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1.  Immunologic consequences of chemotherapy for ovarian cancer: Impaired responses to the influenza vaccine 
Vaccine  2013;31(46):10.1016/j.vaccine.2013.09.001.
Objectives
To examine the effect of chemotherapy for ovarian cancer on immunologic function and to define the effect on the serologic response to the influenza vaccine.
Methods
Under IRB approved protocols, patients with ovarian cancer were administered seasonal trivalent killed influenza vaccines. Peripheral blood was collected for immunologic assessments. Serum was analyzed for hemagglutination inhibition (HAI) antibody titers. Peripheral blood mononuclear cells were isolated to characterize T and B cell populations and function.
Results
Thirty-one patients were recruited: 13 in remission receiving a dendritic cell vaccine with or without a single dose of low-dose cyclophosphamide, 3 in remission not receiving treatment, and 15 undergoing standard therapy. Significant effects on T cell and B cell subset distributions were seen. Functional effects were also seen. Few patients were able to mount a 4-fold HAI antibody response. A 4-fold response was observed for H1N1 in 20%, for H3N2 in 26%, and for influenza B in 6%. Pre-existing exposure to influenza was predictive of responders.
Conclusions
Despite CDC recommendations that patients undergoing chemotherapy receive influenza vaccine, there is little evidence to support its serologic effectiveness in this population. Patients with ovarian cancer are almost uniformly unable to mount a meaningful antibody response. These findings have serious implications for future resource allocation for both seasonal and novel pandemic influenza outbreak and understanding the immunologic deficits as a result of chemotherapy may improve patient care.
doi:10.1016/j.vaccine.2013.09.001
PMCID: PMC3826173  PMID: 24036157
Treg; monoclonal B cell lymphocytosis; DC vaccine; ELISpot; immune compromised; cyclophosphamide; antibody
2.  Transplantation Outcomes for Severe Combined Immunodeficiency, 2000–2009 
The New England journal of medicine  2014;371(5):434-446.
BACKGROUND
The Primary Immune Deficiency Treatment Consortium was formed to analyze the results of hematopoietic-cell transplantation in children with severe combined immunodeficiency (SCID) and other primary immunodeficiencies. Factors associated with a good transplantation outcome need to be identified in order to design safer and more effective curative therapy, particularly for children with SCID diagnosed at birth.
METHODS
We collected data retrospectively from 240 infants with SCID who had received transplants at 25 centers during a 10-year period (2000 through 2009).
RESULTS
Survival at 5 years, freedom from immunoglobulin substitution, and CD3+ T-cell and IgA recovery were more likely among recipients of grafts from matched sibling donors than among recipients of grafts from alternative donors. However, the survival rate was high regardless of donor type among infants who received transplants at 3.5 months of age or younger (94%) and among older infants without prior infection (90%) or with infection that had resolved (82%). Among actively infected infants without a matched sibling donor, survival was best among recipients of haploidentical T-cell–depleted transplants in the absence of any pretransplantation conditioning. Among survivors, reduced-intensity or myeloablative pre-transplantation conditioning was associated with an increased likelihood of a CD3+ T-cell count of more than 1000 per cubic millimeter, freedom from immunoglobulin substitution, and IgA recovery but did not significantly affect CD4+ T-cell recovery or recovery of phytohemagglutinin-induced T-cell proliferation. The genetic subtype of SCID affected the quality of CD3+ T-cell recovery but not survival.
CONCLUSIONS
Transplants from donors other than matched siblings were associated with excellent survival among infants with SCID identified before the onset of infection. All available graft sources are expected to lead to excellent survival among asymptomatic infants. (Funded by the National Institute of Allergy and Infectious Diseases and others.)
doi:10.1056/NEJMoa1401177
PMCID: PMC4183064  PMID: 25075835
3.  Rituximab-Treated Patients Have a Poor Response to Influenza Vaccination* 
Journal of clinical immunology  2012;33(2):388-396.
The efficacy of influenza vaccination in patients treated with rituximab is a clinically important question. Rheumatology clinics are populated with patients receiving rituximab for a broad array of disorders. Although several studies have explored the efficacy of other vaccines in rituximab-treated populations, results have been conflicting. We wished to define influenza vaccine efficacy in a rituximab-treated cohort. We examined 17 evaluable subjects treated with rituximab for rheumatologic conditions. T cell subsets, B cells subsets, T cell function, and B cell function were evaluated at specific time points along with hemagglutinination inhibition titers after receiving the standard inactivated influenza vaccine. T cell subset counts were significantly different than controls but did not change with rituximab. B cells depleted in all patients but were in various stages of recovery at the time of vaccination. Influenza vaccine responsiveness was poor overall, with only 16% of subjects having a four-fold increase in titer. Pre-existing titers were retained throughout the study, however. The ability to respond to the influenza vaccine appeared to be related to the degree of B cell recovery at the time of vaccination. This study emphasizes that antibody responses to vaccine are impaired in subjects treated with rituximab and supports the concept that B cell recovery influences influenza vaccine responsiveness.
doi:10.1007/s10875-012-9813-x
PMCID: PMC3565069  PMID: 23064976
Rituxmab; influenza; antibody; HAI titer; B cell
4.  Protecting Pediatric Oncology Patients From Influenza 
The Oncologist  2013;18(2):204-211.
This review examines evidence to support various strategies to protect pediatric oncology patients from influenza-related morbidity. Influenza vaccination should be considered standard. Additional evidence-supported measures include antiviral treatment, antiviral prophylaxis, cohorting of patients, and hospital infection control measures.
Learning Objectives
Identify optimal vaccination strategies and define the vaccine response rates among pediatric chemotherapy patients.Explain the advantage of beginning empiric antiviral therapy.Describe the need for family member vaccination, hygiene measures, and social distancing.
Influenza is a common respiratory pathogen. Its severity can be unpredictable, but people with chronic illness are at increased risk of severe infection, complications, and death from influenza. This review examines evidence to support various strategies to protect pediatric oncology patients from influenza-related morbidity. Influenza vaccination should be considered standard. Additional evidence-supported measures include antiviral treatment, antiviral prophylaxis, cohorting of patients, and hospital infection control measures. Data from other high-risk populations support the vaccination of family members, double-dose or high-dose vaccination, and the use of barrier methods. These measures have the potential to optimize patient outcomes because there will be fewer treatment interruptions for acute illness. These strategies can also protect patients from prolonged hospitalizations and morbidity related to influenza.
doi:10.1634/theoncologist.2012-0401
PMCID: PMC3579605  PMID: 23370325
Influenza; Vaccine; Chemotherapy; Chemoprophylaxis
5.  Immunologic Consequences of Chemotherapy for Acute Myeloid Leukemia 
There are few data characterizing the immunologic consequences of chemotherapy for AML and almost nothing is known about the effects of chemotherapy in a pediatric AML cohort. We identified T cell subsets, B cell subsets and used ELISPOT analyses to define the function of T cells and B cells in seven pediatric patients with AML on chemotherapy. The data demonstrate that the effects of chemotherapy disproportionately target the B cell and depletion of B cells is associated with impaired responses to the inactivated influenza vaccine. Diminished T cell numbers were also observed although the magnitude of the effect was less than what was seen for B cells. Furthermore, measures of T cell function were largely intact. We conclude that humoral immunity is significantly affected by chemotherapy for AML.
doi:10.1097/MPH.0b013e318266c0c8
PMCID: PMC3526680  PMID: 23018569
6.  Autoimmunity and Inflammation in X-linked Agammaglobulinemia 
Journal of clinical immunology  2014;34(6):627-632.
Purpose
In the past, XLA was described as associated with several inflammatory conditions, but with adequate immune globulin treatment, these are presumed to have diminished. The actual prevalence is not known.
Methods
A web-based patient survey was conducted December 2011- February 2012. Respondents were recruited from the Immune Deficiency Foundation (IDF) patient database, online patient discussion forums and physician recruitment of patients. The questionnaire was developed jointly by IDF and by members of the USIDNET-XLA Disease Specific Working Group. Information regarding inflammatory conditions in patients with XLA was also obtained from the United States Immune Deficiency Network (USIDNET) Registry.
Results
Based on 128 unique patient survey responses, the majority of respondents (69 %) reported having at least one inflammatory symptom, with 53 % reporting multiple symptoms. However, only 28 % had actually been formally diagnosed with an inflammatory condition. Although 20 % reported painful joints and 11 % reported swelling of the joints, only 7 % were given a diagnosis of arthritis. Similarly, 21 % reported symptoms of chronic diarrhea and 17 % reported abdominal pain, however only 4 % had been diagnosed with Crohn’s disease. Data from the USIDNET Registry on 149 patients with XLA, revealed that 12 % had pain, swelling or arthralgias, while 18 % had been diagnosed with arthritis. Similarly, 7 % of these patients had abdominal pain and 9 % chronic diarrhea.
Conclusions
Although patients with XLA are generally considered to have a low risk of autoimmune or inflammatory disease compared to other PIDD cohorts, data from this patient survey and a national registry indicate that a significant proportion of patients with XLA have symptoms that are consistent with a diagnosis of arthritis, inflammatory bowel disease or other inflammatory condition. Documented diagnoses of inflammatory diseases were less common but still increased over the general population. Additional data is required to begin implementation of careful monitoring of patients with XLA for these conditions. Early diagnosis and proper treatment may optimize clinical outcomes for these patients.
doi:10.1007/s10875-014-0056-x
PMCID: PMC4157090  PMID: 24909997
X-linked agammaglobulinemia; primary immunodeficiency; antibody deficiency; autoimmune; inflammation
7.  LPS and Poly I:C Induce Chromatin Modifications at a Novel Upstream Region of the IL-23 p19 Promoter 
Inflammation  2008;31(4):235-246.
IL-23, a heterodimer of IL-12 p40 and IL-23 p19, is critical for an effective immune response to many infections and has been implicated in several autoimmune diseases, however, little is known about the regulation of IL-23 gene expression in monocytes. We found that poly I:C, LPS, flagellin, and zymogen activated significant IL-23 production in primary human monocytes. Using chromatin immunoprecipitation, we found that a distal upstream region of the IL-23 p19 promoter at −601 to −521 underwent extensive histone modifications in response to stimuli. This distal region of the promoter is not highly conserved between species and has not been previously implicated in the regulation of IL-23 expression. Knockdown of CBP markedly decreased IL-23 p19 responses to poly I:C but had a less dramatic effect on LPS responses, confirming different chromatin responses to these two stimuli. Our data suggest that one of the mechanisms regulating IL-23 expression is the regulation of histone modifications at this distal upstream region of the promoter.
doi:10.1007/s10753-008-9070-6
PMCID: PMC4119945  PMID: 18587636
human; monocyte/macrophages; cytokines; histones; chromatin; gene regulation; molecular biology; CBP
8.  Immunologic Features of Cornelia de Lange Syndrome 
Pediatrics  2013;132(2):e484-e489.
OBJECTIVES:
Cornelia de Lange syndrome (CdLS) is a genetic syndrome with multisystem abnormalities. Infections are a significant cause of morbidity and mortality. The goals of our study were to identify the frequency and types of infections in CdLS and to determine if underlying immunodeficiency contributes to the clinical spectrum of this syndrome.
METHODS:
We assessed infectious histories in 45 patients with CdLS and evaluated conventional immunologic screening tests in 27 patients. Among these 27 subjects, additional phenotypic enumeration of T-cell subsets, expression of activation markers in T cells, and production of cytokines in response to T-cell stimulants were studied in 12 CdLS subjects compared with 12 normal case control subjects.
RESULTS:
Recurrent infections were reported at high frequency in CdLS patients and included chronic ear infections (53%), chronic viral respiratory infections (46%), pneumonia (42%), sinus infections (33%), oral candidiasis (13%), sepsis (6%), and bacterial skin infections (4%). Full immune evaluation in 27 subjects led to identification of 9 cases of antibody deficiency syndrome in patients with severe forms of CdLS. Subjects with CdLS had decreased percentages of T regulatory cells and T follicular helper cells compared with normal control subjects (P < .05).
CONCLUSIONS:
This study identified for the first time a high frequency of antibody deficiency in CdLS subjects, indicating a critical need for screening and management of immunodeficiency in CdLS patients with a history of well-documented severe or recurrent infections. Furthermore, our results indicate that impaired T-cell populations may be associated with antibody deficiency in CdLS.
doi:10.1542/peds.2012-3815
PMCID: PMC4074671  PMID: 23821697
Cornelia de Lange syndrome; cohesin; antibody; immunodeficiency
9.  CHARGE Syndrome and Chromosome 22q11.2 Deletion Syndrome: A Comparison of Immunologic and Non-Immunologic Phenotypic Features 
Pediatrics  2009;123(5):e871-e877.
Objectives
CHARGE syndrome and chromosome 22q11.2 deletion syndrome are known to have significant clinical overlap including cardiac anomalies, ear abnormalities, hearing loss, developmental delay, renal abnormalities, hearing loss, and cleft palate. Immunodeficiency has been well documented in 22q11.2 deletion, but there is limited recognition of this potentially serious complication in CHARGE syndrome. The goals of our study were to identify clinical features unique to CHARGE syndrome or 22q11.2 deletion and to describe the spectrum of immune deficiency found in CHARGE patients.
Methods
This study includes 25 children diagnosed with CHARGE syndrome with positive CHD7 mutations, through the Children’s Hospital of Philadelphia genetics program. Clinical features and laboratory findings were reviewed retrospectively. We compared our findings to data available for a large cohort of 22q11.2 deletion syndrome patients followed in our clinical genetics program.
Results
Features found more commonly in CHARGE syndrome included coloboma, choanal atresia, facial nerve palsy, tracheoesophageal fistula, and genital hypoplasia in males. A high incidence of marked hypocalcemia was observed in our study group (72%). We found a spectrum of cell-mediated immune deficiency in our study group, which ranged from lymphopenia (60%) to severe-combined immune deficiency (8%). Defects in humoral immunity were documented in 4 patients and included severe hypogammaglobulinemia with decreased T-cell numbers, transient hypogammaglobulinemia during infancy, and IgA deficiency.
Conclusion
The presence of coloboma, choanal atresia, facial nerve palsy, tracheoesophageal fistula, or genital hypoplasia in males should alert the clinician to the possibility of CHARGE syndrome rather than the 22q11.2 deletion. Molecular testing for CHD7 mutations may help to confirm the diagnosis. In this study, significant hypocalcemia and lymphopenia occurred more frequently in CHARGE syndrome patients than in 22q11.2 deletion syndrome patients. Early inclusion of immunologists to the multi-disciplinary care team (as with 22q11.2 deletion) may be of great benefit to affected patients.
doi:10.1542/peds.2008-3400
PMCID: PMC4098848  PMID: 19403480
CHARGE syndrome; CHD7; DiGeorge syndrome; chromosome 22q11.2 deletion; velocardiofacial syndrome; TBX-1; thymus; SCID; T-cell; immunodeficiency; hypocalcemia
10.  Leucine-Rich Repeat (in Flightless I) Interacting Protein-1 Regulates a Rapid Type I Interferon Response 
The cell autonomous response to viral infection is carefully regulated to induce type I interferons (IFNs), which in turn induce the establishment of an antiviral state. Leucine-rich repeat (in Flightless I) interacting protein-1 (LRRFIP1) and LRRFIP2 are 2 related proteins that have been identified as interacting with MyD88 and Flightless I homolog, a leucine-rich repeat protein. LRRFIP2 positively regulates NFκB and macrophage cytokine production after lipopolysaccharide, but less is known about LRRFIP1. We hypothesized that LRRFIP1 could be more important in antiviral responses, as overexpression led to type I IFN production in a pilot study. The induction of type I IFNs occurred even in the absence of virus, but was enhanced by the presence of virus. Conversely, knockdown of LRRFIP1 compromised IFN expression. We found that LRRFIP1 was rapidly recruited to influenza-containing early endosomes in a p38-dependent fashion. This was specific for virus-containing endosomes as there was almost no colocalization of LRRFIP1 with early endosomes in the absence of virus. Further, LRRFIP1 was recruited to RNA-containing vesicles. Taken together, these data suggest that LRRFIP1 participates in cell responses to virus at early time points and is important for type I IFN induction.
doi:10.1089/jir.2010.0017
PMCID: PMC2992405  PMID: 20586614
11.  The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs 
PLoS ONE  2014;9(5):e93846.
Background
Gene expression studies of peripheral blood mononuclear cells from patients with systemic lupus erythematosus (SLE) have demonstrated a type I interferon signature and increased expression of inflammatory cytokine genes. Studies of patients with Aicardi Goutières syndrome, commonly cited as a single gene model for SLE, have suggested that accumulation of non-coding RNAs may drive some of the pathologic gene expression, however, no RNA sequencing studies of SLE patients have been performed. This study was designed to define altered expression of coding and non-coding RNAs and to detect globally altered RNA processing in SLE.
Methods
Purified monocytes from eight healthy age/gender matched controls and nine SLE patients (with low-moderate disease activity and lack of biologic drug use or immune suppressive treatment) were studied using RNA-seq. Quantitative RT-PCR was used to validate findings. Serum levels of endotoxin were measured by ELISA.
Results
We found that SLE patients had diminished expression of most endogenous retroviruses and small nucleolar RNAs, but exhibited increased expression of pri-miRNAs. Splicing patterns and polyadenylation were significantly altered. In addition, SLE monocytes expressed novel transcripts, an effect that was replicated by LPS treatment of control monocytes. We further identified increased circulating endotoxin in SLE patients.
Conclusions
Monocytes from SLE patients exhibit globally dysregulated gene expression. The transcriptome is not simply altered by the transcriptional activation of a set of genes, but is qualitatively different in SLE. The identification of novel loci, inducible by LPS, suggests that chronic microbial translocation could contribute to the immunologic dysregulation in SLE, a new potential disease mechanism.
doi:10.1371/journal.pone.0093846
PMCID: PMC4010412  PMID: 24796678
12.  Defective actin accumulation impairs human natural killer cell function in DOCK8 deficiency 
Introduction
DOCK8 mutations are responsible for a rare primary combined immunodeficiency syndrome associated with severe cutaneous viral infections, elevated IgE, autoimmunity, and malignancy. Natural killer (NK) cells are essential for tumor surveillance and defense against virally infected cells. NK cell function relies on Wiskott-Aldrich syndrome protein (WASp) for filamentous actin (F-actin) accumulation at the lytic NK cell immunologic synapse (IS). DOCK8 activates Cdc42, which, together with WASp, coordinates F-actin reorganization. While abnormalities in T and B cell function have been described in DOCK8-deficient patients, the role of NK cells in this disease is unclear.
Objectives
Understand the role of DOCK8 in NK cell function in order to determine if NK cell abnormalities explain the pathogenesis of the clinical syndrome of DOCK8 deficiency.
Methods
A cohort of DOCK8-deficient patients was assembled and patient NK cells as well as NK cell lines with stably reduced DOCK8 expression were studied. NK cell cytotoxicity, F-actin content, and lytic immunological synapse formation were measured.
Results
DOCK8-deficient patient NK cells and DOCK8 knockdown cell lines all had decreased NK cell cytotoxicity, which could not be restored after IL-2 stimulation. Importantly, DOCK8 deficiency impaired F-actin accumulation at the lytic immunological synapse without affecting overall NK cell F-actin content.
Conclusions
DOCK8 deficiency results in severely impaired NK cell function owing to an inability to form a mature lytic IS via targeted synaptic F-actin accumulation. This defect may underlie and explain important attributes of the DOCK8 deficiency clinical syndrome including the unusual susceptibility to viral infection and malignancy.
doi:10.1016/j.jaci.2012.12.1568
PMCID: PMC3646579  PMID: 23380217
DOCK8 deficiency; NK cells; actin; cytotoxicity; immunologic synapse
13.  Global H4 acetylation analysis by ChIP-chip in SLE monocytes 
Genes and immunity  2009;11(2):124-133.
Systemic lupus erythematosus is a polygenic disorder affecting approximately 1:1000 adults. Recent data have implicated interferons in the pathogenesis and the expression of many genes downstream of interferons are regulated at the level of histone modifications. We examined H4 acetylation and gene expression in monocytes from patients with systemic lupus erythematosus to define alterations to the epigenome. Monocytes from 14 controls and 24 SLE patients were used for analysis by chromatin immunoprecipitation for H4 acetylation and gene expression arrays. Primary monocytes treated with μ-interferon were used as a comparator. Data were analyzed for concordance of H4 acetylation and gene expression. Network analyses and transcription factor analyses were performed to identify potential pathways. H4 acetylation was significantly altered in monocytes from patients with systemic lupus erythematosus. Sixty three percent of genes with increased H4 acetylation had the potential for regulation by IRF1. IRF1 binding sites were also upstream of nearly all genes with both increased H4 acetylation and gene expression. μ-interferon was a significant contributor to both expression and H4 acetylation patterns but the greatest concordance was seen in the enrichment of certain transcription factor binding sites upstream of genes with increased H4 acetylation in SLE and genes with increased H4 acetylation after μ-interferon treatment.
doi:10.1038/gene.2009.66
PMCID: PMC2832080  PMID: 19710693
SLE; lupus; epigenetics; chromatin; interferon; IRF1
14.  Cytokine-Induced Monocyte Characteristics in SLE 
Monocytes in SLE have been described as having aberrant behavior in a number of assays. We examined gene expression and used a genome-wide approach to study the posttranslational histone mark, H4 acetylation, to examine epigenetic changes in SLE monocytes. We compared SLE monocyte gene expression and H4 acetylation with three types of cytokine-treated monocytes to understand which cytokine effects predominated in SLE monocytes. We found that γ-interferon and α-interferon both replicated a broad range of the gene expression changes seen in SLE monocytes. H4 acetylation in SLE monocytes was overall higher than in controls and there was less correlation of H4ac with cytokine-treated cells than when gene expression was compared. A set of chemokine genes had downregulated expression and H4ac. Therefore, there are significant clusters of aberrantly expressed genes in SLE which are strongly associated with altered H4ac, suggesting that these cells have experienced durable changes to their epigenome.
doi:10.1155/2010/507475
PMCID: PMC2896681  PMID: 20625490
15.  The TNFα locus is Altered in Monocytes from Patients with Systemic Lupus Erythematosus 
In systemic lupus erythematosus, TNFα is elevated in the serum and correlates with disease activity and triglyceride levels. The stimuli that drive TNFα in this setting are incompletely understood. This study was designed to evaluate monocyte chromatin at the TNFα locus to identify semi-permanent changes that might play a role in altered expression of TNFα. SLE patients with relatively quiescent disease (mean Physician Global Assessment=0.6) and healthy controls were recruited for this study. TNFα expression was measured by intracellular cytokine staining of different monocyte subsets in patients (n=24) and controls (n=12). Histone acetylation at the TNFα locus was measured by chromatin immunoprecipitation using a normalized quantitative PCR in patients (n=46) and controls (n=24). There were no differences in the overall fractions of cells expressing CD14 in SLE patients compared to controls, however, the fraction of DR+/CD16+ cells expressing CD14 was slightly higher as was true in the monocyte subset defined by DR+/CD11b+. Within the monocyte population defined by physical characteristics and DR+/CD14+, TNFα expressing cells were more frequent in SLE patients compared to controls. Both the fraction of positive cells and the mean fluorescence intensity were higher in patients than controls. Consistent with this was the finding that monocytes from patients had increased TNFα transcripts and more highly acetylated histones at the TNFα locus compared to controls. Furthermore, patients with the highest levels of TNFα histone acetylation were more likely to have had consistently elevated erythrocyte sedimentation rates, and to have required cytotoxic use. Histone acetylation, associated with increased transcriptional competence of TNFα, may play a role in certain inflammatory aspects of the disease.
doi:10.1016/j.clim.2006.12.008
PMCID: PMC1905860  PMID: 17276734
lupus; epigenetics; histone; TNFalpha
16.  Novel Mutation in Syntaxin-Binding Protein 2 (STXBP2) Prevents IL-2-induced Natural Killer Cell Cytotoxicity 
Capsule Summary
We have identified dizygotic twins with a novel syntaxin-binding protein 2 (STXBP2) mutation, where cytotoxicity cannot be restored with IL-2. This defines STXBP2 as an absolute requirement for NK cell cytotoxic function.
doi:10.1016/j.jaci.2011.12.1003
PMCID: PMC3646578  PMID: 22336081
Familial hemophagocytic lymphohistiocytosis (FHL); syntaxin-binding protein 2 (STXBP2); Munc18-2; syntaxin-11
17.  Genome-Wide Analysis of Interferon Regulatory Factor I Binding in Primary Human Monocytes 
Gene  2011;487(1):21-28.
IRF1 is a transcription factor that participates in interferon signaling. Previous studies of IRF1 binding have utilized in vitro assays. We used ChIP-seq in human monocytes to better define the recognition motif for IRF1. The newly identified 18bp motif (RAAASNGAAAGTGAAASY) is a refinement of the 13bp IRF1 motif commonly used. We utilized the 18bp consensus motif and identified 345 potential target genes. To compare the 18bp motif with the 13bp motif, we compared putative gene targets. Only 56 potential gene targets were defined by both consensus motifs. To compare biological effects of interferon on the 13bp and the 18bp consensus targets, we mined expression data from cells exposed to interferons or transfected with IRF1. In all cases, the 18bp consensus motif was more strongly associated with transcriptional responses than the 13bp motif. Therefore, the new 18bp consensus motif appears to have a greater association with biological activities of IRF1.
doi:10.1016/j.gene.2011.07.004
PMCID: PMC3167955  PMID: 21803131
IRF1; IRF-E; chromatin immunoprecipitation; inflammation; lupus; interferon
18.  Allogeneic Hematopoietic Cell Transplantation for Primary Immune Deficiency Diseases Current Status and Critical Needs 
Allogeneic hematopoietic cell transplantation (HCT) has been employed for 40 years to ameliorate or cure primary immune deficiency (PID) diseases, including severe combined immune deficiency (SCID) and non-SCID PID. There is a critical need for evaluation of the North American experience of different HCT approaches for these diseases, in order to identify best practices and plan future investigative clinical trials. A conference of experts in HCT treatment of PID has recommended: (1) a comprehensive cross-sectional and retrospective analysis of HCT survivors with SCID; (2) a prospective study of SCID patients receiving HCT, with comparable baseline and follow-up testing across participating centers; (3) a pilot study of newborn screening for SCID to identify affected infants prior to compromise by infection; and (4) for the non-SCID diseases, Wiskott-Aldrich syndrome and Chronic Granulomatous Disease, studies of the natural history of disease in patients who do or do not receive HCT. To accomplish these goals, collaboration by a consortium of institutions in North America is proposed. Participation of immunologists and HCT physicians having interest in PID and experts in laboratory methods, clinical outcomes assessment, databases and analysis will be required for the success of these studies.
doi:10.1016/j.jaci.2008.09.045
PMCID: PMC3357108  PMID: 18992926
Allogeneic hematopoietic cell transplantation; primary immunodeficiency; clinical trial
19.  Treatment with sirolimus results in complete responses in patients with autoimmune lymphoproliferative syndrome 
Summary
We hypothesized that sirolimus, an mTOR inhibitor, may be effective in patients with autoimmune lymphoproliferative syndrome (ALPS) and treated patients who were intolerant to or failed other therapies. Four patients were treated for autoimmune cytopenias; all had a rapid complete or near complete response. Two patients were treated for autoimmune arthritis and colitis, demonstrating marked improvement. Three patients had complete resolution of lymphadenopathy and splenomegaly and all patients had a reduction in double negative T cells, a population hallmark of the disease. Based on these significant responses, we recommend that sirolimus be considered as second-line therapy for patients with steroid-refractory disease.
doi:10.1111/j.1365-2141.2009.07595.x
PMCID: PMC2819393  PMID: 19208097
mTOR; autoimmunity; signal transduction; rapamycin
20.  Association of the BANK 1 R61H variant with systemic lupus erythematosus in Americans of European and African ancestry 
Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs10516487, within the B-cell gene BANK1 and systemic lupus erythematosus (SLE) as a consequence of a genome wide association study of this disease in European and Argentinean populations. In a bid for replication, we examined the effects of the R61H non-synonymous variant with respect to SLE in our genotyped American cohorts of European and African ancestry. Utilizing data from our ongoing genome-wide association study in our cohort of 178 Caucasian SLE cases and 1808 Caucasian population-based controls plus 148 African American (AA) SLE cases and 1894 AA population-based controls we investigated the association of the previously described non-synonymous SNP at the BANK1 locus with the disease in the two ethnicities separately. Using a Fisher’s exact test, the minor allele frequency (MAF) of rs10516487 in the Caucasian cases was 22.6% while it was 31.2% in Caucasian controls, yielding a protective odds ratio (OR) of 0.64 (95% CI 0.49-0.85; one-sided p = 7.07 × 10−4). Furthermore, the MAF of rs10516487 in the AA cases was 18.7% while it was 23.3% in AA controls, yielding a protective OR of 0.75 (95% CI 0.55–1.034; one-sided p = 0.039). The OR of the BANK1 variant in our study cohorts is highly comparable with that reported previously in a South American/European SLE case-control cohort (OR = 0.72). As such, R61H in the BANK1 gene confers a similar magnitude of SLE protection, not only in European Americans, but also in African Americans.
PMCID: PMC3681036  PMID: 23776345
systemic lupus erythematosus; African Americans; European Americans; BANK1 gene
21.  GCF2/LRRFIP1 Represses Tumor Necrosis Factor Alpha Expression 
Molecular and Cellular Biology  2005;25(20):9073-9081.
Tumor necrosis factor alpha (TNF-α) is an important mediator of inflammation, apoptosis, and the development of secondary lymphoid structures. Multiple polymorphic microsatellites have been identified in and around the gene, and there are also multiple single-base pair biallelic polymorphisms in the introns and promoter. The TNF-α −308 promoter polymorphism is a G-to-A transition which has been statistically associated with various autoimmune disorders. Some studies have found that it may directly mediate the increased transcription of TNF-α in some circumstances. This study characterizes proteins interacting at the polymorphic promoter site. Affinity purification of binding proteins and confirmatory chromatin immunoprecipitation assays were used to identify the proteins. Electrophoretic mobility shift analyses and surface plasmon resonance were used to define binding characteristics. Proteins interacting at this site include GCF2/LRRFIP1 and Ets-1. GCF2/LRRFIP1 appears to act as a repressor and occupies the −308 site in cells that do not make TNF-α. Cells competent to produce TNF-α have Ets-1 bound to the −308 promoter site. Active transcription is accompanied by NF-κB and c-Jun binding to the proximal promoter. Thus, dynamic changes on the TNF-α promoter, particularly at the −308 site, accompany the transition from repressed to active transcription. GCF2/LRRFIP1 is the first TNF-α repressor identified.
doi:10.1128/MCB.25.20.9073-9081.2005
PMCID: PMC1265793  PMID: 16199883
22.  Infections in Patients with Inherited Defects in Phagocytic Function 
Clinical Microbiology Reviews  2003;16(4):597-621.
Patients with defects in phagocytic function are predisposed to intracellular microorganisms and typically have early dissemination of the infection. Recognition of the underlying disorder and aggressive antimicrobial therapy has been beneficial for the patients. Improved understanding of the pathophysiology has also affected patient management by allowing specific, targeted immunomodulatory intervention. The disorders described in this review are not common but have had a significant impact on our understanding of the role of phagocytic cells in host defense. Conversely, understanding the role of the neutrophil and macrophage in infection has benefited not just the patients described in this review but also other patients with similar disease processes.
doi:10.1128/CMR.16.4.597-621.2003
PMCID: PMC207096  PMID: 14557288
23.  TH1 and TH2 Cytokine mRNA and Protein Levels in Human Immunodeficiency Virus (HIV)-Seropositive and HIV-Seronegative Youths 
The roles of cytokines in the progression of human immunodeficiency virus (HIV)-associated disease are controversial. The patterns of innate cytokine production have been postulated to shift from TH1- to TH2-type cytokines with the progression of HIV-associated disease. Although there have been studies of cytokines in children and adults, no data are available on cytokine production in healthy or HIV-infected adolescents. We analyzed and characterized cytokine mRNA and protein levels for gamma interferon, interleukin 2 (IL-2), IL-4, and tumor necrosis factor alpha and protein levels of IL-6 in both stimulated and unstimulated peripheral blood mononuclear cells obtained from a large longitudinal, observational cohort study of HIV-seropositive and -seronegative adolescents. We correlated cytokine results with viral load and CD4+-T-cell counts as critical markers of disease progression in HIV-infected adolescents. These data were used to examine hypotheses related to the TH1-to-TH2 cytokine shift in a sample of HIV-infected adolescents. Five hundred twenty subjects participating in the REACH (Reaching for Excellence in Adolescent Care and Health) Project of the Adolescent Medicine HIV/AIDS Research Network contributed blood samples. Samples selected for the cross-sectional data set analyzed had to meet selection criteria developed to minimize the potential confounding effects of acute intercurrent illnesses or infections, recent vaccination for hepatitis, and altered hormone status and to optimize congruence of cytokine measurements with assays of viral load and CD4+-T-cell counts. Group differences in the proportions of subjects with detectable levels of each cytokine marker were compared. In the subset of subjects with detectable cytokine values, differences in detected values were compared across subgroups defined by HIV serostatus and among HIV-seropositive subjects by three viral load classifications. The study sample was 65% HIV seropositive, 71% African-American, and 75% female with a mean age of 17.4 years. HIV-seropositive subjects were relatively healthy with mean and median CD4+-T-cell counts of 534 and 499 cells/mm3, respectively. Only 8.1% of subjects had CD4+-T-cell counts below 200 cells/mm3, and 25% had viral loads that were below the threshold of detection (<400 copies/ml). Detailed analyses of these data indicate that there were no differences in cytokines detected in HIV-seropositive and HIV-seronegative adolescents, and there was no apparent relationship between the cytokine measurements and the viral load or CD4+-T-cell categorization, the parameters selected as markers of HIV-associated disease status. These adolescents, including the HIV-seropositive subjects, were relatively healthy, and the HIV-infected subjects were at an early stage in the course of their HIV-associated disease. On the basis of our data, we conclude that, early in the course of HIV-associated disease in adolescents, there are no detectable shifts from TH1 to TH2 cytokine production.
doi:10.1128/CDLI.10.3.399-404.2003
PMCID: PMC154958  PMID: 12738638
24.  CD4+ CD25+ T-Cell Production in Healthy Humans and in Patients with Thymic Hypoplasia 
Regulatory T cells are found primarily in the CD4+ CD25+ fraction of T cells and play an important role in the prevention of autoimmunity. We examined CD4+ CD25+ T cells in 33 healthy children and adults and compared them to a population with an inherited form of thymic hypoplasia and a predisposition to autoimmune disease. Absolute numbers of CD4+ CD25+ T cells were markedly higher in healthy infants than in infants with chromosome 22q11.2 deletion syndrome.
doi:10.1128/CDLI.9.5.1129-1131.2002
PMCID: PMC120063  PMID: 12204972
25.  Gamma Interferon and Lipopolysaccharide Interact at the Level of Transcription To Induce Tumor Necrosis Factor Alpha Expression 
Infection and Immunity  2001;69(5):2847-2852.
Lipopolysaccharide (LPS) is a very potent inducer of tumor necrosis factor alpha (TNF-α) expression from monocytes and macrophages. Another inflammatory cytokine, gamma interferon (IFN-γ), can potentiate the effects of LPS, but the mechanism is not thoroughly understood. Previous reports emphasized the ability of IFN-γ to upregulate CD14 expression (the receptor for LPS), and nearly all studies have utilized sequential stimulation with IFN-γ followed by LPS to exploit this phenomenon. This study demonstrates that IFN-γ can upregulate the effect of LPS at the level of transcription. Human monoblastic Mono-Mac-6 cells produced up to threefold-greater levels of TNF-α when simultaneously stimulated with LPS and IFN-γ compared to treatment with LPS alone. RNase protection studies showed a similar increase in RNA beginning as early as within 30 min. The synthesis of TNF-α mRNA in IFN-γ- and LPS-treated Mono-Mac-6 cells was also temporally prolonged even though the message turnover rate was identical to that seen in LPS stimulated cells. The modulatory effect of IFN-γ may be mediated by Jak2.
doi:10.1128/IAI.69.5.2847-2852.2001
PMCID: PMC98233  PMID: 11292697

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