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Author Lisa F Barcellos

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Global expression and CpG methylation analysis of primary endothelial cells before and after TNFa stimulation reveals gene modules enriched in inflammatory and infectious diseases and associated DMRs.

Brooke Rhead, Xiaorong Shao, Hong Quach, Poonam Ghai, Lisa F Barcellos, Anne M Bowcock,

Endothelial cells are a primary site of leukocyte recruitment during inflammation. An increase in tumor necrosis factor-alpha (TNFa) levels as a result of infection or some autoimmune diseases can trigger this process. Several autoimmune diseases are now treated with TNFa inhibitors. However, genomic alterations that occur as a result of ... Read more >>

PLoS ONE (PloS one)
[2020, 15(3):e0230884]

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Author Correction: A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus.

Cristina M Lanata, Ishan Paranjpe, Joanne Nititham, Kimberly E Taylor, Milena Gianfrancesco, Manish Paranjpe, Shan Andrews, Sharon A Chung, Brooke Rhead, Lisa F Barcellos, Laura Trupin, Patricia Katz, Maria Dall'Era, Jinoos Yazdany, Marina Sirota, Lindsey A Criswell,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):1164]

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Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk.

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Cell (Cell)
[2020, 180(2):403]

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Inherited genetic susceptibility to acute lymphoblastic leukemia in Down syndrome.

Austin L Brown, Adam J de Smith, Vincent U Gant, Wenjian Yang, Michael E Scheurer, Kyle M Walsh, Jonathan M Chernus, Noah A Kallsen, Shanna A Peyton, Gareth E Davies, Erik A Ehli, Naomi Winick, Nyla A Heerema, Andrew J Carroll, Michael J Borowitz, Brent L Wood, William L Carroll, Elizabeth A Raetz, Eleanor Feingold, Meenakshi Devidas, Lisa F Barcellos, Helen M Hansen, Libby Morimoto, Alice Y Kang, Ivan Smirnov, Jasmine Healy, Caroline Laverdière, Daniel Sinnett, Jeffrey W Taub, Jillian M Birch, Pamela Thompson, Logan G Spector, Maria S Pombo-de-Oliveira, Andrew T DeWan, Charles G Mullighan, Stephen P Hunger, Ching-Hon Pui, Mignon L Loh, Michael E Zwick, Catherine Metayer, Xiaomei Ma, Beth A Mueller, Stephanie L Sherman, Joseph L Wiemels, Mary V Relling, Jun J Yang, Philip J Lupo, Karen R Rabin,

Children with Down syndrome (DS) have a 20-fold increased risk of acute lymphoblastic leukemia (ALL) and distinct somatic features, including CRLF2 rearrangement in ∼50% of cases; however, the role of inherited genetic variation in DS-ALL susceptibility is unknown. We report the first genome-wide association study of DS-ALL, comprising a meta-analysis ... Read more >>

Blood (Blood)
[2019, 134(15):1227-1237]

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A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus.

Cristina M Lanata, Ishan Paranjpe, Joanne Nititham, Kimberly E Taylor, Milena Gianfrancesco, Manish Paranjpe, Shan Andrews, Sharon A Chung, Brooke Rhead, Lisa F Barcellos, Laura Trupin, Patricia Katz, Maria Dall'Era, Jinoos Yazdany, Marina Sirota, Lindsey A Criswell,

Systemic lupus erythematous (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. Here, we aim to identify SLE subgroups within a multiethnic cohort using an unsupervised clustering approach based on the American College of Rheumatology (ACR) classification criteria. We identify three patient clusters that vary ... Read more >>

Nat Commun (Nature communications)
[2019, 10(1):3902]

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Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility.

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We analyzed genetic data of 47,429 multiple sclerosis (MS) and 68,374 control subjects and established a reference map of the genetic architecture of MS that includes 200 autosomal susceptibility variants outside the major histocompatibility complex (MHC), one chromosome X variant, and 32 variants within the extended MHC. We used an ... Read more >>

Science (Science (New York, N.Y.))
[2019, 365(6460):]

Cited: 2 times

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Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology.

Elior Rahmani, Regev Schweiger, Brooke Rhead, Lindsey A Criswell, Lisa F Barcellos, Eleazar Eskin, Saharon Rosset, Sriram Sankararaman, Eran Halperin,

High costs and technical limitations of cell sorting and single-cell techniques currently restrict the collection of large-scale, cell-type-specific DNA methylation data. This, in turn, impedes our ability to tackle key biological questions that pertain to variation within a population, such as identification of disease-associated genes at a cell-type-specific resolution. Here, ... Read more >>

Nat Commun (Nature communications)
[2019, 10(1):3417]

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Heritable variation at the chromosome 21 gene ERG is associated with acute lymphoblastic leukemia risk in children with and without Down syndrome.

Adam J de Smith, Kyle M Walsh, Libby M Morimoto, Stephen S Francis, Helen M Hansen, Soyoung Jeon, Semira Gonseth, Minhui Chen, Hanxiao Sun, Sandra Luna-Fineman, Federico Antillón, Verónica Girón, Alice Y Kang, Ivan Smirnov, Xiaorong Shao, Todd P Whitehead, Lisa F Barcellos, Kent W Jolly, Jasmine Healy, Caroline Laverdière, Daniel Sinnett, Jeffrey W Taub, Jillian M Birch, Pamela D Thompson, Maria S Pombo-de-Oliveira, Logan G Spector, Andrew T DeWan, Beth A Mueller, Charleston Chiang, Catherine Metayer, Xiaomei Ma, Joseph L Wiemels,

Leukemia (Leukemia)
[2019, 33(11):2746-2751]

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Author Correction: A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis.

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An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Commun (Nature communications)
[2019, 10(1):2956]

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Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk.

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Cell (Cell)
[2019, 178(1):262]

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miRNA contributions to pediatric-onset multiple sclerosis inferred from GWAS.

Brooke Rhead, Xiaorong Shao, Jennifer S Graves, Tanuja Chitnis, Amy T Waldman, Timothy Lotze, Teri Schreiner, Anita Belman, Lauren Krupp, Benjamin M Greenberg, Bianca Weinstock-Guttman, Gregory Aaen, Jan M Tillema, Moses Rodriguez, Janace Hart, Stacy Caillier, Jayne Ness, Yolanda Harris, Jennifer Rubin, Meghan S Candee, Mark Gorman, Leslie Benson, Soe Mar, Ilana Kahn, John Rose, T Charles Casper, Hong Quach, Diana Quach, Catherine Schaefer, Emmanuelle Waubant, Lisa F Barcellos, ,

Objective:Onset of multiple sclerosis (MS) occurs in childhood for approximately 5% of cases (pediatric MS, or ped-MS). Epigenetic influences are strongly implicated in MS pathogenesis in adults, including the contribution from microRNAs (miRNAs), small noncoding RNAs that affect gene expression by binding target gene mRNAs. Few studies have specifically examined ... Read more >>

Ann Clin Transl Neurol (Annals of clinical and translational neurology)
[2019, 6(6):1053-1061]

Cited: 1 time

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A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis.

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Genome-wide association studies (GWAS) have identified more than 50,000 unique associations with common human traits. While this represents a substantial step forward, establishing the biology underlying these associations has proven extremely difficult. Even determining which cell types and which particular gene(s) are relevant continues to be a challenge. Here, we ... Read more >>

Nat Commun (Nature communications)
[2019, 10(1):2236]

Cited: 2 times

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Vitamin D genes influence MS relapses in children.

Jennifer S Graves, Lisa F Barcellos, Lauren Krupp, Anita Belman, Xiaorong Shao, Hong Quach, Janace Hart, Tanuja Chitnis, Bianca Weinstock-Guttman, Gregory Aaen, Leslie Benson, Mark Gorman, Benjamin Greenberg, Timothy Lotze, Mar Soe, Jayne Ness, Moses Rodriguez, John Rose, Teri Schreiner, Jan-Mendelt Tillema, Amy Waldman, T Charles Casper, Emmanuelle Waubant,

OBJECTIVE:The aim of this study was to determine whether a vitamin D genetic risk score (vitDGRS) is associated with 25-hydroxyvitamin D (25(OH)D) level and multiple sclerosis (MS) relapses in children. METHODS:DNA samples were typed for single nucleotide polymorphisms (SNPs) from four genes previously identified to be associated with 25(OH)D levels. ... Read more >>

Mult. Scler. (Multiple sclerosis (Houndmills, Basingstoke, England))
[2019, :1352458519845842]

Cited: 1 time

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No differential gene expression for CD4+ T cells of MS patients and healthy controls.

Ina S Brorson, Anna Eriksson, Ingvild S Leikfoss, Elisabeth G Celius, Pål Berg-Hansen, Lisa F Barcellos, Tone Berge, Hanne F Harbo, Steffan D Bos,

Background:Multiple sclerosis-associated genetic variants indicate that the adaptive immune system plays an important role in the risk of developing multiple sclerosis. It is currently not well understood how these multiple sclerosis-associated genetic variants contribute to multiple sclerosis risk. CD4+ T cells are suggested to be involved in multiple sclerosis disease ... Read more >>

Mult Scler J Exp Transl Clin (Multiple sclerosis journal - experimental, translational and clinical)
[2019, 5(2):2055217319856903]

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Admixture mapping reveals evidence of differential multiple sclerosis risk by genetic ancestry.

Calvin Chi, Xiaorong Shao, Brooke Rhead, Edlin Gonzales, Jessica B Smith, Anny H Xiang, Jennifer Graves, Amy Waldman, Timothy Lotze, Teri Schreiner, Bianca Weinstock-Guttman, Gregory Aaen, Jan-Mendelt Tillema, Jayne Ness, Meghan Candee, Lauren Krupp, Mark Gorman, Leslie Benson, Tanuja Chitnis, Soe Mar, Anita Belman, Theron Charles Casper, John Rose, Manikum Moodley, Mary Rensel, Moses Rodriguez, Benjamin Greenberg, Llana Kahn, Jennifer Rubin, Catherine Schaefer, Emmanuelle Waubant, Annette Langer-Gould, Lisa F Barcellos,

Multiple sclerosis (MS) is an autoimmune disease with high prevalence among populations of northern European ancestry. Past studies have shown that exposure to ultraviolet radiation could explain the difference in MS prevalence across the globe. In this study, we investigate whether the difference in MS prevalence could be explained by ... Read more >>

PLoS Genet. (PLoS genetics)
[2019, 15(1):e1007808]

Cited: 2 times

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Increased DNA methylation of SLFN12 in CD4+ and CD8+ T cells from multiple sclerosis patients.

Brooke Rhead, Ina S Brorson, Tone Berge, Cameron Adams, Hong Quach, Stine Marit Moen, Pål Berg-Hansen, Elisabeth Gulowsen Celius, Dipen P Sangurdekar, Paola G Bronson, Rodney A Lea, Sean Burnard, Vicki E Maltby, Rodney J Scott, Jeannette Lechner-Scott, Hanne F Harbo, Steffan D Bos, Lisa F Barcellos,

DNA methylation is an epigenetic mark that is influenced by environmental factors and is associated with changes to gene expression and phenotypes. It may link environmental exposures to disease etiology or indicate important gene pathways involved in disease pathogenesis. We identified genomic regions that are differentially methylated in T cells ... Read more >>

PLoS ONE (PloS one)
[2018, 13(10):e0206511]

Cited: 4 times

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Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk.

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Multiple sclerosis is a complex neurological disease, with ∼20% of risk heritability attributable to common genetic variants, including >230 identified by genome-wide association studies. Multiple strands of evidence suggest that much of the remaining heritability is also due to additive effects of common variants rather than epistasis between these variants or mutations exclusive ... Read more >>

Cell (Cell)
[2018, 175(6):1679-1687.e7]

Cited: 10 times

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Several household chemical exposures are associated with pediatric-onset multiple sclerosis.

Soe Mar, Shannon Liang, Michael Waltz, T Charles Casper, Manu Goyal, Benjamin Greenberg, Bianca Weinstock-Guttman, Moses Rodriguez, Gregory Aaen, Anita Belman, Lisa F Barcellos, John Rose, Mark Gorman, Leslie Benson, Meghan Candee, Tanjua Chitnis, Yolanda Harris, Ilana Kahn, Shelly Roalsted, Janace Hart, Timothy Lotze, Manikum Moodley, Jayne Ness, Mary Rensel, Jennifer Rubin, Teri Schreiner, Jan-Mendelt Tillema, Amy Waldman, Lauren Krupp, Jennifer S Graves, Emmanuelle Waubant, ,

Background:There is limited information about the potential associations of multiple sclerosis (MS) and commonly used household chemicals. Methods:We performed a case-control study of exposures to common household chemicals during childhood in children with MS and healthy pediatric controls. Exposures to household products were collected from a comprehensive questionnaire (http://www.usnpmsc.org/Documents/EnvironmentalAssessment.pdf) completed ... Read more >>

Ann Clin Transl Neurol (Annals of clinical and translational neurology)
[2018, 5(12):1513-1521]

Cited: 1 time

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BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia.

Adam J de Smith, Kyle M Walsh, Stephen S Francis, Chenan Zhang, Helen M Hansen, Ivan Smirnov, Libby Morimoto, Todd P Whitehead, Alice Kang, Xiaorong Shao, Lisa F Barcellos, Roberta McKean-Cowdin, Luoping Zhang, Cecilia Fu, Rong Wang, Herbert Yu, Josephine Hoh, Andrew T Dewan, Catherine Metayer, Xiaomei Ma, Joseph L Wiemels,

Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 ... Read more >>

Int. J. Cancer (International journal of cancer)
[2018, 143(11):2647-2658]

Cited: 1 time

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Increased alloreactive and autoreactive antihuman leucocyte antigen antibodies associated with systemic lupus erythematosus and rheumatoid arthritis.

Rachael P Jackman, Giovanna I Cruz, Joanne Nititham, Darrell J Triulzi, Lisa F Barcellos, Lindsey A Criswell, Philip J Norris, Michael P Busch,

Objectives:Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) disproportionately affect women during and following childbearing years. Antihuman leucocyte antigen (HLA) alloantibody responses are common in healthy parous women, and as these diseases are both linked with HLA and immune dysregulation, we sought to evaluate anti-HLA antibodies in RA and SLE. ... Read more >>

Lupus Sci Med (Lupus Science & Medicine)
[2018, 5(1):e000278]

Cited: 1 time

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Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children.

Olivia Solomon, Julie MacIsaac, Hong Quach, Gwen Tindula, Michael S Kobor, Karen Huen, Michael J Meaney, Brenda Eskenazi, Lisa F Barcellos, Nina Holland,

Analysis of DNA methylation helps to understand the effects of environmental exposures as well as the role of epigenetics in human health. Illumina, Inc. recently replaced the HumanMethylation450 BeadChip (450K) with the EPIC BeadChip, which nearly doubles the measured CpG sites to >850,000. Although the new chip uses the same ... Read more >>

Epigenetics (Epigenetics)
[2018, 13(6):655-664]

Cited: 3 times

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Allergies and Childhood Acute Lymphoblastic Leukemia: A Case-Control Study and Meta-analysis.

Amelia D Wallace, Stephen S Francis, Xiomei Ma, Roberta McKean-Cowdin, Steve Selvin, Todd P Whitehead, Lisa F Barcellos, Alice Y Kang, Libby Morimoto, Theodore B Moore, Joseph L Wiemels, Catherine Metayer,

Background: Allergic disease is suspected to play a role in the development of childhood acute lymphoblastic leukemia (ALL). Studies conducted over the last several decades have yielded mixed results.Methods: We examined the association between allergy, a common immune-mediated disorder, and ALL in the California Childhood Leukemia Study (CCLS), a case-control ... Read more >>

Cancer Epidemiol. Biomarkers Prev. (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology)
[2018, 27(10):1142-1150]

Cited: 0 times

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Incorporating machine learning approaches to assess putative environmental risk factors for multiple sclerosis.

Ellen M Mowry, Anna K Hedström, Milena A Gianfrancesco, Xiaorong Shao, Catherine A Schaefer, Ling Shen, Kalliope H Bellesis, Farren B S Briggs, Tomas Olsson, Lars Alfredsson, Lisa F Barcellos,

BACKGROUND:Multiple sclerosis (MS) incidence has increased recently, particularly in women, suggesting a possible role of one or more environmental exposures in MS risk. The study objective was to determine if animal, dietary, recreational, or occupational exposures are associated with MS risk. METHODS:Least absolute shrinkage and selection operator (LASSO) regression was ... Read more >>

Mult Scler Relat Disord (Multiple sclerosis and related disorders)
[2018, 24:135-141]

Cited: 0 times

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Alloreactive fetal T cells promote uterine contractility in preterm labor via IFN-γ and TNF-α.

Michela Frascoli, Lacy Coniglio, Russell Witt, Cerine Jeanty, Shannon Fleck-Derderian, Dana E Myers, Tzong-Hae Lee, Sheila Keating, Michael P Busch, Philip J Norris, Qizhi Tang, Giovanna Cruz, Lisa F Barcellos, Nardhy Gomez-Lopez, Roberto Romero, Tippi C MacKenzie,

Healthy pregnancy is the most successful form of graft tolerance, whereas preterm labor (PTL) may represent a breakdown in maternal-fetal tolerance. Although maternal immune responses have been implicated in pregnancy complications, fetal immune responses against maternal antigens are often not considered. To examine the fetal immune system in the relevant ... Read more >>

Sci Transl Med (Science translational medicine)
[2018, 10(438):]

Cited: 8 times

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MS Sunshine Study: Sun Exposure But Not Vitamin D Is Associated with Multiple Sclerosis Risk in Blacks and Hispanics.

Annette Langer-Gould, Robyn Lucas, Anny H Xiang, Lie H Chen, Jun Wu, Edlin Gonzalez, Samantha Haraszti, Jessica B Smith, Hong Quach, Lisa F Barcellos,

Multiple sclerosis (MS) incidence and serum 25-hydroxyvitamin D (25OHD) levels vary by race/ethnicity. We examined the consistency of beneficial effects of 25OHD and/or sun exposure for MS risk across multiple racial/ethnic groups. We recruited incident MS cases and controls (blacks 116 cases/131 controls; Hispanics 183/197; whites 247/267) from the membership ... Read more >>

Nutrients (Nutrients)
[2018, 10(3):]

Cited: 9 times

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