motor neurons, skeletal muscle cells, and Schwann cells controls the formation and maintenance of neuromuscular synapses. Deficits in the signaling pathway for building synapses, caused by mutations in critical genes or autoantibodies against key proteins, are responsible for several neuromuscular diseases, which cause muscle weakness and fatigue. Here, we describe the role that four key genes, Agrin, Lrp4, MuSK, and Dok7, play in this signaling pathway, how an understanding of their mechanisms of action has led to an understanding of several neuromuscular diseases, and how this knowledge has contributed to emerging therapies for treating neuromuscular diseases.

Attenuation of Polycyclic Aromatic Hydrocarbon (PAH)-Induced Carcinogenesis and Tumorigenesis by Omega-3 Fatty Acids in Mice In Vivo.

Lung cancer is the leading cause of cancer death worldwide. Polycyclic aromatic hydrocarbons (PAHs) are metabolized by the cytochrome P450 (CYP)1A and 1B1 to DNA-reactive metabolites, which could lead to mutations in critical genes, eventually resulting in cancer. Omega-3 fatty acids, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are beneficial against cancers. In this investigation, we elucidated the mechanisms by which omega-3 fatty acids EPA and DHA will attenuate PAH-DNA adducts and lung carcinogenesis and tumorigenesis mediated by the PAHs BP and MC. Adult wild-type (WT) (A/J) mice, Cyp1a1-null, Cyp1a2-null, or Cyp1b1-null mice were exposed to PAHs benzo[a]pyrene (BP) or 3-methylcholanthrene (MC), and the effects of omega-3 fatty acid on PAH-mediated lung carcinogenesis and tumorigenesis were studied. The major findings were as follows: (i) omega-3 fatty acids significantly decreased PAH-DNA adducts in the lungs of each of the genotypes studied; (ii) decreases in PAH-DNA adduct levels by EPA/DHA was in part due to inhibition of CYP1B1; (iii) inhibition of soluble epoxide hydrolase (sEH) enhanced the EPA/DHA-mediated prevention of pulmonary carcinogenesis; and (iv) EPA/DHA attenuated PAH-mediated carcinogenesis in part by epigenetic mechanisms. Taken together, our results suggest that omega-3 fatty acids have the potential to be developed as cancer chemo-preventive agents in people.

RidA proteins contribute to fitness of S. enterica and E. coli by reducing 2AA stress and moderating flux to isoleucine biosynthesis.

Defining the physiological role of a gene product relies on interpreting phenotypes caused by the lack, or alteration, of the respective gene product. Mutations in critical genes often lead to easily recognized phenotypes that can include changes in cellular growth, metabolism, structure etc. However, mutations in many important genes may fail to generate an obvious defect unless additional perturbations are caused by medium or genetic background. The latter scenario is exemplified by RidA proteins. In vitro RidA proteins deaminate numerous imine/enamines, including those generated by serine/threonine dehydratase IlvA (EC:4.3.1.19) from serine or threonine - 2-aminoacrylate (2AA) and 2-aminocrotonate (2AC), respectively. Despite this demonstrable biochemical activity, a lack of RidA has little to no effect on growth of E. coli or S. enterica without the application of additional metabolic perturbation. A cellular role of RidA is to prevent accumulation of 2AA which, if allowed to persist, can irreversibly damage pyridoxal 5'-phosphate (PLP)-dependent enzymes, causing global metabolic stress. Because the phenotypes caused by a lack of RidA are dependent on the unique structure of each metabolic network, the link between RidA function and 2AA stress is difficult to demonstrate in some organisms. The current study used coculture experiments to exacerbate differences in growth caused by the lack of RidA in S. enterica and E. coli. Results described here solidify the established role of RidA in removing 2AA, while also presenting evidence for a role of RidA in enhancing flux towards isoleucine biosynthesis in E. coli. Overall, these data emphasize that metabolic networks can generate distinct responses to perturbation, even when the individual components are conserved.

Metformin reduces the cellular DNA repair capacity and enhances the effect of curcumin on the induction of apoptosis in AGS gastric cancer cells

BackgroundCancer results from the accumulation of mutations in critical genes, such as DNA repair genes. But these genes are a double-edged sword, because the basis of current cancer treatment is DNA damage from chemotherapy and radiation, and the repair system can slow the healing process by repairing the induced damage. Therefore, any substance that can reduce the DNA repair capacity of cancer cells can make the cells more sensitive to treatment. Metformin and curcumin, as low-complication compounds, can play this role well.MethodsIn the present work, changes in the expression of CASP3, BAX, and BCL2L1 apoptotic genes, and nine genes involved in DNA repair pathways (XRCC1, XRCC2, XRCC3, XRCC4, XRCC5, XRCC6, XRCC7, BRCA1 and BRAC2) were measured comparatively by real-time PCR in AGS gastric cancer cell line under single and co-treatments with metformin and curcumin.ResultsOur findings showed that co-treatment of metformin and curcumin induced decreasing the expression of anti-apoptotic BCL2L1 and increasing expression of proapoptotic CASP3 and BAX. Metformin decreased the expression levels of seven genes, while curcumin did not alter the expression levels. The co-treatment of metformin and curcumin showed that although the XRCC2, XRCC3, XRCC4, XRCC5, XRCC6, XRCC7, BRCA1, and BRCA2 were down-regulated, there was no difference between metformin and co-treatment for mRNA levels.ConclusionOur results suggest that metformin increases the sensitivity of cancer cells to anticancer drugs by suppressing several DNA repair pathways and that curcumin may induce apoptosis.

Arterial dissections: Common features and new perspectives.

Arterial dissections, which involve an abrupt tear in the wall of a major artery resulting in the intramural accumulation of blood, are a family of catastrophic disorders causing major, potentially fatal sequelae. Involving diverse vascular beds, including the aorta or coronary, cervical, pulmonary, and visceral arteries, each type of dissection is devastating in its own way. Traditionally they have been studied in isolation, rather than collectively, owing largely to the distinct clinical consequences of dissections in different anatomical locations - such as stroke, myocardial infarction, and renal failure. Here, we review the shared and unique features of these arteriopathies to provide a better understanding of this family of disorders. Arterial dissections occur commonly in the young to middle-aged, and often in conjunction with hypertension and/or migraine; the latter suggesting they are part of a generalized vasculopathy. Genetic studies as well as cellular and molecular investigations of arterial dissections reveal striking similarities between dissection types, particularly their pathophysiology, which includes the presence or absence of an intimal tear and vasa vasorum dysfunction as a cause of intramural hemorrhage. Pathway perturbations common to all types of dissections include disruption of TGF-β signaling, the extracellular matrix, the cytoskeleton or metabolism, as evidenced by the finding of mutations in critical genes regulating these processes, including LRP1, collagen genes, fibrillin and TGF-β receptors, or their coupled pathways. Perturbances in these connected signaling pathways contribute to phenotype switching in endothelial and vascular smooth muscle cells of the affected artery, in which their physiological quiescent state is lost and replaced by a proliferative activated phenotype. Of interest, dissections in various anatomical locations are associated with distinct sex and age predilections, suggesting involvement of gene and environment interactions in disease pathogenesis. Importantly, these cellular mechanisms are potentially therapeutically targetable. Consideration of arterial dissections as a collective pathology allows insight from the better characterized dissection types, such as that involving the thoracic aorta, to be leveraged to inform the less common forms of dissections, including the potential to apply known therapeutic interventions already clinically available for the former.

Incidence of BRAF V600E Gene Mutation Among Lebanese Population in Melanoma and Colorectal Cancer: A Retrospective Study Between 2010 and 2019

Introduction: Cancers arise owing to the accumulation of mutations in critical genes that leads to uncontrolled cell division and the avoidance of apoptosis. Among these oncogenes, BRAF is a potent mitogen-activated protein kinase (MAPK) pathway activator known to be somatically mutated by a glutamic acid to valine substitution at codon 600 (V600E). It is a common finding in various types of human cancers, including malignant melanoma and colorectal cancer (CRC), and is considered a poor prognostic factor and a predictive biomarker. The study aims to determine the incidence of BRAF V600E gene mutation in Lebanese patients with melanoma and CRC and its correlation with gender and age.Methods: We conducted a retrospective cohort design study in which 210 and 132 patients diagnosed to have melanoma and CRC, respectively, were recruited from 2010 to 2019 from "L’Institut National de Pathologie," where a specific polymerase chain reaction is used to detect BRAF mutations. Data from digitized records were collected, including demographic characteristics (age and gender), cancer type, and BRAF mutation. The collected data were analyzed using SPSS Statistics version 20.0 (IBM Corp., Armonk, NY). A p-value < 0.05 was considered significant.Results: The incidence of BRAF mutation in melanoma is 88.10%. There is female predominance with a ratio of 2.6:1 (p = 0.240) and the majority of patients aged between 40 and 60 years (51.2%) with a mean age of 53.74 years. While in CRC, BRAF is mutated in 7.5% with a ratio of 1.2:1 of male predominance (p = 0.999). The majority of patients (54.8%) were between the ages of 60 and 80 years, with a mean age of 65.5 years.Conclusion: BRAF is a frequent oncogenic mutation that is found in lethal tumors. Targeted therapies for these cancers interfere with developing more effective therapeutic strategies, which affect the treatment response in BRAF mutants and improve the prognosis of the patients.

Identification of a Genomic Instability-Related Long Noncoding RNA Prognostic Model in Colorectal Cancer Based on Bioinformatic Analysis

Background In recent years, a growing body of research has revealed that long noncoding RNAs (lncRNAs) participate in regulating genomic instability. Materials and Methods We obtained RNA expression profiles, somatic mutation profiles, clinical information, and pathological features of colorectal cancer (CRC) from The Cancer Genome Atlas project. We divided the cohort into two groups based on mutation frequency and identified genomic instability-related lncRNAs (GI-lncRNAs) using R software. We further analyzed the function of identified GI-lncRNAs and established a prognostic model through Cox regression. Using the established prognostic model, we divided the cohort into the high- and low-risk groups and further verified the prognostic differences between the two groups as well as the predictive power of prognosis-related lncRNAs in the genomic instability of CRC. Results We identified a total of 143 GI-lncRNAs that were differentially expressed between the higher mutation frequency group and the lower mutation frequency group. According to Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses, a series of cancer-associated terms were enriched. We further constructed a prognostic model that included five GI-lncRNAs (lncRNA PTPRD-AS1, lncRNA AC009237.14, lncRNA LINC00543, lncRNA AP003555.1, and lncRNA AL109615.3). We confirmed that the expression of the five GI-lncRNAs was associated with prognosis and the mutation of critical genes in the CRC patient cohort. Conclusions The present research further confirmed the vital function of GI-lncRNAs in the genomic instability of CRC. The five GI-lncRNAs identified in our study are potential biomarkers and need to be studied in more depth.

A novel immune signature to predict the prognosis of patients with hepatocellular carcinoma.

Aberrant immunity has been associated with the initiation and progression of cancers such as hepatocellular carcinoma (HCC). Here, we aim to develop a signature based on immune-related genes (IRGs) to predict the prognosis of HCC patients. The gene expression profiles of 891 HCC samples were derived from 4 publicly accessible datasets. A total of 1534 IRGs from Immunology Database and Analysis Portal website were obtained as candidate genes for prognostic assessment. Using least absolute shrinkage and selection operator (LASSO) regression analysis, 12 IRGs were selected as prognostic biomarkers and were then aggregated to generate an IRG score for each HCC sample. In the training dataset (n = 365), patients with high IRG scores showed a remarkably poorer overall survival than those with low IRG scores (log-rank P < .001). Similar results were documented in 3 independent testing datasets (n = 226, 221, 79, respectively). Multivariate Cox regression and stratified analyses indicated that the IRG score was an independent and robust signature to predict the overall survival in HCC patients. Patients with high IRG scores tended to be in advanced TNM stages, with increased risks of tumor recurrence and metastasis. More importantly, the IRG score was strongly associated with certain immune cell counts, gene expression of immune checkpoints, estimated immune score, and mutation of critical genes in HCC. In conclusion, the proposed IRG score can predict the prognosis and reflect the tumor immune microenvironment of HCC patients, which may facilitate the individualized treatment and provide potential immunotherapeutic targets.

Therapeutic opportunities for pancreatic β-cell ER stress in diabetes mellitus.

Diabetes mellitus is characterized by the failure of insulin-secreting pancreatic β-cells (or β-cell death) due to either autoimmunity (type 1 diabetes mellitus) or failure to compensate for insulin resistance (type 2 diabetes mellitus; T2DM). In addition, mutations of critical genes cause monogenic diabetes. The endoplasmic reticulum (ER) is the primary site for proinsulin folding; therefore, ER proteostasis is crucial for both β-cell function and survival under physiological and pathophysiological challenges. Importantly, the ER is also the major intracellular Ca2+ storage organelle, generating Ca2+ signals that contribute to insulin secretion. ER stress is associated with the pathogenesis of diabetes mellitus. In this Review, we summarize the mutations in monogenic diabetes that play causal roles in promoting ER stress in β-cells. Furthermore, we discuss the possible mechanisms responsible for ER proteostasis imbalance with a focus on T2DM, in which both genetics and environment are considered important in promoting ER stress in β-cells. We also suggest that controlled insulin secretion from β-cells might reduce the progression of a key aspect of the metabolic syndrome, namely nonalcoholic fatty liver disease. Finally, we evaluate potential therapeutic approaches to treat T2DM, including the optimization and protection of functional β-cell mass in individuals with T2DM.

Rapid repair of human disease-specific single-nucleotide variants by One-SHOT genome editing

Many human diseases ranging from cancer to hereditary disorders are caused by single-nucleotide mutations in critical genes. Repairing these mutations would significantly improve the quality of life for patients with hereditary diseases. However, current procedures for repairing deleterious single-nucleotide mutations are not straightforward, requiring multiple steps and taking several months to complete. In the current study, we aimed to repair pathogenic allele-specific single-nucleotide mutations using a single round of genome editing. Using high-fidelity, site-specific nuclease AsCas12a/Cpf1, we attempted to repair pathogenic single-nucleotide variants (SNVs) in disease-specific induced pluripotent stem cells. As a result, we achieved repair of the Met918Thr SNV in human oncogene RET with the inclusion of a single-nucleotide marker, followed by absolute markerless, scarless repair of the RET SNV with no detected off-target effects. The markerless method was then confirmed in human type VII collagen-encoding gene COL7A1. Thus, using this One-SHOT method, we successfully reduced the number of genetic manipulations required for genome repair from two consecutive events to one, resulting in allele-specific repair that can be completed within 3 weeks, with or without a single-nucleotide marker. Our findings suggest that One-SHOT can be used to repair other types of mutations, with potential beyond human medicine.

Genetic Anomalies of the Respiratory Tract

Hereditary lung diseases can affect the airways, parenchyma and vasculature of the lung. Such diseases comprehend simple monogenic disorders such as Kartagener syndrome and α1-antitrypsin deficiency, in which mutations of critical genes are sufficient to induce well‐defined disease phenotypes. A major comprehension of the genetic basis of pulmonary diseases has produced new investigations into their underlying pathophysiology and contributed sometimes to clarify on more frequent sporadic forms. The presence of these structural abnormalities of the respiratory tract can be fatal, so that the identification of causative genes has allowed prenatal diagnosis for many diseases giving a greater hope of survival thanks to a more adequate and prompt management.

A Maturation Index Defines Newly Diagnosed Multiple Myeloma Patients with Advanced Immunophenotypic and Molecular Differentiation Profiles Associated with Poor Prognosis

A Maturation Index Defines Newly Diagnosed Multiple Myeloma Patients with Advanced Immunophenotypic and Molecular Differentiation Profiles Associated with Poor Prognosis

PF560 A MATURATION INDEX DEFINES NEWLY DIAGNOSED MULTIPLE MYELOMA PATIENTS WITH ADVANCED IMMUNOPHENOTYPIC AND MOLECULAR DIFFERENTIATION PROFILES ASSOCIATED WITH POOR PROGNOSIS

Background:The differentiation status plasticity of Multiple Myeloma (MM) plasma cells (PC) is an adaptive strategy that might confer a specific fitness to tumour cells, enabling their interaction to an evolving microenvironment. Therefore, MM clones are not constantly “fit”, and the immunophenotypic profile of the fittest MM PCs might be the expression of specific genetic and genomic programs, emerging under therapeutic pressure and promoting tumour development. However, the genomic background that supports any diverse plasma cell differentiation phenotypes has not yet been inferred.Aims:To correlate the genetic and genomic background with the immunophenotypic profile of MM clones at diagnosis, in order to stratify patients (pts) according to a Maturation Index, and ultimately to evaluate the impact of this stratification on the disease outcome.Methods:114 newly diagnosed MM pts were included in the study. For each pts, both the neoplastic PCs and CD19+ B cells compartments were characterized by 6‐color multi‐parameter flow cytometry analysis, combining CD138‐PE, CD38‐PE‐Cy7, CD56‐APC‐Cy7, CD20‐APC, CD19‐FITC, CD27‐APC, CD45‐PerCp, CD28‐APC, CD117‐FITC, CD28‐APC, CD81‐APC, IgK‐APC and IgL‐FITC. Both whole‐genome copy number alterations (CNAs) and a 25‐genes targeted mutational panel were assessed in CD138+ PCs. A custom ddPCR assay was employed to evaluate the self‐renewal status of PCs.Results:In order to define a Maturation Index, pts were evaluated for: a) differential expression of CD19/CD81 markers; b) level of chromosomal instability (CIN); c) self‐renewal status.According to the CD19 and CD81 markers co‐expression, we were able to stratify pts in 3 different subgroups, recapitulating a progressive PC maturation process: the most immature, which included pts with PCs CD19+/CD81+ (20/114 = 17%); an intermediate CD19‐/CD81+ phenotype subgroup (40/114 = 35%); and the CD19‐/CD81‐ PC subgroup (54/114 = 48%), whose clone was mainly composed by most mature plasma cells.CIN was defined according to both the total CNAs count and the portion of genome changed (GC). Pts with an advanced differentiation status (CD19‐/CD81‐) were more frequently associated to a high CIN (medium tot. CNAs = 550, % GC ≥ 25%), including a higher prevalence of high‐risk features. Indeed, 1p deletion (FAF1), 16q deletion (WWOX, FANCA) and 17p deletion (TP53) were the most recurrent abnormalities. Genomic instability was also confirmed by a higher incidence of clonal pathogenic mutations in critical genes (e.g. NRAS, KRAS, TP53). Interestingly, the application of a 10 Hh‐genes signature, resuming the Hedgehog pathway, demonstrated that PCs with more advanced differentiation status displayed a substantial overexpression of all the genes, indicating a more proliferative, aggressive and, possibly, persistent phenotype.Finally, the presence of a more mature PCs characterized pts carrying baseline clinical features associated to bad prognosis (e.g. n. PET lesions, k/l ratio, ISS III, β2‐microglobulin; p &lt; .05). In addition, these pts tended to obtain high quality response rates (≥VGPR) to PI induction therapy.Summary/Conclusion:An iMMature index defined pts with an advanced differentiation status both at immunophenotypic as well as at molecular level, and this is lastly associated with a prevalence of bad prognosis features. Chromosomal instability, together with cellular phenotypic plasticity, represents an important, yet poorly defined, mechanism by which MM clones accelerate their own evolution and survival.Acknowledgements: AIRC IG2014, Fondazione Berlucchi.

Oncogenic Y68 frame shift mutation of PTEN represents a mechanism of docetaxel resistance in endometrial cancer cell lines

In this study, we aimed to identify mutations of key genes associated with docetaxel resistance in nine endometrial cancer cell lines. Endometrial cancers are associated with several critical gene mutations, including PIK3A, PTEN, and KRAS. Different gene mutations in endometrial cancer cells have varied responses to anticancer drugs and cancer therapies. The most frequently altered gene in endometrioid endometrial carcinoma tumors is PTEN. PTEN protein has lipid phosphatase and protein phosphatase activity, as well as other functions in the nucleus. Although the tumor-suppressive function of PTEN has mainly been attributed to its lipid phosphatase activity, a role for PTEN protein phosphatase activity in cell cycle regulation has also been suggested. Various tumor type-specific PTEN mutations are well documented. Here, nine endometrioid endometrial cancer cell lines with PIK3A, PTEN, and KRAS gene mutations were treated with docetaxel and radiation. One mutation with a docetaxel drug-resistant effect was a truncated form of PTEN. Among PTEN mutations in endometrial cancer cells, the Y68 frame shift mutation of PTEN constitutes a major mechanism of resistance to docetaxel treatment. The molecular mechanism involves truncation of the 403 amino acid PTEN protein at amino acid 68 by the Y68 frame shift, leading to the loss of PTEN protein phosphatase and lipid phosphatase activities.

EGFR mono-antibody salvage therapy for locally advanced and distant metastatic penile cancer: Clinical outcomes and genetic analysis

PurposeThere are limited therapeutic options for patients with advanced penile squamous cell carcinoma (PSCC) after chemotherapy failure. Thus, we evaluated the feasibility of salvage treatment using the epidermal growth factor receptor (EGFR) mono-antibody nimotuzumab in chemotherapy-failed PSCC patients and explored potential response or resistance biomarkers. Materials and methodsSix chemotherapy-failed PSCC patients with locally advanced disease or distant metastasis were enrolled consecutively to nimotuzumab treatment. Clinical responses and side effects were evaluated, and genetic characteristics of cancer specimens were analyzed through the next-generation sequencing of hotspot regions in cancer-related genes. ResultsTwo of 6 patients showed partial responses, one was identified as having stable disease, while the other 3 had disease progression after nimotuzumab therapy. Side effects were all welltolerated. Genetic analysis revealed that TP53, CDKN2A, RB1, SMAD4, FLT3, and PIK3CA were the most frequently mutated genes in PSCC specimens, while altered KRAS, HRAS, EGFR, ERBB2, and FLT3 may be correlated with nimotuzumab resistance. Furthermore, 3 patients that were human papillomavirus-positive each showed clinical response or stable disease. ConclusionsEGFR mono-antibody may be a potential modality for locally advanced PSCC patients after chemotherapy failure. Further large-scale clinical studies are needed to elucidate the role of human papillomavirus status and critical gene mutations in the clinical response to EGFR-targeted therapy.

Enfermedades pulmonares hereditarias

Hereditary lung diseases can affect the respiratory tract, parenchyma and the vascular structures of the lung. These conditions include simple monogenic disorders such as Kartagener syndrome and α1-antitrypsin deficiency, where critical gene mutations are sufficient to cause well defined phenotypes of the disease. However, most of these diseases include complex genetic traits in which heredity affects the pathogenesis in a more subtle way, for example, asthma and idiopathic pulmonary fibrosis. A greater understanding of the genetic basis of lung conditions has provided new knowledge regarding its pathophysiology, and in some cases has helped to cast light on the more sporadic forms. It is important to stress that identification of the causative genes has also enabled prenatal diagnosis and genetic counselling for many diseases. We provide an update in this article of the three most relevant genetically based diseases in our environment.

Levels and prognostic impact of circulating markers of inflammation, endothelial activation and extracellular matrix remodelling in patients with lung cancer and chronic obstructive pulmonary disease

BackgroundThe development of both chronic obstructive pulmonary disease (COPD) and lung cancer (LC) is influenced by smoking related chronic pulmonary inflammation caused by an excessive innate immune response to smoke exposure. In addition, the smoking induced formation of covalent bonds between the carcinogens and DNA and the accumulation of permanent somatic mutations in critical genes are important in the carcinogenic processes, and can also induce inflammatory responses.How chronic inflammation is mirrored by serum markers in COPD and LC and if these markers reflect prognosis in patients with LC is, however, largely unknown.MethodsSerum levels of 18 markers reflecting inflammation, endothelial activation and extracellular matrix remodelling were analysed in 207 patients with non-small lung carcinoma (NSCLC) before surgery and 42 COPD patients. 56% of the LC patients also suffered from COPD. The serum samples were analysed by enzyme immunoassays.ResultsSerum levels of OPG, PTX3, AXL, ALCAM, sCD163, CD147, CatS and DLL1 were significantly higher in patients with COPD as compared to patients with LC. High sTNFR1 levels were associated with improved progression free survival (PFS) and overall survival (OS) in LC patients with (PFS hazard ratio (HR) 0.49, OS HR 0.33) and without COPD (OS HR 0.30). High levels of OPG were associated with improved PFS (HR 0.17) and OS (HR 0.14) for LC with COPD. CRP was significantly associated with overall survival regardless of COPD status.ConclusionSeveral markers reflecting inflammation, endothelial activation and extracellular matrix remodelling are elevated in serum from patients with COPD compared to LC patients. Presence of COPD might influence the levels of circulating biomarkers. Some of these markers are also associated with prognosis.

Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains.

Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever. During 2007–2010 the largest Q fever outbreak ever reported occurred in The Netherlands. It is anticipated that strains from this outbreak demonstrated an increased zoonotic potential as more than 40,000 individuals were assumed to be infected. The acquisition of novel genetic factors by these C. burnetii outbreak strains, such as virulence-related genes, has frequently been proposed and discussed, but is not proved yet. In the present study, the whole genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few additionally selected strains from different geographical locations and publicly available genome sequences were used for a comparative bioinformatics approach. The study focuses on the identification of specific genetic differences in the outbreak related CbNL01 strains compared to other C. burnetii strains. In this approach we investigated the phylogenetic relationship and genomic aspects of virulence and host-specificity. Phylogenetic clustering of whole genome sequences showed a genotype-specific clustering that correlated with the clustering observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA). Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP) analysis of complete genome sequences demonstrated the presence of genotype-specific gene contents and SNP variations in C. burnetii strains. It also demonstrated that the currently used MLVA genotyping methods are highly discriminatory for the investigated outbreak strains. In the fully reconstructed genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a relatively large number of transposon-linked genes were identified as compared to the other published complete genome sequences of C. burnetii. Additionally, large numbers of SNPs in its membrane proteins and predicted virulence-associated genes were identified in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.