Monday, January 29, 2007

Infectious Cancer Cells

Some cancers are caused by infectious agents, such as viruses that cause cancer by infecting and transforming host cells. For example, Epstein-Barr virus (EBV) is implicated in Burkitt's lymphoma, nasopharyngeal carcinoma, and other cancers (review). For canine transmissible venereal tumor (CTVT), however, the tumor cell itself was thought to be the agent. To test this hypothesis, Murgia and colleagues isolated CTVT cells and non-cancerous blood cells from 40 different dogs on 5 continents, and determined their relationships by comparing nuclear and mitochondrial genetic markers. They conclude that all the tumors are clones of a single tumor that arose between 200 and 2,500 years ago. Although the tumor has a very unusual chromosome arrangement (aneuploid), it is stable. They also studied the highly polymorphic histocompatibility genes. Expression of histocompatibility proteins, which would block transplantation between different animals, is reduced but not extinguished on CTVT cells. Another study demonstrated that CTVT cells make TGF-beta1, which could also reduce the immune response. This surprising cell could provide ideas for inducing tolerance of allografts.
Claudio Murgia, Jonathan K. Pritchard, Su Yeon Kim, Ariberto Fassati, and Robin A. Weiss "Clonal Origin and Evolution of a Transmissible Cancer" Cell 126, 477–487, August 11, 2006

Saturday, January 27, 2007

How Peptides bind Proteins

Peptides are short proteins (polypeptides) -- up to about 50 amino acids. They can convey signals and mediate some of the activities of modular proteins. For example, peptides regulate behavior (neuropeptides), mood (substance P), and digestion (glucagon) The rules for peptides binding to proteins are not established, so Hertz and Yanover developed a new “framework” called PepDist for analyzing these interactions computationally. They say that most previous methods used only “binary” (binding/not-binding) classifiers, but a better method would rank peptides and the best would predict affinity. PepDist learns peptide-peptide distance functions and uses these to predict affinity. They trained their model peptides bound to histocompatibility proteins, which constitute a large and diverse family. They claim that PepDist outperforms the (formerly) state of the art models, including SVMHC, NetMHC (these links work, theirs don't!), and RANKPEP. The best part is that you can easily test it yourself – they provide an on-line service.
Hertz T and Yanover C, "PepDist: a new framework for protein-peptide binding prediction based on learning peptide distance functions." BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S3.

Genes and obesity

Gnome writes "Obese people, defined as a body mass index (BMI) over 30 (weight/(height)^2 in kg/m^2), are at increased risk of disease (including type 2 diabetes, heart disease, stroke, some types of cancer) and death. Unlike risk that is clearly behavioral, such as smoking, or genetic, such as some BRCA alleles, obesity is itself caused by a combination of factors. Though the recent increase in obesity rates results largely from behavioral changes, BMI is partially heritable. Herbert and colleagues looked through the whole genome for common variants associated with obesity among participants in the Framingham Heart Study. They avoided the statistical problem of multiple comparisons by first screening using parental genotypes to identify SNPs and inheritance models that best predict offspring phenotypes and then performing a family based association test (FBAT, a type of transmission disequilibrium test (TDT)) to test the selected SNPs for their association with BMI. In step 1, they tested 116,204 SNPs in 694 participants. In step 2, the top 10 SNPs were tested using a recessive model, yielding only 1 significant SNP: rs7566605, which defines a single haplotype and is near INSIG2 (insulin-induced gene 2). “For all exams, rs7566605 CC homozygotes are about 1 BMI unit heavier than individuals with GC or GG genotypes (P <0.0001). They replicated this correlation in a cohort from a town near Munich, Germany, in a combination of Caucasian cohorts from Poland and the USA, and in two samples from an African American population from Illinois, USA. However, the rs7566605 SNP was not correlated with BMI among the Nurses Health Study cohort, perhaps because the cohort contained fewer individuals with a high BMI or because of differences in environment and lifestyle. This is one gene among several associated with obesity and leanness.
Herbert A, Gerry NP, McQueen MB, Heid IM, Pfeufer A, Illig T, Wichmann HE, Meitinger T, Hunter D, Hu FB, Colditz G, Hinney A, Hebebrand J, Koberwitz K, Zhu X, Cooper R, Ardlie K, Lyon H, Hirschhorn JN, Laird NM, Lenburg ME, Lange C, Christman MF. "A common genetic variant is associated with adult and childhood obesity." Science 2006; 312:279-83."Science. 2006 Apr 14;312(5771):279-83.

Intermediate Avidity T Cells Regulated Through Qa-1

Jiang and colleagues have developed a model of immune regulation based on the details of antigen recognition: T cell receptors (TCRs) engaging peptides held by histocompatibility (MHC) molecules on an antigen presenting cell (APC). The strength of multivalent binding, or avidity, such as occurs between T cell and APC, depends on the affinity of individual receptor-ligand pairs (TCR-peptide/MHC) and the number of pairs engaged. They propose that autoimmunity may be avoided by controlling T cells with intermediate avidity for self proteins, since autoreactive T cells with high and low avidity are deleted during T cell maturation in the thymus (positive and negative selection). They suggest that T cells recognizing antigen with intermediate avidity are triggered to express non-classical MHC molecules (class Ib: Qa-1 in mice, HLA-E in humans), which are recognized by regulatory CD8+ T cells (Treg). Previously, they had shown that some pathogenic CD4+ T cells expressed Qa-1 and were suppressed by CD8+ Treg in experimental allergic encephalomyelitis, a mouse model of multiple sclerosis. Here, they analyze the immune response to the protein hen-egg lysozyme (HEL). The susceptibility of the HEL-specific CD4+ T cells to suppression was strikingly dependent on their avidity. (Avidity was estimated by titering HEL into a fixed number of APC and measuring proliferation.) Intermediate-avidity clones, but not high- or low-avidity clones, were suppressed. Though they demonstrate that this suppression can be blocked by Qa-1-specific antibodies, they do not report the correlation with Qa-1 expression. Qa-1 has an established role as a checkpoint for classical MHC molecule expression and regulator of Natural Killer cells but they cite previous studies of a Qa-1 knockout mouse to discount these mechanisms in this model. An intriguing, though incomplete, model.
Jiang H, Wu Y, Liang B, Zheng Z, Tang G, Kanellopoulos J, Soloski M, Winchester R, Goldstein I, Chess L. "An affinity/avidity model of peripheral T cell regulation." J Clin Invest. 2005 Feb;115(2):302-12.

Picosecond Protein Movements

Protein structure can be studied by crystallography or spectroscopy, which can also probe movement. Mukherjee and colleagues used 2 dimensional infrared spectroscopy (2D IR) to study the motions of a peptide on the scale of picoseconds, or trillionths of a second. (Interactions between proteins occur about a million times slower, on the mico- to millisecond time scales probed by NMR.) The 27 amino acid peptide that they studied spans the transmembrane region of CD3zeta, a signaling subunit of T lymphocyte antigen receptor. The peptide forms an alpha helix within the membrane. They synthesized 11 peptides, each with an amide [13]C labeled at a different position. Using a vibrational echo pulse sequence to resolve fast and slow molecular dynamics, they varied the delay between the pulses to measure motion on the picosecond scale. This revealed that all amino acids along the peptide showed the same relaxation times, which were similar to those observed in other peptides in solution, suggesting that this behavior is intrinsic to peptides. Comparisons with a molecular dynamic simulation confirmed that the peptides formed tetramers. They also found 2 'kinks' in the alpha helix, causing a 'funnel' structure to form in the membrane. Based on their observations of how the polar water molecules and lipid headgroups interact with the labeled amides, they predict that the IR patterns of amino acids lining the pores of transmembrane channel proteins will be easily distinguished from those facing the membrane.
Mukherjee P, Kass I, Arkin I, Zanni MT. "Picosecond dynamics of a membrane protein revealed by 2D IR." Proc. Natl. Acad. Sci. U S A. 2006 Feb 27;

Children helping Strangers

Altruism is helping unrelated individuals (non-kin) without expectation of reward. Effective helping in simple tasks requires an understanding of the intentions and needs of the other person (empathy). When does the capacity for altruism develop? These investigators tested 24, 18 month old children. In one test, an adult male experimenter who was unknown to the child dropped a marker (or a paper ball, or a clothespin, or a cup) on the floor. The experimenter focused first on the object for 10 s then alternated their gaze between the object and the child while saying something like "my marker". In the control situation, the experimenter threw the object down to the floor and then looked at it with a "neutral facial expression" for 20 s. "No reward or praise" was given. Most children (22 of 24) helped in at least one task. For 6 of the 10 tasks, the children helped in the experimental situation significantly more often than in the control situation. Three young chimpanzees were also tested. All three were raised by humans and tested by their caretakers. All 3 chimps helped in some tasks and helped "reliably" in the tasks involving reaching. This was also the type of task helped most often by children. The authors concluded that young children and, to a lesser degree, chimpanzees can be altruistic.
Warneken F, Tomasello M. "Altruistic helping in human infants and young chimpanzees." Science. 2006 Mar 3;311(5765):1301-3.

Evolution and Extreme Polymorphism

Many disease-related genes have been mapped to the major histocompatibility complex (MHC), a polymorphic 4 Mbp region on human chromosome 6. The extreme polymorphism of this region stymies some conventional whole genome analysis techniques. Here, Traherne et al. solved this by cloning and sequencing large chromosome fragments using bacterial artificial chromosomes (BACs). They compared in detail two new haplotypes (QBL: HLA-A26-B18-Cw5-DR3-DQ2; and COX: HLA-A1-B8-Cw7-DR3-DQ2), which share the centromeric DR-DQ alleles, to the 'reference' MHC haplotype. This region encompasses more than 259 loci and 20,000 single nucleotide polymorphisms (SNPs). They identified the site where these 2 new haplotypes recombined, probably within the last 3,400 generations. They provide evidence that recombination shuffles haplotype blocks containing certain allelic combinations favored by immunological functions. Moreover, these haplotype blocks appear to spread across haplotypes and populations through recombination suppression, selection, and population expansion.
Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, et al. "Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history." PLoS Genetics 2(1):e9

RNA interference protects worms from viruses

Caenorhabditis elegans (C. elegans) is a small worm (~1000 cells) that is widely used to study development. There are no known natural viral pathogens of C. elegans. Wilkins and colleagues suspected a protective role for RNA interference (RNAi), an anti-viral system that was discovered in plants and subsequently implicated in insect immunity. RNAi acts through small interfering RNA (siRNA) that matches the target sequence (animation from Nature). They tried infecting primary cell cultures with vesicular stomatitis virus (VSV), which is a negative sense RNA virus with a broad host range. To make the measurement easier, they used a virus marked with green fluorescent protein (VSV-GFP). The system worked: replication competent viruses infected wild-type worm cells. Infection could be monitored by fluorescence or by measuring the virus transcripts. Cells from two different mutants defective in RNAi -- one (eri-1) that reduces siRNA cleavage and a second (rrf-3) that permits siRNA amplification -- supported higher levels of virus infection and amplification. Moreover, they could detect a 20-30 nucleotide endogenous siRNA that matches the VSV nucleoprotein. They conclude that RNAi blocks virus replication and reduces virus infection and expression.
Wilkins C, Dishongh R, Moore SC, Whitt MA, Chow M, Machaca K. "RNA interference is an antiviral defence mechanism in Caenorhabditis elegans." Nature. 2005 Aug 18; 436(7053):1044-7.

Toxoplasmosis is mood altering?

Recent reports in the popular press suggest that infection by Toxoplasma gondii (toxoplasmosis) may alter human behavior and cause schizophrenia. T. gondii is a common infection of domestic cats. Unfortunately, the full text of this science paper is not available for free. However, we can analyze in depth these findings from a comprehensive study of young children, comparing those who were infected congenitally with those who were not. This study was aimed at addressing understandable “parental concerns and anxiety”. In a prospective study, pregnant women and neonates were screened for toxoplasmosis between 1996 and 2000 in ten European centers. At 3 years of age, parents of children with and without congenital toxoplasmosis were surveyed about their child's development and behavior using a postal questionnaire. Parents of 178/223 (80%) infected, and 527/821 (64%) uninfected children responded. The researchers “found no evidence that impaired development or behavior were more common in infected children”. Well, that's certainly reassuring though it's not nearly as “newsworthy”.
Freeman K, Salt A, Prusa A, Malm G, Ferret N, Buffolano W, Schmidt D, Tan HK, Gilbert RE; European Multicentre Study on Congenital Toxoplasmosis. "Association between congenital toxoplasmosis and parent-reported developmental outcomes, concerns, and impairments, in 3 year old children." BMC Pediatr. 2005 Jul 13;5:23.

T cell changes in chronic infection

What happens to lymphocytes that are specific for persistent infections? Most adult humans are chronically infected with several viruses, including Epstein-Barr virus and cytomegalovirus. Chronic HIV and Hepatitis C virus infections are large public health concerns. Here, investigators analyzed T cells in mice infected with one of two strains of a virus: one strain is quickly cleared while a nearly identical strain becomes a chronic infection. They found that a protein, programmed cell death 1 or PD-1, was increased on the surface of CD8+ “killer” T lymphocytes in chronically infected mice. PD-1 is previously identified as an inhibitory molecule on T cells that binds PD-L1, which is expressed on most cells in the body. (PD-1 also binds PD-L2, expressed on dendritic cells and macrophages.) PD-1 expression normally increases transiently after infection but remains elevated on specific T cells in chronically infected mice. Could persistent infections be cleared through PD-1 blockade? The final result presented here sounds a cautionary note: these viruses kill mice genetically deficient in PD-1 (knockouts), apparently due to an excessive immune response.
Barber DL, Wherry EJ, Masopust D, Zhu B, Allison JP, Sharpe AH, Freeman GJ, Ahmed R.. "Restoring function in exhausted CD8 T cells during chronic viral infection." Nature. 2006 Feb 9;439:682-7.

Sunday, January 21, 2007

Many more than 23,000 Genes?

A gene, the unit of heredity that encodes a trait, is hard to define in molecular terms. The best known examples of genes encode proteins that contribute to observable phenotypes, such as purple flowers or blue eyes. The genome sequencers have identified about 23,000 genes in the human genome, mostly protein coding. The FANTOM (Functional Annotation of Mouse) Consortium took a broader view, using a number of technologies to identify full length RNA transcripts with unique starts (5’) and stops (3’). They identified 181,047 independent transcripts! Previously unidentified proteins are encoded by 5,154 transcripts. Over one-half of the genome is transcribed on one or both strands without gaps, forming 18,461 transcription “forests” separated by deserts devoid of transcripts. The lengths of these transcripts show 2 major peaks around 2 kb and 20 kb and a minor peak at ~100 Mb. Unbiased analysis of transcription using “tiling arrays”, which probe continuous lengths of the genome exhaustively, have also suggested that there are many more genes than earlier estimates. The authors point out that these results raise concerns about the interpretation of microarray expression studies and gene manipulated mice (knock-ins and -outs). They conclude by estimating the enormous scale of the reevaluated genome code.
Carninci et all FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). "The transcriptional landscape of the mammalian genome." Science 2005 309:1559-63.

Neutralizing antibodies drive HIV mutation

Gnome writes "HIV mutants accumulate rapidly due to a short generation time, a sloppy replication mechanism, and the large number of viruses within the host. The viral envelope (env) gene mutates especially quickly (1-2% per year) because of the selective pressure of neutralizing antibodies. The resulting heterogeneity poses a challenge to vaccine development. Frost and colleagues sought to understand the patterns of rapid mutation and escape by analyzing 13 people recently infected with HIV. They compared the initial env sequence with sequences obtained at yearly intervals and measured neutralizing antibodies in the blood. They found that HIV escape from neutralizing antibodies strongly correlated with changes in the amino acid sequence of env. Escape did not correlate with changes in N-linked glycosylation sites or insertions or deletions (indels). Their data support a simple model for escape from neutralizing antibodies proposed by Haraguchi and Sasaki, which incorporates cross-reactivity. The inability of the immune system to 'catch up' with the continually escaping virus is an example of the 'Red Queen' (running to stay in place) evolutionary dynamics.
Frost SD, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, Paxinos E, Chappey C, Galovich J, Beauchaine J, Petropoulos CJ, Little SJ, Richman DD. "Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection." Proc Natl Acad Sci USA. 2005 Dec 20;102(51):18514-9.

Autoantibodies may influence memory

Most lupus patients have serum autoantibodies against double-stranded DNA (dsDNA) and some suffer from cognitive impairment and mood disturbance, symptoms of neuropsychiatric lupus (NPSLE). These researchers previously used phage display to find a pentapeptide that crossreacts with a pathogenic, monoclonal, dsDNA-specific autoantibody. They further found that the mouse and human receptors for the neurotransmitters NMDA (N-methyl-D-aspartate) and glutamate, NR2a and NR2b, contain this pentapeptide. They also showed that mice immunized with the pentapeptide developed antibodies that bound NR2 but did not cause neural injury unless the blood-brain-barrier (BBB) was disturbed. Similar antibodies can be detected in the cerebrospinal fluid of SLE patients but not healthy control subjects. Administering LPS to these immunized mice opened the BBB in the hippocampus, leading to antibody binding and cell loss in this area of the brain. The treated mice performed poorly in maze tests, suggesting memory impairment. Now, they show that administering epinephrine opened the BBB in the amygdala, exposing cells there to the toxic autoantibodies. The treated mice were less fearful. These may be seminal papers in understanding cognitive defects."
Huerta PT, Kowal C, Degiorgio LA, Volpe BT, Diamond B. "Immunity and behavior: Antibodies alter emotion." Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):678-83.

TWEAK Regulates Cellular Immunity

TNF-related weak inducer of apoptosis (TWEAK) is a member of the TNF superfamily, alias TNFSF12. The mouse gene was cloned by chance and the human gene was identified among EST clones. TWEAK is secreted by several cell types and binds, naturally, TWEAK-R, which is also known as FN14 because it is a 14 kDa protein that is inducible by fibroblast growth factor. FN14 is also distantly related to the TNFR family. Despite all this talk of families, TWEAK was an orphan when it came to functional relationships. Now, Maecker and colleagues report that TWEAK-knockout (TWEAK-KO) mice have altered immune systems. Specifically, the deficient mice have more natural killer cells and T helper type 1 (Th1) cells and their stimulated lymphocytes secrete more interferon-gamma and interleukin-12, suggesting that TWEAK normally acts to reduce these responses. TWEAK-KO mice succumb to shock caused by endotoxin, the bacterial cell wall component lipopolysaccharide (LPS), at lower doses than normal mice. On the other hand, TWEAK-KO mice resisted transplanted tumor cells better than normal mice. The authors also observed that TWEAK stimulates the rapid and prolonged association of NF-kappaB p65, a key transcription factor and intracellular signal, with the histone deacetylase HDAC-1, whereas TNF stimulates p65 association with the transciption coactivator p300. This intriguing observation is the likely molecular basis for the difference between TWEAK and TNF.
Maecker et al "TWEAK attenuates the transition from innate to adaptive immunity." Cell. 2005 123:931-44

What makes stem cells special?

Stem cells are self-renewing and pluripotent, meaning that they can develop into any of the over 200 unique cell types in the body. Three transcription factors, Oct4, Sox2, and Nanog were previously identified as crucial for stem cell development. Oct4 binds Sox2 and together they regulate Nanog. Boyer and colleagues used chromatin immuno-precipitation (ChIP) to determine which genes these proteins bind (and presumably regulate). They found that they bind the promoters of many of the same genes and that many of these genes encode transcription factors that are important in development. Several genes encoding micro RNAs (miRNA) were also bound, which is particularly interesting since stem cells lacking miRNA processing cannot differentiate. Oct4 and Sox2 can activate or repress gene transcription. After correlating with expression profiles, the 3 factors bound 1303 active genes and 957 inactive genes. If the master switches and pathways are identified, it may be possible to convert any cell into a stem cell by activating the correct, hopefully few, genes.
Boyer et al Core transcriptional regulatory circuitry in human embryonic stem cells." Cell. 2005 Sep 23;122(6):947-56

ATP Generator Structure – Function

Almost incredibly, a sedentary adult makes and uses 40 kg of ATP per day! ATP is made by the F0-F1 ATPase, a molecular motor with a rotating shaft and fixed "stator". One end of the shaft, F0, is buried in the mitochondrial inner membrane where the proton gradient causes it to rotate. A single gamma subunit connects the F0 to three alpha and beta subunits, together F1, which are responsible for synthesizing ATP from ADP and Pi (H2PO4-). As a catalytic motor and not just a catalyst, the F0-F1 ATPase is able to increase the rate of reaction away from the equilibrium (which strongly favors the reverse reaction, hydrolysis, because the concentrations of reactants and product in mitochondria are similar). The gamma subunit rotates too slowly, in the microsecond-to-millisecond range, for standard molecular dynamics simulation. To solve this, the authors applied "biasing forces" as the motor moved and assumed these forces would not change the mechanism. Positively charged amino acids on the gamma subunit attract negative amino acids on beta subunit, producing smooth and efficient ionic coupling. Rotation of the gamma subunit induces the opening of the beta subunits. The beta subunit closes spontaneously. Synthesis is not the reverse of hydrolysis, explaining why high concentrations of free ATP does not inhibit synthesis. Gao and colleagues propose a detailed model of how the motor harnesses the proton gradient to act against the equilibrium. Their quantitative model is based on the conceptual “binding change mechanism” model proposed by Boyer, where ATP synthesis proceeds by each beta subunit changing from “open”, weak nucleotide binding, to “tight”, high affinity ATP binding, to “loose”, with the release of ATP. The authors used this model to make accurate predictions about synthesis and hydrolysis kinetics and they invite others to test their detailed model.
Yi Qin Gao, Wei Yang and Martin Karplus, "A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1-ATPase" Cell Oct 21, 2005; 123(2):195-205

Biology of the 1918 Flu

Gnome writes "The 1918 flu caused an unusually high death rate among healthy young adults (ages 15-34). Genomic RNA was recovered several years ago from autopsy material and victims buried in the Alaskan permafrost. The 1918 flu had unique hemagglutinin and neuraminidase proteins on its surface (H1N1). However, they did not cause its pathogenicity because later viruses with this combination are not particularly deadly (e.g., Texas/91). Now, Tumpey and colleagues have reconstructed the entire 1918 virus and tested it. Unlike current flu viruses, the 1918 virus does not require an exogenous protease to infect cells in culture. Moreover, all 13 mice infected through the nose by the 1918 virus developed severe lung inflammation and died within 7 days, while none infected with the Texas/91 strain died. Surprisingly, recombinants between 1918 flu and Texas/91 suggest that the viral polymerase acts in concert with the other 7 proteins to increase virulence. On the bright side, existing antiviral drugs and a novel siRNA therapy were previously shown to protect mice against certain 1918 recombinant viruses.
Tumpey et al., "Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus" Science. 2005 Oct 7;310(5745):77-80.

1 protein = 2 opposing weight-control hormones

Obesity, a body mass index over 30 kg/m^2, is increasing in America and many western societies. Obesity is correlated with poor health, including diabetes and cardiovascular disease. Body weight is regulated by peptide hormones secreted from the gut and brain. Zhang and colleagues noted that ghrelin, a 28 amino acid, gut-derived peptide that stimulates appetite, is post-translationally trimmed from a larger, 117 amino acid protein. They identified in this larger protein not only a signal sequence but also a whole new, 23 amino acid peptide downstream of a potential convertase cleavage site. They named this second protein obestatin, for obesity-suppressing. They found obestatin in rat gut tissue. Whereas fasting rats had more ghrelin in their blood and fed rats had less, obestatin was stable between the groups. Injecting mice with synthetic obestatin blocked ghrelin-induced weight gains. Finally, they identified the hitherto orphan GPR39 as the G protein-coupled receptor. One gene encodes one protein that yields two antagonist peptides! This story promises to be an interesting and important example of post-translationally regulated protein expression.
Zhang et al., "Obestatin, a Peptide Encoded by the Ghrelin Gene, Opposes Ghrelin's Effects on Food Intake" Science 11 November 2005.

Interleukin-1 in Systemic Juvenile arthritis

Juvenile idiopathic arthritis (JIA), joint inflammation with unknown cause in children, affects an estimated 250,000 children in the US alone. About 10% of these cases begin with fevers and/or rash that precede joint symptoms by months or years, a subset called systemic onset JIA (SoJIA). These are hard to diagnose and most do not respond to TNF blockade, a therapy that helps many adult rheumatoid arthritis patients. Here, Pascual and colleagues show that the disease is instead driven by the other major proinflammatory cytokine, interleukin 1 (IL-1). They found that activate peripheral blood leukocytes from SoJIA patients make more IL-1 than do those from healthy people. Sera from SoJIA patients increased the expression of immune-related genes by leukocytes from healthy people. Most strikingly, an IL-1 receptor antagonist (IL-1Ra, Anakinra) reduced fever, arthritis, and other symptoms or markers of disease in all 9 SoJIA patients treated.
Pascual et al., J Exp. Med. 201(9) 1479-1486.

Publishing your mistakes?

Most scientists suspect that erroneous results occasionally make their way into publication. Now, Ioannidis confirms these suspicions, and worse, with statistical simulations. In a remarkably readable paper, he shows that "most published research findings are false"! Not surprisingly, bias increases the chances that the finding is false and large effects are more likely to be true than are small effects. Less expected is the conclusion that "a research finding is less likely to be true... when more teams are involved in a scientific field". In other words, "hot" fields have more mistakes published. The analysis is straightforward and may suggest reasonable ways to reduce the errors in publications.
Ioannidis, JPA. August 2005 PLoS Medicine 2(8):696-701

Insulin-Specific T Cells in Long-Term Diabetics

Type 1 diabetes is unusual among autoimmune diseases because diagnosis is greatly aided by laboratory tests. Levels of blood sugar and glycosylated hemoglobin are excellent measures of disease progression. The symptoms of disease are treated with insulin, which would normally be produced by the pancreatic beta cells that are destroyed in the autoimmune process. In common with other autoimmune diseases, the cause of type 1 diabetes is not known, though insulin itself has been a leading candidate autoantigen. Here, Kent and colleagues show they could find insulin-specific T lymphocytes in the lymph nodes draining the pancreas in 2 long-term diabetics, but not in 3 non-diabetic individuals or 1 recently-diagnosed diabetic. They argue against the T cells having been stimulated by therapeutic insulin because none were found in the spleen of one diabetic. They convincingly demonstrate that the T cell response is specific for the insulin peptide (residues 1-15 of the A chain) bound by host histocompatibility molecules (HLA-DR). The insulin-specific T cells were helper (CD4+) cells and, curiously, secreted a suspected tolerogenic helper type 2 cytokine (interleukin-13) and not a proinflamatory helper type 1 cytokine (interferon-gamma) in vitro. These observations strengthen the argument that long-term diabetes correlates with increased immune reactivity against
Kent et al., Nature, May 12, 2005. 435(7039):224-8.

Alternate splicing may generate a fly immune receptor

Fruit flies have a large protein called Dscam (Down syndrome cell adhesion molecule) with 24 exons. Four of these exons are alternatively spliced from 12, 48, 33, and 2 variants, potentially generating over 18,000 slightly different Dscam proteins. The protein is expressed by brain cells and cells involved with protection against infectious agents: called fat bodies and hemocytes. Dscam is found on the surface of these cells and the extracellular portion of the protein, clearved from the cytoplasmic portion, is found in the insect equivalent of blood, called the hemolymph. The function of Dscam was not known, but Schmucker and colleagues suspected a role in immune protection. They found that many of the gene variants are expressed in the fat bodies and hemocytes, though even more variants are expressed in the brain. Most strikingly, reducing expression of Dscam with RNA inhibition or using null mutants reduces the phagocytosis of bacteria by hemocytes. Two Dscam variants, but not a third, bind one strain of bacteria, supporting the notion that these variants might protect against different pathogens. Moreover, the alternative splicing of Dscam is conserved in other insects. Although the human homologue is not alternatively spliced, might there be other Dscam-like receptors, analogous to Toll-like-receptors (TLRs) in the mammalian genome?"
Watson et al., Science. 2005 Sep 16 309(5742):1874

Immune Recognition of Vascular Endothelial Cells

Immunologists think about central or peripheral tolerance, depending on whether the potential antigen is found within the lymphoid tissues. The central immune system includes the bloodstream, lymph, and primary lymphoid organs such as the thymus and lymph nodes. From an immunologist's perspective, the "periphery" is all the body's non-lymphoid organs and tissues. This distinction overlooks the interface between these tissues - the endothelium - the single cell layer that lines the blood and lymph vessels. Given the pervasiveness of blood vessels, it is not surprising that endothelial cells (EC) have been implicated in many immune processes, most notably atherosclerosis and transplant rejection. These investigators directly tested the ability of the immune system to recognize a new protein expressed by EC using two strains of transgenic mice that express beta-galactosidase only in their EC because their genomes have the beta-gal gene, lacZ , under control of promoters specific for endothelial cells. One transgenic line, VWF-lacZ, expresses beta-gal only in heart and brain endothelium. A second line, TIE2-lacZ, expresses beta-gal in practically all endothelial cells. Upon immunization with beta-gal protein, these mice responded normally, generating strong antibodies and T cell responses. They also responded normally after immunization with a DNA vector driving expression of beta-gal. After immunization, vascular EC in the transgenic mice continued to express beta-gal and the vessels showed no signs of inflammation when analyzed microscopically. This suggested the EC were simply ignored. However, TIE2-lacZ skin (which contains beta-gal+ EC) stimulated
beta-gal specific antibodies when it was transplanted onto non-transgenic littermates. Moreover, no antibodies were stimulated upon transplantation onto VWF-lacZ mice, suggesting that the immune system in these mice were tolerant, not ignorant, of the beta-gal expressed by EC. They conclude that the immune system subtly tolerates and does not ignore EC proteins.
Annette L Rothermel, Yinong Wang, Jeffrey Schechner, Barry Mook-Kanamori, William C Aird, Jordan S Pober, George Tellides and David R Johnson. Endothelial cells present antigens in vivo BMC Immunology March 2004, 5:5

Mitochondrial tRNA mutant causes metabolic defects

Mitochondria are cellular organelles that use oxidative phosphorylation to convert the energy of reduced dietary carbon into ATP, which provides energy for practically all processes. Human mitochondria possess a mostly vestigial 16 kb genome, which encodes ribosomal and 22 transfer RNAs along with 13 proteins. There are more mitochondria in cells with high energy needs such as heart muscle cells, where mitochondria and myofibrils make up 85% of cell volume. Cardiovascular disease is associated with high blood pressure and high serum cholesterol. These investigators analyzed the genetics of a syndrome that includes hypertension (blood pressure >140/90 mm Hg), hypercholesterolemia (serum cholesterol >200 mg/dl), and hypomagnesemia (serum magnesium below 1.8 mg/dl) in 4 generations of a large family. A genome-wide linkage
analysis yielded no candidates. They found that the 32 family members of both sexes with hypomagnesemia all descended from one female, suggesting a mitochondrial defect. Upon sequencing and single-strand conformational polymorphism analysis, they found 14 variants, 13 of which were previously described, and one new variant at nucleotide 4291 of the mitochondrial genome, within an isoleucine tRNA. This tRNA mutation is found only on this maternal lineage, not among the thousands of previously sequenced mitochondrial genomes.
Wilson et al. Science 306: 1190, November 2004

Common infection might set stage for lupus

Infection is known to trigger certain autoimmune diseases, e.g., rheumatic fever and ankylosing spondylitis. The initial immune response against the pathogen is thought to also recognize "self" proteins called autoantigens and may later spread to recognize additional autoantigens. These investigators wished to test their suspicion that Epstein Barr virus (EBV) triggers systemic lupus erythematosus (SLE). They previously showed that the first SLE autoantigen is the RNA-binding protein Ro. Here, they analyzed blood samples from a repository drawn from more than 5 million people. They found 29 people who later developed lupus and who had donated a blood sample before they developed Ro-specific autoantibodies. Nine of these early sera contained autoantibodies that recognized only a single small portion of Ro. All of these early, Ro-specific antibodies cross-reacted with a completely different small fragment of the EBV nuclear protein EBNA-1, suggesting that the crossreaction could be an early event in the disease. To test this, they immunized rabbits with peptides matching Ro or EBNA-1. Strikingly, both groups of rabbits developed lupus-like symptoms, including reduced numbers of white blood cells (leukopenia), clotting factors (thrombocytopenia) and kidney function. This paper connects a common infection with lupus. It remains to be determined why lupus develops in relatively few of the many EBV infected adults.
McClain et al. Nat.Med. 11, 85 - 89 (2004) "Early events in lupus humoral autoimmunity suggest initiation through molecular mimicry"