FinnGen provides genetic insights from a well-phenotyped isolated population

Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored^1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10^-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.

Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes

Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

Live fast, die young: Behavioural and physiological impacts of light pollution on a marine fish during larval recruitment

Artificial light at night (ALAN) is a recently acknowledged form of anthropogenic pollution of growing concern to the biology and ecology of exposed organisms. Though ALAN can have detrimental effects on physiology and behaviour, we have little understanding of how marine organisms in coastal areas may be impacted. Here, we investigated the effects of ALAN exposure on coral reef fish larvae during the critical recruitment stage, encompassing settlement, metamorphosis, and post-settlement survival. We found that larvae avoided illuminated settlement habitats, however those living under ALAN conditions for 10 days post-settlement experienced changes in swimming behaviour and higher susceptibility to nocturnal predation. Although ALAN-exposed fish grew faster and heavier than control fish, they also experienced significantly higher mortality rates by the end of the experimental period. This is the first study on the ecological impacts of ALAN during the early life history of marine fish.

Hospital management of colonic perforations complicating ambulatory outpatient colonoscopy via over-the-scope clips or surgery: a case series

BACKGROUND

Colonoscopy is the standard of care for the diagnosis and treatment of many colonic disorders. Over the past few years, endoscopic closure of colonoscopy-related perforation has become more common. Endoscopic closure of perforation secondary to colonoscopy has been undertaken in patients in the hospital setting and often during the same colonoscopic procedure in which the perforation itself occurred. The aim of our study was to analyze our experience with emergency endoscopic closure of colonoscopy-related perforation with over-the-scope clip (OTSC) technique.

METHODS

We report five cases of colonic perforation that occurred during colonoscopy in an outpatient facility remotely located from our hospital and then referred as an emergency to our institution for endoscopic closure.

RESULTS

Bowel preparation was reported to be adequate in all cases. Prior to attempting endoscopic closure of colonic perforation, all patients were in stable clinical condition, early broad-spectrum antibiotic coverage was initiated, and a surgical consult was obtained. All patients had sigmoidoscopy and were found to have sigmoid colon perforations. In three cases, the perforations were closed successfully using an OTSC clip device 14 mm type t. Two patients were found to have greater than 4-cm sigmoid perforations with irregular margins, incompatible with OTSC closure, and were referred for emergency surgery. All patients had an uneventful course following either OTSC closure or surgery.

CONCLUSIONS

Based on the characteristics of the five cases and a review of the literature, we suggest a practical approach for undertaking closure of colonic perforations occurring during colonoscopy in the outpatient setting, focusing on clinical criteria to determine eligibility of patients for attempted endoscopic closure and outlining required therapeutic and monitoring steps needed to optimize outcomes.

Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics

Although cystic fibrosis (CF) is attributed to dysfunction of a single gene, the relationships between the abnormal gene product and the development of inflammation and progression of lung disease are not fully understood, which limits our ability to predict an individual patient's clinical course and treatment response. To better understand CF progression, we characterized the molecular signatures of CF disease status with plasma-based functional genomics. Peripheral blood mononuclear cells (PBMCs) from healthy donors were cultured with plasma samples from CF patients ( n = 103) and unrelated, healthy controls ( n = 31). Gene expression levels were measured with an Affymetrix microarray (GeneChip Human Genome U133 Plus 2.0). Peripheral blood samples from a subset of the CF patients ( n = 40) were immunophenotyped by flow cytometry, and the data were compared with historical data for age-matched healthy controls ( n = 351). Plasma samples from another subset of CF patients ( n = 56) and healthy controls ( n = 16) were analyzed by multiplex enzyme-linked immunosorbent assay (ELISA) for numerous cytokines and chemokines. Principal component analysis and hierarchical clustering of induced transcriptional data revealed disease-specific plasma-induced PBMC profiles. Among 1,094 differentially expressed probe sets, 51 genes were associated with pancreatic sufficient status, and 224 genes were associated with infection with Pseudomonas aeruginosa. The flow cytometry and ELISA data confirmed that various immune modulators are relevant contributors to the CF molecular signature. This study provides strong evidence for distinct molecular signatures among CF patients. An understanding of these molecular signatures may lead to unique molecular markers that will enable more personalized prognoses, individualized treatment plans, and rapid monitoring of treatment response.

Genetic mapping and characterization of the bleeding disorder in the fawn-hooded hypertensive rat

Release of platelet dense granule contents occurs in response to vascular injury, playing an important role in platelet aggregation and primary hemostasis. Abnormalities of the platelet dense granules results in a bleeding disorder of variable severity termed “storage pool defect” (SPD). We have examined the fawn-hooded hypertensive (FHH) rat as a model of SPD in order to genetically map the locus (Bd) responsible for prolonged bleeding. Platelet function assays of the FHH rat confirmed the presence of a platelet dense granule SPD. However electron microscopy and lysosomal enzyme assays indicated differences between the FHH rat and other rodent models of SPD. Genetic mapping through the use of congenic FHH rats localized the Bd locus to an approximately 1 cM region on rat chromosome 1. Through the use of comparative mapping between species and analysis of the initial draft of the rat genome assembly, six known and thirty-four putative genes were identified in the Bd locus. None of these genes have been previously implicated in platelet function. Therefore positional cloning of the gene responsible for the bleeding disorder in the FHH rat will lead to new insights in platelet physiology, with implications for diagnosis and management of hemostatic and thrombotic disorders.

From rat pathophysiology to genomic medicine: an interview with Howard Jacob

Howard Jacob is best known for pioneering genomic sequencing of a patient to solve a mysterious pediatric case in 2010. With roots in pharmacology and cardiovascular disease, however, his career has largely been dedicated to dissecting the physiology and genetics of the rat to help understand complex human diseases. Howard was Director of the Human and Molecular Genetics Center at the Medical College of Wisconsin for 16 years, during which time he applied a combination of approaches, including quantitative genetics, integrative physiology and next-generation sequencing, in rat models to shed light on cardiovascular, metabolic and renal disorders. He was a key contributor to the genomic toolbox for rat research, and generated the first targeted-knockout rat models using zinc-finger-nuclease technology. He also contributed to sequencing of the rat genome and establishment of the Rat Genome Database. In this interview, Howard provides his perspectives on the past, present and future of rat-based translational research and explains why, despite his many successes as the leader of a rat group, he recently made the transition to clinical genomics.

Summary: Howard Jacob describes some of the key moments and breakthroughs in his remarkable career, and the path that led him from his research roots in cardiovascular disease and rat physiology to becoming Director of a clinical genomic sequencing program.

Abstract 1556: Algorithms for discovery of somatic single nucleotide mutation display specific artifacts and different detection capabilities under the effect of read coverage and sample heterogeneity

Understanding the performance and capability of different bioinformatics algorithms used for the discovery of somatic variants is very important for helping scientists choose an appropriate tool for cancer research. In this study, we developed a comparison approach and created a series of data sets that could be used to provide such guidance. We mixed reads from two well characterized individuals, NA12878 and NA24385, and generated a series of data sets with different coverages and sample heterogeneity. We then used these data sets to evaluate five commonly utilized somatic mutation detection tools. Our results indicate that read coverage has a significant impact on the accuracy and capability of mutation calling by individual bioinformatics algorithms. The mutation caller that performs well with high read coverage may perform poorly with low read coverage. On the other hand, the tool that performed well in calling variants in a relatively higher homogeneity sample may not have the same power to detect rare variants with low mutation allele frequency. In addition, we demonstrated that different mutation calling algorithms are associated with specific artifacts that were sensitive to read coverage. Furthermore, there were large numbers of false positives and false negatives shared by five callers, indicating that other factors, such as read alignment, library preparation, and even the properties of the sequencing platform could be the sources of false discovery for somatic variants. We observed similar behavior of the five variant calling algorithms using the sequencing data of a pair of matched tumor/normal cell lines, confirming the findings from the comparative analyses on the mixture of reads from the two normal individuals. Our findings are expected to facilitate selection of bioinformatics pipelines that fit for specific purposes in cancer research based on sequencing data.

Citation Format: Wenming Xiao, Leihong Wu, Gokhan Yavas, Huixiao Hong, Baitang Ning, Weida Tong, Eric F. Donaldson, Zivana Tezak, Reena Philip, Howard Jacob, Louis M. Staudt. Algorithms for discovery of somatic single nucleotide mutation display specific artifacts and different detection capabilities under the effect of read coverage and sample heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1556. doi:10.1158/1538-7445.AM2017-1556

First description of the neuro-anatomy of a larval coral reef fish Amphiprion ocellaris

The present study described the neuro-anatomy of a larval coral reef fish Amphiprion ocellaris and hypothesized that morphological changes during the transition from the oceanic environment to a reef environment (i.e. recruitment) have the potential to be driven by changes to environmental conditions and associated changes to cognitive requirements. Quantitative comparisons were made of the relative development of three specific brain areas (telencephalon, mesencephalon and cerebellum) between 6 days post-hatch (dph) larvae (oceanic phase) and 11 dph (at reef recruitment). The results showed that 6 dph larvae had at least two larger structures (telencephalon and mesencephalon) than 11 dph larvae, while the size of cerebellum remained identical. These results suggest that the structure and organization of the brain may reflect the cognitive demands at every stage of development. This study initiates analysis of the relationship between behavioural ecology and neuroscience in coral reef fishes.

Abstract B07: Utilizing consomic xenograft models to identify genetic variants in the tumor microenvironment that determine breast cancer radiation responses

Progress in elucidating the molecular basis of breast cancer has allowed for treatment breakthroughs such as anti-estrogen and Her2-targeted therapy. It has also shaped the approaches to both surgical and systemic therapy. However, no similar use of molecular information has been utilized to better direct the use of radiation therapy. The development of predictive tools for the radiosensitivity of tumors could allow for personally tailored radiation doses, with treatment de-escalation for radiosensitive tumors, or dose escalation or the use of adjunct treatments in the case of radioresistant tumors. Communication between malignant tumor cells and the tumor microenvironment (TME) underlies most aspects of tumor biology, including chemotherapy and radiation resistance. We have developed a Consomic Xenograft Model (CXM), which maps germline variants that impact only the TME, as well as a species-specific RNA-seq (SSRS) protocol which allows detection of expression changes in the malignant and nonmalignant cellular compartments of tumor xenografts, in parallel and without cell-sorting. Here we utilize these unique techniques to identify genetic variants in the TME that can affect radiation sensitivity. In CXM, human triple negative breast cancer MDA-MD-231 cells are orthotopically implanted into immunodeficient (IL2Rγ-/-) consomic rat strains, which are rat strains in which an entire chromosome is introgressed into the isogenic background of another inbred strain by selective breeding. Because the strain backgrounds are different but the tumor cells are not varied, the observed changes in tumor progression are due to genetic differences in the non-malignant TME. We hypothesized that the tumors in SS.BN3 rats (identical to SS rats but with BN strain chromosome 3) would be more sensitive to radiation due to increased tumor vascularity via CD31 staining, and increased tumor blood volume capacity, as measured by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Our studies demonstrate differential responses to radiation in the CXM model comparing parental SS (IL2Rγ) rats to SS.BN3 (IL2Rγ) rats treated with fractionated radiation therapy (4 Gray x 3), with altered tumor growth kinetics and tumor recurrence rates. A difference was seen in time to 5-fold increase in tumor growth, with 44 vs. &gt;130 days for SS versus SS.BN3 rats (supra-additive, p&lt;0.05). There was a recurrence-free survival of 30% vs. 67% at 130 days, with a median time to recurrence of 57 days vs. time not reached (&gt;130 days) in the SS versus SS.BN3 rats (p=0.02). These results suggest that genetic determinants in the TME affect the radiation sensitivity of genetically identical tumor cells. Using SSRS, we identified a number of candidates on rat chromosome 3 that may potentially influence radiation sensitivity by altering the tumor vasculature. Future studies will further dissect the pathways responsible for the changes in radiation sensitivity. Determining TME factors that affect the radiation sensitivity of tumors has the potential to allow for more tailored and effective radiation treatments in breast cancer.

Citation Format: Carmen Bergom, Michael Straza, Amy Rymaszewski, Anne Frei, Angela Lemke, Shirng-Wern Tsaih, Howard Jacob, Michael J. Flister. Utilizing consomic xenograft models to identify genetic variants in the tumor microenvironment that determine breast cancer radiation responses. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr B07.

Plasma genetic and genomic abnormalities predict treatment response and clinical outcome in advanced prostate cancer

Liquid biopsies, examinations of tumor components in body fluids, have shown promise for predicting clinical outcomes. To evaluate tumor-associated genomic and genetic variations in plasma cell-free DNA (cfDNA) and their associations with treatment response and overall survival, we applied whole genome and targeted sequencing to examine the plasma cfDNAs derived from 20 patients with advanced prostate cancer. Sequencing-based genomic abnormality analysis revealed locus-specific gains or losses that were common in prostate cancer, such as 8q gains, AR amplifications, PTEN losses and TMPRSS2-ERG fusions. To estimate tumor burden in cfDNA, we developed a Plasma Genomic Abnormality (PGA) score by summing the most significant copy number variations. Cox regression analysis showed that PGA scores were significantly associated with overall survival (p < 0.04). After androgen deprivation therapy or chemotherapy, targeted sequencing showed significant mutational profile changes in genes involved in androgen biosynthesis, AR activation, DNA repair, and chemotherapy resistance. These changes may reflect the dynamic evolution of heterozygous tumor populations in response to these treatments. These results strongly support the feasibility of using non-invasive liquid biopsies as potential tools to study biological mechanisms underlying therapy-specific resistance and to predict disease progression in advanced prostate cancer.

Abstract PR16: New tools for mapping genetic modifiers of cancer risk in the tumor microenvironment

The majority of heritable breast cancer risk is unknown. One potential source of “missing heritability” is genetic modifiers in the tumor microenvironment (TME). Although genetic modifiers in the TME have long been suspected, they have rarely been studied and are largely unknown. Here, we used two new techniques: the Consomic Xenograft Model (CXM) and species-specific RNA-seq (SSRS) to map genetic modifiers in the TME. In CXM, human breast cancer xenografts are implanted in immunodeficient consomic rat strains and tracked for tumor progression. Because the rat strains vary by one chromosome (i.e., consomic), whereas the malignant tumor cells do not differ, any observed changes in tumor phenotypes are due to genetic modifiers in the TME and can be localized to one chromosome. The SSRS method uses probabilistic mapping of RNAseq reads to a joint human and rat transcriptome to assess differential expression (DE) in malignant (human) tumor cells and the nonmalignant (rat) TME. Validation of SSRS revealed &gt;99.4% specificity in calling human or rat reads, which was significantly better than conventional RNA-seq. Using CXM, we found that BN-derived genetic variant(s) on rat chromosome 3 significantly reduced growth of MDA-MB-231-Luc (231Luc+) tumors by 49% (P&lt;0.05) in the SS.BN3IL2Rγ CXM strain compared with parental SSIL2Rγ. This coincided with a 3.1-fold (P&lt;0.001) decrease in blood vascular invasion by 231Luc+ tumor cells and 7.3-fold (P&lt;0.05) lower metastatic burden in the lungs in SS.BN3IL2Rγ compared with SSIL2Rγ, despite a paradoxical 27% (P&lt;0.05) increase in blood vessel density (BVD) in SS.BN3IL2Rγ rats. The tumor-associated blood vessels in SS.BN3IL2Rγ rats appeared collapsed and dysfunctional, possibly explaining the decreased tumor growth and metastasis, despite increased BVD. Lymphatic vasculature and lymphogenous metastasis were completely unaffected by the SS.BN3IL2Rγ background, suggesting that the causative variant(s) on BN rat chromosome 3 are vascular cell-type specific. We used SSRS to begin identifying the TME-specific mediators on rat chromosome 3 (RNO3) that inhibit growth and hematogenous metastasis of human 231Luc+ breast cancer xenografts implanted in the SS.BN3IL2Rγ. Compared with SSIL2Rγ tumors, we identified a network of 539 DE transcripts in the TME of SS.BN3IL2Rγ rats, of which 28% (150 genes) reside on RNO3, which was significantly higher (&gt;4-fold; P&lt;0.001) than any other rat chromosome. Moreover, a two-sample Kolmogorov-Smirnov test revealed that the difference in distributions of adjusted p-values for RN03 versus the rest of the genome was highly significantly higher for DE genes (P=3.152e-08) or DE transcripts (P=3.441e-16). Compared with other rat chromosomes, RNO3 also had by far the highest incidence of alternative isoform usage (91% of all instances). Pathway analysis of DE genes using DAVID revealed that the two most significant GO clusters were extracellular matrix (49 genes; P&lt;10-20) and blood vessel development (43 genes; P&lt;10-17), which recapitulated the vascular defects observed in the SS.BN3IL2Rγ tumors. Collectively, our data demonstrate that CXM and SSRS can be used to detect genetic modifiers in the TME.

Citation Format: Michael J. Flister, Alexander Stoddard, Shirng-Wern Tsaih, Angela Lemke, Jozef Lazar, Howard Jacob. New tools for mapping genetic modifiers of cancer risk in the tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr PR16.

Abstract PR08: New tools for mapping genetic modifiers of cancer risk in the tumor microenvironment

The majority of heritable breast cancer risk is unknown. One potential source of “missing heritability” is genetic modifiers in the tumor microenvironment (TME). Although genetic modifiers in the TME have long been suspected, they have rarely been studied and are largely unknown. Here, we used two new techniques: the Consomic Xenograft Model (CXM) and species-specific RNA-seq (SSRS) to map genetic modifiers in the TME. In CXM, human breast cancer xenografts are implanted in immunodeficient consomic rat strains and tracked for tumor progression. Because the rat strains vary by one chromosome (i.e., consomic), whereas the malignant tumor cells do not differ, any observed changes in tumor phenotypes are due to genetic modifiers in the TME and can be localized to one chromosome. The SSRS method uses probabilistic mapping of RNAseq reads to a joint human and rat transcriptome to assess differential expression (DE) in malignant (human) tumor cells and the nonmalignant (rat) TME. Validation of SSRS revealed &gt;99.4% specificity in calling human or rat reads, which was significantly better than conventional RNA-seq. Using CXM, we found that BN-derived genetic variant(s) on rat chromosome 3 significantly reduced growth of MDA-MB-231-Luc (231Luc+) tumors by 49% (P&lt;0.05) in the SS.BN3IL2Rγ CXM strain compared with parental SSIL2Rγ. This coincided with a 3.1-fold (P&lt;0.001) decrease in blood vascular invasion by 231Luc+ tumor cells and 7.3-fold (P&lt;0.05) lower metastatic burden in the lungs in SS.BN3IL2Rγ compared with SSIL2Rγ, despite a paradoxical 27% (P&lt;0.05) increase in blood vessel density (BVD) in SS.BN3IL2Rγ rats. The tumor-associated blood vessels in SS.BN3IL2Rγ rats appeared collapsed and dysfunctional, possibly explaining the decreased tumor growth and metastasis, despite increased BVD. Lymphatic vasculature and lymphogenous metastasis were completely unaffected by the SS.BN3IL2Rγ background, suggesting that the causative variant(s) on BN rat chromosome 3 are vascular cell-type specific. We used SSRS to begin identifying the TME-specific mediators on rat chromosome 3 (RNO3) that inhibit growth and hematogenous metastasis of human 231Luc+ breast cancer xenografts implanted in the SS.BN3IL2Rγ. Compared with SSIL2Rγ tumors, we identified a network of 539 DE transcripts in the TME of SS.BN3IL2Rγ rats, of which 28% (150 genes) reside on RNO3, which was significantly higher (&gt;4-fold; P&lt;0.001) than any other rat chromosome. Moreover, a two-sample Kolmogorov-Smirnov test revealed that the difference in distributions of adjusted p-values for RN03 versus the rest of the genome was highly significantly higher for DE genes (P=3.152e-08) or DE transcripts (P=3.441e-16). Compared with other rat chromosomes, RNO3 also had by far the highest incidence of alternative isoform usage (91% of all instances). Pathway analysis of DE genes using DAVID revealed that the two most significant GO clusters were extracellular matrix (49 genes; P&lt;10-20) and blood vessel development (43 genes; P&lt;10-17), which recapitulated the vascular defects observed in the SS.BN3IL2Rγ tumors. Collectively, our data demonstrate that CXM and SSRS can be used to detect genetic modifiers in the TME.

Citation Format: Michael J. Flister, Alexander Stoddard, Shirng-Wern Tsaih, Angela Lemke, Jozef Lazar, Howard Jacob. New tools for mapping genetic modifiers of cancer risk in the tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR08.

Pappa2 is linked to salt-sensitive hypertension in Dahl S rats

A 1.37 Mbp region of chromosome 13 previously identified by exclusion mapping was consistently associated with a reduction of salt-induced hypertension in the Dahl salt-sensitive (SS) rat. This region contained five genes that were introgressed from the salt-insensitive Brown Norway (BN) rat. The goal of the present study was to further narrow that region to identify the gene(s) most likely to protect from salt-induced hypertension. The studies yielded a subcongenic SS rat strain containing a 0.71 Mbp insert from BN (26-P strain) in which salt-induced hypertension was reduced by 24 mmHg. The region contained two protein-coding genes (Astn1 and Pappa2) and a microRNA (miR-488). Pappa2 mRNA in the renal cortex of the protected 26-P was 6- to 10-fold greater than in SS fed a 0.4% NaCl diet but was reduced to levels observed in SS when fed 8.0% NaCl diet for 7 days. Compared with brain nuclei (NTS, RVLM, CVLM) and the adrenal gland, Pappa2 in the renal cortex was the only gene found to be differentially expressed between SS and 26-P and that responded to changes of salt diet. Immunohistochemistry studies found Pappa2 localized in the cytosol of the epithelial cells of the cortical thick ascending limbs. In more distal segments of the renal tubules, it was observed within tubular lumens and most notably bound to the apical membranes of the intercalated cells of collecting ducts. We conclude that we have identified a variant form of Pappa2 that can protect against salt-induced hypertension in the Dahl S rat.

Abstract 044: Pappa2 is Linked to Salt-sensitive Hypertension in Dahl SS Rats

The goal of the present study was to narrow a 1.37 Mbp region containing five genes on chromosome 13 (positions 80.92-82.29 Mbp in the Rn5 genome assembly) that we have previously found to influence the mean arterial pressure (MAP) by at least 25 mmHg in SS rats fed a high salt diet (8.0% NaCl for 14 days). The creation of 6 overlapping subcongenic strains that cover this region identified a 0.71 Mbp region (positions 81.01-81.72 Mbp) in which substitution of SS alleles with BN alleles reduced salt-induced hypertension in congenic SS rats by nearly 30 mmHg and significantly reduced urinary albumin excretion (UalbV) (see figure below; n=10-15/strain; * significant difference from SS; p<0.05). Analysis of the narrow candidate region revealed the presence of two protein-coding genes ( Pappa2 and Astn1 ) and a microRNA ( miR488 ), none of which are known to be mechanistically involved in hypertension. Pappa2 mRNA in these rat strains fed 0.4% NaCl diet was expressed at 6-10 fold higher levels in the renal cortex of the salt-resistant congenic strains with the BN allele (26-N, -O, and [[Unable to Display Character: &#8211;]]P) compared to strains with the SS allele (26-Q, -R, and [[Unable to Display Character: &#8211;]]S). A Pappa2 coding sequence variant of unknown functional importance was identified. Immunohistochemistry and fluorescence in situ hybridization studies localized Pappa2 to intercalated cells of the cortical and medullary collecting duct. Astn1 and miR-488 were not differentially expressed in renal tissue. Together, these findings point towards Pappa2 as a candidate gene for salt-induced hypertension in SS rats.

Abstract 3217: NextGen strategies for mapping genetic modifiers in the tumor microenvironment

The majority of heritable breast cancer risk is unknown. One potential source of “missing heritability” is genetic modifiers in the tumor microenvironment (TME). Although genetic modifiers in the TME have long been suspected, they have rarely been studied and are largely unknown. Here, we used two new techniques: the Consomic Xenograft Model (CXM) and species-specific RNA-seq (SSRS) to map genetic modifiers in the TME. In CXM, human breast cancer xenografts are implanted in immunodeficient consomic rat strains and tracked for tumor progression. Because the rat strains vary by one chromosome (i.e., consomic), whereas the malignant tumor cells do not differ, any observed changes in tumor phenotypes are due to genetic modifiers in the TME and can be localized to one chromosome. The SSRS method uses probabilistic mapping of RNAseq reads to a joint human and rat transcriptome to assess differential expression (DE) in malignant (human) tumor cells and the nonmalignant (rat) TME. Validation of SSRS revealed &gt;99.4% specificity in calling human or rat reads, which was significantly better than conventional RNA-seq. Using CXM, we found that BN-derived genetic variant(s) on rat chromosome 3 significantly reduced growth of MDA-MB-231-Luc (231Luc+) tumors by 49% (P&lt;0.05) in the SS.BN3IL2Rγ CXM strain compared with parental SSIL2Rγ. This coincided with a 3.1-fold (P&lt;0.001) decrease in blood vascular invasion by 231Luc+ tumor cells and 7.3-fold (P&lt;0.05) lower metastatic burden in the lungs in SS.BN3IL2Rγ compared with SSIL2Rγ, despite a paradoxical 27% (P&lt;0.05) increase in blood vessel density (BVD) in SS.BN3IL2Rγ rats. The tumor-associated blood vessels in SS.BN3IL2Rγ rats appeared collapsed and dysfunctional, possibly explaining the decreased tumor growth and metastasis, despite increased BVD. We used SSRS to begin identifying the TME-specific mediators on rat chromosome 3 (RNO3) that inhibit growth and hematogenous metastasis of human 231Luc+ breast cancer xenografts implanted in the SS.BN3IL2Rγ. Compared with SSIL2Rγ tumors, we identified a network of 539 DE transcripts in the TME of SS.BN3IL2Rγ rats, of which 28% (150 genes) reside on RNO3, which was significantly higher (&gt;4-fold; P&lt;0.001) than any other rat chromosome. Moreover, a two-sample Kolmogorov-Smirnov test revealed that the difference in distributions of adjusted p-values for RN03 versus the rest of the genome was highly significantly higher for DE genes (P = 3.152e-08) or DE transcripts (P = 3.441e-16). Compared with other rat chromosomes, RNO3 also had by far the highest incidence of alternative isoform usage (91% of all instances). Pathway analysis of DE genes using DAVID revealed that the two most significant GO clusters were extracellular matrix (49 genes; P&lt;10−20) and blood vessel development (43 genes; P&lt;10−17), which recapitulated the vascular defects observed in the SS.BN3IL2Rγ tumors. Collectively, our data demonstrate that CXM and SSRS can be used to detect genetic modifiers in the TME.

Citation Format: Michael Flister, Angela Lemke, Michael Dwinell, Carmen Bergom, James Shull, Howard Jacob. NextGen strategies for mapping genetic modifiers in the tumor microenvironment. [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 3217. doi:10.1158/1538-7445.AM2015-3217

Zinc-finger nuclease knockout of dual-specificity protein phosphatase-5 enhances the myogenic response and autoregulation of cerebral blood flow in FHH.1BN rats

We recently reported that the myogenic responses of the renal afferent arteriole (Af-Art) and middle cerebral artery (MCA) and autoregulation of renal and cerebral blood flow (RBF and CBF) were impaired in Fawn Hooded hypertensive (FHH) rats and were restored in a FHH.1^BN congenic strain in which a small segment of chromosome 1 from the Brown Norway (BN) containing 15 genes including dual-specificity protein phosphatase-5 (Dusp5) were transferred into the FHH genetic background. We identified 4 single nucleotide polymorphisms in the Dusp5 gene in FHH as compared with BN rats, two of which altered CpG sites and another that caused a G155R mutation. To determine whether Dusp5 contributes to the impaired myogenic response in FHH rats, we created a Dusp5 knockout (KO) rat in the FHH.1^BN genetic background using a zinc-finger nuclease that introduced an 11 bp frame-shift deletion and a premature stop codon at AA121. The expression of Dusp5 was decreased and the levels of its substrates, phosphorylated ERK1/2 (p-ERK1/2), were enhanced in the KO rats. The diameter of the MCA decreased to a greater extent in Dusp5 KO rats than in FHH.1^BN and FHH rats when the perfusion pressure was increased from 40 to 140 mmHg. CBF increased markedly in FHH rats when MAP was increased from 100 to 160 mmHg, and CBF was better autoregulated in the Dusp5 KO and FHH.1^BN rats. The expression of Dusp5 was higher at the mRNA level but not at the protein level and the levels of p-ERK1/2 and p-PKC were lower in cerebral microvessels and brain tissue isolated from FHH than in FHH.1^BN rats. These results indicate that Dusp5 modulates myogenic reactivity in the cerebral circulation and support the view that a mutation in Dusp5 may enhance Dusp5 activity and contribute to the impaired myogenic response in FHH rats.

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are curated from published literature, submitted by researchers and integrated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature. Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease.

Abstract 222: Upregulation Of Cyp4a1 Gene Expression Restores The Impaired Myogenic Response And Autoregulation Of Cerebral Blood Flow In Dahl Salt Sensitive Rats

We have reported that a reduction in the expression of CYP4A and the production of 20-HETE in the renal outer medulla contributes to development of hypertension in Dahl salt sensitive (SS) rats. The present study examined whether 20-HETE production is also reduced in the vasculature and if a deficiency in the formation of 20-HETE in the vasculature alters vascular tone and promotes end organ damage. The production of 20-HETE, the myogenic response of middle cerebral arteries (MCA) and autoregulation of cerebral blow flow (CBF) was compared in SS, CYP4A1 transgenic SS rats and SS.5BN consomic rats in which chromosome 5 from Brown Norway (BN) was transferred into the SS genetic background. 20-HETE production was 6-fold higher in cerebral arteries obtained from CYP4A1 transgenic (n=25) and SS.5BN (n=4)rats than in SS (n=17) rats 0.77 ± 0.08 versus 0.12 ± 0.03 pmol/mg/min). The luminal diameter of MCA decreased to 70 ± 3 % in CYP4A1 transgenic rats and to 65 ± 6 in SS.5BN when perfusion pressure was increased from 40 to 140 mmHg, whereas it remained unaltered in SS rats. Administration of the inhibitor of the synthesis of 20-HETE, HET0016 (10 uM), abolished the myogenic response in MCA of CYP4A1 transgenic and SS.5BN rats but had no effect in SS rats. CBF was poorly autoregulated and increased by 49 ± 6% in SS rats as MAP was increased by 60% from 100 to 160 mmHg. In contrast, CBF was only increased by 26 ± 5% and in SS.5BN rats and by 19 ± 2% in CYP4A1 transgenic rats when MAP was increased in the same range. These results indicate that a genetic deficiency of 20-HETE contributes to an impaired myogenic response in autoregulation of CBF in SS rats which may contribute to vascular remodeling, stroke and dementia following the onset of hypertension.

Abstract 223: Zinc-finger Nuclease Knockout Of Dual-specificity Protein Phosphatase-5 Enhances Myogenic Response In Autoregulation Of Cerebral Blood Flow In Fhh.1bn Rats

We recently reported that the pressure-induced myogenic responses of afferent arteries (Af-Art) and middle cerebral arteries (MCAs) were impaired in the fawn hooded hypertensive (FHH) rats and were restored in FHH.1BN congenic strain in which chromosome 1 from the Brown Norway (BN) rats containing 11 genes including dual-specificity protein phosphatase-5 (Dusp5) was transferred into FHH genetic background. There are 4 single nucleotide polymorphisms (SNP) in Dusp5 in FHH as compared with BN rats, one of which causes G155R mutation. To determine whether Dusp5 contributes to the impaired vascular myogenic response in FHH rats, we created a Dusp5 knockout (KO) rats in the FHH.1BN genetic background using zinc-finger nuclease (ZFN) that introduced a premature stop codon at amino acid (AA) 121. The expression of Dusp5 in KO rats were significantly decreased and the level of phosphorylated ERK2 (p-ERK2) was significantly increased in multiple organs including liver, spleen and white blood cells (WBCs). The luminal diameter of the MCAs in FHH.1BN rats (n=12) decreased 20 ± 2 % when the perfusion pressure was increased from 40 to 140 mmHg, whereas it decreased 34 ± 7 % in Dusp5 KO rats (n=6) and increased 10 ± 4% in FHH strain (n=8). Autoregulation was markedly impaired and CBF increased by 54 ± 6% in FHH rats when MAP was increased from 100 to 160 mmHg. CBF was better autoregulated in FHH.1BN strain and Dusp5 KO rats increased by only 26 ± 3% and 12 ± 3% when MAP was increased over the same range. However, the range of autoregulation of CBF was extended in the FHH rats (n=7) in that CBF rose to 107 ± 6% in FHH.1BN rats (n=7) when pressure was increased to 190 mmHg versus 33 ± 4% in the Dusp5 KO animals (n=6). These results suggest that Dusp5 plays an important role in modulating of myogenic tone in the cerebral circulation. Unless the G155R mutation activates Dusp5 in FHH rats, it is unlikely that Dusp5 is responsible for the impaired myogenic response in FHH rats.

Abstract 298: Protective Role of Endogenous 20-HETE in Renal Ischemia-Reperfusion Injury

The present study compared renal ischemia-reperfusion (IR) injury in Dahl salt-sensitive (SS) rats that have a deficiency in the renal formation of 20-HETE versus CYP4A1 transgenic SS (SS.4A1) rats in which the renal production of 20-HETE is restored. The concentrations of free 20-HETE in the renal cortex and outer medulla were significantly greater in SS.4A1 than in SS rats. Renal 20-HETE levels rose to a greater extent in SS.4A1 than in SS rats following renal IR. Plasma creatinine level rose to 3.7 ± 0.1 in SS versus 1.8 ± 0.3 mg/dl in SS.4A1 rats (respectively, n=6) following 30 min of ischemia and 24 h reperfusion. The % of necrotic tubules and apoptotic cells were 4-fold higher in SS than in SS.4A1 rats. Administration of the 20-HETE synthesis inhibitor (HET0016, 10 mg/kg) abolished the resistance of SS.4A1 rats to renal IR injury and plasma creatinine level rose to 3.8 ± 0.1 mg/dl (n=6). Cortical blood flow in SS, SS.4A1 and HET0016 treated SS.4A1 rats immediately returned to control following IR. However, medullary blood flow in SS and HET0016 treated SS.4A1 rats fell to 30 % of control 3 h after IR (n=5), and it remained depressed for 24 h. In contrast, medullary blood flow did not decline following IR in SS.4A1 rats. Proximal intratubular pressure rose from 13 to approximately 40 mmHg, 2 h after IR in both SS and SS.4A1 rats. Proximal intratubular pressure remained much higher in SS than in SS.4A1 rats 24 h after IR (32 vs 19 mmHg). These data indicate that normalization of renal CYP4A activity and 20-HETE production opposes renal IR injury by preventing secondary fall in medullary blood flow and the prolonged renal medullary ischemia.

Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome

Chromosome 8q24 locus contains regulatory variants that modulate genetic risk to various cancers including prostate cancer (PC). However, the biological mechanism underlying this regulation is not well understood. Here, we developed a chromosome conformation capture (3C)-based multi-target sequencing technology and systematically examined three PC risk regions at the 8q24 locus and their potential regulatory targets across human genome in six cell lines. We observed frequent physical contacts of this risk locus with multiple genomic regions, in particular, inter-chromosomal interaction with CD96 at 3q13 and intra-chromosomal interaction with MYC at 8q24. We identified at least five interaction hot spots within the predicted functional regulatory elements at the 8q24 risk locus. We also found intra-chromosomal interaction genes PVT1, FAM84B and GSDMC and inter-chromosomal interaction gene CXorf36 in most of the six cell lines. Other gene regions appeared to be cell line-specific, such as RRP12 in LNCaP, USP14 in DU-145 and SMIN3 in lymphoblastoid cell line. We further found that the 8q24 functional domains more likely interacted with genomic regions containing genes enriched in critical pathways such as Wnt signaling and promoter motifs such as E2F1 and TCF3. This result suggests that the risk locus may function as a regulatory hub by physical interactions with multiple genes important for prostate carcinogenesis. Further understanding genetic effect and biological mechanism of these chromatin interactions will shed light on the newly discovered regulatory role of the risk locus in PC etiology and progression.

Abstract 41: SH2B3 Is a Genetic Determinant of Cardiac Inflammation and Fibrosis

Background: Genome wide association studies (GWAS) are powerful tools for nominating pathogenic variants, but offer little insight as to how candidate genes impact disease outcome. Such is the case for SH2B adaptor protein 3 (SH2B3), which is associated with coronary artery disease (CAD), atherosclerosis, and risk of myocardial infarction (MI), but its role in post-MI response is completely unknown.

Methods: Using an experimental model of MI (left anterior descending artery [LAD] occlusion) in wild-type (WT) and Sh2b3 knockout (KO) rats, we assessed the role of Sh2b3 in post-MI fibrosis, leukocyte infiltration, angiogenesis, left ventricle (LV) contractility, and inflammatory gene expression. We also confirmed our findings in LV samples from end-stage heart failure patients with or without the MI-associated SH2B3 risk allele.

Results: Compared with WT, Sh2b3 KO rats had significantly increased fibrosis (2.2-fold; P2-fold; P<0.001), which coincided with decreased LV fractional shortening (FS) (-Δ11%; P<0.05) at 7 days post-LAD occlusion. Despite an increased angiogenic potential in Sh2b3 KO rats (1.7-fold; P<0.05), we observed no significant differences in LV capillary density between WT and Sh2b3 KO rats. Of the 903 genes examined, 19 were significantly elevated in the post-LAD occluded hearts of Sh2b3 KO rats relative to WT, of which three (NLRP12, CCR2, and IFNγ) were also significantly elevated in the LV of heart failure (HF) patients carrying the MI-associated rs3184504 [T] SH2B3 risk allele.

Conclusions: These data suggest for the first time that SH2B3 is a master risk factor for MI by impacting both MI incidence and post-MI response.

Abstract 48: Targeting the Endothelial Progenitor Cell Surface Proteome to Identify Novel Mechanisms that Mediate Angiogenic Efficacy and Restore Angiogenesis in a Rodent Model of Vascular Disease

Bone-marrow derived endothelial progenitor cells (EPCs) promote angiogenesis, and clinical trials suggest autologous EPC-based therapy may be effective in treatment of vascular diseases. Albeit promising, variability in the efficacy of EPCs associated with underlying disease states has hindered the realization of EPC-based therapy. Here we identify and characterize EPC dysfunction in a rodent model of vascular disease (SS/Mcwi rat) that exhibits impaired angiogenesis under physiological conditions, and develops cardiovascular disease on a high salt diet. First, we compared the angiogenic responses to EPCs delivered into the skeletal muscle of SS/Mcwi recipient prior to electrical stimulation. Delivery of EPCs from SS/Mcwi donors had no effect on angiogenesis compared to stimulation alone (9.2± 2.2% vs. 7.6 ± 1.7%, respectively). In contrast, introgression of chromosome 13 from a Brown Norway rat onto the SS/Mcwi background (SS-13 BN /Mcwi rat) significantly enhanced the angiogenic function of EPCs (22.3 ± 3.7%) and suggests involvement of genes on chromosome 13. To identify molecular candidates that mediate the angiogenic potential of these cells, we performed a cell surface proteomic analysis. Analysis revealed that EPCs derived from SS/Mcwi rats express significantly more type 2 low-affinity immunoglobulin Fc-gamma (FCGR2, 25% increase) and Natural Killer 2B4 (CD244, 67% increase) receptors than EPCs from the SS-13 BN /Mcwi rat. Genome-wide mRNA sequencing (RNAseq) revealed differential expression of multiple isoforms encoding FCGR2a and CD244 proteins, and qt-PCR confirmed an increase in CD244 and FCGR2a transcripts in SS/Mcwi EPCs. Increased expression of FCGR2a and CD244 receptors are predicted to increase the probability of SS/Mcwi EPCs being targeted for death, providing a mechanistic explanation for their reduced angiogenic efficacy in vivo . Pathway analysis supported this contention, as ‘key’ molecules annotated to cell death paths were differentially expressed in the SS/Mcwi EPC transcriptome. We speculate that screening and neutralization of cell surface proteins that tag ‘diseased’ EPCs for death will enhance regenerative potential of EPC-based therapies, providing a major advance in the field of regenerative medicine.

Abstract 39: Cyp4a1 Transgenic Rats Generated Using Sleeping Beauty Transposon System Restores the Impaired Myogenic Responses in the Afferent Arteriole of Dahl S Rats

We have reported that the production of 20-HETE is reduced in the renal vasculature of Dahl S rats and that myogenic and TGF responses of afferent arteries (Af-Art) are impaired in Dahl S rats. In this study we generated CYP4A1 transgenic rats in the Dahl S inbred strain background utilizing the enhanced Sleeping Beauty (SB100X) transposon system to determine if upregulation of 20-HETE production can restore vascular reactivity and oppose the development of renal injury. Fertilized eggs collected from female Dahl S rats were microinjected with a transposon vector harboring the rat CYP4A1 cDNA under the control of the ubiquitous CAG promoter along with SB100X transposase mRNA to produce transgenic founders. Heterozygous founders were backcrossed to Dahl S rats, transgene insertion sites were identified by Ligation Mediated PCR and sequencing, and the progeny were brother-sister mated to derive homozygous transgenic lines. The expression of CYP4A protein was significantly elevated and the production of 20-HETE was 3-fold higher in the renal outer medullary tissue of CYP4A1 transgenic (n=17) compared to Dahl S rats (n=17). 20-HETE production was 10-fold higher in renal microvessels of CYP4A1 transgenic animals than Dahl S rats. (0.2±0.3, n=22 versus 1.9±0.1 pmol/mg/min, n=14). The luminal diameter of the Af-Art decreased significantly from 15.9 ± 0.6 to 14.1 ± 0.5 μm in CYP4A1 transgenic rats (n=5) when the perfusion pressure was increased from 60 to 120 mmHg, whereas it remained unaltered in Dahl S rats (from 19.4 ± 2.3 to 20.6 ± 5.6 μm, n=22). These studies further support the view that a deficiency in the formation of 20-HETE in the renal microcirculation contributes to the marked susceptibility of Dahl S rats to develop of hypertension and diabetic induced renal injury, and the new CYP4A1 transposon transgenic rat model may be useful for determining the mechanisms involved.

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat

Large numbers of inbred laboratory rat strains have been developed for a range of complex disease phenotypes. To gain insights into the evolutionary pressures underlying selection for these phenotypes, we sequenced the genomes of 27 rat strains, including 11 models of hypertension, diabetes, and insulin resistance, along with their respective control strains. Altogether, we identified more than 13 million single-nucleotide variants, indels, and structural variants across these rat strains. Analysis of strain-specific selective sweeps and gene clusters implicated genes and pathways involved in cation transport, angiotensin production, and regulators of oxidative stress in the development of cardiovascular disease phenotypes in rats. Many of the rat loci that we identified overlap with previously mapped loci for related traits in humans, indicating the presence of shared pathways underlying these phenotypes in rats and humans. These data represent a step change in resources available for evolutionary analysis of complex traits in disease models.

PaperClip

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Genomes of 27 rat strains were sequenced; >13 million sequence variants identified

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Selective sweeps and coevolved gene clusters were detected in 11 disease models

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Previously identified and new disease genes and pathways were identified

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This is first evolutionary analysis of artificial selection for disease phenotypes

Characterization of human plasma-derived exosomal RNAs by deep sequencing

BACKGROUND

Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using three human plasma samples and evaluated the efficacies of small RNA library preparation protocols from three manufacturers. In all we evaluated 14 libraries (7 replicates).

RESULTS

From the 14 size-selected sequencing libraries, we obtained a total of 101.8 million raw single-end reads, an average of about 7.27 million reads per library. Sequence analysis showed that there was a diverse collection of the exosomal RNA species among which microRNAs (miRNAs) were the most abundant, making up over 42.32% of all raw reads and 76.20% of all mappable reads. At the current read depth, 593 miRNAs were detectable. The five most common miRNAs (miR-99a-5p, miR-128, miR-124-3p, miR-22-3p, and miR-99b-5p) collectively accounted for 48.99% of all mappable miRNA sequences. MiRNA target gene enrichment analysis suggested that the highly abundant miRNAs may play an important role in biological functions such as protein phosphorylation, RNA splicing, chromosomal abnormality, and angiogenesis. From the unknown RNA sequences, we predicted 185 potential miRNA candidates. Furthermore, we detected significant fractions of other RNA species including ribosomal RNA (9.16% of all mappable counts), long non-coding RNA (3.36%), piwi-interacting RNA (1.31%), transfer RNA (1.24%), small nuclear RNA (0.18%), and small nucleolar RNA (0.01%); fragments of coding sequence (1.36%), 5' untranslated region (0.21%), and 3' untranslated region (0.54%) were also present. In addition to the RNA composition of the libraries, we found that the three tested commercial kits generated a sufficient number of DNA fragments for sequencing but each had significant bias toward capturing specific RNAs.

CONCLUSIONS

This study demonstrated that a wide variety of RNA species are embedded in the circulating vesicles. To our knowledge, this is the first report that applied deep sequencing to discover and characterize profiles of plasma-derived exosomal RNAs. Further characterization of these extracellular RNAs in diverse human populations will provide reference profiles and open new doors for the development of blood-based biomarkers for human diseases.

Genetic mutation of recombination activating gene 1 in Dahl salt-sensitive rats attenuates hypertension and renal damage

Hypertension and renal damage in Dahl SS rats are associated with increased infiltrating immune cells in the kidney. To examine the role of infiltrating immune cells in this disease process, a zinc finger nuclease targeting bases 672-706 of recombination-activating gene 1 (Rag1) was injected into the pronucleus of Dahl SS (SS/JrHsdMcwi) strain embryos and implanted in pseudopregnant females. This strategy yielded a rat strain with a 13-base frame-shift mutation in the target region of Rag1 and a deletion of immunoreactive Rag1 protein in the thymus. Flow cytometry demonstrated that the Rag1-null mutant rats have a significant reduction in T and B lymphocytes in the circulation and spleen. Studies were performed on SS and Rag1-null rats fed a 4.0% NaCl diet for 3 wk. The infiltration of T cells into the kidney following high-salt intake was significantly blunted in the Rag1-null rats (1.7 ± 0.6 × 10(5) cells/kidney) compared with the Dahl SS (5.6 ± 0.9 × 10(5) cells/kidney). Accompanying the reduction in infiltration of immune cells in the kidney, mean arterial blood pressure and urinary albumin excretion rate were significantly lower in Rag1-null mutants (158 ± 3 mmHg and 60 ± 16 mg/day, respectively) than in SS rats (180 ± 11 mmHg and 251 ± 37 mg/day). Finally, a histological analysis revealed that the glomerular and tubular damage in the kidneys of the SS rats fed a high-salt diet was also attenuated in the Rag1 mutants. These studies demonstrate the importance of renal infiltration of immune cells in the pathogenesis of hypertension and renal damage in Dahl SS rats.

Abstract 4: Genetic Deletion of CD247 in Dahl Salt-Sensitive (SS) Rats Attenuates Hypertension and Renal Damage

The CD3 zeta chain (CD247), a gene involved in T cell signaling, has been demonstrated to associate with hypertension in human genetic studies. Hypertension and renal damage in the Dahl SS rat are associated with an increase in infiltrating T cells in the kidney. There are numerous descriptions of the role of CD247 as a modulator of T cell receptor signaling, but little is known about the role of this gene product in hypertension. To test the functional role of CD247 in hypertension and renal disease, zinc finger nucleases targeting exon 1 were injected into Dahl SS/JrHsdMcwi embryos. The resulting mutation is a 13-bp frameshift deletion of bases 155-167 in exon 1 of CD247 leading to a predicted stop codon within 19 bases of the mutation. Western blotting confirmed the absence of CD247 protein in the thymus, demonstrating a null mutation, and flow cytometry of circulating T and B-cells in wild type (WT) and CD247 null mutant rats (n=5-10/group) demonstrated that the mutants have a significant decrease in CD3+ T-cells (0.04±0.01 vs 4.6±0.5 x 10 7 cells/ml) and increased CD45R+ B-cells (4.1±0.4 vs 1.2±0.2 x 10 7 cells/ml). Studies were then performed on age-matched, male, WT and CD247 null mutant rats fed a 4.0% NaCl diet for three weeks. The infiltration of CD3+ T-cells into the kidney following high salt was significantly blunted in the CD247 mutant rats (1.4±0.4 x 10 5 cells/kidney) compared to the WT (8.7±2.0 x 10 5 cells/kidney). Accompanying the reduced infiltration of T-cells, mean arterial blood pressure was significantly lower in the CD247 null mutant rats than the WT (134±1 vs 151±2 mmHg). As an index of kidney disease, urinary albumin and protein excretion rate were significantly reduced in CD247 null mutants (17±1 and 62±2 mg/day, respectively) compared to WT (49±3 and 121±5 mg/day, respectively). Finally, a histological analysis revealed that the glomerular and tubular damage in the kidneys of the WT rats fed high salt was also attenuated in the CD247 null mutants. This new experimental model provides evidence that T cells are required for the full development of Dahl SS hypertension and indicate that the association between CD247 and hypertension in humans may be related to altered immune cell function. Supported by HL-29587, DK-62803, and RC2-HL101681.

Abstract 127: Identification of a Region of Rat Chromosome 1 That Impairs the Myogenic Response and Cerebral Blood Flow Autoregulation in Fawn Hooded Hypertensive Rats

This study examined the effect of transfer of a 2.4 Mbp region of Brown Norway (BN) rat Chr 1 into the Fawn Hooded Hypertensive (FHH) genetic background on autoregulation (AR) of cerebral blood flow (CBF) and the myogenic response of isolated middle cerebral arteries (MCA). Autoregulation of CBF measured by laser Doppler flowmetry was poor in FHH rats (AR index (AI), 0.8±0.1) and in FHH.1BN congenic strains which excluded the critical region (AR-: AI, 0.9± 0.1). In contrast, autoregulation of CBF was completely restored by transfer of the region of BN Chr 1 between 258.8 to 261.2 Mbp in AR+ FHH.1BN congenic strains (AI, 0.3 ± 0.1). The diameter of MCA of FHH rats and AR- congenic strains increased by ∼10% (140 ± 1 to 157± 2 μm), when transmural pressure was increased from 40 to 140 mmHg. In contrast, the diameter of the MCA in AR+ congenic strain fell from 127 ± 2 to 65 ± 1 μm. Whole-cell patch-clamp of cerebral VSM cells revealed a 4.3-fold increase in BK channel current densities at depolarized potentials in FHH versus AR+ rats (105 ± 2 versus 24 ± 4 pA/pF at +80mV). Using single channel analysis we found that the increase in BK channel current was largely due to a marked increase in the NPo of BK channel in FHH as compared to AR+ rats (0.9 ± 0.1 and 0.2 ± 0.1 at +80mV). To explore the significance of the impaired myogenic response, we compared changes in CBF and infarct size following transient occlusion and reperfusion of the MCA in FHH rats and the AR- and AR+ congenic strains. Occlusion of MCA reduced CBF similarly in all the strains. However, the hyperemic response following reperfusion in FHH and AR- strains was significantly greater and more prolonged than that seen in AR+ rats (AR-: 173 ± 1%, 45 min versus AR+: 124 ± 5%, 15 min). Moreover, infarct size and edema formation was significantly greater in the AR- congenic strain (39 ± 3 % and 12 ± 2 %) in comparison to that seen in the AR+ strain (28 ± 2 %; 7 ± 1%). These results indicate that there is a gene that plays a critical role in the regulation of the myogenic response of the cerebral vasculature by altering BK channel activity in the critical 2.4 Mb region of Chr 1 containing just 15 genes and that transfer of this region from BN to FHH rats restores autoregulation of CBF, vascular reactivity and reduces infarct size following ischemia/reperfusion injury.

Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing

Lung cancer is the leading cause of cancer-related death, with non-small cell lung cancer (NSCLC) being the predominant form of the disease. Most lung cancer is caused by the accumulation of genomic alterations due to tobacco exposure. To uncover its mutational landscape, we performed whole-exome sequencing in 31 NSCLCs and their matched normal tissue samples. We identified both common and unique mutation spectra and pathway activation in lung adenocarcinomas and squamous cell carcinomas, two major histologies in NSCLC. In addition to identifying previously known lung cancer genes (TP53, KRAS, EGFR, CDKN2A and RB1), the analysis revealed many genes not previously implicated in this malignancy. Notably, a novel gene CSMD3 was identified as the second most frequently mutated gene (next to TP53) in lung cancer. We further demonstrated that loss of CSMD3 results in increased proliferation of airway epithelial cells. The study provides unprecedented insights into mutational processes, cellular pathways and gene networks associated with lung cancer. Of potential immediate clinical relevance, several highly mutated genes identified in our study are promising druggable targets in cancer therapy including ALK, CTNNA3, DCC, MLL3, PCDHIIX, PIK3C2B, PIK3CG and ROCK2.

Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

Left ventricular mass (LVM) is a highly heritable trait and an independent risk factor for all-cause mortality. So far, genome-wide association studies have not identified the genetic factors that underlie LVM variation, and the regulatory mechanisms for blood-pressure-independent cardiac hypertrophy remain poorly understood. Unbiased systems genetics approaches in the rat now provide a powerful complementary tool to genome-wide association studies, and we applied integrative genomics to dissect a highly replicated, blood-pressure-independent LVM locus on rat chromosome 3p. Here we identified endonuclease G (Endog), which previously was implicated in apoptosis but not hypertrophy, as the gene at the locus, and we found a loss-of-function mutation in Endog that is associated with increased LVM and impaired cardiac function. Inhibition of Endog in cultured cardiomyocytes resulted in an increase in cell size and hypertrophic biomarkers in the absence of pro-hypertrophic stimulation. Genome-wide network analysis unexpectedly implicated ENDOG in fundamental mitochondrial processes that are unrelated to apoptosis. We showed direct regulation of ENDOG by ERR-α and PGC1α (which are master regulators of mitochondrial and cardiac function), interaction of ENDOG with the mitochondrial genome and ENDOG-mediated regulation of mitochondrial mass. At baseline, the Endog-deleted mouse heart had depleted mitochondria, mitochondrial dysfunction and elevated levels of reactive oxygen species, which were associated with enlarged and steatotic cardiomyocytes. Our study has further established the link between mitochondrial dysfunction, reactive oxygen species and heart disease and has uncovered a role for Endog in maladaptive cardiac hypertrophy.