Innate intracellular resistance to HIV-1

drj writes "Human immunodeficiency virus type 1 (HIV-1), the cause of acquired immunodeficiency syndrome (AIDS) in humans, efficiently enters Old World monkey cells but it is not reverse transcribed. This block probably protects monkeys from productive HIV-1 infection and AIDS. Stremlau and colleagues searched for an Old World monkey (rhesus) gene blocking HIV-1 infection by transferring an expression library into a susceptible human cell line (HeLa) and testing for HIV-1 resistance. They found TRIM5a, a 497 amino acid protein located in cytoplasmic bodies and named only for its structural "tripartite motif". Inhibition might result from the ubiquitin ligase activities of TRIM5a, which marks a protein for degradation but here might simply interfere with capsid disassembly. Notably, the rhesus TRIM5a does not block simian immunodeficiency virus (SIV) infection. Human TRIM5a differs in several key residues that are presumably involved in recognizing HIV-1 capsid.
Stremlau et al. Nature 427:858. February 26, 2004.
'The cytoplasmic body component TRIM5a restricts HIV-1 infection in Old World monkeys' Matthew Stremlau, Christopher M. Owens, Michel J. Perron, Michael Kiessling, Patrick Autissier & Joseph Sodroski"

mRNA quality control

drj writes "Messenger RNA (mRNA) with a premature termination codon (PTC) undergoes nonsense mediated decay (NMD). NMD is thought to protect against amino-terminal protein fragments that could be disruptive, for example, by acting as dominant negative mutants. Muscular dystrophy, Marfan syndrome, and other human diseases are caused by premature termination. Hillman and colleagues earlier determined that over one-third of alternatively-spliced human mRNAs have a PTC. Since NMD mechanisms were only recently discovered, they suspected many mRNAs in the databases might contain previously unrecognized PTCs and would have undergone NMD in vivo. Here, they aligned protein sequences from SWISS-PROT with gene sequences from Genbank to identify ~8% of entries that contain a PTC. Important biological effects could be attributed to NMD. For example, an intronic polymorphism linked to type II diabetes reduces 4 of 8 calpain-10 mRNA isoforms. These same 4 isoforms contain a PTC, suggesting NMD underlies reduced expression, causing disease. Similar analysis of CDC-like kinases and a receptor containing a death domain suggests previously unsuspected roles for NMD.
Hillman et al. Genome Biology 5:R8. January 2, 2004
Background: In mammals, "premature" is a stop codon >50 nucleotides upstream of the last intron. mRNAs with PTC are flagged for degradation by the persistent splice junction protein complexes, which are normally cleared by the ribosome.
An unappreciated role for RNA surveillance R Tyler Hillman, Richard E Green and Steven E Brenner. Genome Biology 2004, 5:R8. online at genomebiology"

Lymphocyte migration triggered by sphingosine-1-phosphate

drj writes "Why did the lymphocyte leave the lymphoid organ? A chemical gradient was long suspected and now some details have been identified. Matloubian et al. found very few lymphocytes in the blood of mice with lymphocytes that are deficient in one particular receptor for sphingosine-1-phosphate (S1P), called S1P1. They show that developing S1P1-deficient thymocytes remain in the thymus and B cells remain in peripheral lymphoid organs, though there is only a mild alteration in the the subpopulations within these organs. Normal thymocytes but not deficient thymocytes move in response to a S1P gradient. Antigen stimulated T cells transiently reduce S1P1 expression, which is mostly restored within days, suggesting a molecular basis for transient retention in lymphoid organs. An immunosuppressant drug currently in clinical trials, FTY720, binds S1P1, leading to receptor downregulation and reduced migration. The data strongly support a compelling model, albeit one with many details yet to be determined."
M. Matloubian et al. Nature 427:355-360. January 22, 2004

Enzymology - The Next Generation

drj writes "This thought-provoking overview of current enzymology in The Scientist [free registration required] briefly introduces advances in structural studies, mechanistic theories, ribozymes, and potential commercial applications. My favorite was conceiving of the cell as a network of enzymes operating at rates determined by their (intrinsic) Km and the concentration of substrates and cofactors. Not a new idea, perhaps, but well described and evocative. The network is dramatized by these mapping of metabolic pathways and cellular and molecular processes (through ExPASy, courtesy of Roche). (originally posted on MedDot.org)

"Enzymology's New Frontiers" M. Greener, The Scientist. 2004;Vol. 18 1:16-20 January 19, 2004"

Type 1 Diabetes: a cure? (in mice)

drj writes: "Type 1 diabetes is the culmination of an immune-mediated destruction of the insulin-secreting beta cells, resulting in a loss of blood sugar regulation (normoglycemia). NOD (non-obese diabetic) mice often suffer a similar disease, perhaps due to a proteasome defect that reduces nuclear factor activation and alters lymphocyte development. Kodama and colleagues here demonstrate the potential of one strategy to cure diabetes - by stopping the immune attack and allowing regeneration from residual beta cells or progenitor cells. While maintaining normoglycemia with a beta cell transplant, they “reeducated” the immune system of diabetic NOD mice by treatment with an immune activator (complete Freund's adjuvant) and repeated infusions of normal (non-NOD) spleen cells. After 6 weeks of twice weekly infusions followed by removal of the beta cell transplant, islet structures and functional beta cells could be found within the NOD pancreas and the mice maintained normoglycemia for over 9 weeks. The authors believe these findings suggest a promising therapy for human diabetes, avoiding the complications of islet transplantation or stem cell culture.
Kodama et al. Science 302:1223-1227 (2003)
"Islet Regeneration During the Reversal of Autoimmune Diabetes in NOD Mice" Shohta Kodama, Willem Kühtreiber, Satoshi Fujimura, Elizabeth A. Dale, Denise L. Faustman (posted originally on MedDot.org Jan 17, 2004)

Immunity: Statistically different functional CDR3s in mouse

mhc writes "This article relates interesting differences between the VH CDR3 repertoires of mouse and human. A full analysis was performed of the complete Kabat and IMGT antibody databases to arrive at these conclusions. Among them: that compared to the human sequence, the mouse CDR3 is shorter, more hydrophilic, enriched in tyrosine, and less likely to be structurally constrained by proline or intrachain cys-cys bonding. The functional inference is that the mouse repertoire recognizes the antigen universe in a different manner than human, and that the human response can achieve a much greater divergence than does the mouse. The authors suggest that this analysis can serve as a benchmark by which antigen-specific responses can be compared (e.g. is an anti-DNA response more hydrophilic than the universe of anti-self autoantibody responses, or just more hydrophilic than the "average" response as determined from this analysis?)
Zemlin M, Klinger M, Link J, Zemlin C, Bauer K, Engler JA, Schroeder HW Jr, Kirkham PM. "Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures." J Mol Biol. 2003 Dec 5;334(4):733-49
(ed.) VH CDR3 = variable heavy (chain immunoglobulin) complement determining region 3. (Originally posted on MedDot.org January 6, 2005)

Autoimmune Diabetes: Gene expression changes little in diabetic mouse

drj writes "More than 20 genes are known to influence the development of type 1 (autoimmune) diabetes in mice and at least this number are thought to contribute to the disease in humans. Using microarrays representing over 39,000 transcripts, Eaves et al. compared mice from closely related lines that do, or do not, develop diabetes. They identified over 400 differentially expressed genes in spleen and thymus tissues and 8 candidates for one particular susceptibility locus (Idd9.1). However, the expectation that the susceptibility (Idd) loci cause large scale differences in gene expression proved to be wrong. Instead, few changes were observed, suggesting that general patterns of gene expression resist change even during the development of a serious autoimmune disease.
To avoid excluding “suggestive” changes, the investigators set the level of significant change at 1 per 20,000 transcripts instead of 1 per 20 arrays (~800,000 transcripts). They identified potential cis-acting changes by examining chromosome locations. For example, the Idd3 region derived from B6 mice protects about 2/3 of NOD mice from diabetes (20-25% vs. 75-80%). However, only 8 transcripts change expression in Idd3B6 mice, all only modestly (19-66%), and none map within the 0.35 cM Idd3 region on chromosome 3."
Eaves IA, Wicker LS, Ghandour G, Lyons PA, Peterson LB, Todd JA, Glynne RJ., Combining Mouse Congenic Strains and Microarray Gene Expression Analyses to Study a Complex Trait: The NOD Model of Type 1 Diabetes. Genome Res. 2002;12:232-242"

Transplantation: Manipulated dendritic cells are tolerogenic

drj writes, "Immune suppressive drugs enable clinical transplantation, the only therapy for end-stage organ failure, at the cost of reducing patient protection from infections. Ideally, a patient could be made specifically tolerant of a graft without blocking other immune responses. Using a mouse heart transplantation model, Ichim and colleagues suggest several procedures for doing just that, by manipulating certain costimulatory or antigen presenting skills of allogeneic (donor) dendritic cells (DC).

The authors first induced tolerance through means they have established earlier – treatment of recipient mice with blocking antibodies specific for CD45RB and with LF15-0195 (LF), an analogue of the antirejection drug 15-deoxyspergualin. DC recovered from the spleens of mice with long term surviving grafts stimulate allogeneic (donor) T cells to make interleukin (IL)-4 and IL-10 but not interferon-gamma. Next, they identified 4 treatments that produce similar results: (1) Gene transfer and expression of human Fas ligand (FasL) in DC generate “killer DC” that cause apoptosis of allogeneic T cells. (2) Treatment of DC with LF15-0195 blocked activation of the transcription factor NF-kappaB. (3) DC treated with (MHC) class (II) invariant chain peptide (CLIP). (4) Finally, DC treated with short, interfering RNA (siRNA) corresponding to IL-12 blocked its expression and reduced interferon-gamma while increasing IL-4 expression. Each treatment reduced the ability of DC to specifically stimulate allogeneic T cells, suggesting they could be used to establish transplant tolerance. Although the altered DC phenotype resembles those of DC in demonstrably tolerant mice, it will be necessary to test these treatment are able to induce transplant tolerance.
Ichim et al., Prevention of allograft rejection by in vitro generated tolerogenic dendritic cells. Transpl Immunol. 2003;11:295-306
(Originally posted on MedDot.org Dec. 10, 2003)

Immunity: New T cell Regulatory Proteins

Anonymous writes "Chu and colleagues found 33 proteins that decreased T cell activation induced by triggering the T cell antigen receptor (TCR). They screened for increased CD69, a marker of T activation, induced by antibodies to the TCR in Jurkat cells transduced with a retroviral expression library. Although not exhaustive, the screen identified many truncation mutants of expected (Lck, ZAP70, SHP-1, etc.) and surprising (an integrin, Grb7, etc.) proteins. One new gene was identified, a suspected ubiquitin ligase they named TRAC-1 that previously was only an EST. The proteins’ functions were confirmed in primary T cells. As the authors note, the post genome advances will come from assigning functions to proteins. Their approach may help identify proteins in complex signaling systems. PubMed
J. Biol." (Originally posted on MedDot.org October 2, 2003)
Systematic identification of regulatory proteins critical for T-cell activation
Peter Chu, Jorge Pardo, Haoran Zhao, Connie C Li, Erlina Pali, Mary M Shen, Kunbin Qu, Simon X Yu, Betty CB Huang, Peiwen Yu, Esteban S Masuda1, Susan M Molineaux, Frank Kolbinger, Gregorio Aversa, Jan de Vries, Donald G Payan and X Charlene Liao
Journal of Biology 2003 2:21

Cancer: Reducing tolerance of "self" tumors

CarbonBasedUnit writes "Many human tumor antigens are normal (not mutated) “self” proteins, so Rosenberg’s group treated melanoma (skin cancer) patients by immunizing with a melanocyte peptide while blocking CTLA-4, a protein that is thought to mediate immune self-tolerance. One patient was essentially cured and two improved while the other 11 patients showed no improvement. Nine of the 14 patients developed a remarkable variety of autoimmune complications, severe in 6, stopping the trial (all recovered). This paper also clearly establishes CTLA-4, an inducible protein expressed on activated T lymphocytes, as crucial in maintaining self tolerance in humans.
PubMed Entry" (originally posted on MedDot.org August 29, 2003)

Cancer regression and autoimmunity induced by cytotoxic T lymphocyte-associated antigen 4 blockade in patients with metastatic melanoma.
Phan GQ, Yang JC, Sherry RM, Hwu P, Topalian SL, Schwartzentruber DJ, Restifo NP, Haworth LR, Seipp CA, Freezer LJ, Morton KE, Mavroukakis SA, Duray PH, Steinberg SM, Allison JP, Davis TA, Rosenberg SA. PNAS 2003 Jul 8;100(14):8372-7

Notes:
Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), also designated CD152
Regulatory T lymphocytes express CD4 and CD25 on their surface.