1
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Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol 2019; 20:226. [PMID: 31672156 PMCID: PMC6822431 DOI: 10.1186/s13059-019-1834-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/23/2019] [Indexed: 01/05/2023] Open
Abstract
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.
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Affiliation(s)
- Jon G Sanders
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sergey Nurk
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Rodolfo A Salido
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Jeremiah Minich
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Marcus Fedarko
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Timothy D Arthur
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | | | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - Greg C Humphrey
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - James Gaffney
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mahdieh Khosroheidari
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cliff Green
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marlon Liyanage
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Jason W Dang
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Vanessa V Phelan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA
| | - Robert A Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Anton Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - Tariq M Rana
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Douglas J Conrad
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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Abstract
MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.
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Affiliation(s)
| | - Kendra Walton
- Genomics Facility, Center for Genes, Environment, and Health, Department of Biomedical Research, National Jewish Health, Denver, CO, USA
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3
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Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell 2017; 62:157-168. [PMID: 27105112 DOI: 10.1016/j.molcel.2016.03.019] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 12/29/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022]
Abstract
HIV-infected individuals are living longer on antiretroviral therapy, but many patients display signs that in some ways resemble premature aging. To investigate and quantify the impact of chronic HIV infection on aging, we report a global analysis of the whole-blood DNA methylomes of 137 HIV+ individuals under sustained therapy along with 44 matched HIV- individuals. First, we develop and validate epigenetic models of aging that are independent of blood cell composition. Using these models, we find that both chronic and recent HIV infection lead to an average aging advancement of 4.9 years, increasing expected mortality risk by 19%. In addition, sustained infection results in global deregulation of the methylome across >80,000 CpGs and specific hypomethylation of the region encoding the human leukocyte antigen locus (HLA). We find that decreased HLA methylation is predictive of lower CD4 / CD8 T cell ratio, linking molecular aging, epigenetic regulation, and disease progression.
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Affiliation(s)
- Andrew M Gross
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Philipp A Jaeger
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristen L Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mahdieh Khosroheidari
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brenda M Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Susan Swindells
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Cherie T Ng
- aTyr Pharmaceuticals, San Diego, CA 92121, USA
| | - Ken Flagg
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Guangzhou Kang Rui Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, China
| | - Daniel Chen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kang Zhang
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Veterans Administration Healthcare System, San Diego, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Trey Ideker
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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4
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Alvarez ML, Khosroheidari M, Eddy E, Kiefer J, DiStefano JK. Correction: Role of MicroRNA 1207-5P and Its Host Gene, the Long Non-Coding RNA Pvt1, as Mediators of Extracellular Matrix Accumulation in the Kidney: Implications for Diabetic Nephropathy. PLoS One 2016; 11:e0168353. [PMID: 27936176 PMCID: PMC5148166 DOI: 10.1371/journal.pone.0168353] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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5
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Alvarez ML, Khosroheidari M, Eddy E, Done SC. MicroRNA-27a decreases the level and efficiency of the LDL receptor and contributes to the dysregulation of cholesterol homeostasis. Atherosclerosis 2015; 242:595-604. [PMID: 26318398 DOI: 10.1016/j.atherosclerosis.2015.08.023] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/06/2015] [Accepted: 08/14/2015] [Indexed: 11/29/2022]
Abstract
RATIONALE A strong risk factor for atherosclerosis- the leading cause of heart attacks and strokes- is the elevation of low-density lipoprotein cholesterol (LDL-C) in blood. The LDL receptor (LDLR) is the primary pathway for LDL-C removal from circulation, and their levels are increased by statins -the main treatment for high blood LDL-C. However, statins have low efficiency because they also increase PCSK9 which targets LDLR for degradation. Since microRNAs have recently emerged as key regulators of cholesterol homeostasis, our aim was to identify potential microRNA-based therapeutics to decrease blood LDL-C and prevent atherosclerosis. METHODS AND RESULTS We over expressed and knocked down miR-27a in HepG2 cells to assess its effect on the expression of key players in the LDLR pathway using PCR Arrays, Elisas, and Western blots. We found that miR-27a decreases LDLR levels by 40% not only through a direct binding to its 3' untranslated region but also indirectly by inducing a 3-fold increase in PCSK9, which enhances LDLR degradation. Interestingly, miR-27a also directly decreases LRP6 and LDLRAP1, two other key players in the LDLR pathway that are required for efficient endocytosis of the LDLR-LDL-C complex in the liver. The inhibition of miR-27a using lock nucleic acids induced a 70% increase in LDLR levels and, therefore, it would be a more efficient treatment for hypercholesterolemia because of its desirable effects not only on LDLR but also on PCSK9. CONCLUSION The results presented here provide evidence supporting the potential of miR-27a as a novel therapeutic target for the prevention of atherosclerosis.
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Affiliation(s)
- M Lucrecia Alvarez
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ 85004, USA.
| | - Mahdieh Khosroheidari
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ 85004, USA
| | - Elena Eddy
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ 85004, USA
| | - Stefania C Done
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ 85004, USA
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6
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Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CHM, Carson DA, Kipps TJ, Frazer KA. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J 2015; 5:e303. [PMID: 25860294 PMCID: PMC4450323 DOI: 10.1038/bcj.2015.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023] Open
Abstract
We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.
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Affiliation(s)
- E N Smith
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - E M Ghia
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - C M DeBoever
- Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA
| | - L Z Rassenti
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K Jepsen
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K-A Yoon
- Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA
| | - H Matsui
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - S Rozenzhak
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - H Alakus
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - P J Shepard
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Y Dai
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - M Khosroheidari
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - M Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - K L Gunderson
- Illumina, Inc., 5200 Illumina Way, San Diego, CA, USA
| | - K Messer
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - L Muthuswamy
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - T J Hudson
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - O Harismendy
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C L Barrett
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C H M Jamieson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA [3] Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - D A Carson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - T J Kipps
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K A Frazer
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [3] Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA [4] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
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7
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Boland BS, Widjaja CE, Banno A, Zhang B, Kim SH, Stoven S, Peterson MR, Jones MC, Su HI, Crowe SE, Bui JD, Ho SB, Okugawa Y, Goel A, Marietta EV, Khosroheidari M, Jepsen K, Aramburu J, López-Rodríguez C, Sandborn WJ, Murray JA, Harismendy O, Chang JT. Immunodeficiency and autoimmune enterocolopathy linked to NFAT5 haploinsufficiency. J Immunol 2015; 194:2551-60. [PMID: 25667416 DOI: 10.4049/jimmunol.1401463] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The link between autoimmune diseases and primary immunodeficiency syndromes has been increasingly appreciated. Immunologic evaluation of a young man with autoimmune enterocolopathy and unexplained infections revealed evidence of immunodeficiency, including IgG subclass deficiency, impaired Ag-induced lymphocyte proliferation, reduced cytokine production by CD8(+) T lymphocytes, and decreased numbers of NK cells. Genetic evaluation identified haploinsufficiency of NFAT5, a transcription factor regulating immune cell function and cellular adaptation to hyperosmotic stress, as a possible cause of this syndrome. Inhibition or deletion of NFAT5 in normal human and murine cells recapitulated several of the immune deficits identified in the patient. These results provide evidence of a primary immunodeficiency disorder associated with organ-specific autoimmunity linked to NFAT5 deficiency.
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Affiliation(s)
- Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA 92093
| | | | - Asoka Banno
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Bing Zhang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Stephanie H Kim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | | | - Michael R Peterson
- Western Washington Pathology and Multicare Health System, Tacoma, WA 98405
| | - Marilyn C Jones
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093
| | - H Irene Su
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sheila E Crowe
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Samuel B Ho
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246; Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX 75246
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246; Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX 75246
| | | | - Mahdieh Khosroheidari
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kristen Jepsen
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jose Aramburu
- Immunology Unit, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003 Spain; and
| | - Cristina López-Rodríguez
- Immunology Unit, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003 Spain; and
| | - William J Sandborn
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA 92093
| | | | - Olivier Harismendy
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA 92093;
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8
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Abstract
Identification of biomarkers that allow early detection of kidney diseases in urine and plasma has been an area of active interest for several years. Urinary exosome vesicles, 40-100 nm in size, are released into the urine under normal conditions by cells from all nephron segments and may contain protein, mRNA and microRNA representative of their cell type of origin. Under conditions of renal dysfunction or injury, exosomes may contain altered proportions of these components, which may serve as biomarkers for disease. There are currently several methods available for isolation of urinary exosomes, and we have previously conducted an experimental comparison of each of these approaches, including three based on ultracentrifugation, one using a nanomembrane ultrafiltration concentrator, one using a commercial precipitation reagent and one using a modification of the precipitation technique using ExoQuick reagent that we developed in our laboratory. We found the modified precipitation method produced the highest yield of exosome particles, miRNA, and mRNA, making this approach suitable for the isolation of exosomes for subsequent RNA profiling. We conclude that the modified exosome precipitation method offers a quick, scalable, and effective alternative for the isolation of exosomes from urine. In this report, we describe our modified precipitation technique using ExoQuick reagent for isolating exosomes from human urine.
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Affiliation(s)
- Rupesh Kanchi Ravi
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute (TGen)
| | - Mahdieh Khosroheidari
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute (TGen)
| | - Johanna K DiStefano
- Diabetes, Cardiovascular and Metabolic Diseases Division, Translational Genomics Research Institute (TGen);
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9
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Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol 2014; 15:420. [PMID: 25103687 PMCID: PMC4165357 DOI: 10.1186/s13059-014-0420-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/07/2014] [Indexed: 11/17/2022] Open
Abstract
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.
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Alvarez ML, Khosroheidari M, Eddy E, Kiefer J. Role of microRNA 1207-5P and its host gene, the long non-coding RNA Pvt1, as mediators of extracellular matrix accumulation in the kidney: implications for diabetic nephropathy. PLoS One 2013; 8:e77468. [PMID: 24204837 PMCID: PMC3808414 DOI: 10.1371/journal.pone.0077468] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/02/2013] [Indexed: 01/13/2023] Open
Abstract
Diabetic nephropathy is the most common cause of chronic kidney failure and end-stage renal disease in the Western World. One of the major characteristics of this disease is the excessive accumulation of extracellular matrix (ECM) in the kidney glomeruli. While both environmental and genetic determinants are recognized for their role in the development of diabetic nephropathy, epigenetic factors, such as DNA methylation, long non-coding RNAs, and microRNAs, have also recently been found to underlie some of the biological mechanisms, including ECM accumulation, leading to the disease. We previously found that a long non-coding RNA, the plasmacytoma variant translocation 1 (PVT1), increases plasminogen activator inhibitor 1 (PAI-1) and transforming growth factor beta 1 (TGF-β1) in mesangial cells, the two main contributors to ECM accumulation in the glomeruli under hyperglycemic conditions, as well as fibronectin 1 (FN1), a major ECM component. Here, we report that miR-1207-5p, a PVT1-derived microRNA, is abundantly expressed in kidney cells, and is upregulated by glucose and TGF-β1. We also found that like PVT1, miR-1207-5p increases expression of TGF-β1, PAI-1, and FN1 but in a manner that is independent of its host gene. In addition, regulation of miR-1207-5p expression by glucose and TGFβ1 is independent of PVT1. These results provide evidence supporting important roles for miR-1207-5p and its host gene in the complex pathogenesis of diabetic nephropathy.
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Affiliation(s)
- M. Lucrecia Alvarez
- Diabetes, Cardiovascular, and Metabolic Diseases Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
| | - Mahdieh Khosroheidari
- Diabetes, Cardiovascular, and Metabolic Diseases Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Elena Eddy
- Diabetes, Cardiovascular, and Metabolic Diseases Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jeff Kiefer
- Diabetes, Cardiovascular, and Metabolic Diseases Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
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