Publications by authors named "Megan A Cooper"

60 Publications

Immunological Findings and Clinical Outcomes of Infants With Positive Newborn Screening for Severe Combined Immunodeficiency From a Tertiary Care Center in the U.S.

Front Immunol 2021 3;12:734096. Epub 2021 Sep 3.

The Division of Allergy and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.

The implementation of severe combined immunodeficiency (SCID) newborn screening has played a pivotal role in identifying these patients early in life as well as detecting various milder forms of T cell lymphopenia (TCL). In this study we reviewed the diagnostic and clinical outcomes, and interesting immunology findings of term infants referred to a tertiary care center with abnormal newborn SCID screens over a 6-year period. Key findings included a 33% incidence of non-SCID TCL including infants with novel variants in , , , and ; 57% positivity rate of newborn SCID screening among infants with DiGeorge syndrome; and earlier diagnosis and improved transplant outcomes for SCID in infants diagnosed after compared to before implementation of routine screening. Our study is unique in terms of the extensive laboratory workup of abnormal SCID screens including lymphocyte subsets, measurement of thymic output (TREC and CD4TE), and lymphocyte proliferation to mitogens in nearly all infants. These data allowed us to observe a stronger positive correlation of the absolute CD3 count with CD4RTE than with TREC copies, and a weak positive correlation between CD4RTE and TREC copies. Finally, we did not observe a correlation between risk of TCL and history of prenatal or perinatal complications or low birth weight. Our study demonstrated SCID newborn screening improves disease outcomes, particularly in typical SCID, and allows early detection and discovery of novel variants of certain TCL-associated genetic conditions.
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http://dx.doi.org/10.3389/fimmu.2021.734096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8446381PMC
September 2021

Economic burden of congenital athymia in the United States for patients receiving supportive care during the first 3 years of life.

J Med Econ 2021 Jan-Dec;24(1):962-971

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA.

Aims: Congenital athymia is an ultra-rare pediatric condition characterized by the lack of thymus in utero and the naïve T cells critical for infection defense and immune regulation. Patients with congenital athymia receive supportive care to minimize and treat infections, autoimmune phenomena, and autologous graft-versus-host disease (aGVHD) manifestations, but historically, die within the first 3 years of life with supportive care only. We estimated the healthcare resource utilization and economic burden of supportive care over patients' first 3 years of life in the United States.

Methods: A medical chart audit by the treating physician was used to collect patient data from birth to age 3 on clinical manifestations associated with congenital athymia (clinical manifestations due to underlying syndromic conditions excluded). Using costs and charges from publicly available sources, the total economic burden of direct medical costs and charges for the first 3 years of life (considered "lifetime" for patients receiving supportive care) and differences in economic burden between patients with higher and lower inpatient hospitalization durations were estimated.

Results: All patients ( = 10) experienced frequent infections and aGVHD manifestations; 40% experienced ≥1 episode of sepsis, and 20% had recurrent sepsis episodes annually. The estimated mean 3-year economic burden per patient was US$5,534,121 (2020 US dollars). The annual mean inpatient hospitalization duration was 150.6 days. Inpatient room charges accounted for 79% of the economic burden, reflecting the high costs of specialized care settings required to prevent infection, including isolation. Patients with high inpatient utilization ( = 5; annual mean inpatient hospitalization duration, 289.6 days) had an estimated 3-year economic burden of US$9,926,229.

Limitations: The total economic burden may not be adequately represented due to underestimation of some direct costs or overestimation of others.

Conclusions: Current treatment of patients with congenital athymia (supportive care) presents a high economic burden to the healthcare system.
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http://dx.doi.org/10.1080/13696998.2021.1962129DOI Listing
September 2021

Monogenic autoimmunity and infectious diseases: the double-edged sword of immune dysregulation.

Curr Opin Immunol 2021 Jul 12;72:230-238. Epub 2021 Jul 12.

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, 63110, United States. Electronic address:

The study of monogenic autoimmune diseases has provided key insights into molecular mechanisms involved in development of autoimmunity and immune tolerance. It has also become clear that such inborn errors of immunity (IEIs) frequently present clinically not only with autoimmune diseases, but also frequently have increased susceptibility to infection. The genes associated with monogenic autoimmunity influence diverse functional pathways, and the resulting immune dysregulation also impacts the complex and coordinated immune response to pathogens, for example type I interferon and cytokine signaling, the complement pathway and proper differentiation of the immune response. The SARS-CoV-2 pandemic has highlighted how monogenic autoimmunity can increase risk for serious infection with the discovery of severe disease in patients with pre-existing antibodies to Type I IFNs. This review discusses recent insight into the relationship between monogenic autoimmunity and infectious diseases.
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http://dx.doi.org/10.1016/j.coi.2021.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8452259PMC
July 2021

Toll-Like Receptor Signaling in the Establishment and Function of the Immune System.

Cells 2021 06 2;10(6). Epub 2021 Jun 2.

Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Toll-like receptors (TLRs) are pattern recognition receptors that play a central role in the development and function of the immune system. TLR signaling promotes the earliest emergence of hematopoietic cells during development, and thereafter influences the fate and function of both primitive and effector immune cell types. Aberrant TLR signaling is associated with hematopoietic and immune system dysfunction, and both loss- and gain-of- function variants in TLR signaling-associated genes have been linked to specific infection susceptibilities and immune defects. Herein, we will review the role of TLR signaling in immune system development and the growing number of heritable defects in TLR signaling that lead to inborn errors of immunity.
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http://dx.doi.org/10.3390/cells10061374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8228919PMC
June 2021

Reliance on Cox10 and oxidative metabolism for antigen-specific NK cell expansion.

Cell Rep 2021 Jun;35(9):109209

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

Natural killer (NK) cell effector functions are dependent on metabolic regulation of cellular function; however, less is known about in vivo metabolic pathways required for NK cell antiviral function. Mice with an inducible NK-specific deletion of Cox10, which encodes a component of electron transport chain complex IV, were generated to investigate the role of oxidative phosphorylation in NK cells during murine cytomegalovirus (MCMV) infection. Ncr1-Cox10 mice had normal numbers of NK cells but impaired expansion of antigen-specific Ly49H NK cells and impaired NK cell memory formation. Proliferation in vitro and homeostatic expansion were intact, indicating a specific metabolic requirement for antigen-driven proliferation. Cox10-deficient NK cells upregulated glycolysis, associated with increased AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) activation, although this was insufficient to protect the host. These data demonstrate that oxidative metabolism is required for NK cell antiviral responses in vivo.
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http://dx.doi.org/10.1016/j.celrep.2021.109209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8229496PMC
June 2021

Genetic Mosaicism as a Cause of Inborn Errors of Immunity.

J Clin Immunol 2021 05 16;41(4):718-728. Epub 2021 Apr 16.

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, 660 S. Euclid Ave. Box 8208, St. Louis, MO, 63110, USA.

Inborn errors of immunity (IEIs) are a heterogeneous group of disorders due to genetic defects in the immune response that have a broad clinical spectrum. Diagnosis of the precise genetic cause of IEI has led to improved care and treatment of patients; however, genetic diagnosis using standard approaches is only successful in ~40% of patients and is particularly challenging in "sporadic" cases without a family history. Standard genetic testing for IEI evaluates for germline changes in genes encoding proteins important for the immune response. It is now clear that IEI can also arise from de novo mutations leading to genetic variants present in germ cells and/or somatic cells. In particular, somatic mosaicism, i.e., post-zygotic genetic changes in DNA sequence, is emerging as a significant contributor to IEI. Testing for somatic mosaicism can be challenging, and both older sequencing techniques such as Sanger sequencing and newer next-generation sequencing may not be sensitive enough to detect variants depending on the platform and analysis tools used. Investigation of multiple tissue samples and specifically targeting sequence technologies to detect low frequency variants is important for detection of variants. This review examines the role and functional consequences of genetic mosaicism in IEI. We emphasize the need to refine the current exome and genome analysis pipeline to efficiently identify mosaic variants and recommend considering somatic mosaicism in disease discovery and in the first-tier of genetic analysis.
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http://dx.doi.org/10.1007/s10875-021-01037-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068627PMC
May 2021

A Case of Severe Combined Immunodeficiency Missed by Newborn Screening.

J Clin Immunol 2021 Aug 12;41(6):1352-1355. Epub 2021 Mar 12.

Department of Pediatrics, Division of Hematology/Oncology, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1007/s10875-021-01020-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954206PMC
August 2021

Lifelong Immune Modulation Versus Hematopoietic Cell Therapy for Inborn Errors of Immunity.

J Allergy Clin Immunol Pract 2021 02;9(2):628-639

Department of Blood and Marrow Transplant, Royal Manchester Children's Hospital, Manchester, United Kingdom. Electronic address:

Advances in diagnosis of inborn errors of immunity (IEI) and an understanding of the molecular and immunologic mechanisms of these disorders have led to both the development of new therapies and improved approaches to hematopoietic cell transplantation (HCT). For example, monoclonal antibodies (mAbs) and small molecules, such as Janus tyrosine kinase inhibitors, that can modulate immunologic pathways have been designed for or repurposed for management of IEI. A better understanding of molecular mechanisms of IEI has led to use of drugs typically considered "immunosuppressive" to modulate the immune response, such as mammalian target of rapamycin inhibitors in disorders of phosphoinositide 3-kinase gain of function. Since the first HCT in a patient with severe combined immunodeficiency (SCID) in 1968, transplantation strategies have improved, with more than 90% probability of survival after allogeneic HCT in SCID and hence HCT is now the therapeutic standard for SCID and many other IEI. When tailoring treatment for IEI, multiple disease-specific and individual factors should be considered. In diseases such as SCID or agammaglobulinemia, the choice between HCT or medical management is straightforward. However, in many IEI, the choice between the options is challenging. This review focuses on the factors that should be taken into account in the quest for the optimal treatment for patients with IEI.
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http://dx.doi.org/10.1016/j.jaip.2020.11.055DOI Listing
February 2021

Genetics of Pediatric Immune-Mediated Diseases and Human Immunity.

Annu Rev Immunol 2021 04 3;39:227-249. Epub 2021 Feb 3.

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine in St. Louis, Missouri 63110, USA; email:

Primary immunodeficiency diseases (PIDs) are a rapidly growing, heterogeneous group of genetically determined diseases characterized by defects in the immune system. While individually rare, collectively PIDs affect between 1/1,000 and 1/5,000 people worldwide. The clinical manifestations of PIDs vary from susceptibility to infections to autoimmunity and bone marrow failure. Our understanding of the human immune response has advanced by investigation and discovery of genetic mechanisms of PIDs. Studying patients with isolated genetic variants in proteins that participate in complex signaling pathways has led to an enhanced understanding of host response to infection, and mechanisms of autoimmunity and autoinflammation. Identifying genetic mechanisms of PIDs not only furthers immunological knowledge but also benefits patients by dictating targeted therapies or hematopoietic stem cell transplantation. Here, we highlight several of these areas in the field of primary immunodeficiency, with a focus on the most recent advances.
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http://dx.doi.org/10.1146/annurev-immunol-093019-124513DOI Listing
April 2021

Immunodeficiency and bone marrow failure with mosaic and germline TLR8 gain of function.

Blood 2021 May;137(18):2450-2462

Division of Allergy and Immunology, Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR.

Inborn errors of immunity (IEI) are a genetically heterogeneous group of disorders with a broad clinical spectrum. Identification of molecular and functional bases of these disorders is important for diagnosis, treatment, and an understanding of the human immune response. We identified 6 unrelated males with neutropenia, infections, lymphoproliferation, humoral immune defects, and in some cases bone marrow failure associated with 3 different variants in the X-linked gene TLR8, encoding the endosomal Toll-like receptor 8 (TLR8). Interestingly, 5 patients had somatic variants in TLR8 with <30% mosaicism, suggesting a dominant mechanism responsible for the clinical phenotype. Mosaicism was also detected in skin-derived fibroblasts in 3 patients, demonstrating that mutations were not limited to the hematopoietic compartment. All patients had refractory chronic neutropenia, and 3 patients underwent allogeneic hematopoietic cell transplantation. All variants conferred gain of function to TLR8 protein, and immune phenotyping demonstrated a proinflammatory phenotype with activated T cells and elevated serum cytokines associated with impaired B-cell maturation. Differentiation of myeloid cells from patient-derived induced pluripotent stem cells demonstrated increased responsiveness to TLR8. Together, these findings demonstrate that gain-of-function variants in TLR8 lead to a novel childhood-onset IEI with lymphoproliferation, neutropenia, infectious susceptibility, B- and T-cell defects, and in some cases, bone marrow failure. Somatic mosaicism is a prominent molecular mechanism of this new disease.
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http://dx.doi.org/10.1182/blood.2020009620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8109013PMC
May 2021

Multiplexed Functional Assessment of Genetic Variants in CARD11.

Am J Hum Genet 2020 12 16;107(6):1029-1043. Epub 2020 Nov 16.

Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA. Electronic address:

Genetic testing has increased the number of variants identified in disease genes, but the diagnostic utility is limited by lack of understanding variant function. CARD11 encodes an adaptor protein that expresses dominant-negative and gain-of-function variants associated with distinct immunodeficiencies. Here, we used a "cloning-free" saturation genome editing approach in a diploid cell line to simultaneously score 2,542 variants for decreased or increased function in the region of CARD11 associated with immunodeficiency. We also described an exon-skipping mechanism for CARD11 dominant-negative activity. The classification of reported clinical variants was sensitive (94.6%) and specific (88.9%), which rendered the data immediately useful for interpretation of seven coding and splicing variants implicated in immunodeficiency found in our clinic. This approach is generalizable for variant interpretation in many other clinically actionable genes, in any relevant cell type.
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http://dx.doi.org/10.1016/j.ajhg.2020.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820631PMC
December 2020

Recovery from COVID-19 in a Child with Chronic Granulomatous Disease and T Cell Lymphopenia.

J Clin Immunol 2021 01 27;41(1):23-25. Epub 2020 Oct 27.

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.

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http://dx.doi.org/10.1007/s10875-020-00896-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588587PMC
January 2021

ETV6 germline mutations cause HDAC3/NCOR2 mislocalization and upregulation of interferon response genes.

JCI Insight 2020 09 17;5(18). Epub 2020 Sep 17.

Department of Pediatrics, Washington University at St. Louis, St. Louis, Missouri, USA.

ETV6 is an ETS family transcription factor that plays a key role in hematopoiesis and megakaryocyte development. Our group and others have identified germline mutations in ETV6 resulting in autosomal dominant thrombocytopenia and predisposition to malignancy; however, molecular mechanisms defining the role of ETV6 in megakaryocyte development have not been well established. Using a combination of molecular, biochemical, and sequencing approaches in patient-derived PBMCs, we demonstrate abnormal cytoplasmic localization of ETV6 and the HDAC3/NCOR2 repressor complex that led to overexpression of HDAC3-regulated interferon response genes. This transcriptional dysregulation was also reflected in patient-derived platelet transcripts and drove aberrant proplatelet formation in megakaryocytes. Our results suggest that aberrant transcription may predispose patients with ETV6 mutations to bone marrow inflammation, dysplasia, and megakaryocyte dysfunction.
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http://dx.doi.org/10.1172/jci.insight.140332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526537PMC
September 2020

Siblings with a novel MED12 variant and Odho syndrome with immune defects.

Clin Genet 2020 09 26;98(3):308-310. Epub 2020 Jul 26.

Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1111/cge.13806DOI Listing
September 2020

Stage-Specific Requirement for Eomes in Mature NK Cell Homeostasis and Cytotoxicity.

Cell Rep 2020 06;31(9):107720

Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

Natural killer (NK) cells are cytotoxic innate lymphoid cells (ILCs) that mediate antiviral and antitumor responses and require the transcriptional regulator Eomesodermin (Eomes) for early development. However, the role of Eomes and its molecular program in mature NK cell biology is unclear. To address this, we develop a tamoxifen-inducible, type-1-ILC-specific (Ncr1-targeted) cre mouse and combine this with Eomes-floxed mice. Eomes deletion after normal NK cell ontogeny results in a rapid loss of NK cells (but not ILC1s), with a particularly profound effect on penultimately mature stage III NK cells. Mechanisms responsible for stage III reduction include increased apoptosis and impaired maturation from stage II precursors. Induced Eomes deletion also decreases NK cell cytotoxicity and abrogates in vivo rejection of major histocompatibility complex (MHC)-class-I-deficient cells. However, other NK cell functional responses, and stage IV NK cells, are largely preserved. These data indicate that mature NK cells have distinct Eomes-dependent and -independent stages.
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http://dx.doi.org/10.1016/j.celrep.2020.107720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265846PMC
June 2020

Responsiveness of sphingosine phosphate lyase insufficiency syndrome to vitamin B6 cofactor supplementation.

J Inherit Metab Dis 2020 09 4;43(5):1131-1142. Epub 2020 May 4.

Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California, USA.

Sphingosine-1-phosphate (S1P) lyase is a vitamin B6-dependent enzyme that degrades sphingosine-1-phosphate in the final step of sphingolipid metabolism. In 2017, a new inherited disorder was described caused by mutations in SGPL1, which encodes sphingosine phosphate lyase (SPL). This condition is referred to as SPL insufficiency syndrome (SPLIS) or alternatively as nephrotic syndrome type 14 (NPHS14). Patients with SPLIS exhibit lymphopenia, nephrosis, adrenal insufficiency, and/or neurological defects. No targeted therapy for SPLIS has been reported. Vitamin B6 supplementation has therapeutic activity in some genetic diseases involving B6-dependent enzymes, a finding ascribed largely to the vitamin's chaperone function. We investigated whether B6 supplementation might have activity in SPLIS patients. We retrospectively monitored responses of disease biomarkers in patients supplemented with B6 and measured SPL activity and sphingolipids in B6-treated patient-derived fibroblasts. In two patients, disease biomarkers responded to B6 supplementation. S1P abundance and activity levels increased and sphingolipids decreased in response to B6. One responsive patient is homozygous for an SPL R222Q variant present in almost 30% of SPLIS patients. Molecular modeling suggests the variant distorts the dimer interface which could be overcome by cofactor supplementation. We demonstrate the first potential targeted therapy for SPLIS and suggest that 30% of SPLIS patients might respond to cofactor supplementation.
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http://dx.doi.org/10.1002/jimd.12238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8072405PMC
September 2020

Hematopoietic Cell Transplantation in Patients With Primary Immune Regulatory Disorders (PIRD): A Primary Immune Deficiency Treatment Consortium (PIDTC) Survey.

Front Immunol 2020 21;11:239. Epub 2020 Feb 21.

Department of Pediatrics, Immunology, Allergy, and Retrovirology Baylor College of Medicine, Texas Children's Hospital William T. Shearer Center for Human Immunobiology, Houston, TX, United States.

Primary Immune Regulatory Disorders (PIRD) are an expanding group of diseases caused by gene defects in several different immune pathways, such as regulatory T cell function. Patients with PIRD develop clinical manifestations associated with diminished and exaggerated immune responses. Management of these patients is complicated; oftentimes immunosuppressive therapies are insufficient, and patients may require hematopoietic cell transplant (HCT) for treatment. Analysis of HCT data in PIRD patients have previously focused on a single gene defect. This study surveyed transplanted patients with a phenotypic clinical picture consistent with PIRD treated in 33 Primary Immune Deficiency Treatment Consortium centers and European centers. Our data showed that PIRD patients often had immunodeficient and autoimmune features affecting multiple organ systems. Transplantation resulted in resolution of disease manifestations in more than half of the patients with an overall 5-years survival of 67%. This study, the first to encompass disorders across the PIRD spectrum, highlights the need for further research in PIRD management.
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http://dx.doi.org/10.3389/fimmu.2020.00239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046837PMC
March 2021

NAPDH Oxidase-Specific Flow Cytometry Allows for Rapid Genetic Triage and Classification of Novel Variants in Chronic Granulomatous Disease.

J Clin Immunol 2020 01 8;40(1):191-202. Epub 2019 Dec 8.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.

Purpose: Chronic granulomatous disease (CGD) is an innate immune deficiency, primarily affecting the phagocytic compartment, and presenting with a diverse phenotypic spectrum ranging from severe childhood infections to monogenic inflammatory bowel disease. Dihydrorhodamine (DHR) flow cytometry is the standard diagnostic test for CGD, and correlates with NADPH oxidase activity. While there may be genotype correlation with the DHR flow pattern in some patients, in several others, there is no correlation. In such patients, assessment by flow cytometric evaluation of NADPH oxidase-specific (NOX) proteins provides a convenient and rapid means of genetic triage, though immunoblotting has long been used for this purpose.

Methods And Results: We describe the clinical utility of the NOX flow cytometry assay through assessment of X-linked and autosomal recessive CGD patients and their first-degree relatives. The assessment of specific NOX proteins was correlated with overall NADPH oxidase function (DHR flow), clinical phenotype and genotype. NOX-specific protein assessment is a valuable adjunct to DHR assessment and genotyping to classify and characterize CGD patients.

Conclusions: The atypical clinical presentation of some CGD patients can make genotype-phenotype correlation with DHR flow data challenging. Genetic testing, while useful for confirmation of diagnosis, can take several weeks, and in some patients does not provide a conclusive answer. However, NADPH-oxidase-specific protein flow assessment offers a rapid alternative to identification of the underlying genetic defect in cellular subsets, and can be utilized as a reflex test to an abnormal DHR flow. Further, it can provide insight into correlation between oxidative burst relative to protein expression in granulocytes and monocytes.
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http://dx.doi.org/10.1007/s10875-019-00712-6DOI Listing
January 2020

Heterozygous FOXN1 Variants Cause Low TRECs and Severe T Cell Lymphopenia, Revealing a Crucial Role of FOXN1 in Supporting Early Thymopoiesis.

Am J Hum Genet 2019 09 22;105(3):549-561. Epub 2019 Aug 22.

Division of Allergy and Immunology, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA.

FOXN1 is the master regulatory gene of thymic epithelium development. FOXN1 deficiency leads to thymic aplasia, alopecia, and nail dystrophy, accounting for the nude/severe combined immunodeficiency (nu/SCID) phenotype in humans and mice. We identified several newborns with low levels of T cell receptor excision circles (TRECs) and T cell lymphopenia at birth, who carried heterozygous loss-of-function FOXN1 variants. Longitudinal analysis showed persistent T cell lymphopenia during infancy, often associated with nail dystrophy. Adult individuals with heterozygous FOXN1 variants had in most cases normal CD4 but lower than normal CD8 cell counts. We hypothesized a FOXN1 gene dosage effect on the function of thymic epithelial cells (TECs) and thymopoiesis and postulated that these effects would be more prominent early in life. To test this hypothesis, we analyzed TEC subset frequency and phenotype, early thymic progenitor (ETP) cell count, and expression of FOXN1 target genes (Ccl25, Cxcl12, Dll4, Scf, Psmb11, Prss16, and Cd83) in Foxn1 (nu/+) mice and age-matched wild-type (+/+) littermate controls. Both the frequency and the absolute count of ETP were significantly reduced in nu/+ mice up to 3 weeks of age. Analysis of the TEC compartment showed reduced expression of FOXN1 target genes and delayed maturation of the medullary TEC compartment in nu/+ mice. These observations establish a FOXN1 gene dosage effect on thymic function and identify FOXN1 haploinsufficiency as an important genetic determinant of T cell lymphopenia at birth.
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http://dx.doi.org/10.1016/j.ajhg.2019.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731368PMC
September 2019

Rheumatologic and autoimmune manifestations in primary immune deficiency.

Curr Opin Allergy Clin Immunol 2019 12;19(6):545-552

Division of Rheumatology.

Purpose Of Review: Here we review the rheumatologic and autoimmune features of primary immune deficiencies with a focus on recently recognized genetic diseases, the spectrum of autoimmunity in PID, and targeted therapies.

Recent Findings: Primary immune deficiencies (PIDs) were initially described as genetic diseases of the immune system leading to susceptibility to infection. It is now well recognized that immune dysfunction and dysregulation also cause noninfectious complications including autoimmunity. The increased application of molecular testing for PID has revealed the diversity of clinical disease. Recent discoveries of diseases with prominent autoimmunity include activated phosphoinositide 3-kinase δ syndrome and PIDs caused by gain-of-function in STAT1 and STAT3. Similarly, identification of larger cohorts of patients with molecular diagnoses in more common PIDs, such as common variable immune deficiency (CVID), has led to increased understanding of the range of autoimmunity in PIDs. Understanding the molecular basis of these PIDs has the potential to lead to targeted therapy to treat associated autoimmunity.

Summary: Autoimmunity and rheumatologic disease can be presenting symptoms and/or complicating features of primary immunodeficiencies. Evaluation for PIDs in patients who have early-onset, multiple, and/or atypical autoimmunity can enhance diagnosis and therapeutic options.
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http://dx.doi.org/10.1097/ACI.0000000000000583DOI Listing
December 2019

MicroRNA-142 Is Critical for the Homeostasis and Function of Type 1 Innate Lymphoid Cells.

Immunity 2019 09 8;51(3):479-490.e6. Epub 2019 Aug 8.

Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA. Electronic address:

Natural killer (NK) cells are cytotoxic type 1 innate lymphoid cells (ILCs) that defend against viruses and mediate anti-tumor responses, yet mechanisms controlling their development and function remain incompletely understood. We hypothesized that the abundantly expressed microRNA-142 (miR-142) is a critical regulator of type 1 ILC biology. Interleukin-15 (IL-15) signaling induced miR-142 expression, whereas global and ILC-specific miR-142-deficient mice exhibited a cell-intrinsic loss of NK cells. Death of NK cells resulted from diminished IL-15 receptor signaling within miR-142-deficient mice, likely via reduced suppressor of cytokine signaling-1 (Socs1) regulation by miR-142-5p. ILCs persisting in Mir142 mice demonstrated increased expression of the miR-142-3p target αV integrin, which supported their survival. Global miR-142-deficient mice exhibited an expansion of ILC1-like cells concurrent with increased transforming growth factor-β (TGF-β) signaling. Further, miR-142-deficient mice had reduced NK-cell-dependent function and increased susceptibility to murine cytomegalovirus (MCMV) infection. Thus, miR-142 critically integrates environmental cues for proper type 1 ILC homeostasis and defense against viral infection.
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http://dx.doi.org/10.1016/j.immuni.2019.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6750984PMC
September 2019

Lymphocyte-driven regional immunopathology in pneumonitis caused by impaired central immune tolerance.

Sci Transl Med 2019 06;11(495)

Translational Hepatology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.

Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), a monogenic disorder caused by mutations, presents with several autoimmune diseases. Among these, endocrine organ failure is widely recognized, but the prevalence, immunopathogenesis, and treatment of non-endocrine manifestations such as pneumonitis remain poorly characterized. We enrolled 50 patients with APECED in a prospective observational study and comprehensively examined their clinical and radiographic findings, performed pulmonary function tests, and analyzed immunological characteristics in blood, bronchoalveolar lavage fluid, and endobronchial and lung biopsies. Pneumonitis was found in >40% of our patients, presented early in life, was misdiagnosed despite chronic respiratory symptoms and accompanying radiographic and pulmonary function abnormalities, and caused hypoxemic respiratory failure and death. Autoantibodies against BPIFB1 and KCNRG and the homozygous c.967_979del13 mutation are associated with pneumonitis development. APECED pneumonitis features compartmentalized immunopathology, with accumulation of activated neutrophils in the airways and lymphocytic infiltration in intraepithelial, submucosal, peribronchiolar, and interstitial areas. Beyond APECED, we extend these observations to lung disease seen in other conditions with secondary AIRE deficiency (thymoma and RAG deficiency). Aire-deficient mice had similar compartmentalized cellular immune responses in the airways and lung tissue, which was ameliorated by deficiency of T and B lymphocytes. Accordingly, T and B lymphocyte-directed immunomodulation controlled symptoms and radiographic abnormalities and improved pulmonary function in patients with APECED pneumonitis. Collectively, our findings unveil lung autoimmunity as a common, early, and unrecognized manifestation of APECED and provide insights into the immunopathogenesis and treatment of pulmonary autoimmunity associated with impaired central immune tolerance.
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http://dx.doi.org/10.1126/scitranslmed.aav5597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6647037PMC
June 2019

Natural killer cells might adapt their inhibitory receptors for memory.

Authors:
Megan A Cooper

Proc Natl Acad Sci U S A 2018 11 18;115(45):11357-11359. Epub 2018 Oct 18.

Division of Pediatric Rheumatology, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110

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http://dx.doi.org/10.1073/pnas.1815756115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233136PMC
November 2018

Identification of enhanced IFN-γ signaling in polyarticular juvenile idiopathic arthritis with mass cytometry.

JCI Insight 2018 08 9;3(15). Epub 2018 Aug 9.

Division of Pediatric Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.

Polyarticular juvenile idiopathic arthritis (JIA) is among the most challenging of the JIA subtypes to treat. Even with current biologic therapies, the disease remains difficult to control in a substantial subset of patients, highlighting the need for new therapies. The aim of this study was to use the high dimensionality afforded by mass cytometry with phospho-specific antibodies to delineate signaling abnormalities in immune cells from treatment-naive polyarticular JIA patients. Peripheral blood mononuclear cells were isolated from 17 treatment-naive polyarticular JIA patients, 10 of the patients after achieving clinical remission, and 19 healthy controls. Samples were stimulated for 15 minutes with IL-6 or IFN-γ and analyzed by mass cytometry. Following IFN-γ stimulation, increased STAT1 and/or STAT3 phosphorylation was observed in subsets of CD4 T cells and classical monocytes from treatment-naive patients. The enhanced IFN-γ signaling was associated with increased expression of JAK1 and SOCS1 in CD4 T cells. Furthermore, substantial heterogeneity in surface marker expression was observed among the subsets of CD4 T cells and classical monocytes with increased IFN-γ responsiveness. The identification of enhanced IFN-γ signaling in CD4 T cells and classical monocytes from treatment-naive polyarticular JIA patients provides mechanistic support for investigations into therapies that attenuate IFN-γ signaling in this disease.
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http://dx.doi.org/10.1172/jci.insight.121544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129135PMC
August 2018

Comment on: Evidence of innate lymphoid cell redundancy in humans.

Nat Immunol 2018 08;19(8):788-789

Department of Pediatrics, Division of Rheumatology, Washington University, St. Louis, MO, USA.

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http://dx.doi.org/10.1038/s41590-018-0164-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736524PMC
August 2018

Is There Natural Killer Cell Memory and Can It Be Harnessed by Vaccination? Vaccination Strategies Based on NK Cell and ILC Memory.

Cold Spring Harb Perspect Biol 2018 10 1;10(10). Epub 2018 Oct 1.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110.

Studies over the last decade have decisively shown that innate immune natural killer (NK) cells exhibit enhanced long-lasting functional responses following a single activation event. With the increased recognition of memory and memory-like properties of NK cells, questions have arisen with regard to their ability to effectively mediate vaccination responses in humans. Moreover, recently discovered innate lymphoid cells (ILCs) could also potentially exhibit memory-like functions. Here, we review different forms of NK cell memory, and speculate about the ability of these cells and ILCs to meaningfully contribute to vaccination responses.
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http://dx.doi.org/10.1101/cshperspect.a029512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169813PMC
October 2018

Glycolytic requirement for NK cell cytotoxicity and cytomegalovirus control.

JCI Insight 2017 12 7;2(23). Epub 2017 Dec 7.

Department of Pediatrics, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA.

NK cell activation has been shown to be metabolically regulated in vitro; however, the role of metabolism during in vivo NK cell responses to infection is unknown. We examined the role of glycolysis in NK cell function during murine cytomegalovirus (MCMV) infection and the ability of IL-15 to prime NK cells during CMV infection. The glucose metabolism inhibitor 2-deoxy-ᴅ-glucose (2DG) impaired both mouse and human NK cell cytotoxicity following priming in vitro. Similarly, MCMV-infected mice treated with 2DG had impaired clearance of NK-specific targets in vivo, which was associated with higher viral burden and susceptibility to infection on the C57BL/6 background. IL-15 priming is known to alter NK cell metabolism and metabolic requirements for activation. Treatment with the IL-15 superagonist ALT-803 rescued mice from otherwise lethal infection in an NK-dependent manner. Consistent with this, treatment of a patient with ALT-803 for recurrent CMV reactivation after hematopoietic cell transplant was associated with clearance of viremia. These studies demonstrate that NK cell-mediated control of viral infection requires glucose metabolism and that IL-15 treatment in vivo can reduce this requirement and may be effective as an antiviral therapy.
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http://dx.doi.org/10.1172/jci.insight.95128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5752285PMC
December 2017

Somatic mutations and clonal hematopoiesis in congenital neutropenia.

Blood 2018 01 1;131(4):408-416. Epub 2017 Nov 1.

Division of Oncology, Department of Internal Medicine.

Severe congenital neutropenia (SCN) and Shwachman-Diamond syndrome (SDS) are congenital neutropenia syndromes with a high rate of leukemic transformation. Hematopoietic stressors may contribute to leukemic transformation by increasing the mutation rate in hematopoietic stem/progenitor cells (HSPCs) and/or by promoting clonal hematopoiesis. We sequenced the exome of individual hematopoietic colonies derived from 13 patients with congenital neutropenia to measure total mutation burden and performed error-corrected sequencing on a panel of 46 genes on 80 patients with congenital neutropenia to assess for clonal hematopoiesis. An average of 3.6 ± 1.2 somatic mutations per exome was identified in HSPCs from patients with SCN compared with 3.9 ± 0.4 for healthy controls ( = NS). Clonal hematopoiesis due to mutations in was present in 48% (13/27) of patients with SDS but was not seen in healthy controls (0/17, < .001) or patients with SCN (0/40, < .001). Our SDS cohort was young (median age 6.3 years), and many of the patients had multiple mutations. Conversely, clonal hematopoiesis due to mutations of was present in patients with SCN but was not detected in healthy controls or patients with SDS. These data show that hematopoietic stress, including granulocyte colony-stimulating factor, do not increase the mutation burden in HSPCs in congenital neutropenia. Rather, distinct hematopoietic stressors result in the selective expansion of HSPCs carrying specific gene mutations. In particular, in SDS there is enormous selective pressure to expand -mutated HSPCs, suggesting that acquisition of mutations is an early, likely initiating event, in the transformation to myelodysplastic syndrome/acute myeloid leukemia in patients with SDS.
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http://dx.doi.org/10.1182/blood-2017-08-801985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790127PMC
January 2018
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