Identifying transcript-level differential expression in primary human immune cells

BACKGROUND

Multipotential hematopoietic stem cells differentiate into a wide variety of immune cells with a diversity of functions, including the ability to respond to a variety of stimuli. Importantly, numerous studies have demonstrated the importance of gene transcription in defining cell identity and functions. While these studies have primarily been performed at the level of the gene, it is known that key immune genes such as CD44 and CD45 generate multiple different transcripts that are differentially expressed across different immune cells, and that encode proteins with different sequences and functions. Prior genomic surveys have shown that the mechanisms for generating diversity in expressed transcripts (alternate splicing, alternate transcription start sites, etc.) are very active in immune cells, but have been lacking in terms of identifying genes with multiple transcripts, that are differentially expressed, and likely to affect cell functions.

METHODS

We first identified the set of genes that had at least two transcripts expressed in our RNA sequencing dataset generated from purified populations of neutrophils, monocytes and five lymphocyte populations (B, NK, γδ T, CD4 + T and CD8 + T) from twelve healthy donors. Next, we developed a heuristic approach to identify genes where two or more transcripts have distinct expression patterns across lymphoid and/or myeloid populations. We then focused our annotation and interpretation on differentially expressed transcripts that affect the coding sequence. This process was repeated to identify transcripts that were differentially expressed between monocytes and populations of macrophages and LPS-stimulated macrophages derived from these monocytes in vitro.

RESULTS

We found that over 55 % of genes had two or more expressed transcripts, with an average ∼3 transcripts per gene, and that 70 % of these had at least two of the transcripts that encoded proteins with different sequences. As expected, we identified a complex pattern of differential expression for multiple transcripts encoding the CD45 transmembrane protein, but we also found similar evidence for ten other genes (CD300A, FYB1, GPI, LITAF, PSMA1, PTMA, RPL32, SEPTIN9, SH3BP2, SH3KBP1) when comparing the expression patterns of transcripts within myeloid and lymphoid cells. We also identified five genes with differentially expressed transcripts associated with the transition from monocytes to macrophages (FNBP1, KLF6, and SEPTIN9) or between macrophages and LPS-stimulated macrophages (CD44, OAZ2, and SEPTIN9). For the most part, we found that the different transcripts of these genes are expected to impact specific biological functions, for example the different transcripts of SEPTIN9 likely regulate the cytoskeleton in immune cells via their interactions with actins filaments and microtubules.

CONCLUSIONS

This analytic approach successfully identified multi-transcript genes that are differentially expressed across immune cells and could be applied to other transcriptomic data.

DATA AVAILABILITY STATEMENT

Researchers can request access to the individual-level data from the current study by contacting the Montreal Heart Institute ethics committee at the following institutional email address: cer.icm@icm-mhi.org.

Prostaglandins and calprotectin are genetically and functionally linked to the Inflammatory Bowel Diseases

Background

Genome wide association studies (GWAS) have identified and validated more than 200 genomic loci associated with the inflammatory bowel disease (IBD), although for most the causal gene remains unknown. Given the importance of myeloid cells in IBD pathogenesis, the current study aimed to uncover the role of genes within IBD genetic loci that are endogenously expressed in this cell lineage.

Methods

The open reading frames (ORF) of 42 genes from IBD-associated loci were expressed via lentiviral transfer in the THP-1 model of human monocytes and the impact of each of these on the cell’s transcriptome was analyzed using a RNA sequencing-based approach. We used a combination of genetic and pharmacologic approaches to validate our findings in the THP-1 line with further validation in human induced pluripotent stem cell (hiPSC)-derived-monocytes.

Results

This functional genomics screen provided evidence that genes in four IBD GWAS loci (PTGIR, ZBTB40, SLC39A11 and NFKB1) are involved in controlling S100A8 and S100A9 genes expression, which encode the two subunits of calprotectin (CP). We demonstrated that increasing PTGIR expression and/or stimulating PTGIR signaling resulted in increased CP expression in THP-1.

This was further validated in hiPSC-derived monocytes. Conversely, knocking-down PTGIR endogenous expression and/or inhibiting PTGIR signaling led to decreased CP expression. These analyses were extended to the known IBD gene PTGER4, whereby its specific agonist also led to increased CP expression. Furthermore, we demonstrated that the PTGIR and PTGER4 mediated control of CP expression was dependent on signaling via adenylate cyclase and STAT3. Finally, we demonstrated that LPS-mediated increases in CP expression could be potentiated by agonists of PTGIR and PTGER4, and diminished by their antagonists.

Conclusion

Our results support a causal role for the PTGIR, PTGER4, ZBTB40, SLC39A11 and NFKB1 genes in IBD, with all five genes regulating the expression of CP in myeloid cells, as well as potential roles for the prostacyclin/prostaglandin biogenesis and signaling pathways in IBD susceptibility and pathogenesis.

Epigenetic reader SP140 loss of function drives Crohn's disease due to uncontrolled macrophage topoisomerases

How mis-regulated chromatin directly impacts human immune disorders is poorly understood. Speckled Protein 140 (SP140) is an immune-restricted PHD and bromodomain-containing epigenetic "reader," and SP140 loss-of-function mutations associate with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the relevance of these mutations and mechanisms underlying SP140-driven pathogenicity remains unexplored. Using a global proteomic strategy, we identified SP140 as a repressor of topoisomerases (TOPs) that maintains heterochromatin and macrophage fate. In humans and mice, SP140 loss resulted in unleashed TOP activity, de-repression of developmentally silenced genes, and ultimately defective microbe-inducible macrophage transcriptional programs and bacterial killing that drive intestinal pathology. Pharmacological inhibition of TOP1/2 rescued these defects. Furthermore, exacerbated colitis was restored with TOP1/2 inhibitors in Sp140-/- mice, but not wild-type mice, in vivo. Collectively, we identify SP140 as a TOP repressor and reveal repurposing of TOP inhibition to reverse immune diseases driven by SP140 loss.

Functional screen of inflammatory bowel disease genes reveals key epithelial functions

BACKGROUND

Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants, and their functional impacts has been more limited.

METHODS

We identified 145 genes from IBD-associated genomic loci having endogenous expression within the intestinal epithelial cell compartment. We evaluated the impact of lentiviral transfer of the open reading frame (ORF) of these IBD genes into the HT-29 intestinal epithelial cell line via transcriptomic analyses. By comparing the genes in which expression was modulated by each ORF, as well as the functions enriched within these gene lists, we identified ORFs with shared impacts and their putative disease-relevant biological functions.

RESULTS

Analysis of the transcriptomic data for cell lines expressing the ORFs for known causal genes such as HNF4a, IFIH1, and SMAD3 identified functions consistent with what is already known for these genes. These analyses also identified two major clusters of genes: Cluster 1 contained the known IBD causal genes IFIH1, SBNO2, NFKB1, and NOD2, as well as genes from other IBD loci (ZFP36L1, IRF1, GIGYF1, OTUD3, AIRE and PITX1), whereas Cluster 2 contained the known causal gene KSR1 and implicated DUSP16 from another IBD locus. Our analyses highlight how multiple IBD gene candidates can impact on epithelial structure and function, including the protection of the mucosa from intestinal microbiota, and demonstrate that DUSP16 acts a regulator of MAPK activity and contributes to mucosal defense, in part via its regulation of the polymeric immunoglobulin receptor, involved in the protection of the intestinal mucosa from enteric microbiota.

CONCLUSIONS

This functional screen, based on expressing IBD genes within an appropriate cellular context, in this instance intestinal epithelial cells, resulted in changes to the cell's transcriptome that are relevant to their endogenous biological function(s). This not only helped in identifying likely causal genes within genetic loci but also provided insight into their biological functions. Furthermore, this work has highlighted the central role of intestinal epithelial cells in IBD pathophysiology, providing a scientific rationale for a drug development strategy that targets epithelial functions in addition to the current therapies targeting immune functions.

Bottom-Up Gold Filling in New Geometries and Yet Higher Aspect Ratio Gratings for Hard X-Ray Interferometry

An extreme bottom-up filling variant of superconformal Au electrodeposition yielding void-free filling of recessed features is demonstrated with diffraction gratings composed of a two-dimensional patterned "chessboard" array of square vias of aspect ratio (depth/width) ≈ 23 as well as one-dimensional arrays of trenches having aspect ratios exceeding 50 and 65. Deposition on planar and patterned substrates is examined in several near-neutral x mol·L^-1 Na₃Au(SO₃)₂ + 0.64 mol·L^-1 Na₂SO₃ electrolytes (x = [0.08, 0.16, 0.32]) containing ≈ 50 μmol·L^-1 Bi³⁺ additive. The electrolytes are similar to those used in earlier work, although the upper bound on Au(SO₃)₂ concentration is twofold greater than previously described. Filling results are complemented by associated current and deposition charge transients whose features, particularly with well controlled pH, exhibit repeatable behaviors and timescales for incubation of passive deposition followed by bottom-up, void-free filling. While incompletely filled features can exhibit substantial via-to-via variation in fill height, self-passivation that follows complete bottom-up filling results in highly uniform filling profiles across the substrates. Visibility measurements capture the quality and uniformity of the as-formed wafer scale gratings. X-ray phase contrast imaging demonstrates their potential for imaging applications.

Lrrk2 alleles modulate inflammation during microbial infection of mice in a sex-dependent manner

Variants in the leucine-rich repeat kinase-2 (LRRK2) gene are associated with Parkinson's disease, leprosy, and Crohn's disease, three disorders with inflammation as an important component. Because of its high expression in granulocytes and CD68-positive cells, LRRK2 may have a function in innate immunity. We tested this hypothesis in two ways. First, adult mice were intravenously inoculated with Salmonella typhimurium, resulting in sepsis. Second, newborn mouse pups were intranasally infected with reovirus (serotype 3 Dearing), which induced encephalitis. In both mouse models, wild-type Lrrk2 expression was protective and showed a sex effect, with female Lrrk2-deficient animals not controlling infection as well as males. Mice expressing Lrrk2 carrying the Parkinson's disease-linked p.G2019S mutation controlled infection better, with reduced bacterial growth and longer animal survival during sepsis. This gain-of-function effect conferred by the p.G2019S mutation was mediated by myeloid cells and was abolished in animals expressing a kinase-dead Lrrk2 variant, p.D1994S. Mouse pups with reovirus-induced encephalitis that expressed the p.G2019S Lrrk2 mutation showed increased mortality despite lower viral titers. The p.G2019S mutant Lrrk2 augmented immune cell chemotaxis and generated more reactive oxygen species during virulent infection. Reovirus-infected brains from mice expressing the p.G2019S mutant Lrrk2 contained higher concentrations of α-synuclein. Animals expressing one or two p.D1994S Lrrk2 alleles showed lower mortality from reovirus-induced encephalitis. Thus, Lrrk2 alleles may alter the course of microbial infections by modulating inflammation, and this may be dependent on the sex and genotype of the host as well as the type of pathogen.

A transcriptome-based approach to identify functional modules within and across primary human immune cells

Genome-wide transcriptomic analyses have provided valuable insight into fundamental biology and disease pathophysiology. Many studies have taken advantage of the correlation in the expression patterns of the transcriptome to infer a potential biologic function of uncharacterized genes, and multiple groups have examined the relationship between co-expression, co-regulation, and gene function on a broader scale. Given the unique characteristics of immune cells circulating in the blood, we were interested in determining whether it was possible to identify functional co-expression modules in human immune cells. Specifically, we sequenced the transcriptome of nine immune cell types from peripheral blood cells of healthy donors and, using a combination of global and targeted analyses of genes within co-expression modules, we were able to determine functions for these modules that were cell lineage-specific or shared among multiple cell lineages. In addition, our analyses identified transcription factors likely important for immune cell lineage commitment and/or maintenance.

Characterization of a Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Model for the Study of Variant Pathogenicity: Validation of a KCNJ2 Mutation

BACKGROUND

Long-QT syndrome is a potentially fatal condition for which 30% of patients are without a genetically confirmed diagnosis. Rapid identification of causal mutations is thus a priority to avoid at-risk situations that can lead to fatal cardiac events. Massively parallel sequencing technologies are useful for the identification of sequence variants; however, electrophysiological testing of newly identified variants is crucial to demonstrate causality. Long-QT syndrome could, therefore, benefit from having a standardized platform for functional characterization of candidate variants in the physiological context of human cardiomyocytes.

METHODS AND RESULTS

Using a variant in Kir2.1 (Gly52Val) revealed by whole-exome sequencing in a patient presenting with symptoms of long-QT syndrome as a proof of principle, we demonstrated that commercially available human induced pluripotent stem cell-derived cardiomyocytes are a powerful model for screening variants involved in genetic cardiac diseases. Immunohistochemistry experiments and whole-cell current recordings in human embryonic kidney cells expressing the wild-type or the mutant Kir2.1 demonstrated that Kir2.1-52V alters channel cellular trafficking and fails to form a functional channel. Using human induced pluripotent stem cell-derived cardiomyocytes, we not only confirmed these results but also further demonstrated that Kir2.1-52V is associated with a dramatic prolongation of action potential duration with evidence of arrhythmic activity, parameters which could not have been studied using human embryonic kidney cells.

CONCLUSIONS

Our study confirms the pathogenicity of Kir2.1-52V in 1 patient with long-QT syndrome and also supports the use of isogenic human induced pluripotent stem cell-derived cardiomyocytes as a physiologically relevant model for the screening of variants of unknown function.

Loss of hepatic LRPPRC alters mitochondrial bioenergetics, regulation of permeability transition and trans-membrane ROS diffusion

The French-Canadian variant of Leigh Syndrome (LSFC) is an autosomal recessive oxidative phosphorylation (OXPHOS) disorder caused by a mutation in LRPPRC, coding for a protein involved in the stability of mitochondrially-encoded mRNAs. Low levels of LRPPRC are present in all patient tissues, but result in a disproportionately severe OXPHOS defect in the brain and liver, leading to unpredictable subacute metabolic crises. To investigate the impact of the OXPHOS defect in the liver, we analyzed the mitochondrial phenotype in mice harboring an hepatocyte-specific inactivation of Lrpprc. Loss of LRPPRC in the liver caused a generalized growth delay, and typical histological features of mitochondrial hepatopathy. At the molecular level, LRPPRC deficiency caused destabilization of polyadenylated mitochondrial mRNAs, altered mitochondrial ultrastructure, and a severe complex IV (CIV) and ATP synthase (CV) assembly defect. The impact of LRPPRC deficiency was not limited to OXPHOS, but also included impairment of long-chain fatty acid oxidation, a striking dysregulation of the mitochondrial permeability transition pore, and an unsuspected alteration of trans-membrane H2O2 diffusion, which was traced to the ATP synthase assembly defect, and to changes in the lipid composition of mitochondrial membranes. This study underscores the value of mitochondria phenotyping to uncover complex and unexpected mechanisms contributing to the pathophysiology of mitochondrial disorders.

IL23R (Interleukin 23 Receptor) Variants Protective against Inflammatory Bowel Diseases (IBD) Display Loss of Function due to Impaired Protein Stability and Intracellular Trafficking

Genome-wide association studies as well as murine models have shown that the interleukin 23 receptor (IL23R) pathway plays a pivotal role in chronic inflammatory diseases such as Crohn disease (CD), ulcerative colitis, psoriasis, and type 1 diabetes. Genome-wide association studies and targeted re-sequencing studies have revealed the presence of multiple potentially causal variants of the IL23R. Specifically the G149R, V362I, and R381Q IL23Rα chain variants are linked to protection against the development of Crohn disease and ulcerative colitis in humans. Moreover, the exact mechanism of action of these receptor variants has not been elucidated. We show that all three of these IL23Rα variants cause a reduction in IL23 receptor activation-mediated phosphorylation of the signal-transducing activator of transcription 3 (STAT3) and phosphorylation of signal transducing activator of transcription 4 (STAT4). The reduction in signaling is due to lower levels of cell surface receptor expression. For G149R, the receptor retention in the endoplasmic reticulum is due to an impairment of receptor maturation, whereas the R381Q and V362I variants have reduced protein stability. Finally, we demonstrate that the endogenous expression of IL23Rα protein from V362I and R381Q variants in human lymphoblastoid cell lines exhibited lower expression levels relative to susceptibility alleles. Our results suggest a convergent cause of IL23Rα variant protection against chronic inflammatory disease.

Specific targeting of the IL-23 receptor, using a novel small peptide noncompetitive antagonist, decreases the inflammatory response

IL-23 is part of the IL-12 family of cytokines and is composed of the p19 subunit specific to IL-23 and the p40 subunit shared with IL-12. IL-23 specifically contributes to the inflammatory process of multiple chronic inflammatory autoimmune disorders, including psoriasis, multiple sclerosis, inflammatory bowel disease, and rheumatoid arthritis. So far, one antibody targeting the shared p40 subunit of IL-12 and IL-23, Ustekinumab, is approved clinically to treat psoriasis. However, there are no treatments inhibiting specifically the IL-23 proinflammatory response. We have developed small IL-23R-specific antagonists by designing all D-peptides arising from flexible regions of IL-23R. Of these peptides, we selected 2305 (teeeqqly), since in addition to its soluble properties, it inhibited IL-23-induced STAT3 phosphorylation in spleen cells. Peptide 2305 specifically binds to IL-23R/IL-12Rβ1-expressing HEK-293 cells and not to cells devoid of the receptor. Peptide 2305 showed functional selectivity by modulating IL-23-induced gene expression in IL-23R/IL-12Rβ1-expressing cells and in Jurkat cells; 2305 does not inhibit IL-12-induced cytokine expression in IL-12Rβ-IL-12Rβ2-HEK-293 cells. Finally, compared with anti-p40 treatment, 2305 effectively and selectively inhibits IL-23-induced inflammation in three in vivo mouse models: IL-23-induced ear inflammation, anti-CD40-induced systemic inflammatory response, and collagen-induced arthritis. We, hereby, describe the discovery and characterization of a potent IL-23R small-peptide modulator, 2305 (teeeqqly), that is effective in vivo. 2305 may be more convenient, less cumbersome, less costly, and most importantly, more specific than current biologics for the treatment of inflammatory conditions, and conceivably complement the actual therapies for these chronic and debilitating inflammatory diseases.

The dichotomous pattern of IL-12r and IL-23R expression elucidates the role of IL-12 and IL-23 in inflammation

IL-12 and IL-23 cytokines respectively drive Th1 and Th17 type responses. Yet, little is known regarding the biology of these receptors. As the IL-12 and IL-23 receptors share a common subunit, it has been assumed that these receptors are co-expressed. Surprisingly, we find that the expression of each of these receptors is restricted to specific cell types, in both mouse and human. Indeed, although IL-12Rβ2 is expressed by NK cells and a subset of γδ T cells, the expression of IL-23R is restricted to specific T cell subsets, a small number of B cells and innate lymphoid cells. By exploiting an IL-12- and IL-23-dependent mouse model of innate inflammation, we demonstrate an intricate interplay between IL-12Rβ2 NK cells and IL-23R innate lymphoid cells with respectively dominant roles in the regulation of systemic versus local inflammatory responses. Together, these findings support an unforeseen lineage-specific dichotomy in the in vivo role of both the IL-12 and IL-23 pathways in pathological inflammatory states, which may allow more accurate dissection of the roles of these receptors in chronic inflammatory diseases in humans.

The non-classical MAP kinase ERK3 controls T cell activation

The classical mitogen-activated protein kinases (MAPKs) ERK1 and ERK2 are activated upon stimulation of cells with a broad range of extracellular signals (including antigens) allowing cellular responses to occur. ERK3 is an atypical member of the MAPK family with highest homology to ERK1/2. Therefore, we evaluated the role of ERK3 in mature T cell response. Mouse resting T cells do not transcribe ERK3 but its expression is induced in both CD4⁺ and CD8⁺ T cells following T cell receptor (TCR)-induced T cell activation. This induction of ERK3 expression in T lymphocytes requires activation of the classical MAPK ERK1 and ERK2. Moreover, ERK3 protein is phosphorylated and associates with MK5 in activated primary T cells. We show that ERK3-deficient T cells have a decreased proliferation rate and are impaired in cytokine secretion following in vitro stimulation with low dose of anti-CD3 antibodies. Our findings identify the atypical MAPK ERK3 as a new and important regulator of TCR-induced T cell activation.

Prevalence and predictive factors of the need for surgery for advanced colorectal adenoma

AIM

Endoscopic resection is the primary treatment for colorectal adenoma, but in some cases surgery is necessary. The aim of this retrospective study was to define the prevalence and predictive factors for surgery in patients with advanced colorectal adenoma managed in a referral endoscopy centre.

METHOD

Consecutive patients diagnosed with advanced adenoma (Class 4 in the Vienna classification) during a colonoscopy from 2007 to 2009 in the endoscopy centre of the University Hospital of Rennes were included. Predictive factors of surgery were determined by univariate and multivariate analysis.

RESULTS

Two-hundred and twelve (135 male) patients with a mean age of 65.8 years were included. The reason for colonoscopy was for diagnosis in 63.2%, surveillance in 25.5% and screening in 11.3%. These referred patients amounted to 20.8% of all patients having colonoscopy. Surgery was performed in 13.7% of the 212 patients and in 16 (8.3%) of the 192 patients in whom endoscopic removal was attempted. In the subgroup of 192 patients, univariate analysis revealed that body mass index (P = 0.04), histology (P = 0.002), size (P = 0.03) and macroscopic appearance (P < 0.001) of the polyp were associated with surgery. Multivariate analysis revealed that the macroscopic appearance and histology only were significantly associated with surgery.

CONCLUSION

Surgery was needed in 13.7% of patients with an advanced adenoma, but in only 8.3% of the subgroup of 192 patients in whom endoscopic removal was attempted. Factors associated with surgery included macroscopic appearance and histology.

Unusual selection and peripheral homeostasis for immunoregulatory CD4(-) CD8(-) T cells

Immunoregulatory CD4(-)  CD8(-) (double-negative; DN) T cells exhibit a unique antigen-specific mode of suppression, yet the ontogeny of DN T cells remains enigmatic. We have recently shown that 3A9 T-cell receptor (TCR) transgenic mice bear a high proportion of immunoregulatory 3A9 DN T cells, facilitating their study. The 3A9 TCR is positively selected on the H2(k) MHC haplotype, is negatively selected in mice bearing the cognate antigen, namely hen egg lysozyme, and there is absence of positive selection on the H2(b) MHC haplotype. Herein, we take advantage of this well-defined 3A9 TCR transgenic model to assess the thymic differentiation of DN T cells and its impact on determining the proportion of these cells in secondary lymphoid organs. We find that the proportion of DN T cells in the thymus is not dictated by the nature of the MHC-selecting haplotype. By defining DN T-cell differentiation in 3A9 TCR transgenic CD47-deficient mice as well as in mice bearing the NOD.H2(k) genetic background, we further demonstrate that the proportion of 3A9 DN T cells in the spleen is independent of the MHC selecting haplotype. Together, our findings suggest that immunoregulatory DN T cells are subject to rules distinct from those imposed upon CD4 T cells.

Case report: reconstruction of the distal tibia with porous tantalum spacer after resection for giant cell tumor

Treatment options for giant cell tumors of the distal tibia include curettage and cement packing, curettage and bone grafting, or resection and reconstruction for aggressive tumors. Curettage of aggressive tumors often leads to severe bone loss requiring reconstruction. Allograft and autograft may be effective options for reconstruction, but each is associated with drawbacks including the possibility of infection and collapse. We present a case of giant cell tumor of the distal tibia treated with curettage and arthrodesis using a porous tantalum spacer. Complete removal of the tumor and successful arthrodesis of the ankle were accomplished using the spacer. The patient returned to pain-free walking along with eradication of the giant cell tumor. We believe porous tantalum spacers are a reasonable option for reconstructing the distal tibia after curettage of a giant cell tumor with extensive bone loss.

REGULATORY CD4-CD8- T CELLS PREVENT AUTOIMMUNE DIABETES (143.4)

Regulatory T cells show great potential for use in cellular therapy. In particular, CD4-CD8- (DN) T cells, which compose 1 to 3% of total T lymphocytes, exhibit prominent antigen-specific immune tolerance properties in models of allografts and xenografts, as well as in an induced model of autoimmune diabetes. Here, we evaluate the immunoregulatory properties of DN T cells in the autoimmune-prone NOD genetic background. Using the 3A9 TCR transgenic mice, we demonstrate that DN T cells from both autoimmune-resistant and -prone mice are equally effective at eliminating potentially autoreactive B cells in vitro. However, autoimmune-prone mice carry at least three fold fewer DN T cells than autoimmune-resistant mice, in both TCR transgenic and non-transgenic setting. Interestingly, a single transfer of DN T cells is sufficient to prevent autoimmune diabetes onset in autoimmune-prone mice. These results suggest that increasing DN T cell number is sufficient to confer protection from autoimmune diabetes onset. Further functional and genetic characterization of DN T cells in NOD mice highlighted a potential role for both CD172a and IL-10 in the regulation of DN T cell homeostasis. Importantly, genetic polymorphisms in both CD172a and IL-10 are associated with diabetes susceptibility in humans. Taken together, our results strongly suggest a role for DN T cell in peripheral tolerance and the association of genetic defects in DN T cell homeostasis with the development of diabetes.

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

Ulcerative colitis is a chronic, relapsing inflammatory condition of the gastrointestinal tract with a complex genetic and environmental etiology. In an effort to identify genetic variation underlying ulcerative colitis risk, we present two distinct genome-wide association studies of ulcerative colitis and their joint analysis with a previously published scan, comprising, in aggregate, 2,693 individuals with ulcerative colitis and 6,791 control subjects. Fifty-nine SNPs from 14 independent loci attained an association significance of P < 10(-5). Seven of these loci exceeded genome-wide significance (P < 5 x 10(-8)). After testing an independent cohort of 2,009 cases of ulcerative colitis and 1,580 controls, we identified 13 loci that were significantly associated with ulcerative colitis (P < 5 x 10(-8)), including the immunoglobulin receptor gene FCGR2A, 5p15, 2p16 and ORMDL3 (orosomucoid1-like 3). We confirmed association with 14 previously identified ulcerative colitis susceptibility loci, and an analysis of acknowledged Crohn's disease loci showed that roughly half of the known Crohn's disease associations are shared with ulcerative colitis. These data implicate approximately 30 loci in ulcerative colitis, thereby providing insight into disease pathogenesis.

Absence of CD47 in vivo influences thymic dendritic cell subset proportions but not negative selection of thymocytes

CD47 is a ubiquitously expressed molecule which has been attributed a role in many cellular processes. Its role in preventing cellular phagocytosis has defined CD47 as an obligatory self-molecule providing a 'don't-eat-me-signal'. Additionally, CD47-CD172a interactions are important for cellular trafficking. Yet, the contribution of CD47 to T cell stimulation remains controversial, acting sometimes as a co-stimulator and sometimes as an inhibitor of TCR signalling or peripheral T cell responses. Most of the experiments leading to this controversy have been carried in in vitro systems. Moreover, the role of CD47 on thymocyte differentiation, which precisely relies on TCR signal strength, has not been evaluated. Here, we examine the in vivo role of CD47 in T cell differentiation using CD47-deficient mice. We find that, in the absence of CD47, thymocyte positive and negative selection processes are not altered. Indeed, our data demonstrate that the absence of CD47 does not influence the strength of TCR signalling in thymocytes. Furthermore, in agreement with a role for CD47-CD172a interactions in CD172a(+) dendritic cell migration, we report a reduced proportion of thymic dendritic cells expressing CD172a in CD47-deficient mice. As the total proportion of dendritic cells is maintained, this creates an imbalance in the proportion of CD172a(+) and CD172a(low) dendritic cells in the thymus. Together, these data indicate that the altered proportion of thymic dendritic cell subsets does not have a primordial influence on thymic selection processes.

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Jusque vers 1970, la question de l'extinction mondiale du paludisme, maladie dont on nous dit qu'elle est aussi ancienne que l'humanité elle-même, se posait en termes relativement simples. A la régression spontanée du mal, telle qu'elle s'était opérée en Europe du Nord et de l'Ouest à la fin du XIXe siècle et au début du XXe, on opposait les programmes d'éradication systématiques, menés avec des moyens prophylactiques et thérapeutiques scientifiquement définis ; les succès de la lutte médicale, particulièrement nets dans plusieurs pays méditerranéens, ont mis en lumière l'efficacité des politiques volontaires et organisées d'éradication, contribuant ainsi à laisser dans l'ombre ce que ces résultats pouvaient devoir à d'autres facteurs.

Development of a FLP/frt system for generating helper-dependent adenoviral vectors

Helper-dependent (HD) adenoviral vectors devoid of all viral coding sequences have a large cloning capacity and have been reported to provide long-term transgene expression in vivo with negligible toxicity, making them attractive vectors for gene therapy. Currently, the most efficient means of generating HD vectors involves co-infecting 293 cells expressing Cre with the HD vector and a helper virus bearing a packaging signal flanked by loxP sites. Cre-mediated excision of the packaging signal renders the helper virus genome unpackageable but still able to replicate and to provide helper functions for HD vector propagation. HD vector titer is increased by serial co-infections. Typically, helper virus contamination is < or =1% pre- and < or =0.1% postpurification by CsCl banding. While these contamination levels are low, further reduction is desirable. Alternative methods of selection against the helper virus may achieve this goal, especially when combined with Cre/loxP. We describe the development of a system for generating HD vectors based on site-specific recombination between frt sites catalyzed by FLP recombinase and show by direct comparison that the FLP/frt and Cre/loxP systems are equivalent with respect to HD vector amplification efficiency and helper virus contamination levels. Availability of a second recombinase system for HD vector production will enhance the utility and flexibility of HD vectors.

Improving residents' compliance with standards of ambulatory care: results from the VA Cooperative Study on Computerized Reminders

CONTEXT

Computerized systems to remind physicians to provide appropriate care have not been widely evaluated in large numbers of patients in multiple clinical settings.

OBJECTIVE

To examine whether a computerized reminder system operating in multiple Veterans Affairs (VA) ambulatory care clinics improves resident physician compliance with standards of ambulatory care.

DESIGN, SETTING, AND PARTICIPANTS

A total of 275 resident physicians at 12 VA medical centers were randomly assigned in firms or half-day clinic blocks to either a reminder group (n = 132) or a control group (n = 143). During a 17-month study period (January 31, 1995-June 30, 1996), the residents cared for 12,989 unique patients for whom at least 1 of the studied standards of care (SOC) was applicable.

MAIN OUTCOME MEASURES

Compliance with 13 SOC, tracked using hospital databases and encounter forms completed by residents, compared between residents in the reminder group vs those in the control group.

RESULTS

Measuring compliance as the proportion of patients in compliance with all applicable SOC by their last visit during the study period, the reminder group had statistically significantly higher rates of compliance than the control group for all standards combined (58.8% vs 53.5%; odds ratio [OR], 1.24; 95% confidence interval [CI], 1.08-1.42; P =.002) and for 5 of the 13 standards examined individually. Measuring compliance as the proportion of all visits for which care was indicated in which residents provided proper care, the reminder group also had statistically significantly higher rates of compliance than the control group for all standards combined (17.9% vs 12.2%; OR, 1.57; 95% CI, 1.45-1.71; P<.001) and for 9 of the 13 standards examined individually. The benefit of reminders, however, declined throughout the course of the study, even though the reminders remained active.

CONCLUSIONS

Our data indicate that reminder systems installed at multiple sites can improve residents' compliance to multiple SOC. The benefits of such systems, however, appear to deteriorate over time. Future research needs to explore methods to better sustain the benefits of reminders. JAMA. 2000;284:1411-1416.

AANA journal course: update for nurse anesthetists--serotonin agonists and antagonists: anesthetic implications

A number of important new pharmacologic agents in widespread clinical use share the ability of manipulate serotonin as their mechanism of action. Drugs as diverse as the antidepressants fluoxetine (Prozac), sertraline (Zoloft), paroxetine (Paxil), and venlafaxine (Effexor); the antimigraine agent sumatriptan (Imitrex); the antiobesity agent dexfenfluramine (Redux); and the antiemetics ondansetron (Zofran) and granisetron (Kytril) are routinely encountered in the perioperative patient. A thorough understanding of the pharmacology, physiologic effects, significant drug interactions and anesthetic implications of serotonin agonists or antagonists is vital for proper anesthetic management of patients receiving these drugs.

Overutilization of acute-care beds in Veterans Affairs hospitals

The authors tested the hypothesis that the Department of Veterans Affairs (VA) hospitals would have substantial overutilization of acute care beds and services because of policies that emphasize inpatient care over ambulatory care. Reviewers from 24 randomly selected VA hospitals applied the InterQual ISD* (Intensity, Severity, Discharge) criteria for appropriateness concurrently to a random sample of 2,432 admissions to acute medical, surgical, and psychiatry services. Reliability of hospital reviewers in applying the ISD* criteria was tested by comparing their reviews with those of a small group of expert reviewers. Validity of the ISD* criteria was tested by comparing the assessments of master reviewers with the implicit judgments of panels of nine physicians. The physician panels validated the ISD* admission criteria for medicine and surgery (74% agreement with master reviewers, kappa > 0.4), whereas the psychiatry criteria were not validated (66% agreement, kappa 0.29). Hospital reviewers reliably used all three criteria sets (> 83% agreement with master reviewers, kappa > 0.6). Rates of nonacute admissions to acute medical and surgical services were > 38% as determined by the hospital and master reviewers and by the physician panels. Nonacute rates of continued stay were > 32% for both medicine and surgery services. Similar rates of nonacute admissions and continued stay were found for all 24 hospitals. Reasons for nonacute admissions and continued stay included lack of an ambulatory care alternative, conservative physician practices, delays in discharge planning, and social factors such as homelessness and long travel distances to the hospital. Using criteria that the authors showed to be reliable and valid, substantial overutilization of acute medicine and surgical beds was found in a representative sample of VA hospitals. Correcting this situation will require changes in physician practice patterns, development of ambulatory care alternatives to inpatient care, and modification of current VA policies determining eligibility for care.

A managed care workstation for support of ambulatory care in Veterans Health Administration medical centers

This paper describes the development of a Managed Care Workstation for implementation in a Department of Veterans Affairs hospital. Each VA hospital information system contains a wealth of information in a comprehensive and well integrated M database, however, a clinician's access to the information is hampered by a lack of usable database tools. The Managed Care Workstation is designed to enhance access to VA databases. The workstation uses M (Mumps) and SQL to present the VA's M hierarchical database as relational tables on the workstation. This work reveals the benefits of using a SQL-M workstation to access data contained in an M based hospital information system and demonstrates how the workstation architecture supports the information model necessary for management of patient care outcomes.

Hip arthrodesis: an important option for advanced disease in the young adult

Despite increasing confidence in the intermediate and long-term results of total hip replacement, considerable and justifiable concern remains about its use in young, active adults. Hip arthrodesis is a valuable, although unpopular, option in this group of patients. The authors describe, step by step, the standardized technique of arthrodesis that they first used in 1981, and they review the results of their experience. The importance of precise positioning of the fusion is emphasized: 20 degrees of flexion, 5 degrees of external rotation and neutral abduction-adduction. Intraoperative radiography to check the positioning is strongly advised. Because total hip arthroplasty will likely be necessary at a later date, every effort should be made to preserve the abductors, and the greater trochanter should be fixed in place at its normal level. If these precautions are taken and if the patient is carefully selected and properly educated preoperatively, a high success rate can be expected for hip arthrodesis.

Soft tissue sarcomas: a plea for proper management

Although soft tissue sarcomas are relatively uncommon, they often occur in young patients and if properly treated are often curable. Unfortunately, inappropriate approaches to biopsy before adequate staging may compromise a successful outcome. The roles of diagnostic imaging (particularly magnetic resonance imaging) in adequate preoperative evaluation and staging and the fundamental principles of surgical management are discussed.

A clinical database management system for improved integration of the Veterans Affairs Hospital Information System

The Department of Veterans Affairs (VA) Decentralized Hospital Computer Program (DHCP) contains data modules derived from separate ancillary services (e.g., Lab, Pharmacy and Radiology). It is currently difficult to integrate information between the modules. A prototype is being developed aimed at integrating ancillary data by storing clinical data oriented to the patient so that there is easy interaction of data from multiple services. A set of program utilities provides for user-defined functions of decision support, queries, and reports. Information can be used to monitor quality of care by providing feedback in the form of reports, and reminders. Initial testing has indicated the prototype's design and implementation are feasible (in terms of space requirements, speed, and ease of use) in outpatient and inpatient settings. The design, development, and clinical use of this prototype are described.

"Computers in medicine"--a course for students at the USD School of Medicine

The University of South Dakota School of Medicine offers an elective course for senior medical students in the use of computer technology for patient care. The philosophy of the course, its current composition, and changes to the course in the future are described. By organizing topic information using computer tools for text, outline, data item, math, and image processing, students learn formats for information storage in the computer. In the near future, students will have the opportunity to make a hypothesis and test it with decision support tools that are present in an integrated hospital database.

Medical student attention to preventive medicine: change with time and reinforcement

We followed medical students' attention to documentation in their write-ups of appropriate preventive medicine information, based upon a patient's age, sex, and existing medical conditions, as well as the translation of critical findings to the problem list, for three years. The proportion of relevant items documented was .50 in year one, .80 in year two, and .69 in year three. Significant differences (p less than .001) were found between all three years. Similarly, the proportion of important items translated to the problem list was .04 in year one, .22 in year two, and .18 in year three. There was significant improvement in years two and three as compared to year one (p less than .001). The impact of interventions designed to reinforce the medical student's attention to preventive medicine was also studied. Cued forms on which to record the patient's history were compared to written feedback regarding the student's write-ups. Both significantly improved student performance. The effect of the written feedback also persisted in the follow-up period.

Changing orientations of medical students to patients' care: biomedical versus biopsychosocial models

The instructional effectiveness of a new biopsychosocial medicine curriculum model was evaluated using criterion-based measures of medical students' patient-history taking. Students ( n = 63) who received the new biopsychosocial curriculum were significantly more skilled in identifying, documenting and translating patients' psychosocial data and predisposing risk, factors than students ( n = 56) receiving the prior biomedical, disease-oriented curriculum. Implications for medical education and practice are also discussed.

Amphetamine-induced perseverative behavior in a radial arm maze following DSP4 or 6-OHDA pretreatment

Mice permitted to explore an 8-arm radial maze tended to visit those arms least recently entered. Treatment with D-amphetamine engendered a perseverative tendency, wherein mice repeatedly visited two arms of the maze. Administration of the norepinephrine (NE) neurotoxin, N-2-chloroethyl-N-ethyl-2-bromo-benzylamine (DSP4), appreciably reduced NE in the hippocampus and cortex, moderately reduced NE in the locus coeruleus, and had only a small effect on hypothalamic NE. The DSP4 treatment resulted in a decrease of locomotor activity among amphetamine-treated mice, coupled with an increase of stereotyped response patterns. Although the NE depletion did not affect the pattern of exploration that mice ordinarily displayed, DSP4 appreciably increased the perseverative tendency provoked by amphetamine. Reduction of dopamine (DA) and NE by intraventricular administration of the catecholamine neurotoxin, 6-hydroxydopamine (6-OHDA), antagonized the effects of amphetamine, such that the frequency of alternation responses was increased and the proportion of perseverative responses was reduced. The effectiveness of the 6-OHDA treatment in antagonizing the amphetamine-induced perseveration was not reduced among mice that were pretreated with desmethylimipramine, which resulted in partial prevention of the NE reduction by 6-OHDA administration. It is suggested that DA neuronal activity contributes to the amphetamine -provoked perseveration , whereas NE stimulation modifies the perseverative tendency by influencing exploration or habituation.

Evaluating the medical history: observation versus write-up review

The ability to develop a medical history data base relevant to the total care of a patient is a requisite skill for clinical problem-solving. Assessment of this skill by faculty members in medical students has been based on direct observation of the student-patient encounter as well as on evaluation of the student's written patient history. In the study reported here, both methods were compared by the authors for the same student-patient interview. Preceptor ratings of the students' data-elicitation skills were correlated with their ratings of the students' interview-process skills and the time spent by the preceptor observing the interview. A criterion-based, checklist scoring of the student's write-up was not correlated with preceptor ratings. In this study, the authors suggest that a criterion-based evaluation of the student's patient write-up is a less faculty-intensive and more reliable method of evaluating medical student data-collection skills than direct observation of the student-patient encounter.

Effects of inescapable shock and norepinephrine depletion induced by DSP4 on escape performance

The potential contribution of dorsal bundle norepinephrine (NE) in the induction of escape disturbances engendered by inescapable shock was evaluated following administration of the NE neurotoxin, DSP4. Treatment with DSP4 produced marked NE reductions in the hippocampus and cortex, a moderate reduction of NE in the locus coeruleus, but only small effects on hypothalamic NE. In contrast to the effect of inescapable shock, DSP4 was found not to influence escape behavior among naive mice or mice that had received inescapable shock. Moreover, DSP4 was without effect on escape performance irrespective of whether animals were individually or group housed, a treatment that has been shown to be sensitive to manipulations that influence escape performance. Treatment with DSP4 was found not to influence the escape interference ordinarily provoked by either haloperidol or alpha-MpT. Interestingly, the escape interference ordinarily engendered by the dopamine-beta-hydroxylase inhibitor, FLA-63, was eliminated among mice that had been pretreated with DSP4. The interference effect induced by inescapable shock is probably not attributable to NE alterations in the hippocampus and locus coeruleus. Serial or parallel effects of shock on more than a single transmitter system are likely to be responsible for the behavioral interference.

Cross-stressor immunization against the behavioral deficits introduced by uncontrollable shock

Exposure to inescapable shock disrupted performance in both shock- and water-escape tasks. These deficits were prevented in mice that were previously trained in the same task. However, an asymmetrical immunization effect was seen in a cross-stressor paradigm. Whereas deficits of water-escape performance engendered by inescapable shock were prevented by prior shock-escape training, the deficits of shock-escape performance were not eliminated by prior water-escape training. Evidently, the immunization effect occurs when initial training and subsequent testing are conducted in the same task, or when the initial training and uncontrollable stress session involve the same aversive stimulus. Norepinephrine determinations revealed that reductions of the amine introduced by inescapable shock were unaffected by prior shock-escape training and were enhanced by prior exposure to the stress of water immersion. Thus, although the performance deficit introduced by inescapable shock may be related to variations of norepinephrine, the immunization effect probably was unrelated to alterations of this transmitter. Rather, the data provisionally suggested that the immunization stems from two independent factors: Namely, initially training animals in an active escape task may (a) disrupt subsequent learning that the inescapable stress actually is uncontrollable and (b) limit the influence of the motor deficits introduced by uncontrollable shock on subsequent escape performance.