Resistance-associated Genes Research Articles

The applications of CRISPR screen in functional genomics.

CRISPR technology has rapidly changed the face of biological research, such that precise genome editing has now become routine for many labs within several years of its initial development. CRISPR/Cas9 (Clustered Regularly Interspace Short Palindromic Repeat/CRISPR-associated nuclease 9) gene editing system is a powerful and groundbreaking programmable genome editing technology developed based on an adaptive bacterial and archaea immune system resisting the invasion of exogenous nucleic acid. Compared with traditional genome editing technology, CRISPR/Cas9 system is easier, efficient and less cytotoxic. CRISPR/Cas9 gene editing technology has been applied to many aspects of cancer research, including research on tumor genes, constructing animal tumor models, screening tumor phenotypic-related and resistance-associated gene and cancer gene therapy. In this review, we focus on the application of the CRISPR screen for this fast moving field. Finally, we discuss practical aspects of screen design, and outline a further step forward in the rapidly expanding field of genome editing.

How Antiparasitic Drugs Work-And Sometimes Stop Working!

How Antiparasitic Drugs Work-And Sometimes Stop Working!

Genome Sequence of Riemerella anatipestifer Strain RCAD0122, a Multidrug-Resistant Isolate from Ducks

Riemerella anatipestifer is an important pathogenic bacterium in waterfowl and other avian species. We present here the genome sequence of R. anatipestifer RCAD0122, a multidrug-resistant strain isolated from infected ducks. The isolate contains at least nine types of antibiotic resistance-associated genes.

Autophagic UVRAG Promotes UV-Induced Photolesion Repair by Activation of the CRL4DDB2 E3 Ligase

UV-induced DNA damage, a major risk factor for skin cancers, is primarily repaired by nucleotide excision repair (NER). UV radiation resistance-associated gene (UVRAG) is a tumor suppressor involved in autophagy. It was initially isolated as a cDNA partially complementing UV sensitivity in xeroderma pigmentosum (XP), but this was not explored further. Here we show that UVRAG plays an integral role in UV-induced DNA damage repair. It localizes to photolesions and associates with DDB1 to promote the assembly and activity of the DDB2-DDB1-Cul4A-Roc1 (CRL4(DDB2)) ubiquitin ligase complex, leading to efficient XPC recruitment and global genomic NER. UVRAG depletion decreased substrate handover toXPC and conferred UV-damage hypersensitivity. We confirmed the importance of UVRAG for UV-damage tolerance using a Drosophila model. Furthermore, increased UV-signature mutations in melanoma correlate with reduced expression of UVRAG. Our results identify UVRAG as a regulator of CRL4(DDB2)-mediated NER and suggest that its expression levels may influence melanoma predisposition.

Molecular Detection of Bru1 Gene and Identification of Brown Rust Resistance in Chinese Sugarcane Germplasm

Sugarcane brown rust induced by Puccinia melanocephala is an important global disease. Bru1 is a major brown rust resistance gene and has been shown to provide broad-spectrum resistance against various brown rust pathogen strains originating from different countries. Thus, brown rust resistance genes have important implications for sugarcane brown rust resistance breeding programs. The objectives of this study were to (1) assess the level of resistance of common sugarcane crossbreeding parents to P. melanocephala, (2) determine the distribution of the Bru1 gene in common sugarcane crossbreeding parents in China, (3) screen, evaluate, and select rust-resistant parental lines to improve the efficiency of breeding for brown rust resistance. Brown rust resistance in 101 common sugarcane breeding parents was collected from the Chinese National Nursery of Sugarcane Germplasm Resources and was scored and identified at the seedling stage and was assayed for the presence of the brown rust resistance gene Bru1. The results showed that Bru1 was detected in 48 (47.5 %) resistant clones out of the 101 tested parental lines, indicating that brown rust resistance in common sugarcane breeding parents in China is primarily controlled by Bru1. The apparent absence of Bru1 from the other 29 resistant and 24 susceptible parental lines suggested that they may carry brown rust resistance-associated genes other than Bru1. These results may facilitate future efforts to breed varieties with improved resistance to brown rust and may provide additional resistant parental lines for selecting and planting elite-resistant varieties to effectively control brown rust disease in sugarcane.

Characterization of Virulence-Associated Genes, Antimicrobial Resistance Genes, and Class 1 Integrons in Salmonella enterica serovar Typhimurium Isolates from Chicken Meat and Humans in Egypt.

Foodborne pathogens are leading causes of illness especially in developing countries. The current study aimed to characterize virulence-associated genes and antimicrobial resistance in 30 Salmonella Typhimurium isolates of chicken and human origin at Mansoura, Egypt. The results showed that invA, avrA, mgtC, stn, and bcfC genes were identified in all the examined isolates, while 96.7% and 6.7% were positive for sopB and pef genes, respectively. The highest resistance frequencies of the isolates were to chloramphenicol and trimethoprim-sulfamethoxazole (73.3%, each), followed by streptomycin (56.7%), tetracycline and ampicillin (53.3%, each), and gentamicin (30%). However, only 2.7% of the isolates were resistant to cefotaxime and ceftriaxone each. Different resistance-associated genes, including blaTEM, aadB, aadC, aadA1, aadA2, floR, tetA(A), tetA(B), and sul1, were identified in Salmonella Typhimurium isolates with the respective frequencies of 53.3%, 6.7%, 23.3%, 46.7%, 63.3%, 73.3%, 60%, 20%, and 96.7%. None of the isolates was positive for blaSHV, blaOXA, and blaCMY genes. The results showed that the intI1 gene was detected in 24 (80%) of the examined Salmonella Typhimurium isolates. Class 1 integrons were found in 19 (79.2%) isolates that were intI1 positive. Seven integron profiles (namely: P-I to P-VII) were identified with P-V (gene cassette dfrA15, aadA2), the most prevalent profile. To the best of our knowledge, this is the first study to characterize the unusual gene cassette array dfrA12-OrfF-aadA27 from Salmonella Typhimurium isolates in Egypt.

Stem-cell-specific endocytic degradation defects lead to intestinal dysplasia in Drosophila.

ABSTRACTUV radiation resistance-associated gene (UVRAG) is a tumor suppressor involved in autophagy, endocytosis and DNA damage repair, but how its loss contributes to colorectal cancer is poorly understood. Here, we show that UVRAG deficiency in Drosophila intestinal stem cells leads to uncontrolled proliferation and impaired differentiation without preventing autophagy. As a result, affected animals suffer from gut dysfunction and short lifespan. Dysplasia upon loss of UVRAG is characterized by the accumulation of endocytosed ligands and sustained activation of STAT and JNK signaling, and attenuation of these pathways suppresses stem cell hyperproliferation. Importantly, the inhibition of early (dynamin-dependent) or late (Rab7-dependent) steps of endocytosis in intestinal stem cells also induces hyperproliferation and dysplasia. Our data raise the possibility that endocytic, but not autophagic, defects contribute to UVRAG-deficient colorectal cancer development in humans.

Whole Genome Expression Profiling Analysis of Metastasis and Drug-resistance-related Genes in Epithelial Ovarian Cancer Cells

Objective To investigate the genes associated with higher ability of metastasis and chemotherapic resistance in epithelial ovarian carcinoma (EOC) by using Agilent whole genome oligonucleotide gene chip,with an attempt to further investigate the molecular mechanism of metastasis and chemotherapic resistance of EOC. Methods Oligonucleotide microarrays were used to determine whether gene expression profile might differentiate EOC cell lines (RMG-1-C,COC1 and HO8910) from their sub-lines (RMG-1-H,COC1/DDP and HO8910/PM) with higher ability of metastasis and chemotherapic resistance. Quantitative real-time polymerase chain reaction and immunohistochemical staining validated the microarray results. Results Gene expression profile identified 49 differentially expressed genes that showed≥2.0 fold change. All these differentially expressed genes were involved mainly in gene expression and biopolymer biosynthesis. Interaction network analysis predicted 21 genes participating in the regulatory connection. Highly differential expression of GCET2,CFTR,FOXP1 and GARS genes was validated by quantitative realtime polymerase chain reaction in all cell line samples,and the Results were consistent with microarray findings. Conclusion The change in the metastasis and chemotherapic resistance-associated gene expression profiles may provide a theoretical basis for studies on the molecular mechanisms of metastasis and chemotherapic resistance in EOC.

Systematic analyses of the ultraviolet radiation resistance-associated gene product (UVRAG) protein interactome by tandem affinity purification.

Ultraviolet radiation resistance-associated gene product (UVRAG) was originally identified as a protein involved in cellular responses to UV irradiation. Subsequent studies have demonstrated that UVRAG plays as an important role in autophagy, a lysosome-dependent catabolic program, as a part of a pro-autophagy PIK3C3/VPS34 lipid kinase complex. Several recent studies have shown that UVRAG is also involved in autophagy-independent cellular functions, such as DNA repair/stability and vesicular trafficking/fusion. Here, we examined the UVRAG protein interactome to obtain information about its functional network. To this end, we screened UVRAG-interacting proteins using a tandem affinity purification method coupled with MALDI-TOF/MS analysis. Our results demonstrate that UVRAG interacts with various proteins involved in a wide spectrum of cellular functions, including genome stability, protein translational elongation, protein localization (trafficking), vacuole organization, transmembrane transport as well as autophagy. Notably, the interactome list of high-confidence UVRAG-interacting proteins is enriched for proteins involved in the regulation of genome stability. Our systematic UVRAG interactome analysis should provide important clues for understanding a variety of UVRAG functions.

Genomic Analysis of Detoxification Supergene Families in the Mosquito Anopheles sinensis.

Anopheles sinensis is an important malaria vector in China and other Southeast Asian countries, and the emergence of insecticide resistance in this mosquito poses a serious threat to the efficacy of malaria control programs. The recently published An. sinensis genome and transcriptome provide an opportunity to understand the molecular mechanisms of insecticide resistance. Analysis of the An. sinensis genome revealed 174 detoxification genes, including 93 cytochrome P450s (P450s), 31 glutathione-S-transferases (GSTs), and 50 choline/carboxylesterases (CCEs). The gene number was similar to that in An. gambiae, but represented a decrease of 29% and 42% compared with Aedes aegypti and Culex quinquefasciatus, respectively. The considerable contraction in gene number in Anopheles mosquitoes mainly occurred in two detoxification supergene families, P450s and CCEs. The available An. sinensis transcriptome was also re-analyzed to further identify key resistance-associated detoxification genes. Among 174 detoxification genes, 124 (71%) were detected. Several candidate genes overexpressed in a deltamethrin-resistant strain (DR-strain) were identified as belonging to the CYP4 or CYP6 family of P450s and the Delta GST class. These generated data provide a basis for identifying the resistance-associated genes of An. sinensis at the molecular level.

Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Genotypes That Are Susceptible, Resistant, and Hypersensitive to Reniform Nematode (Rotylenchulus reniformis).

Reniform nematode is a semi-endoparasitic nematode species causing significant yield loss in numerous crops, including cotton (Gossypium hirsutum L.). An RNA-sequencing analysis was conducted to measure transcript abundance in reniform nematode susceptible (DP90 & SG747), resistant (BARBREN-713), and hypersensitive (LONREN-1) genotypes of cotton (Gossypium hirsutum L.) with and without reniform nematode infestation. Over 90 million trimmed high quality reads were assembled into 84,711 and 80, 353 transcripts using the G. arboreum and the G. raimondii genomes as references. Many transcripts were significantly differentially expressed between the three different genotypes both prior to and during nematode pathogenesis, including transcripts corresponding to the gene ontology categories of cell wall, hormone metabolism and signaling, redox reactions, secondary metabolism, transcriptional regulation, stress responses, and signaling. Further analysis revealed that a number of these differentially expressed transcripts mapped to the G. raimondii and/or the G. arboreum genomes within 1 megabase of quantitative trait loci that had previously been linked to reniform nematode resistance. Several resistance genes encoding proteins known to be strongly linked to pathogen perception and resistance, including LRR-like and NBS-LRR domain-containing proteins, were among the differentially expressed transcripts mapping near these quantitative trait loci. Further investigation is required to confirm a role for these transcripts in reniform nematode susceptibility, hypersensitivity, and/or resistance. This study presents the first systemic investigation of reniform nematode resistance-associated genes using different genotypes of cotton. The candidate reniform nematode resistance-associated genes identified in this study can serve as the basis for further functional analysis and aid in further development of reniform a nematode resistant cotton germplasm.

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.

Motivation: A major goal of biomedical research is to identify molecular features associated with a biological or clinical class of interest. Differential expression analysis has long been used for this purpose; however, conventional methods perform poorly when applied to data with high within class heterogeneity.Results: To address this challenge, we developed EMDomics, a new method that uses the Earth mover’s distance to measure the overall difference between the distributions of a gene’s expression in two classes of samples and uses permutations to obtain q-values for each gene. We applied EMDomics to the challenging problem of identifying genes associated with drug resistance in ovarian cancer. We also used simulated data to evaluate the performance of EMDomics, in terms of sensitivity and specificity for identifying differentially expressed gene in classes with high within class heterogeneity. In both the simulated and real biological data, EMDomics outperformed competing approaches for the identification of differentially expressed genes, and EMDomics was significantly more powerful than conventional methods for the identification of drug resistance-associated gene sets. EMDomics represents a new approach for the identification of genes differentially expressed between heterogeneous classes and has utility in a wide range of complex biomedical conditions in which sample classes show within class heterogeneity.Availability and implementation: The R package is available at http://www.bioconductor.org/packages/release/bioc/html/EMDomics.htmlContact: abeck2@bidmc.harvard.eduSupplementary information: supplementary data are available at Bioinformatics online.

Carriage of Haemophilus influenzae in the oropharynx of young children and molecular epidemiology of the isolates after fifteen years of H. influenzae type b vaccination in Italy

BackgroundHaemophilus influenzae is an important pathogen able to cause a wide spectrum of diseases in children. Colonization of the upper respiratory tract is a risk factor for developing disease. This study aimed to investigate the oropharyngeal carriage rate of H. influenzae in young children in two Italian cities, 15 years after H. influenzae type b (Hib) vaccination was introduced. Antibiotic resistant traits and genotypes of the colonizing H. influenzae isolates were investigated. MethodsOropharyngeal swabs were obtained from 717 healthy children aged <6 years (June 2012–July 2013). Potential risk factors for H. influenzae colonization were investigated. H. influenzae isolates from carriage were characterized by PCR capsular typing, ampicillin susceptibility testing, resistance-associated gene sequencing and multilocus sequence typing (MLST). For comparison purposes, 38 non-typeable H. influenzae (NTHi) isolates from invasive disease were genotyped by MLST. ResultsThe overall H. influenzae carriage rate was 14.1% (101/717). Age, study site, presence of young siblings, and complete Hib vaccination status were independently associated with colonization. Of 101 isolates, 98 were NTHi, 2 were type e and 1 was type f. The overall ampicillin resistance rate was 15.8% (16/101). Resistance was mediated by TEM-1 β-lactamase production in half of isolates (n=8) or modifications in penicillin-binding protein (PBP) 3 in the other half (n=8). Several substitutions were discovered in PBP3 including the Asn526Lys change. Seventy-six different STs were identified among 98 NTHi isolates from carriage, with only 4 STs (ST12, ST57, ST238, ST1238) encompassing ≥3 isolates. Comparison of carriage and disease isolates found that several STs were shared between the two sources, although none of the major disease-associated STs were observed in carriage isolates. ConclusionsNTHi is the predominant serotype in carriage. The importance of monitoring both NTHi colonization rate and circulating genotypes should be emphasized in the era of the Hib conjugate vaccines.

Class III PI3K regulates organismal glucose homeostasis by providing negative feedback on hepatic insulin signalling.

Defective hepatic insulin receptor (IR) signalling is a pathogenic manifestation of metabolic disorders including obesity and diabetes. The endo/lysosomal trafficking system may coordinate insulin action and nutrient homeostasis by endocytosis of IR and the autophagic control of intracellular nutrient levels. Here we show that class III PI3K—a master regulator of endocytosis, endosomal sorting and autophagy—provides negative feedback on hepatic insulin signalling. The ultraviolet radiation resistance-associated gene protein (UVRAG)-associated class III PI3K complex interacts with IR and is stimulated by insulin treatment. Acute and chronic depletion of hepatic Vps15, the regulatory subunit of class III PI3K, increases insulin sensitivity and Akt signalling, an effect that requires functional IR. This is reflected by FoxO1-dependent transcriptional defects and blunted gluconeogenesis in Vps15 mutant cells. On depletion of Vps15, the metabolic syndrome in genetic and diet-induced models of insulin resistance and diabetes is alleviated. Thus, feedback regulation of IR trafficking and function by class III PI3K may be a therapeutic target in metabolic conditions of insulin resistance.

Application Progress of CRISPR/Cas9 System for Gene Editing in Tumor Research

CRISPR/Cas9（Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated nuclease 9）基因编辑系统是基于古细菌抵御外源核酸入侵的免疫机制为基础开发出来的一种新型的基因编辑技术。相对于传统的基因编辑系统，该系统具有更加高效、操作简单、细胞毒性小等特点。目前，CRISPR/Cas9基因编辑技术已经在肿瘤研究的诸多方面中得到应用，包括肿瘤相关基因的功能研究、构建动物肿瘤模型、筛选肿瘤细胞表型及耐药相关基因以及肿瘤的基因治疗等诸多方面。本文就其在肿瘤研究中的应用进展进行综述。

Comparative transcriptome analyses of deltamethrin-susceptible and -resistant Culex pipiens pallens by RNA-seq.

The widespread and improper use of pyrethroid insecticides, such as deltamethrin, has resulted in the evolution of resistance in many mosquito species, including Culex pipiens pallens. With the development of high-throughput sequencing, it is possible to massively screen pyrethroid resistance-associated gene. In this study, we used Illumina-Solexa transcriptome sequencing to identify genes that are expressed differently in deltamethrin-susceptible and -resistant strains of Culex pipiens pallens as a critical knowledge base for further studies. A total of 4,961,197,620 base pairs and 55,124,418 reads were sequenced, mapped to the Culex quinquefasciatus genome and assembled into 17,679 known genes. We recorded 1826 significantly differentially expressed genes (DEGs). Among them, 1078 genes were up-regulated and 748 genes were down-regulated in the deltamethrin-resistant strain compared to -susceptible strain. These DEGs contained cytochrome P450s, cuticle proteins, UDP-glucuronosyltransferases, lipases, serine proteases, heat shock proteins, esterases and others. Among the 1826 DEGs, we found that the transcriptional levels of CYP6AA9 in the laboratory populations was elevated as the levels of deltamethrin resistance increased. Moreover, the expression levels of the CYP6AA9 were significantly higher in the resistant strains than the susceptible strains in three different field populations. We further confirmed the association between the CYP6AA9 gene and deltamethrin resistance in mosquitoes by RNA interfering (RNAi). Altogether, we explored massive potential pyrethroid resistance-associated genes and demonstrated that CYP6AA9 participated in the pyrethroid resistance in mosquitoes.

Identification and antimicrobial susceptibility of obligate anaerobic bacteria from clinical samples of animal origin

The etiology of veterinary infectious diseases has been the focus of considerable research, yet relatively little is known about the causative agents of anaerobic infections. Susceptibility studies have documented the emergence of antimicrobial resistance and indicate distinct differences in resistance patterns related to veterinary hospitals, geographic regions, and antibiotic-prescribing regimens. The aim of the present study was to identify the obligate anaerobic bacteria from veterinary clinical samples and to determinate the in vitro susceptibility to eight antimicrobials and their resistance-associated genes. 81 clinical specimens obtained from food-producing animals, pets and wild animals were examined to determine the relative prevalence of obligate anaerobic bacteria, and the species represented. Bacteroides spp, Prevotella spp and Clostridium spp represented approximately 80% of all anaerobic isolates. Resistance to metronidazole, clindamycin, tetracycline and fluoroquinolones was found in strains isolated from food-producing animals. Ciprofloxacin, enrofloxacin and cephalotin showed the highest resistance in all isolates. In 17%, 4% and 14% of tetracycline-resistant isolates, the resistance genes tetL, tetM and tetW were respectively amplified by PCR whereas in 4% of clindamycin-resistant strains the ermG gene was detected. 26% of the isolates were positive for cepA, while only 6% harbored the cfxA (resistance-conferring genes to beta-lactams). In this study, the obligate anaerobic bacteria from Costa Rica showed a high degree of resistance to most antimicrobials tested. Nevertheless, in the majority of cases this resistance was not related to the resistance acquired genes usually described in anaerobes. It is important to address and regulate the use of antimicrobials in the agricultural industry and the empirical therapy in anaerobic bacterial infections in veterinary medicine, especially since antibiotics and resistant bacteria can persist in the environment.

Analysis of UB and L40 resistance related to deltamethrin in Drosophila kc cells

Pests have been subjected to heavy selection pressure, and the development of resistance to pyrethroid has been recorded. It is extremely valuable to identify the resistance genes that are relevant for pest control. In our previous studies, we reported that UBL40 is the deltamethrin resistance-associated gene. UBL40 is cleaved by specific endopeptidases to release UB and L40. Whether UB or L40 participates in deltamethrin resistance requires further study. In this study, quantitative real-time PCR was applied to reveal that UB and L40 were both overexpressed in Drosophila kc cells after deltamethrin stimulation. To investigate the roles of UB and L40 further, RNA interferences (RNAi) and cell transfections were utilized. UB and L40 knockdown both significantly reduced the level of resistance of RNAi-treated cells after 48h, and the overexpressions of UB and L40 in Drosophila kc cells conferred a degree of protection against deltamethrin. These results represent the first evidence that UB and L40 both play roles in the regulation of deltamethrin resistance and that this study could help us to elucidate the resistance mechanisms and identify new target genes associated with resistance.

Transcription factors, CncC and Maf, regulate expression of CYP6BQ genes responsible for deltamethrin resistance in Tribolium castaneum

Insecticide resistance is a global problem that presents an ongoing challenge to control insects that destroy crops, trees and transmit diseases. Dramatic progress has been made during the last decade on identification of insecticide resistance-associated genes. In one of the most common resistance mechanisms, insects acquire resistance by increasing the levels of their detoxification enzymes especially the cytochrome P450 monooxygenases (P450's). Previous studies in our laboratory showed that the pyrethroid resistance in QTC279 strain of Tribolium castaneum is achieved through constitutive overexpression of the P450 gene CYP6BQ9 by 200-fold higher in the resistant strain as compared to that in the susceptible strain. RNAi-aided knockdown in the expression of probable genes that regulate P450 gene expression in QTC279 identified cap ‘n’ collar C (CncC) and muscle aponeurosis fibromatosis (Maf) family transcription factors as the key regulator of these genes, CncC and Maf regulate expression of multiple genes in the CYP6BQ cluster. Studies on the promoters of these genes using reporter assays identified binding sites that mediate CncC and Maf regulation of CYP6BQ gene expression.

Abstract 4245: Detection of fusion genes in lung cancer biopsies of crizotinib resistant patients

Abstract Purpose: A small proportion of lung cancer patients have an inversion involving the ALK gene on chromosome 2. These ALK+ patients initially respond to crizotinib, but later develop progressive disease. This resistance can be due to gatekeeper mutations in the kinase domain of the ALK gene like L1196M and G1269A, copy number gain of the EML4-ALK fusion gene, and mutations in EGFR and KRAS. We aimed at identifying fusion genes that may explain the resistance mechanism in patients progressing on crizotinib. Materials and Methods: Frozen tissue of the resistant tumor samples was available for four EML4-ALK positive patients (Table 1). Paired end RNA sequencing was performed using the Illumina TruSeq RNA platform. DeFuse (v.0.6.1) was used to identify fusion products. Candidate fusion genes were validated by RT-PCR. In addition, we used the IGV browser to identify mutations in resistance-associated genes in the RNA-seq data. Results: Thirteen fusions genes were identified with high confidence (Table 1). In three of the four patients we detected an EML4-ALK fusion product. Four novel fusion products with a functional ORF were confirmed by RT-PCR. Three of these fusion products were present in patient 1 (Table 1). The fourth fusion involving CLIP4-VSNL1 was detected in patient 3. Interestingly, three of the 4 fusion products observed in patient 3 involved 5 genes that are all close to the ALK locus, i.e. EML4, ALK, CLIP4, VSNL1 and MCFD2 (Table 1). In addition, we found two resistance-related mutations in the tyrosine kinase domain of the ALK gene, i.e. p.C1156Y and p.G1269A, in patients 2 and 3, respectively. Fusion products in four crizotinib resistant lung cancer patientsPatientAgeSmokingALK immunohistochemistryTumor response (PFS in months)Fusion genesORF147CurrentNot availableNo (1.4)RAB35-ATP2A2YesSLC10A7-TTC29YesSTAB2-NUAK1YesKMT2B-AC002115.9NoPIAS1-SLC24A6NoZNF827-ARHGAP10No227None+Yes (9.2)EML4-ALKYesNRG1-RBPMSNo342None+Yes (10.4)EML4-ALKYesCLIP4-VSNL1YesMCFD2-CLIP4NoCPSF6-RBMS2No456Current+Yes (15.7)EML4-ALKYes Conclusion: We found four new fusion products with a functional ORF using RNA sequencing of crizotinib resistant tumor samples. Further analysis of the primary tumor samples is ongoing and will reveal if these fusion genes might have been induced by the crizotinib treatment. Two of the four patients have a known resistance-inducing mutation in the ALK gene. Citation Format: Ali Saber, Anthonie van der Wekken, Klaas Kok, Martijn M. Terpstra, Mirjam F. Mastik, Wim Timens, Ed M.D. Schuuring, T. Jeroen Hiltermann, Harry J.M. Groen, Anke van den Berg. Detection of fusion genes in lung cancer biopsies of crizotinib resistant patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4245. doi:10.1158/1538-7445.AM2015-4245