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Wassman ER, Chettier R, Nelson LM, Serrano MA, Zdunich D, Ward K. COPY NUMBER LOSSES IN SPECIFIC REGIONS OF COMMON VARIATION ARE SIGNIFICANTLY MORE PREVALENT IN INFERTILITY PATIENTS COMPARED WITH A POPULATION OF DEMONSTRATED FERTILITY AND LOW FETAL WASTAGE. Fertil Steril 2020. [DOI: 10.1016/j.fertnstert.2020.08.245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gilad O, Li D, George E, Chettier R, Simpkins F, Ward K, Brown EJ. Synthetic-lethal interactions between ATR inhibition and functional genetic and proteomic biomarkers to predict responses in endometriosis-associated cancers. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e18000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e18000 Background: Endometriosis is a common gynecologic disorder proven to be a precursor to several cancer types. We developed a potent and selective inhibitor (ATRN-119) of a critical DNA damage response (DDR) protein kinase: the ataxia telangiectasia and Rad3-related protein (ATR). Treatment with ATRN-119 is synthetically lethal with multiple cancer-associated changes in DDR pathways, representing a new and effective strategy to treat cancer. The objective of this study is to evaluate the overlap of DDR genes that respond to ATRN-119 and those mutated in endometriosis. Methods: We sequenced the exomes of 2,932 unrelated women with surgically-confirmed endometriosis (GERMLINE) and 274 tissue blocks containing endometriosis lesions (LESION). DNA was extracted using standard methods. Missense and truncation variants were analyzed. These data were compared to analysis of a whole proteome screen for factors that respond to exposure to ATRN-119 and may influence responsiveness to treatment. Factors observed in both methods were considered high-priority biomarker candidates and were experimentally tested for synthetic lethality with ATRN-119 treatment. Results: Analysis of endometriosis patients found 89% of the LESION samples had 2 or more DDR mutations vs 83% of the GERMLINE samples. There is an excess of DDR mutations per sample in LESION (5.5 mutations) vs GERMLINE (3.89 mutations) [p = 4.66x10-6, Mann Whitney test]. In parallel, we identified 92 genes as protein responders to ATRN-119 treatment. Mutations in 21 of these 92 genes show nominal association with surgical endometriosis (p < 0.05). However, of these responsive genes, 18 are known TIER 1 cancer-driver genes and well-characterized mutations were found in three dominant genes in the LESION tissue (ATM, DDB1, and ARID1A). Overall 20% of the patients who’s LESION we examined subsequently developed an endometriosis-associated cancer. Both in vitro and in vivo studies confirmed synthetic-lethal interactions between ATRN-119 treatment and alteration of these genes. Conclusions: The overlap between DDR genes responding to ATRN-119 and those mutated in endometriosis-associated cancer suggest that genetic markers underlying response and resistance will be critical to extend the use of these drugs while increasing efficacy and minimizing toxicities. Furthermore, our data support the inclusion of endometriosis-associated cancer patients in planned ATRN-119 clinical trials.
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Affiliation(s)
| | - Dansu Li
- Atrin Pharmaceuticals, Doylestown, PA
| | - Erin George
- Perelman School of Medicine, Philadelphia, PA
| | | | - Fiona Simpkins
- University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | - Eric J Brown
- University of Pennsylvania School of Medicine, Philadelphia, PA
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Ward K, Chettier R, Albertsen HM. Endometriosis risk allele in Wnt4 may interact with rare mutations in HDAC2 gene. Fertil Steril 2019. [DOI: 10.1016/j.fertnstert.2019.07.952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ward K, Chettier R, Albertsen HM, Morgan T, Williams T. Somatic cancer driver mutations in endometriosis lesions contribute to secondary cancer risk. Fertil Steril 2019. [DOI: 10.1016/j.fertnstert.2019.07.328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Albertsen HM, Chettier R, Ward K. Cytoskeletal and extra cellular matrix genes are key contributors in the pathogenesis of endometriosis. Fertil Steril 2019. [DOI: 10.1016/j.fertnstert.2019.07.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Albertsen HM, Matalliotaki C, Matalliotakis M, Zervou MI, Matalliotakis I, Spandidos DA, Chettier R, Ward K, Goulielmos GN. Whole exome sequencing identifies hemizygous deletions in the UGT2B28 and USP17L2 genes in a three‑generation family with endometriosis. Mol Med Rep 2019; 19:1716-1720. [PMID: 30628680 PMCID: PMC6390005 DOI: 10.3892/mmr.2019.9818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/05/2018] [Accepted: 12/28/2018] [Indexed: 12/22/2022] Open
Abstract
Endometriosis is an enigmatic condition with an unknown etiology and a poorly understood pathogenesis. It is considered to appear from the interplay of many genetic and environmental factors, affecting up to 10% of women and represents a major cause of pain and infertility. The familial association of endometriosis, as demonstrated through monozygotic twin and family studies suggests a genetic contribution to the disease, with further case-control and genome-wide association studies (GWAS) detecting various endometriosis risk factors. In a recent study, we described a unique, three-generation family of Cretan origin (Greece) with 7 females with surgically confirmed endometriosis (grandmother, 3 daughters and 3 granddaughters). All the affected members of this family displayed a variety of clinical manifestations and complications. In the present study, to further analyze the genetic variants conferring the risk of developing endometriosis, whole exome sequencing (WES) was performed, using the AmpliSeq technology on the Ion Proton platform. An initial analysis of 64 variants that were detected across the 14 genes previously confirmed to be associated with endometriosis, did not identify any deleterious exonic variants in these genes. However, further analysis revealed 2 hemizygous deletions in the grandmother that segregate in several of her affected offspring. The first deletion was found in the UGT2B28 locus, spanning 7 informative sequence variants across at least 14 kb. The second deletion, located in USP17L2, spans 3 informative variants across at least 2 kb. On the whole, the findings of the presents study implicate 2 additional genes in the pathogenesis of endometriosis, apart from those already identified by GWAS.
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Affiliation(s)
| | - Charoula Matalliotaki
- 3rd Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki 541 24, Greece
| | - Michail Matalliotakis
- 3rd Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki 541 24, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, University of Crete, Heraklion 710 03, Crete, Greece
| | - Ioannis Matalliotakis
- Department of Obstetrics and Gynecology, Venizeleio General Hospital of Heraklion, Heraklion 714 09, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 710 03, Crete, Greece
| | | | - Kenneth Ward
- Juneau Biosciences, LLC, Salt Lake City, UT, USA
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, University of Crete, Heraklion 710 03, Crete, Greece
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Affiliation(s)
- Hilary S. Gammill
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Washington, Seattle (H.S.G., R.S.)
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle (H.S.G.)
| | - Rakesh Chettier
- Taueret Laboratories LLC, Salt Lake City, UT (R.C., A.B., K.W.)
| | - Alina Brewer
- Taueret Laboratories LLC, Salt Lake City, UT (R.C., A.B., K.W.)
- The Preeclampsia Registry, Preeclampsia Foundation, Melbourne, FL (A.B., E.T.)
| | - James M. Roberts
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, Epidemiology and Clinical and Translational Research, University of Pittsburgh, PA (J.M.R.)
| | - Raj Shree
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Washington, Seattle (H.S.G., R.S.)
| | - Eleni Tsigas
- The Preeclampsia Registry, Preeclampsia Foundation, Melbourne, FL (A.B., E.T.)
| | - Kenneth Ward
- Taueret Laboratories LLC, Salt Lake City, UT (R.C., A.B., K.W.)
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Matalliotaki C, Matalliotakis M, Zervou MI, Trivli A, Matalliotakis I, Mavromatidis G, Spandidos DA, Albertsen HM, Chettier R, Ward K, Goulielmos GN. Co-existence of endometriosis with 13 non-gynecological co-morbidities: Mutation analysis by whole exome sequencing. Mol Med Rep 2018; 18:5053-5057. [PMID: 30272298 PMCID: PMC6236265 DOI: 10.3892/mmr.2018.9521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022] Open
Abstract
Endometriosis is an enigmatic condition with an unknown etiology and poorly understood pathogenesis and women with endometriosis represent a high-risk population group for a large category of chronic conditions. The study focused on a 67-year-old woman who presented with a 40-year history of familial endometriosis associated with various non-gynecological co-morbidities, thus representing a unique case from a cohort of 1,000 patients with endometriosis. Her family history included infertile members suffering from endometriosis. Thirteen non-gynecological co-morbidities were documented throughout the years, including five autoimmune diseases (i.e., systemic lupus erythematosus, ankylosing spondylitis, multiple sclerosis, bronchial asthma and Crohn's disease), urinary bladder diverticulum, osteoporosis, multinodular goiter, cardiovascular diseases, gastroesophageal reflux disease, malignant tumor of urinary bladder, Barrett's esophagus and bilateral cataract. In order to understand the potential role of gene mutations in the development of all those co-morbidities, whole exome sequencing was performed and the presence of various disease-associated, potentially causal missense variants, were observed. These findings are in accordance with the previously suggested common underlying etiologic pathway for some, but not all, autoimmune disorders. This unusual case provides novel insights demonstrating that endometriosis can coexist with various chronic autoimmune diseases and other conditions, including non-gynecological malignancies, which possibly share a common genetic cause, a fact that should be taken into consideration seriously by clinicians.
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Affiliation(s)
- Charoula Matalliotaki
- 3rd Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Michail Matalliotakis
- 3rd Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion 71003, Greece
| | - Alexandra Trivli
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion 71003, Greece
| | - Ioannis Matalliotakis
- Department of Obstetrics and Gynecology, Venizeleio General Hospital of Heraklion, Heraklion 71409, Greece
| | - George Mavromatidis
- 3rd Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71003, Greece
| | | | | | - Kenneth Ward
- Juneau Biosciences, Salt Lake City, UT 84109, USA
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion 71003, Greece
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Fogelson N, Chettier R, Ward K. DNA Testing to Predict Endometriosis: Implications for Referral for Minimally Invasive Surgery. J Minim Invasive Gynecol 2017. [DOI: 10.1016/j.jmig.2017.08.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ward K, Chettier R, Albertsen H, Farrington P. Exome sequencing of women with surgically confirmed endometriosis identifies new candidate genes. Fertil Steril 2015. [DOI: 10.1016/j.fertnstert.2015.07.208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chettier R, Nelson L, Ogilvie JW, Albertsen HM, Ward K. Haplotypes at LBX1 have distinct inheritance patterns with opposite effects in adolescent idiopathic scoliosis. PLoS One 2015; 10:e0117708. [PMID: 25675428 PMCID: PMC4326419 DOI: 10.1371/journal.pone.0117708] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 09/25/2014] [Accepted: 12/30/2014] [Indexed: 11/19/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is a clinically significant disorder with high heritability that affects 2–4% of the population. Genome-wide association studies have identified LBX1 as a strong susceptibility locus for AIS in Asian and Caucasian populations. Here we further dissect the genetic association with AIS in a Caucasian population. To identify genetic markers associated with AIS we employed a genome-wide association study (GWAS) design comparing 620 female Caucasian patients who developed idiopathic scoliosis during adolescence with 1,287 ethnically matched females who had normal spinal curves by skeletal maturity. The genomic region around LBX1 was imputed and haplotypes investigated for genetic signals under different inheritance models. The strongest signal was identified upstream of LBX1 (rs11190878, Ptrend = 4.18×10-9, OR = 0.63[0.54–0.74]). None of the remaining SNPs pass the genome-wide significance threshold. We found rs11190870, downstream of LBX1 and previously associated with AIS in Asian populations, to be in modest linkage disequilibrium (LD) with rs11190878 (r2 = 0.40, D' = 0.81). Haplotype analysis shows that rs11190870 and rs11190878 track a single risk factor that resides on the ancestral haplotype and is shared across ethnic groups. We identify six haplotypes at the LBX1 locus including two strongly associated haplotypes; a recessive risk haplotype (TTA, Controlfreq = 0.52, P = 1.25×10-9, OR = 1.56), and a co-dominant protective haplotype (CCG, Controlfreq = 0.28, P = 2.75×10-7, OR = 0.65). Together the association signals from LBX1 explain 1.4% of phenotypic variance. Our results identify two clinically relevant haplotypes in the LBX1-region with opposite effects on AIS risk. The study demonstrates the utility of haplotypes over un-phased SNPs for individualized risk assessment by more strongly delineating individuals at risk for AIS without compromising the effect size.
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Affiliation(s)
- Rakesh Chettier
- Affiliated Genetics, Inc., Salt Lake City, Utah, 84109, United States of America
| | - Lesa Nelson
- Affiliated Genetics, Inc., Salt Lake City, Utah, 84109, United States of America
| | - James W. Ogilvie
- Lucina Foundation, Salt Lake City, Utah, 84109, United States of America
| | - Hans M. Albertsen
- Juneau Biosciences, LLC., Salt Lake City, Utah, 84109, United States of America
| | - Kenneth Ward
- Affiliated Genetics, Inc., Salt Lake City, Utah, 84109, United States of America
- Juneau Biosciences, LLC., Salt Lake City, Utah, 84109, United States of America
- * E-mail:
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Chettier R, Albertsen H, Ward K. Next generation sequencing of families with endometriosis identifies new genomic regions likely to contribute to heritability. Fertil Steril 2014. [DOI: 10.1016/j.fertnstert.2014.07.260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Chettier R, Albertsen H, Ward K. Comparing apples and oranges: molecular pathogenesis of endometriosis varies by patient ancestry. Fertil Steril 2012. [DOI: 10.1016/j.fertnstert.2012.07.488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ward K, Chettier R, Farrington P, Albertsen H. Rare genetic variants useful for non-invasive diagnosis and prediction of endometriosis. Fertil Steril 2012. [DOI: 10.1016/j.fertnstert.2012.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ward K, Chettier R, Farrington P, Albertsen H. KRAS and LCS6 show no evidence of association with endometriosis. Fertil Steril 2012. [DOI: 10.1016/j.fertnstert.2012.07.785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ward K, Chettier R, Ward J, Nelson L. 723: Genome-wide association study of preeclampsia points to several novel genes. Am J Obstet Gynecol 2011. [DOI: 10.1016/j.ajog.2010.10.745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ward K, Ogilvie J, Argyle V, Nelson L, Meade M, Braun J, Chettier R. Polygenic inheritance of adolescent idiopathic scoliosis: A study of extended families in Utah. Am J Med Genet A 2010; 152A:1178-88. [DOI: 10.1002/ajmg.a.33145] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ogilvie J, Nelson L, Chettier R, Ward K. Does bracing alter the natural history of Adolescent Idiopathic Scoliosis? Scoliosis 2009. [PMCID: PMC2793488 DOI: 10.1186/1748-7161-4-s2-o59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bell R, Hubbard A, Chettier R, Chen D, Miller JP, Kapahi P, Tarnopolsky M, Sahasrabuhde S, Melov S, Hughes RE. A human protein interaction network shows conservation of aging processes between human and invertebrate species. PLoS Genet 2009; 5:e1000414. [PMID: 19293945 PMCID: PMC2657003 DOI: 10.1371/journal.pgen.1000414] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 02/10/2009] [Indexed: 01/08/2023] Open
Abstract
We have mapped a protein interaction network of human homologs of proteins that modify longevity in invertebrate species. This network is derived from a proteome-scale human protein interaction Core Network generated through unbiased high-throughput yeast two-hybrid searches. The longevity network is composed of 175 human homologs of proteins known to confer increased longevity through loss of function in yeast, nematode, or fly, and 2,163 additional human proteins that interact with these homologs. Overall, the network consists of 3,271 binary interactions among 2,338 unique proteins. A comparison of the average node degree of the human longevity homologs with random sets of proteins in the Core Network indicates that human homologs of longevity proteins are highly connected hubs with a mean node degree of 18.8 partners. Shortest path length analysis shows that proteins in this network are significantly more connected than would be expected by chance. To examine the relationship of this network to human aging phenotypes, we compared the genes encoding longevity network proteins to genes known to be changed transcriptionally during aging in human muscle. In the case of both the longevity protein homologs and their interactors, we observed enrichments for differentially expressed genes in the network. To determine whether homologs of human longevity interacting proteins can modulate life span in invertebrates, homologs of 18 human FRAP1 interacting proteins showing significant changes in human aging muscle were tested for effects on nematode life span using RNAi. Of 18 genes tested, 33% extended life span when knocked-down in Caenorhabditis elegans. These observations indicate that a broad class of longevity genes identified in invertebrate models of aging have relevance to human aging. They also indicate that the longevity protein interaction network presented here is enriched for novel conserved longevity proteins. Studies of longevity in model organisms such as baker's yeast, roundworm, and fruit fly have clearly demonstrated that a diverse array of genetic mutations can result in increased life span. In fact, large-scale genetic screens have identified hundreds of genes that when mutated, knocked down, or deleted will significantly enhance longevity in these organisms. Despite great progress in understanding genetic and genomic determinants of life span in model organisms, the general relevance of invertebrate longevity genes to human aging and longevity has yet to be fully established. In this study, we show that human homologs of invertebrate longevity genes change in their expression levels during aging in human tissue. We also show that human genes encoding proteins that interact with human longevity homolog proteins are also changed in expression during human aging. These observations taken together indicate that the broad patterns underlying genetic control of life span in invertebrates is highly relevant to human aging and longevity. We also present a collection of novel candidate genes and proteins that may influence human life span.
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Affiliation(s)
- Russell Bell
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Alan Hubbard
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- Buck Institute for Age Research, Novato, California, United States of America
| | - Rakesh Chettier
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Di Chen
- Buck Institute for Age Research, Novato, California, United States of America
| | - John P. Miller
- Buck Institute for Age Research, Novato, California, United States of America
| | - Pankaj Kapahi
- Buck Institute for Age Research, Novato, California, United States of America
| | | | | | - Simon Melov
- Buck Institute for Age Research, Novato, California, United States of America
| | - Robert E. Hughes
- Buck Institute for Age Research, Novato, California, United States of America
- * E-mail:
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Vignali M, McKinlay A, LaCount DJ, Chettier R, Bell R, Sahasrabudhe S, Hughes RE, Fields S. Interaction of an atypical Plasmodium falciparum ETRAMP with human apolipoproteins. Malar J 2008; 7:211. [PMID: 18937849 PMCID: PMC2577112 DOI: 10.1186/1475-2875-7-211] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [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: 04/01/2008] [Accepted: 10/20/2008] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In order to establish a successful infection in the human host, the malaria parasite Plasmodium falciparum must establish interactions with a variety of human proteins on the surface of different cell types, as well as with proteins inside the host cells. To better understand this aspect of malaria pathogenesis, a study was conducted with the goal of identifying interactions between proteins of the parasite and those of its human host. METHODS A modified yeast two-hybrid methodology that preferentially selects protein fragments that can be expressed in yeast was used to conduct high-throughput screens with P. falciparum protein fragments against human liver and cerebellum libraries. The resulting dataset was analyzed to exclude interactions that are not likely to occur in the human host during infection. RESULTS An initial set of 2,200 interactions was curated to remove proteins that are unlikely to play a role in pathogenesis based on their annotation or localization, and proteins that behave promiscuously in the two-hybrid assay, resulting in a final dataset of 456 interactions. A cluster that implicates binding between P. falciparum PFE1590w/ETRAMP5, a putative parasitophorous vacuole membrane protein, and human apolipoproteins ApoA, ApoB and ApoE was selected for further analysis. Different isoforms of ApoE, which are associated with different outcomes of malaria infection, were shown to display differential interactions with PFE1590w. CONCLUSION A dataset of interactions between proteins of P. falciparum and those of its human host was generated. The preferential interaction of the P. falciparum PFE1590w protein with the human ApoE epsilon3 and ApoE epsilon4 isoforms, but not the ApoE epsilon2 isoform, supports the hypothesis that ApoE genotype affects risk of malaria infection. The dataset contains other interactions of potential relevance to disease that may identify possible vaccine candidates and drug targets.
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Affiliation(s)
- Marissa Vignali
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA.
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Kaltenbach LS, Romero E, Becklin RR, Chettier R, Bell R, Phansalkar A, Strand A, Torcassi C, Savage J, Hurlburt A, Cha GH, Ukani L, Chepanoske CL, Zhen Y, Sahasrabudhe S, Olson J, Kurschner C, Ellerby LM, Peltier JM, Botas J, Hughes RE. Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet 2007; 3:e82. [PMID: 17500595 PMCID: PMC1866352 DOI: 10.1371/journal.pgen.0030082] [Citation(s) in RCA: 299] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 04/06/2007] [Indexed: 12/25/2022] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative condition caused by expansion of the polyglutamine tract in the huntingtin (Htt) protein. Neuronal toxicity in HD is thought to be, at least in part, a consequence of protein interactions involving mutant Htt. We therefore hypothesized that genetic modifiers of HD neurodegeneration should be enriched among Htt protein interactors. To test this idea, we identified a comprehensive set of Htt interactors using two complementary approaches: high-throughput yeast two-hybrid screening and affinity pull down followed by mass spectrometry. This effort led to the identification of 234 high-confidence Htt-associated proteins, 104 of which were found with the yeast method and 130 with the pull downs. We then tested an arbitrary set of 60 genes encoding interacting proteins for their ability to behave as genetic modifiers of neurodegeneration in a Drosophila model of HD. This high-content validation assay showed that 27 of 60 orthologs tested were high-confidence genetic modifiers, as modification was observed with more than one allele. The 45% hit rate for genetic modifiers seen among the interactors is an order of magnitude higher than the 1%–4% typically observed in unbiased genetic screens. Genetic modifiers were similarly represented among proteins discovered using yeast two-hybrid and pull-down/mass spectrometry methods, supporting the notion that these complementary technologies are equally useful in identifying biologically relevant proteins. Interacting proteins confirmed as modifiers of the neurodegeneration phenotype represent a diverse array of biological functions, including synaptic transmission, cytoskeletal organization, signal transduction, and transcription. Among the modifiers were 17 loss-of-function suppressors of neurodegeneration, which can be considered potential targets for therapeutic intervention. Finally, we show that seven interacting proteins from among 11 tested were able to co-immunoprecipitate with full-length Htt from mouse brain. These studies demonstrate that high-throughput screening for protein interactions combined with genetic validation in a model organism is a powerful approach for identifying novel candidate modifiers of polyglutamine toxicity. Huntington's Disease (HD) is a fatal inherited neurodegenerative disease, which typically begins in middle age and progresses with symptoms of severe uncontrolled movements and cognitive dysfunction. HD is uniformly fatal with death occurring ten to 15 years after onset of symptoms. There is currently no effective treatment for HD. The genetic mutation underlying HD causes a protein called huntingtin (Htt) to contain an abnormally long tract of the amino acid glutamine. This extended span of glutamines changes the shape of the Htt protein, which can cause it to interact in abnormal ways with other cellular proteins. In this study, we have identified a large number of new proteins that bind to normal and mutant forms of the Htt protein. To establish a potential role for these interacting proteins in HD, we show that changing the expression of many of these proteins can modulate the pathological effects of mutant Htt on fly neurons that deteriorate when they express mutant Htt. Identifying cellular proteins that bind to Htt and modulate its pathological activity may facilitate the discovery of an effective treatment for HD.
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Affiliation(s)
- Linda S Kaltenbach
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Eliana Romero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Robert R Becklin
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Rakesh Chettier
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Russell Bell
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Amit Phansalkar
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Andrew Strand
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Cameron Torcassi
- Buck Institute for Age Research, Novato, California, United States of America
| | - Justin Savage
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Anthony Hurlburt
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Guang-Ho Cha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lubna Ukani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Yuejun Zhen
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | | | - James Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Cornelia Kurschner
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Lisa M Ellerby
- Buck Institute for Age Research, Novato, California, United States of America
| | - John M Peltier
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail: (JB); (REH)
| | - Robert E Hughes
- Prolexys Pharmaceuticals, Salt Lake City, Utah, United States of America
- Buck Institute for Age Research, Novato, California, United States of America
- * To whom correspondence should be addressed. E-mail: (JB); (REH)
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LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C, Fields S, Hughes RE. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 2005; 438:103-7. [PMID: 16267556 DOI: 10.1038/nature04104] [Citation(s) in RCA: 402] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 08/01/2005] [Indexed: 11/08/2022]
Abstract
Plasmodium falciparum causes the most severe form of malaria and kills up to 2.7 million people annually. Despite the global importance of P. falciparum, the vast majority of its proteins have not been characterized experimentally. Here we identify P. falciparum protein-protein interactions using a high-throughput version of the yeast two-hybrid assay that circumvents the difficulties in expressing P. falciparum proteins in Saccharomyces cerevisiae. From more than 32,000 yeast two-hybrid screens with P. falciparum protein fragments, we identified 2,846 unique interactions, most of which include at least one previously uncharacterized protein. Informatic analyses of network connectivity, coexpression of the genes encoding interacting fragments, and enrichment of specific protein domains or Gene Ontology annotations were used to identify groups of interacting proteins, including one implicated in chromatin modification, transcription, messenger RNA stability and ubiquitination, and another implicated in the invasion of host cells. These data constitute the first extensive description of the protein interaction network for this important human pathogen.
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Affiliation(s)
- Douglas J LaCount
- Howard Hughes Medical Institute, University of Washington, Box 357730, Seattle, Washington 98195, USA
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