Glynn Dennis

DAVID: Database for Annotation, Visualization, and Integrated Discovery

The distributed nature of biological knowledge poses a major challenge to the interpretation of genome-scale datasets, including those derived from microarray and proteomic studies. This report describes DAVID, a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries. Lists of gene or protein identifiers are rapidly annotated and summarized according to shared categorical data for Gene Ontology, protein domain, and biochemical pathway membership. DAVID assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.

Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals

The presence of HIV-1 in latently infected, resting CD4+ T cells has been clearly demonstrated in infected individuals; however, the extent of viral expression and the underlying mechanisms of the persistence of HIV-1 in this viral reservoir have not been fully delineated. Here, we show that resting CD4+ T cells from the majority of viremic patients are capable of producing cell-free HIV-1 spontaneously ex vivo. The levels of HIV-1 released by resting CD4+ T cells were not significantly reduced in the presence of inhibitors of cellular proliferation and viral replication. However, resting CD4+ T cells from the majority of aviremic patients failed to produce virions, despite levels of HIV-1 proviral DNA and cell-associated HIV-1 RNA comparable to viremic patients. The DNA microarray analysis demonstrated that a number of genes involving transcription regulation, RNA processing and modification, and protein trafficking and vesicle transport were significantly upregulated in resting CD4+ T cells of viremic patients compared to those of aviremic patients. These results suggest that active viral replication has a significant impact on the physiologic state of resting CD4+ T cells in infected viremic patients and, in turn, allows release of HIV-1 without exogenous activation stimuli. In addition, given that no quantifiable virions were produced by the latent viral reservoir in the majority of aviremic patients despite the presence of cell-associated HIV-1 RNA, evidence for transcription of HIV-1 RNA in resting CD4+ T cells of aviremic patients should not necessarily be taken as direct evidence for ongoing viral replication during effective therapy.

HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication

Certain HIV-encoded proteins modify host-cell gene expression in a manner that facilitates viral replication. These activities may contribute to low-level viral replication in nonproliferating cells. Through the use of oligonucleotide microarrays and high-throughput Western blotting we demonstrate that one of these proteins, gp120, induces the expression of cytokines, chemokines, kinases, and transcription factors associated with antigen-specific T cell activation in the absence of cellular proliferation. Examination of transcriptional changes induced by gp120 in freshly isolated peripheral blood mononuclear cells and monocyte-derived-macrophages reveals a broad and complex transcriptional program conducive to productive infection with HIV. Observations include the induction of nuclear factor of activated T cells, components of the RNA polymerase II complex including TFII D, proteins localized to the plasma membrane, including several syntaxins, and members of the Rho protein family, including Cdc 42. These observations provide evidence that envelope-mediated signaling contributes to the productive infection of HIV in suboptimally activated T cells.

Fc receptor homologs: newest members of a remarkably diverse Fc receptor gene family.

Summary: Newfound relatives of the classical Fc receptors (FcR) have been provisionally named the Fc receptor homologs (FcRH). The recent identification of eight human and six mouse FcRH genes substantially increases the size and functional potential of the FcR family. The extended family of FcR and FcRH genes spans ∼15 Mb of the human chromosome 1q21–23 region, whereas in mice this family is split between chromosomes 1 and 3. The FcRH genes encode molecules with variable combinations of five subtypes of immunoglobulin (Ig) domains. The presence of a conserved sequence motif in one Ig domain subtype implies Ig Fc binding capability for many FcRH family members that are preferentially expressed by B lineage cells. In addition, most FcRH family members have consensus tyrosine‐based activating and inhibitory motifs in their cytoplasmic domains, while the others lack features typical of transmembrane receptors. The FcRH family members, like the classical FcRs, come in multiple isoforms and allelic variations. The unique individual and polymorphic properties of the FcR/FcRH members indicate a remarkably diverse Fc receptor gene family with immunoregulatory function.

Cutting Edge: L-Selectin (CD62L) Expression Distinguishes Small Resting Memory CD4+ T Cells That Preferentially Respond to Recall Antigen

Naive CD4+ T cells use L-selectin (CD62L) expression to facilitate immune surveillance. However, the reasons for its expression on a subset of memory CD4+ T cells are unknown. We show that memory CD4+ T cells expressing CD62L were smaller, proliferated well in response to tetanus toxoid, had longer telomeres, and expressed genes and proteins consistent with immune surveillance function. Conversely, memory CD4+ T cells lacking CD62L expression were larger, proliferated poorly in response to tetanus toxoid, had shorter telomeres, and expressed genes and proteins consistent with effector function. These findings suggest that CD62L expression facilitates immune surveillance by programming CD4+ T cell blood and lymph node recirculation, irrespective of naive or memory CD4+ T cell phenotype.

Fc receptor homologs (FcRH1-5) extend the Fc receptor family.

Receptors for the Fc portion of immunoglobulins (FcR) are expressed broadly among cells of the immune system (Ravetch and Kinet 1991; Daeron 1997). The differential expression of these Ig isotope-specific receptors enable them to modulate cellular and humoral immunity by linking their antibody ligands with effector cells. These cellular receptors have the ability to sense humoral concentrations of antibody, initiate cellular responses in host defense, and participate in autoimmune disorders (Ravetch and Bolland 2001). The diverse regulatory roles of FcR depend upon their Ig isotype specificity, cellular distribution, and cytoplasmic signaling elements. The different FcR molecules share similarities in their ligand-binding subunits and overall extracellular structures, but they differ in their transmembrane and cytoplasmic regions in two major ways. These receptors either have self-contained inhibitory or activating signaling motifs or instead they use charged residues in their transmembrane region to pair with signal-transducing adaptor chains possessing activating signaling motifs.

Phylogeny of Paired Ig-like Receptors

The mouse paired immunoglobulin-like receptors of activating (PIR-A) and inhibitory (PIR-B) types exemplify an emerging family of hematopoietic cell surface receptors whose roles in natural and acquired immunity have yet to be fully elucidated. As implied by their name, coordinate expression of PIR-A and PIR-B is seen on myeloid, dendritic, and B cell lineages. PIR-A and PIR-B share similar ligand-binding extracellular regions composed of six Ig-like domains, but they differ in their signaling potentials on the basis of differences in their transmembrane and cytoplasmic regions. Although PIR-A and PIR-B themselves are not conserved beyond rodents, PIR homologs have been identified in other mammals and birds, suggesting that the PIR genes belong to an ancient ancestral lineage of related Ig-like receptor families. A phylogenetic analysis, employing primary amino acid sequences and three-dimensional protein structures of the PIR homologs and their relatives, suggests a common ancestry for the PIR and Fc receptor families.