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12 results on '"Ramnauth, Andrew"'

4. Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing

Author

Zhang, Zhengmao, primary, Bai, Hanwen, additional, Blumenfeld, Jon, additional, Ramnauth, Andrew B., additional, Barash, Irina, additional, Prince, Martin, additional, Tan, Adrian Y., additional, Michaeel, Alber, additional, Liu, Genyan, additional, Chicos, Ines, additional, Rennert, Lior, additional, Giannakopoulos, Stavros, additional, Larbi, Karen, additional, Hughes, Stuart, additional, Salvatore, Steven P., additional, Robinson, Brian D., additional, Kapur, Sandip, additional, and Rennert, Hanna, additional

Published
2021
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5. A common intronic single nucleotide variant modifies PKD1 expression level.

Author

Zhang, Zhengmao, Blumenfeld, Jon, Ramnauth, Andrew, Barash, Irina, Zhou, Pengbo, Levine, Daniel, Parker, Thomas, and Rennert, Hanna

Subjects
SINGLE nucleotide polymorphisms, RNA splicing, POLYCYSTIC kidney disease, FRAMESHIFT mutation, MOLECULAR genetics, NATURAL selection, DATA libraries
Abstract

Autosomal dominant polycystic kidney disease (ADPKD), caused by mutations in PKD1 and PKD2 (PKD1/2), has unexplained phenotypic variability likely affected by environmental and other genetic factors. Approximately 10% of individuals with ADPKD phenotype have no causal mutation detected, possibly due to unrecognized risk variants of PKD1/2. This study was designed to identify risk variants of PKD genes through population genetic analyses. We used Wright's F‐statistics (Fst) to evaluate common single nucleotide variants (SNVs) potentially favored by positive natural selection in PKD1 from 1000 Genomes Project (1KG) and genotyped 388 subjects from the Rogosin Institute ADPKD Data Repository. The variants with >90th percentile Fst scores underwent further investigation by in silico analysis and molecular genetics analyses. We identified a deep intronic SNV, rs3874648G> A, located in a conserved binding site of the splicing regulator Tra2‐β in PKD1 intron 30. Reverse‐transcription PCR (RT‐PCR) of peripheral blood leukocytes (PBL) from an ADPKD patient homozygous for rs3874648‐A identified an atypical PKD1 splice form. Functional analyses demonstrated that rs3874648‐A allele increased Tra2‐β binding affinity and activated a cryptic acceptor splice‐site, causing a frameshift that introduced a premature stop codon in mRNA, thereby decreasing PKD1 full‐length transcript level. PKD1 transcript levels were lower in PBL from rs3874648‐G/A carriers than in rs3874648‐G/G homozygotes in a small cohort of normal individuals and patients with PKD2 inactivating mutations. Our findings indicate that rs3874648G > A is a PKD1 expression modifier attenuating PKD1 expression through Tra2‐β, while the derived G allele advantageously maintains PKD1 expression and is predominant in all subpopulations. [ABSTRACT FROM AUTHOR]

Published
2022
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6. Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV‐CATCHER): A customizable purification assay designed for small‐RNA biomarker identification and evaluation of circulating small‐EVs

Author

Mitchell, Megan I., primary, Ben‐Dov, Iddo Z., additional, Liu, Christina, additional, Ye, Kenny, additional, Chow, Kar, additional, Kramer, Yael, additional, Gangadharan, Anju, additional, Park, Steven, additional, Fitzgerald, Sean, additional, Ramnauth, Andrew, additional, Perlin, David S., additional, Donato, Michele, additional, Bhoy, Emily, additional, Manouchehri Doulabi, Ehsan, additional, Poulos, Michael, additional, Kamali‐Moghaddam, Masood, additional, and Loudig, Olivier, additional

Published
2021
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7. Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV-CATCHER) : A customizable purification assay designed for small-RNA biomarker identification and evaluation of circulating small-EVs

Author

Mitchell, Megan, I, Ben-Dov, Iddo Z., Liu, Christina, Ye, Kenny, Chow, Kar, Kramer, Yael, Gangadharan, Anju, Park, Steven, Fitzgerald, Sean, Ramnauth, Andrew, Perlin, David S., Donato, Michele, Bhoy, Emily, Doulabi, Ehsan Manouchehri, Poulos, Michael, Kamali-Moghaddam, Masood, Loudig, Olivier, Mitchell, Megan, I, Ben-Dov, Iddo Z., Liu, Christina, Ye, Kenny, Chow, Kar, Kramer, Yael, Gangadharan, Anju, Park, Steven, Fitzgerald, Sean, Ramnauth, Andrew, Perlin, David S., Donato, Michele, Bhoy, Emily, Doulabi, Ehsan Manouchehri, Poulos, Michael, Kamali-Moghaddam, Masood, and Loudig, Olivier

Abstract

Circulating nucleic acids, encapsulated within small extracellular vesicles (EVs), provide a remote cellular snapshot of biomarkers derived from diseased tissues, however selective isolation is critical. Current laboratory-based purification techniques rely on the physical properties of small-EVs rather than their inherited cellular fingerprints. We established a highly-selective purification assay, termed EV-CATCHER, initially designed for high-throughput analysis of low-abundance small-RNA cargos by next-generation sequencing. We demonstrated its selectivity by specifically isolating and sequencing small-RNAs from mouse small-EVs spiked into human plasma. Western blotting, nanoparticle tracking, and transmission electron microscopy were used to validate and quantify the capture and release of intact small-EVs. As proof-of-principle for sensitive detection of circulating miRNAs, we compared small-RNA sequencing data from a subset of small-EVs serum-purified with EV-CATCHER to data from whole serum, using samples from a small cohort of recently hospitalized Covid-19 patients. We identified and validated, only in small-EVs, hsa-miR-146a and hsa-miR-126-3p to be significantly downregulated with disease severity. Separately, using convalescent sera from recovered Covid-19 patients with high anti-spike IgG titers, we confirmed the neutralizing properties, against SARS-CoV-2 in vitro, of a subset of small-EVs serum-purified by EV-CATCHER, as initially observed with ultracentrifuged small-EVs. Altogether our data highlight the sensitivity and versatility of EV-CATCHER.

Published
2021
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10. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

Author

Loudig, Olivier, primary, Wang, Tao, additional, Ye, Kenny, additional, Lin, Juan, additional, Wang, Yihong, additional, Ramnauth, Andrew, additional, Liu, Christina, additional, Stark, Azadeh, additional, Chitale, Dhananjay, additional, Greenlee, Robert, additional, Multerer, Deborah, additional, Honda, Stacey, additional, Daida, Yihe, additional, Spencer Feigelson, Heather, additional, Glass, Andrew, additional, Couch, Fergus, additional, Rohan, Thomas, additional, and Ben-Dov, Iddo, additional

Published
2017
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12. Hsa-miR-375 is differentially expressed during breast lobular neoplasia and promotes loss of mammary acinar polarity

Author

Giricz, Orsi, primary, Reynolds, Paul A, additional, Ramnauth, Andrew, additional, Liu, Christina, additional, Wang, Tao, additional, Stead, Lesley, additional, Childs, Geoffrey, additional, Rohan, Thomas, additional, Shapiro, Nella, additional, Fineberg, Susan, additional, Kenny, Paraic A, additional, and Loudig, Olivier, additional

Published
2011
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