Over-expression of CYP6A2 is associated with spirotetramat resistance and cross-resistance in the resistant strain of Aphis gossypii Glover

A laboratory-selected spirotetramat-resistant strain (SR) of cotton aphid developed 579-fold and 15-fold resistance to spirotetramat in adult aphids and 3rd instar nymphs, respectively, compared with a susceptible strain (SS) [26]. The SR strain developed high-level cross-resistance to alpha-cypermethrin and bifenthrin and very low or no cross-resistance to the other tested insecticides. Synergist piperonyl butoxide (PBO) dramatically increased the toxicity of spirotetramat and alpha-cypermethrin in the resistant strain. RT-qPCR results demonstrated that the transcriptional levels of CYP6A2 increased significantly in the SR strain compared with the SS strain, which was consistent with the transcriptome results [30]. The depletion of CYP6A2 transcripts by RNAi also significantly increased the sensitivity of the resistant aphid to spirotetramat and alpha-cypermethrin. These results indicate the possible involvement of CYP6A2 in spirotetramat resistance and alpha-cypermethrin cross-resistance in the cotton aphid. These together with other cross-resistance results have implications for the successful implementation of resistance management strategies for Aphis gossypii.

Diaphragm muscle fiber injury after inspiratory resistive breathing

Five awake previously tracheotomized mongrel dogs were challenged with inspiratory resistive breathing (IRB). The mean peak tracheal pressure = -35.4 +/- 1.1 cmH2O, ETCO2 = 39.8 +/- 1.5 mmHg was sustained for 2 h/d over 4 consecutive d. On the fourth day, following IRB, the dogs were placed under general anaesthesia, and the diaphragm was perfused via the internal mammary artery with a low molecular weight fluorescent tracer (Procion orange, FW = 631), to which normal muscle fibers are impermeable. Muscle fiber membrane damage was identified on tissue sections by using fluorescent microscopy showing the presence of the tracer in the cytoplasm. Four dogs undergoing the same protocol (except IRB) served as control. The dye was seen in 7.6 +/- 2.6% and in 0.3 +/- 0.1% of fibers in the IRB and control groups, respectively (p < 0.05). Via ATPase staining, it was found that fibers of type I were predominantly affected as compared to type II (p < 0.05). In addition, an increased area fraction of fibers demonstrating sarcomere disruption was found after IRB (2.4 +/- 0.5%) compared to pre-IRB (0.4 +/- 0.1%; p < 0.05). We conclude that resistive breathing of a magnitude similar to that seen in some respiratory diseases, or used in respiratory muscle training programs induces muscle membrane and sarcomere injury.

Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors

Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93.3% sensitivity and 100% specificity for fusion detection. Assessment of repeatability and reproducibility revealed 96.3% and 94.4% concordance between intrarun and interrun technical replicates, respectively. Application of this assay on prospective patient samples uncovered OLFM4 as a novel RET fusion partner in a small-bowel cancer and led to the discovery of a KLK2-FGFR2 fusion in a patient with prostate cancer who subsequently underwent treatment with a pan-fibroblast growth factor receptor inhibitor. Beyond fusion detection, OSU-SpARKFuse has built-in capabilities for discovery research, including gene expression analysis, detection of single-nucleotide variants, and identification of alternative splicing events.

Dystonin-deficient mice exhibit an intrinsic muscle weakness and an instability of skeletal muscle cytoarchitecture

Dystonia musculorum (dt) was originally described as a hereditary sensory neurodegeneration syndrome of the mouse. The gene defective in dt encodes a cytoskeletal linker protein, dystonin, that is essential for maintaining neuronal cytoskeletal integrity. In addition to the nervous system, dystonin is expressed in a variety of other tissues, including muscle. We now show that dystonin cross-links actin and desmin filaments and that its levels are increased during myogenesis, coinciding with the progressive reorganization of the intermediate filament network. A disorganization of cytoarchitecture in skeletal muscle from dt/dt mice was observed in ultrastructural studies. Myoblasts from dt/dt mice fused to form myotubes in culture; however, terminally differentiated myotubes contained incompletely assembled myofibrils. Another feature observed in dt/dt myotubes in culture and in skeletal muscle in situ was an accumulation and abnormal distribution of mitochondria. The diaphragm muscle from dt/dt mice was weak in isometric contractility measurements in vitro and was susceptible to contraction-induced sarcolemmal damage. Altogether, our data indicate that dystonin is a cross-linker of actin and desmin filaments in muscle and that it is essential for establishing and maintaining proper cytoarchitecture in mature muscle.

Expression of myosin heavy-chain isoforms in the respiratory muscles following inspiratory resistive breathing

We investigated the effect of inspiratory resistive breathing (IRB) on the expression of the genes encoding fast and slow isoforms of myosin heavy chain (MyHC) in respiratory muscles. Eleven mongrel dogs were studied for baseline MyHC messenger RNA (mRNA) expression, seven of which were also used to study the effects of IRB. For this latter objective, awake and spontaneously breathing animals were subjected to 2 h of IRB (80 cm H(2)O/L/s) per day for four consecutive days. mRNA expression was assessed in the diaphragm, external intercostal muscle, and a limb muscle, using both slot- blot and in situ hybridizations with isoform-specific probes. A current semiquantitative scoring method (from 0 to 4) was used to quantify the in situ mRNA expression levels, and slot-blot data were analyzed with densitometry. Prior to IRB, slow- and fast-MyHC mRNA expression was moderate, similar, and homogeneous throughout the different regions of the diaphragm, with scores of 1.50 +/- 0.54 (mean +/- SD) for slow and 2.13 +/- 0.35 for fast mRNAs in the costal region of the diaphragm, and of 1.81 +/- 0.37 for slow and 2. 13 +/- 0.64 for fast mRNAs in the crural region of the diaphragm. Although expression of fast-MyHC mRNA remained unchanged after IRB, the relative expression of the mRNA for the slow isoform increased in costal (+30%), crural (+12%), and external intercostal (+27%) muscles. MyHC mRNA expression did not change in limb muscles. We conclude that breathing with a moderate inspiratory resistance for a short period induces the expression of slow MyHC in respiratory muscles.

Cancer Driver Log (CanDL): Catalog of Potentially Actionable Cancer Mutations

Massively parallel sequencing technologies have enabled characterization of genomic alterations across multiple tumor types. Efforts have focused on identifying driver mutations because they represent potential targets for therapy. However, because of the presence of driver and passenger mutations, it is often challenging to assign the clinical relevance of specific mutations observed in patients. Currently, there are multiple databases and tools that provide in silico assessment for potential drivers; however, there is no comprehensive resource for mutations with functional characterization. Therefore, we created an expert-curated database of potentially actionable driver mutations for molecular pathologists to facilitate annotation of cancer genomic testing. We reviewed scientific literature to identify variants that have been functionally characterized in vitro or in vivo as driver mutations. We obtained the chromosome location and all possible nucleotide positions for each amino acid change and uploaded them to the Cancer Driver Log (CanDL) database with associated literature reference indicating functional driver evidence. In addition to a simple interface, the database allows users to download all or selected genes as a comma-separated values file for incorporation into their own analysis pipeline. Furthermore, the database includes a mechanism for third-party contributions to support updates for novel driver mutations. Overall, this freely available database will facilitate rapid annotation of cancer genomic testing in molecular pathology laboratories for mutations.

Spirotetramat resistance adaption analysis of Aphis gossypii Glover by transcriptomic survey

A resistant strain of the cotton aphid (SR) developed 441.26-fold and 11.97-fold resistance to spirotetramat for adult aphids and nymphs, respectively, compared with the susceptible (SS) strain. Solexa sequencing technology was employed to identify differentially expressed genes (DEGs) in the spirotetramat-resistant cotton aphid. Respective totals of 22,430,522 and 21,317,732 clean reads were obtained from SR and SS cDNA libraries and assembled into 35,222 non-redundant (Nr) consensus sequences. A total of 14,913, 9,220, 7,922, 4,314 and 4,686 sequences were annotated using Nr, Swiss-Prot, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), respectively. Compared with the SS strain, the SR strain had 1287 significantly changed unigenes, of which 130 genes were up-regulated and 1157 genes were down-regulated (P ≤ 0.001). Among these genes, 440 unigenes were annotated, consisting of 114 up-regulated and 326 down-regulated genes. The expression levels of heat shock protein 70 (Hsp70) and UDP-glucuronosyltransferase were significantly up-regulated in the SR strain compared to the SS strain. The genes encoding cuticle proteins, salivary glue protein, fibroin heavy chain, energy ATP synthase, and cytochrome c oxidase were dramatically decreased. Among the DEGs, cytochrome P450 6A2 (c20965.graph_c0) was the only P450 gene up-regulated in the SR strain. The expression levels of 10 DEGs were confirmed by real-time qPCR, and the trends in gene expression observed by qPCR matched those of the Solexa expression profiles. The acetyl-CoA carboxylase (ACC) genes in the SR and SS libraries both contain four single nucleotide polymorphisms (SNPs), with three common SNPs: 1227 (C/T), 1811 (A/T: F/Y) and 3759 (C/T); however, 7540 (A/T) and 108 (G/A) occurred solely in the SS and SR strains, respectively.

Functional magnetic stimulation for conditioning of expiratory muscles in patients with spinal cord injury

OBJECTIVE

To evaluate the effectiveness of functional magnetic stimulation (FMS) in conditioning expiratory muscles patients with spinal cord injury (SCI).

DESIGN

A prospective before-after trial.

SETTING

The Functional Magnetic Stimulation Laboratory of the SCI Health Care Group, VA Long Beach Health Care System, and the Spinal Cord Injury Services, Department of Veterans Affairs, Palo Alto Health Care System.

PARTICIPANTS

Eight men with tetraplegia.

INTERVENTION

Expiratory muscle training was achieved by placing a magnetic stimulator with a round magnetic coil along subjects' lower thoracic spine.

MAIN OUTCOME MEASURES

Measures taken were the maximal expired pressure at total lung capacity (MEP-TLC) and at functional residual capacity (MEP-FRC), expiratory reserve volume (ERV), and the forced expiratory flow rate at TLC (FEF-TLC) and at FRC (FEF-FRC) by subjects' voluntary maximal efforts.

RESULTS

After 4 weeks of conditioning, the mean +/- standard error of the mean values were: MEP-TLC, 55.3 +/- 8.6cmH(2)O; MEP-FRC, 29.6 +/- 5.6cmH(2)O; ERV,.57 +/-.08L; FEF-TLC, 4.3 +/- 0.5L/s; and FEF-FRC, 1.9 +/- 0.2L/s. These values correspond to, respectively, 129%, 137%, 162%, 109%, and 127% of pre-FMS conditioning values. When FMS was discontinued for 2 weeks, the MEP-TLC returned to its pre-FMS training value.

CONCLUSION

A 4-week protocol of FMS of the expiratory muscles improves voluntary expiratory muscle strength significantly, indicating that FMS can be a noninvasive therapeutic technology in respiratory muscle training for persons with tetraplegia.

Ontogenesis of nitric oxide synthases in the ventilatory muscles

Nitric oxide (NO) acts as an endogenous mediator in mature skeletal muscle. In this study, we investigated the regulation of the endothelial (eNOS) and neuronal (nNOS) isoforms of nitric oxide synthase (NOS) in skeletal-muscle development (rat diaphragm). Muscle NOS activity, nNOS and eNOS protein, and mRNA expressions were markedly increased during the late gestational and early postnatal periods. Expression of both isoforms, however, declined progressively thereafter. Similarly, argininosuccinate lyase and argininosuccinate synthetase, both involved in the recycling of L-citrulline to L-arginine, were expressed at high levels in rat embryonic and neonatal diaphragms, with gradual reduction in their expression during late postnatal development. Immunostaining revealed extensive nNOS expression at the sarcolemma in neonatal and mature diaphragms, whereas eNOS expression was limited to the endothelium. Both neonatal and adult diaphragms expressed an alternatively spliced nNOS isoform with an insert of 34 amino acids between exons 16 and 17. In vitro-generated muscle force rose significantly after NOS inhibition in both neonatal and adult diaphragms, but the magnitude of force augmentation was larger in adult than in neonatal diaphragm. These results indicate that constitutive NOS isoforms are developmentally regulated in skeletal muscles, suggesting multiple roles for NO in developing and mature skeletal-muscle fibers.

Toxin-antitoxin operon kacAT of Klebsiella pneumoniae is regulated by conditional cooperativity via a W-shaped KacA-KacT complex

Bacterial toxin–antitoxin pairs play important roles in bacterial multidrug tolerance. Gcn5-related N-acetyltransferase (GNAT) toxins inhibit translation by acetylation of aminoacyl-tRNAs and are counteracted by direct contacts with cognate ribbon–helix–helix (RHH) antitoxins. Our previous analysis showed that the GNAT toxin KacT and RHH antitoxin KacA of Klebsiella pneumoniae form a heterohexamer in solution and that the complex interacts with the cognate promoter DNA, resulting in negative autoregulation of kacAT transcription. Here, we present the crystal structure of DNA-bound KacAT complex at 2.2 Å resolution. The crystal structure revealed the formation of a unique heterohexamer, KacT–KacA₂–KacA₂–KacT. The direct interaction of KacA and KacT involves a unique W-shaped structure with the two KacT molecules at opposite ends. Inhibition of KacT is achieved by the binding of four KacA proteins that preclude the formation of an active KacT dimer. The kacAT operon is auto-regulated and we present an experimentally supported molecular model proposing that the KacT:KacA ratio controls kacAT transcription by conditional cooperativity. These results yield a profound understanding of how transcription GNAT–RHH pairs are regulated.

Influence of tension time on muscle fiber sarcolemmal injury in rat diaphragm

We hypothesized that the amount of sarcolemmal injury is directly related to the total tension time (TT(tot)), calculated as mean tension x total stimulation time. Diaphragm strips from Sprague-Dawley rats were superfused at optimal muscle length with Krebs containing procion orange to identify sarcolemmal injury. TT(tot) was induced by stimulation with 100 Hz for 3 min at duty cycles of 0.02, 0.15, 0.3, and 0.6, or with continuous contractions at 0.2, 0.4, 0.6, and 1.0 of maximal tension. A significant positive correlation between TT(tot) and the percentage of fibers with injured sarcolemma (r(2) = 0.63, P < 0.05) is seen. Stimulation (at 100 Hz, duty cycle = 1) resulted in fast fatigue with low injury, likely caused by altered membrane conductivity. Stimulations inducing the largest injury are those showing progressive force loss and high TT(tot), where injury may be due to activation of membrane degradative enzymes. The maximal tension measured at 20 min poststimulation was inversely related to the number of fibers injured, suggesting loss of force is caused by cellular injury.

Induction of the ATP-sensitive potassium (uK(ATP)-1) channel by endotoxemia

The effect of sepsis on the ubiquitously expressed ATP-sensitive potassium (uK(ATP)-1) channel expression was measured in Sprague-Dawley rat diaphragms. Rats were treated with either 0.5 ml saline or 20 mg/Kg E. coli lipopolysaccharides and sacrificed at 3, 6, 12, 24, or 48 h later. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that channel mRNA expression was increased at 3 h and continued to rise up to 48 h. Western blotting analysis showed a approximately 9-fold increase in channel protein expression 24 h after sepsis. Our results demonstrate that sepsis upregulates the uK(ATP)-1 channel.

Src-Dependent DBL Family Members Drive Resistance to Vemurafenib in Human Melanoma

The use of selective BRAF inhibitors (BRAFi) has produced remarkable outcomes for patients with advanced cutaneous melanoma harboring a BRAFV600E mutation. Unfortunately, the majority of patients eventually develop drug-resistant disease. We employed a genetic screening approach to identify gain-of-function mechanisms of BRAFi resistance in two independent melanoma cell lines. Our screens identified both known and unappreciated drivers of BRAFi resistance, including multiple members of the DBL family. Mechanistic studies identified a DBL/RAC1/PAK signaling axis capable of driving resistance to both current and next-generation BRAFis. However, we show that the SRC inhibitor, saracatinib, can block the DBL-driven resistance. Our work highlights the utility of our straightforward genetic screening method in identifying new drug combinations to combat acquired BRAFi resistance. SIGNIFICANCE: A simple, rapid, and flexible genetic screening approach identifies genes that drive resistance to MAPK inhibitors when overexpressed in human melanoma cells.

SRC-RAC1 signaling drives drug resistance to BRAF inhibition in de-differentiated cutaneous melanomas

Rare gain-of-function mutations in RAC1 drive drug resistance to targeted BRAF inhibition in cutaneous melanoma. Here, we show that wildtype RAC1 is a critical driver of growth and drug resistance, but only in a subset of melanomas with elevated markers of de-differentiation. Similarly, SRC inhibition also selectively sensitized de-differentiated melanomas to BRAF inhibition. One possible mechanism may be the suppression of the de-differentiated state, as SRC and RAC1 maintained markers of de-differentiation in human melanoma cells. The functional differences between melanoma subtypes suggest that the clinical management of cutaneous melanoma can be enhanced by the knowledge of differentiation status. To simplify the task of classification, we developed a binary classification strategy based on a small set of ten genes. Using this gene set, we reliably determined the differentiation status previously defined by hundreds of genes. Overall, our study informs strategies that enhance the precision of BRAFi by discovering unique vulnerabilities of the de-differentiated cutaneous melanoma subtype and creating a practical method to resolve differentiation status.

Machine learning approach informs biology of cancer drug response

Background

The mechanism of action for most cancer drugs is not clear. Large-scale pharmacogenomic cancer cell line datasets offer a rich resource to obtain this knowledge. Here, we present an analysis strategy for revealing biological pathways that contribute to drug response using publicly available pharmacogenomic cancer cell line datasets.

Methods

We present a custom machine-learning based approach for identifying biological pathways involved in cancer drug response. We test the utility of our approach with a pan-cancer analysis of ML210, an inhibitor of GPX4, and a melanoma-focused analysis of inhibitors of BRAF^V600. We apply our approach to reveal determinants of drug resistance to microtubule inhibitors.

Results

Our method implicated lipid metabolism and Rac1/cytoskeleton signaling in the context of ML210 and BRAF inhibitor response, respectively. These findings are consistent with current knowledge of how these drugs work. For microtubule inhibitors, our approach implicated Notch and Akt signaling as pathways that associated with response.

Conclusions

Our results demonstrate the utility of combining informed feature selection and machine learning algorithms in understanding cancer drug response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04720-z.

[Dental lamina as presumptive source of odontogenic cyst]

The possibility of the dental lamina as a source of odontogenic cyst was investigated. The mandibular first molar tooth germs with the dental lamina and surface oral epithelium were cut from 17.5-day-old C3H mouse embryos. The following 5 kinds of grafts were prepared: (I) recombinant of the dental lamina and dental papilla, (II) dental lamina, (III) dental papilla, (IV) recombinant of the oral epithelium and dental papilla and (V) oral epithelium. After the renal subcapsular transplantation to the 3-month-old syngenic male mice, each graft was harvested at timed sequences from 2 to 24 weeks and was examined histopathologically. The recombinant of the dental lamina and dental papilla (1) grew into a cyst lined by para-keratinized stratified squamous epithelium. The cyst enlarged gradually and might be compared to the odontogenic keratocyst of the human being. The recombinant of the oral epithelium and dental papilla (IV) and the oral epithelium (V) developed into a cyst lined by orthokeratinized stratified squamous epithelium which differed from the epithelium seen in Experiment (I). The dental papilla (III) grew to be a bone tissue while nothing developed from the dental lamina (II). These results suggest that the dental lamina is one of the sources of the odontogenic keratocyst and the dental papilla plays an important role in its histogenesis.

A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells

BACKGROUND

The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression libraries or the CRISPR activation system. However, a variety of technical and logistical challenges make these approaches difficult for many labs to execute. In addition, genome-wide shRNA or CRISPR libraries typically contain of hundreds of thousands of individual engineered elements, and the associated complexity creates issues with replication and reproducibility for these methods.

RESULTS

Here we describe a simple, reproducible approach using the SB transposon system to perform phenotypic cell-based genetic screens. This approach employs only three plasmids to perform unbiased, whole-genome transposon mutagenesis. We also describe a ligation-mediated PCR method that can be used in conjunction with the included software tools to map raw sequence data, identify candidate genes associated with phenotypes of interest, and predict the impact of recurrent transposon insertions on candidate gene function. Finally, we demonstrate the high reproducibility of our approach by having three individuals perform independent replicates of a mutagenesis screen to identify drivers of vemurafenib resistance in cultured melanoma cells.

CONCLUSIONS

Collectively, our work establishes a facile, adaptable method that can be performed by labs of any size to perform robust, genome-wide screens to identify genes that influence phenotypes of interest.

[Increasing number and improved survival of patients with hepatocellular carcinoma from 1988 to 2007: data of a German university clinic]

BACKGROUND AND OBJECTIVES

Hepatocellular carcinoma (HCC) ranks sixth regarding prevalence and third regarding mortality among malignant tumours worldwide. The aim of the present study was to determine changes of clinical-epidemiological parameters and survival rates during two decades.

PATIENTS AND METHODS

A total of 441 consecutive patients with HCC admitted to the University Clinic Düsseldorf between January 1988 and December 2007 were included. For comparison, this time period was divided into two decades (1988 - 1997 and 1998 - 2007).

RESULTS

The number of newly diagnosed HCCs has tripled in the years 1998 - 2007 compared to the years 1988 - 1997. HCV-associated HCCs increased from 28 % in the years 1988 - 1997 to 38 % (p < 0.05) in the years 1998 - 2007. Tumour size, Okuda and BCLC stages decreased during the observation period (both p < 0.001 and p < 0.05). Median overall survival improved during the observation period from 6 [95 % CI: 4.83 - 7.17] to 9 months ]95 % CI: 7.31 - 10.69]; p < 0.0001) as did the 1-year and 5-year survival rates from 22 % to 42 % (p < 0.019) and from 0 % to 9 % (p < 0.001), respectively. The proportion of treated patients compared to patients with best supportive care as well as the proportion of patients receiving a multimodal therapy compared to patients with a single treatment regimen increased in the second decade (55 % vs. 79 %: p < 0.005; 5.4 % vs. 23 %: p < 0.0001). Multimodal therapy was an independent predictor for prolonged survival in a multivariate analysis including Child-Pugh score, BCLC stage, tumour size, and gender (odds ratio 2,77; 95 % CI: 1.44 - 5.31).

CONCLUSION

Improved screening as well as broader and improved treatment options may have contributed to the increasing survival rates.

Novel mutations and expression changes of acetyl-coenzyme A carboxylase are associated with spirotetramat resistance in Aphis gossypii Glover

Acetyl-coenzyme A carboxylase (ACC) catalyses the carboxylation of acetyl-coenzyme A (acetyl-CoA) to produce malonyl-CoA during the de novo synthesis of fatty acids. Spirotetramat, an inhibitor of ACC, is widely used to control a range of sucking insects, including the Aphis gossypii. In the present study, Reverse transcription quantitative real-time PCR (RT-qPCR) results demonstrated that ACC was significantly overexpressed in a laboratory-selected spirotetramat-resistant strain compared with the susceptible strain. ACC RNA interference significantly suppressed fecundity and led to cuticle formation deficiencies in resistant adults and nymphs compared with the control. The full-length ACC gene was sequenced from both resistant and susceptible cotton aphids, and a strong association was found between spirotetramat resistance and 14 amino acid substitutions in the biotin carboxylase domain and carboxyl transferase domain of the ACC gene. Furthermore, ACC activity was higher in resistant aphids than in the susceptible strain, and ACC in the resistant aphids exhibited significant insensitivity to spirotetramat and spirotetramat-enol. The results indicate that the overexpressed insensitive (mutated) ACC target played an important role in the high levels of spirotetramat resistance observed here. This association of amino acid substitution with resistance is the first report of a potential target site mechanism affecting spirotetramat in the cotton aphid.

Abstract PR17: Sleeping Beauty mutagenesis reveals a Src-dependent DBL GEF family signaling mechanism driving MAPK inhibitor resistance in BRAF mutant melanoma

BRAF/MEK inhibition remains an important treatment option for patients with BRAF V600 mutant melanoma who show disease progression on immunotherapy; however, the majority of patients treated with BRAF/MEK (MAPKi) therapy develop MAPKi-resistant disease within two years of initiating treatment. Genomic analysis of drug-resistant melanomas has identified somatic mutations associated with resistance, including BRAF amplification or truncation and RAS mutation. In addition, other forms of acquired resistance involving adaptation and reprogramming have been described, with different studies identifying different drivers in different melanoma cell lines and patient-derived xenografts. The heterogeneity of acquired resistance mechanisms presents a major clinical challenge for identifying novel drug combinations with potential activity in significant subsets of patients. To enable the rapid identification of context-dependent drivers of MAPKi resistance, we adapted our Sleeping Beauty (SB) transposon mutagenesis for use in cell culture. SB mutagenesis in this setting identifies predominantly gain-of-function mechanisms and thus has the ability to identify both genetic mutations (such as expression of truncated proteins) and genes within alternative acquired resistance pathways whose upregulated expression drives MAPKi resistance. Validating our approach, our screen identified N-terminal truncation of BRAF—a known mechanism of vemurafenib resistance. In addition, we identified DBL family guanine exchange factors (GEFs), MCF2 and VAV1, as drivers of MAPKi resistance that we have functionally validated in multiple BRAF V600E mutant melanoma cell lines. Crucially, many DBL family GEFs are well known to be regulated by Src family kinases (SFKs), and our data indicate that GEF-driven MAPKi resistance can be blocked by combination treatment with vemurafenib and saracatinib, a selective SFK inhibitor. Expansion of resistant cells in the presence of vemurafenib or vemurafenib with cobimetinib can be reversed by switching to vemurafenib plus saracatinib. Consistently, we find that adding saracatinib converts MAPKi-mediated cytostasis into cell killing and blocks spontaneous MAPKi resistance in responsive melanoma cell lines. The GEFs signal downstream to a RAC1-PAK kinase module that is required for GEF-driven resistance. Importantly, the potential utility of both SFK inhibitors and PAK inhibitors for overcoming MAPKi resistance has been proposed, but the connection between SFK-dependent and PAK-dependent resistance mechanisms had not been obvious. We show that combined BRAF/SFK inhibition is effective in cell lines in which the GEF-driven mechanism operates, but not in cell lines in which the GEFs do not drive resistance. Our SB mutagenesis system has the ability to rapidly survey the context-dependent landscape of MAPKi resistance in any transfectable cell system, with the potential to reveal connections between seemingly disparate resistance mechanisms.

This abstract is also being presented as Poster B04.

Citation Format: Charlotte R. Feddersen, Jacob Schillo, Afshin Varzavand, Hayley Vaughn, Andrew Voight, Eliot Zhu, Jesse D Riordan, Christopher S. Stipp, Adam J. Dupuy. Sleeping Beauty mutagenesis reveals a Src-dependent DBL GEF family signaling mechanism driving MAPK inhibitor resistance in BRAF mutant melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR17.

[Software development of multi-element transient signal acquisition and processing with multi-channel ICP-AES]

A software for multi-channel ICP-AES multi-element transient signal acquisition and processing were developed in this paper. It has been successfully applied to signal acquisition and processing in many transient introduction techniques on-line hyphenated with multi-channel ICP-AES.

Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma

Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.

Patient characteristics and treatment patterns for patients with benign prostatic hyperplasia, erectile dysfunction or co-occurring benign prostatic hyperplasia and erectile dysfunction in general practices in the UK: a retrospective observational study

AIMS

The aim of this study was to assess patient characteristics, medication treatment patterns and healthcare resource utilization among men with existing erectile dysfunction (ED) or benign prostatic hyperplasia (BPH), who are newly diagnosed with the second condition (BPH or ED) compared with those with only one condition.

METHODS

This retrospective cohort study utilized the Clinical Practice Research Datalink. Males, aged 40 years or older, newly diagnosed with ED or symptomatic BPH between 1 June 2010 and 31 May 2011, were selected. Patient demographics, existing comorbidities and baseline medication use were analysed. Treatments initiated for the incident condition and treatment patterns were reported at 6, 12, 18 and 24-months postdiagnosis. Referrals to urologists and visits to general practitioners were reported around diagnosis and during follow-up.

RESULTS

This study included 11,501 incident patients with BPH, of which 23% had a prior ED diagnosis and 9,734 incident patients with ED, of which 17% had a prior BPH diagnosis. The average age at diagnosis of BPH was similar across both cohorts. Among incident patients with ED, those with prior diagnosis of BPH were diagnosed at an older average age (65 ± 9.2 years) compared to those without BPH (57 ± 9.1 years). The majority of patients in both incident BPH cohorts (62.9-65.5%) were prescribed alpha-blockers as initial treatment. The majority of patients in both incident ED cohorts (49.6-51.6%) were prescribed sildenafil as initial treatment followed by tadalafil (24.3-26.0%). At 12 months, 50% of incident patients with BPH and 80% of patients with ED had discontinued the therapy initiated.

CONCLUSION

This study found that in the UK, patients with co-occurring BPH and ED when newly diagnosed with the second condition initiated the same treatments as those without prior ED or BPH. During the first year, treatment patterns including discontinuation were comparable in the groups with one of the conditions and co-occurring BPH and ED.

Abstract LB-096: A gain-of-function screen identifies drivers of drug resistance in BRAFV600E melanoma cell lines

Melanoma is the deadliest form of skin cancer, and until recently patients had few treatment options upon diagnosis. Fortunately, this lack of treatment options changed with the discovery of vemurafenib, a highly selective kinase inhibitor that specifically targets the BRAFV600E mutant protein, found in ~50% of all melanoma cases. Initially, the kinase inhibitor provided complete or partial response to over 50% of patients and prolonged progression-free survival. However, the majority of patients relapse once tumors acquire resistance to vemurafenib. Some of the genetic resistance mechanisms are known, including BRAF amplification, expression of truncated BRAF, and RAS mutation. However, a significant portion of vemurafenib resistance cases is unexplained. While drug resistance can be delayed by combining vemurafenib with cobimetinib, a MEK inhibitor, mechanisms of resistance to this drug combination are not well characterized.

We performed a gain-of-function screen to identify drivers of drug resistance to vemurafenib or vemurafenib combined with cobimetinib. Briefly, A375 melanoma cells were engineered to express the hyperactive transposase SB100. These cells were then subsequently transfected with the mutagenic T2Onc3 transposon to produce a population of mutagenized A375 cells. Three weeks of vemurafenib treatment selected for cells with the acquired ability to grow in the presence of drug. Candidate driver mutations were then identified by profiling the sites of transposon insertion in drug-resistant cells to find genes that were recurrently over-expressed by transposon insertions. This led to the discovery of five genes that act as drivers of vemurafenib resistance when overexpressed in the human melanoma cell line A375. Candidate genes were then validated in multiple melanoma cell lines by assessing cell growth and viability in varying concentrations of vemurafenib.

An analogous screen was performed in A375 to identify drivers of resistance to the combination of vemurafenib and cobimetinib. In addition, we are assessing the diversity of drug resistance mechanisms by performing mutagenesis in three additional human melanoma cell lines.

The characterization of the novel drug resistance pathways identified here will improve treatment outcomes for patients with BRAFV600E mutant melanoma.

Citation Format: Charlotte R. Feddersen, Jacob L. Schillo, Hayley R. Vaughn, Andrew P. Voigt, Eliot Y. Zhu, Lexy S. Wadsworth, Christopher S. Stipp, Adam J. Dupuy. A gain-of-function screen identifies drivers of drug resistance in BRAFV600E melanoma cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-096.