Meredith P. Millis

Identification of PVT1 as a Candidate Gene for End-Stage Renal Disease in Type 2 Diabetes Using a Pooling-Based Genome-Wide Single Nucleotide Polymorphism Association Study

To identify genetic variants contributing to end-stage renal disease (ESRD) in type 2 diabetes, we performed a genome-wide analysis of 115,352 single nucleotide polymorphisms (SNPs) in pools of 105 unrelated case subjects with ESRD and 102 unrelated control subjects who have had type 2 diabetes for ≥10 years without macroalbuminuria. Using a sliding window statistic of ranked SNPs, we identified a 200-kb region on 8q24 harboring three SNPs showing substantial differences in allelic frequency between case and control pools. These SNPs were genotyped in individuals comprising each pool, and strong evidence for association was found with rs2720709 (P = 0.000021; odds ratio 2.57 [95% CI 1.66–3.96]), which is located in the plasmacytoma variant translocation gene PVT1. We sequenced all exons, exon-intron boundaries, and the promoter of PVT1 and identified 47 variants, 11 of which represented nonredundant markers with minor allele frequency ≥0.05. We subsequently genotyped these 11 variants and an additional 87 SNPs identified through public databases in 319-kb flanking rs2720709 (∼1 SNP/3.5 kb); 23 markers were associated with ESRD at P < 0.01. The strongest evidence for association was found for rs2648875 (P = 0.0000018; 2.97 [1.90–4.65]), which maps to intron 8 of PVT1. Together, these results suggest that PVT1 may contribute to ESRD susceptibility in diabetes.

Genome‐wide SNP genotyping study using pooled DNA to identify candidate markers mediating susceptibility to end‐stage renal disease attributed to Type 1 diabetes

Aims  Genetic factors play a major role in the progression of kidney disease in diabetes. To identify candidate single nucleotide polymorphisms (SNPs) with potential effects on susceptibility to end‐stage renal disease (ESRD), we performed a whole genome association scan using pooled DNA from Caucasian individuals with Type 1 diabetes.

Variants in the Plasmacytoma Variant translocation gene ( PVT1 ) are associated with end-stage renal disease attributed to type 1 diabetes

OBJECTIVE— End-stage renal disease (ESRD) attributed to diabetes is strongly dependent on genetic factors. We previously reported association between variants in the plasmacytoma variant translocation gene (PVT1) and ESRD attributed to type 2 diabetes in Pima Indians. The objective of this study was to evaluate the extent to which these variants mediate susceptibility in other populations. RESEARCH DESIGN AND METHODS— We genotyped 24 markers showing the strongest evidence for association in Pima Indians in unrelated Caucasians with type 1 diabetes from the Genetics of Kidneys in Diabetes (GoKinD) study. The study sample was comprised of 531 case subjects with ESRD and 564 control subjects with diabetes duration >20 years and a maximum urinary albumin-to-creatinine ratio <150 mg/g. RESULTS— Markers rs13447075 (odds ratio [OR] 1.47 [95% CI 1.14–1.89] per copy of A allele; P = 0.003) and rs2648862 (2.66 [1.19–5.92] per copy of C allele; P = 0.008) were strongly associated with ESRD in analyses adjusting for age2, age3, duration of diabetes, and smoking status. We further identified a common haplotype containing the C allele at rs10808565 and the A allele at rs13447075 that was associated with ESRD (P = 0.003). PVT1 gene expression yields several isoforms, and rs13447075 is located within the coding region of one of these transcript variants. We identified expression of this isoform in four major human kidney cell types, including mesangial, cortical epithelial, epithelial, and proximal tubule cells. CONCLUSIONS— These results are the first to provide confirmatory evidence supporting a role for PVT1 in mediating susceptibility to ESRD attributable to diabetes.

ELMO1 variants and susceptibility to diabetic nephropathy in American Indians

Variants in the engulfment and cell motility 1 gene, ELMO1, have previously been associated with kidney disease attributed to type 2 diabetes. The Pima Indians of Arizona have high rates of diabetic nephropathy, which is strongly dependent on genetic determinants; thus, we sought to investigate the role of ELMO1 polymorphisms in mediating susceptibility to this disease in this population. Genotype distributions were compared among 141 individuals with nephropathy and 416 individuals without heavy proteinuria in a family study of 257 sibships, and 107 cases with diabetic ESRD and 108 controls with long duration diabetes and no nephropathy. We sequenced 17.4 kb of ELMO1 and identified 19 variants. We genotyped 12 markers, excluding those in 100% genotypic concordance with other variants or with a minor allele frequency <0.05, plus 21 additional markers showing association with ESRD in earlier studies. In the family study, the strongest evidence for association was with rs1345365 (odds ratio [OR]=2.42 per copy of A allele [1.35-4.32]; P=0.001) and rs10951509 (OR=2.42 per copy of A allele [1.31-4.48]; P=0.002), both of which are located in intron 13 and are in strong pairwise linkage disequilibrium (r(2)=0.97). These associations were in the opposite direction from those observed in African Americans, which suggests that the relationship between diabetic kidney disease and ELMO1 variation may involve as yet undiscovered functional variants or complex interactions with other biological variables.

Medium-Throughput SNP Genotyping Using Mass Spectrometry: Multiplex SNP Genotyping Using the iPLEX® Gold Assay

Depending on the scope of the research project, categories of single-nucleotide polymorphism (SNP) genotyping experiments range from low to medium to high throughput, with each approach differing widely in cost, platform, and efficiency. Medium-throughput genotyping is generally appropriate for assaying up to 36 markers in 384 individuals and is commonly used for fine-mapping chromosomal regions identified in genome scans. Multiplexing, which allows for simultaneous assessment of multiple SNPs, is an efficient, rapid, and economic way to augment medium-throughput genotyping output and is readily performed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this chapter, we describe a technique for medium-throughput genotyping using the iPLEX® Gold assay available from Sequenom, Inc. (San Diego, CA). This multiplex SNP genotyping platform incorporates locus-specific PCR amplification of genomic DNA, followed by shrimp alkaline phosphatase treatment to inactivate unincorporated nucleotides, single-base primer extension using mass-modified terminators, and MALDI-TOF MS for allele-specific detection. This protocol utilizes proprietary enzymes, software and SpectroCHIP® Arrays that are pre-spotted with a MALDI matrix.

Association of variants in the carnosine peptidase 1 gene (CNDP1) with diabetic nephropathy in American Indians

CNDP1 is located on 18q22.3, where linkage with diabetic nephropathy has been observed in several populations, including Pima Indians. However, evidence for association between CNDP1 alleles and diabetic nephropathy is equivocal and population-dependent. This study investigated CNDP1 as a candidate for diabetic kidney disease in Pima Indians. Nineteen tag single nucleotide polymorphisms spanning the CNDP1 locus were selected using genotype data from Chinese individuals in the HapMap resource along with 2 variants previously associated with diabetic nephropathy. All variants were genotyped in 3 different samples including a diabetic end-stage renal disease (ESRD) case-control study, a family-based study of diabetic individuals who participated in the linkage study for nephropathy, and a cohort of diabetic individuals in whom longitudinal measures of glomerular filtration rates (GFR) were performed. There was no statistically significant evidence for association with diabetic ESRD. However, nominal evidence for association was found in the family study, where markers rs12957330 (Odds ratio [OR]=0.29 per copy of G allele; p=0.04) and rs17817077 (OR=0.46 per copy of G allele; p=0.05) were associated with diabetic nephropathy. In addition, markers rs12964454, rs7244647, and rs7229005 were associated with changes in GFR (-8.5ml/min per copy of the G allele; p=0.04; 18.8ml/min per copy of the C allele; p=0.03; and -13.4ml/min per copy of the C allele; p=0.001, respectively). These findings provide nominal evidence supporting a role between CNDP1 variants and diabetic kidney disease.

Abstract 3607: Differential protein expression and miR content of sorted subsets of circulating microvesicles from cancer patients and healthy controls

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL MicroRNAs (miRs) are small non-coding RNAs that are 20 to 25 nucleotides in length and regulate expression of entire families of genes. A major source of circulating miRs in cancer patients is believed to be circulating microvesicles (cMV) within biologic fluids such as blood. The transfer of these modifiers of RNA translation from diseased cells into the bloodstream can have broad impacts on disease detection, progression and/or prognosis. The goal of these studies was to determine whether there are differences in miR composition within different subpopulations of cMV based on surface protein composition. We used flow cytometry to phenotype and sort plasma-derived cMV from 20 individuals (3 breast cancer, 2 lung cancer, 6 prostate cancer, 1 bladder cancer and 6 non-cancer controls). cMV were stained for proteins associated with membranes such as tetraspanins (CD9, 63, 81) Ago2 and/or GW182 using a Beckman Coulter MoFlo XDP. For phenotypic analysis, events were gated on tetraspanin expression to distinguish cMV from nano-sized irrelevant debris, and co-expression of GW182 and Ago2 was determined. Quadrant-based sorting was performed for single- and double-positive events. miR content was determined using conventional Taqman probes with the ABI 7900 thermal cycler on extracted RNA from the sorted cMV. The results of these studies demonstrate that unfractionated cMV were not able to discriminate cancers from non-cancers using miRs-let-7a, -16, -22, -148a or -451 in this population of patients. When sorted tetraspanin+, Ago2+ and/or GW182+ populations of cMV were compared, miR expression was generally 5-fold higher in cancer patients than in healthy controls. These studies demonstrate that cMV can be consistently phenotyped, analyzed and sorted using a flow cytometer and that subpopulations of cMV contain unique miR profiles which can be useful in distinguishing cancer plasma from non-cancer plasma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3607. doi:1538-7445.AM2012-3607

Abstract 3610: GW182 associates with circulating microvesicles and microRNA in human plasma

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL To date, microRNAs (miR) in human plasma have been discovered within circulating microvesicles (cMV), bound to Argonaute 2 and associated with HDL and LDL microvesicles. The protein GW182 shares an association with both multivesicular bodies and the Argonaute family of proteins. GW182 has the capacity to bind all human Argonaute proteins (1-4) and their associated miRs. In the cell, GW182 is associated with the membrane of multivesicular bodies and has the ability to congregate Argonaute-loaded RISC complexes. In addition, GW182 has been observed on the surface of purified exosomes. Here we investigated the relationship of GW182 with Argonaute and cMV in human plasma. A monoclonal antibody directed toward GW182 was used to capture the protein. This isolate also contained Argonaute proteins as determined by Western analysis. The co-precipitation of GW182 and Argonaute suggests that these two proteins retain their functional relationship in plasma. RNA was then isolated from precipitates for miR detection and analysis. The GW182-associated miR profile from human plasma contained individual miRs whose abundance either equaled or surpassed that of their matched Argonaute 2 immuno-precipitated miRs. This implies that GW182 maintains an association with the family of Argonaute proteins and a subset of cMV in human plasma. Phenotypic analysis of GW182-associated human plasma microparticles was performed using flow cytometry with a Beckman Coulter MoFlo XDP. A subpopulation of plasma-derived cMV was observed that co-expressed tetraspanins, GW182 and Argonaute 2. Since tetraspanins are transmembrane proteins highly associated with cMV, these results suggest that both GW182 and Argonaute can associate with cMV in human plasma. Thus, precipitation of GW182 enables the isolation and purification of miRs from human plasma including those bound to Argonaute 1-4 and a subset of cMV. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3610. doi:1538-7445.AM2012-3610

Abstract 4530: A novel blood-based method for evaluating KRAS in circulating microvesicles from colorectal cancer patients

Circulating microvesicles (cMV) are lipid-encapsulated bodies that are secreted from various tissues and can be detected in a number of body fluids, including plasma. Once collected from plasma, they can be exploited diagnostically for their protein and RNA signatures. Mutations in KRAS are diagnostically important for predicting response to chemotherapy and prognosis. A blood-based method of assessing KRAS mutation status would be helpful for patients with colorectal cancer (CRC). Traditional methods of KRAS detection examine the genomic DNA sequence. We developed a method to sequence exon 3 from KRAS using Pyrosequencing. The limit of detection for the assay was 0.78 ng/uL of mutant cDNA for both Pyrosequencing and Sanger sequencing. To further enhance mutation detection, we sorted cMV from CRC patients by first capturing cMV with a CRC associated membrane protein and then sorting for CD63 and CD24 positive events. A Taqman gene expression assay was not sensitive enough to detect KRAS in the sorted samples. However, Pyrosequencing was sufficient to identify mutant and wild-type sequences in patient plasma samples. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4530. doi:1538-7445.AM2012-4530

Abstract 4954: Comparison of miR expression patterns in plasma, serum, and cell line cMV

Circulating microvesicles (cMV) isolated from either blood plasma or serum can yield genetic material sufficient for informative microRNA (miR) expression analysis. The ability to purify RNA from cMV isolated from several sources was compared, and the miR expression patterns were determined. cMV were isolated from the blood plasma and serum of men with and without prostate cancer, as well as from healthy and prostate tumor tissue and prostate cancer cell lines. Total RNA was extracted from the plasma and cell line cMV using the Qiagen miReasy kit and from the serum cMV using the ExoMir extraction method. The miR expression was determined for each source using Agilent V3 miRNA microarrays. Each sample (300 ng) was hybridized to the microarrays, and the acquired data were analyzed with the GeneSpring software package. Expression patterns for miR from cMV isolated from the plasma and serum of men with and without prostate cancer were evaluated for significant differences. Hierarchical clustering on both samples and genes demonstrated a distinct expression pattern for miR from plasma cMV compared with miR from cell line and tumor tissue cMV. These findings demonstrate that cMV isolated from the peripheral blood offer a unique and potentially clinically relevant source of miR for blood-based analysis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4954. doi:10.1158/1538-7445.AM2011-4954