Reconstitution of EBV-directed T cell immunity by adoptive transfer of peptide-stimulated T cells in a patient after allogeneic stem cell transplantation for AITL

Reconstitution of the T cell repertoire after allogeneic stem cell transplantation is a long and often incomplete process. As a result, reactivation of Epstein-Barr virus (EBV) is a frequent complication that may be treated by adoptive transfer of donor-derived EBV-specific T cells. We generated donor-derived EBV-specific T cells by stimulation with peptides representing defined epitopes covering multiple HLA restrictions. T cells were adoptively transferred to a patient who had developed persisting high titers of EBV after allogeneic stem cell transplantation for angioimmunoblastic T-cell lymphoma (AITL). T cell receptor beta (TCRβ) deep sequencing showed that the T cell repertoire of the patient early after transplantation (day 60) was strongly reduced and only very low numbers of EBV-specific T cells were detectable. Manufacturing and in vitro expansion of donor-derived EBV-specific T cells resulted in enrichment of EBV epitope-specific, HLA-restricted T cells. Monitoring of T cell clonotypes at a molecular level after adoptive transfer revealed that the dominant TCR sequences from peptide-stimulated T cells persisted long-term and established an EBV-specific TCR clonotype repertoire in the host, with many of the EBV-specific TCRs present in the donor. This reconstituted repertoire was associated with immunological control of EBV and with lack of further AITL relapse.     

The V lambda J lambda repertoire in human fetal spleen: evidence for positive selection and extensive receptor editing

VlambdaJlambda rearrangements obtained from genomic DNA of individual IgM(+) B cells from human fetal spleen were analyzed. A nonrandom pattern of lambda gene rearrangements that differed from the adult Vlambda repertoire was found. The Vlambda distal genes 8A and 4B were absent from the nonproductive fetal repertoire, whereas 2E and 3L were overrepresented and 1B was underrepresented in the productive fetal repertoire. Positive selection of the Vlambda gene, 2E, along with Vlambda rearrangements employing homologous VlambdaJlambda joins were observed in the fetal, but not in the adult Vlambda repertoire. Overrepresentation of Jlambda distal cluster C genes rearranging to the Vlambda distal J segment, Jlambda7, in both productive and nonproductive fetal repertoires suggested that receptor editing/replacement was more active in the fetus than in adults. Numerous identical VlambdaJlambda junctions were observed in both the productive and nonproductive repertoire of the fetus and adult, but were significantly more frequent in the productive repertoire of the fetus, suggesting expansion of B cells expressing particular lambda-light chains in both stages of development, with more profound expansion in the fetal repertoire. Notably, B cells expressing identical lambda-light chains expressed diverse heavy chains. These data demonstrate that three mechanisms strongly influence the shaping of the human fetal lambda-chain repertoire that are less evident in the adult: positive selection, receptor editing, and expansion of B cells expressing specific lambda-light chains. These events imply that the expressed fetal repertoire is shaped by exposure to self Ags.     

A novel virus carrier state to evaluate immunotherapeutic regimens: regulatory T cells modulate the pathogenicity of antiviral memory cells

Restrictions in the diversity of an adaptive immune repertoire can facilitate viral persistence. Because a host afflicted with an immune deficiency is not likely to purge a persistent infection using endogenous mechanisms, it is important to explore adoptive therapies to supplement the host with a functional immune defense. In this study, we describe a virus carrier state that results from introducing lymphocytic choriomeningitis virus (LCMV) into adult mice possessing a restricted T cell repertoire. On infection of these mice, LCMV establishes systemic persistence, and within the CNS the virus infects astrocytes (and later oligodendrocytes) rather than its traditional parenchymal target neurons. To determine whether LCMV could be purged from a novel target selection in the absence of an endogenous immune repertoire, we adoptively transferred virus-specific memory cells into adult carrier mice. The memory cells purged virus from the periphery as well as the CNS, but they induced fatalities not typically associated with adoptive immunotherapy. When the repertoire of the recipient mice was examined, a deficiency in natural regulatory T cells was noted. We therefore supplemented carrier mice with regulatory T cells and simultaneously performed adoptive immunotherapy. Cotransfer of regulatory T cells significantly reduced mortality while still permitting the antiviral memory cells to purge the persistent infection. These data indicate that regulatory T cells can be used therapeutically to lessen the pathogenicity of virus-specific immune cells in an immunodeficient host. We also propose that the novel carrier state described herein will facilitate the study of immunotherapeutic regimens.     

Stability engineering of the human antibody repertoire

Human monoclonal antibodies often display limited thermodynamic and colloidal stabilities. This behavior hinders their production, and places limitations on the development of novel formulation conditions and therapeutic applications. Antibodies are highly diverse molecules, with much of the sequence variation observed within variable domain families and, in particular, their complementarity determining regions. This has complicated the development of comprehensive strategies for the stability engineering of the human antibody repertoire. Here we provide an overview of the field, and discuss recent advances in the development of robust and aggregation resistant antibody therapeutics.     

Song characterization in the spectacled warbler (Sylvia conspicillata): a circum-Mediterranean species with a complex song structure

The spectacled warbler (Sylvia conspicillata) is a small passerine with a patchy distribution throughout the circum-Mediterranean region, including the North Atlantic archipelagos of Madeira, Canary Islands and Cape Verde. Here we characterize the species song structure on the island of Fuerteventura, quantifying repertoire size, inter- and intra-individual spectrographic variation, to determine whether acoustic variation occurred within an island population. Male song display was organized in song bouts of a variable number of song phrases, which in turn were made up of 4–69 syllables. We classified syllable types to derive a measure of repertoire size (number of different syllables) per song bout, and then used rarefaction methods to calculate the estimated repertoire size for our population of males. Three categories of song bout length were considered in analyses: short song bouts of 10 phrases, average bouts of 19 phrases and long bouts of ≥ 29 phrases. The observed and estimated repertoire size per male (between 43 and 126 syllables per male) increased with song bout duration, although the relationship was not significant for the estimated values. To test whether songs could be individually specific, we measured 11 spectrotemporal parameters of the song. A discriminant analysis using these variables performed poorly in classifying songs to the individuals that uttered them, but we found less variation in the individual than in the population for three out of the 11 variables. These individually specific variables, involving the first or the most common syllable of the song, the trill, were the duration of the first syllable of the phrase, the duration and the dominant frequency of the trill syllable. Our study emphasizes the complexity of spectacled warbler songs, in which males continuously add novel syllables over the entire song bout. This complexity appears to be determined by individual innovation capabilities rather than by the behaviour of copying neighbour repertoires, since songs of close birds were not more similar than songs from far-away territories.     

The Effects of Relaxed and Reversed Selection by Predators on the Antipredator Behavior of the Threespine Stickleback, Gasterosteus aculeatus

Isolation from predators can lead to the reduction or loss of ancestral behavioral defenses in prey, but does not always do so. Predators introduced to populations that have experienced relaxed selection from some ancestral predators can favor the evolution of antipredator behavior that has been lost. We examined these possibilities by eliciting antipredator behavior in three populations of threespine stickleback fish, Gasterosteus aculeatus : an oceanic population thought to resemble the ancestral form, and two populations historically (up to 20 000 yr) devoid of piscine predators (relaxed selection), one of which has been stocked with salmonids for nearly 25 yr (reversed selection). We used three kinds of predator models: a sculpin (ambush predator), a rainbow trout (chasing predator), and an overhead silhouette of an arctic tern. Stickleback reacted differently to the three models, indicating that they distinguished among them. Individuals from all populations responded similarly to the tern model. The ancestral population showed the weakest response to the sculpin model despite being the only population that encounters these predators naturally. Stickleback from the trout-free population displayed slightly reduced responses to the trout model, and recovery times like those in the ancestral population providing only weak evidence for loss of the ancestral antipredator repertoire. Fish from the reverse-selected population exhibited fascinating, elevated responses to both the trout and sculpin models relative to the other two populations. These findings offer initial evidence of (1) a partial alteration of the ancestral behavioral repertoire during a long period of relaxed selection from piscine predators, and (2) rapid acquisition of extreme responses to piscine predators under reverse selection.     

Diversity of T cell receptor-alpha chain transcripts from hyperimmune alloreactive T cells.

Alloreactive T cells represent a relatively large fraction of the T cell population compared with the fraction of T cells that are specific for other foreign Ag. Recent findings indicate that most alloreactive T cells recognize endogenous peptides in association with a non-self MHC product. In light of these observations, it is perhaps not surprising that previous studies of the size of the TCR-alpha beta repertoire among alloreactive cells showed that they express many different V alpha and V beta genes. To further access the extent of diversity among alloreactive cells, we examined V alpha J alpha combinatorial diversity in polyclonal populations of a BALB/c anti-BALB.B mixed lymphocyte response. A long term culture from naive mice contained a diverse repertoire of V alpha J alpha combinations that was similar to the diversity present among unstimulated splenic T cells. In contrast, long term cultures from hyperimmunized animals contained "dominant" clones of T cells that expressed a restricted repertoire of V alpha J alpha combinations. Examination of the nucleotide sequences of these alpha-chains suggested that there was selective expansion of T cells with identical alpha-chains. In addition, T cells that express the same V alpha J alpha combination but different junctions were also identified. Consistent with previous results, the isolates from hyperimmune animals did not contain somatic mutations in the CDR3 region of the alpha-chains. Nevertheless, the results suggest that T cells may be subject to in vivo selection and clonal expansion analogous to the process of affinity maturation of Ig.     

The communicative life of a social carnivore: acoustic repertoire of the ring-tailed coati (Nasua nasua)

The coati is a highly social mammal that features sophisticated cognitive and social abilities. We hypothesized that the ring-tailed coati, Nasua nasua, uses an extensive acoustic repertoire that correlates to their diverse range of social interactions. We tested this hypothesis by observing and recording a free-ranging managed population of N. nasua in Tietê Ecological Park (PET), in the municipality of São Paulo, State of São Paulo, Brazil. Of 404 h of sampling, 47 h of coati vocalizations were recorded over 3 years. Additional records were obtained opportunistically on other free-living populations at PET by using passive acoustic monitoring. We describe here an acoustic repertoire composed of 15 calls (12 basic calls, 2 rhythmic calls and the non-random complex calls composed of three or four different units). This diverse repertoire of signals was used in contact/cohesion regulation, foraging activities, alert or potential threat situations, playing and fighting interactions and during social isolation and acute distress. The contact call (chirp) is produced through biphonation, and other non-linear phenomena are present. Our study found a complex vocal repertoire that encourages further studies to describe the evolution of the cognitive characteristics and social abilities of ring-tailed coatis.     

Infant-directed behavior in young rhesus monkeys: Sex differences and effects of prenatal androgens

Young (3–4 years old) laboratory-reared rhesus monkeys were observed in five 15-minute tests with 1–15-day-old infants. Males and females were equally likely to investigate infants. Females communicated more with infants by grin-lipsmacking and gurgling–-gestures that were not shown by any males. More females presented the ventrum to infants than did males. Females contacted infants more than did males by grooming, crouching over, and having full body contact with them. To see whether prenatal androgens produced the male pattern of response, we conducted similar tests with pseudohermaphrodites (prenatally androgenized genetic females) and neonatally castrated males. On most sexually dimorphic behaviors, pseudohermaphrodites behaved more like females than like males. Castrated males, like females and pseudohermaphrodites, crouched over infants more than did intact males. Castrated males differed from females only on one infant-directed response, the grin-lipsmack. These comparisons showed that defeminization of the repertoire of infant-directed responses was measurable only in intact males. We conclude accordingly that prenatal androgens alone are not responsible for defeminization of this repertoire and that a contribution from postnatal androgens is likely to be necessary.     

Structural basis for regulation of the Crk signaling protein by a proline switch

Proline switches, controlled by cis-trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. Here we report the structures of both the cis and trans conformers of a proline switch in the Crk signaling protein. Proline isomerization toggles Crk between two conformations: an autoinhibitory conformation, stabilized by the intramolecular association of two tandem SH3 domains in the cis form, and an uninhibited, activated conformation promoted by the trans form. In addition to acting as a structural switch, the heterogeneous proline recruits cyclophilin A, which accelerates the interconversion rate between the isomers, thereby regulating the kinetics of Crk activation. The data provide atomic insight into the mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency. The results also reveal new SH3 binding surfaces, highlighting the binding versatility and expanding the noncanonical ligand repertoire of this important signaling domain.     

Host-related immunomodulators encoded by poxviruses and herpesviruses

In the past year, important advances have been made in the area of host-related immunomodulatory genes encoded by the larger DNA viruses, particularly for the poxviruses and herpesviruses. Not only has the repertoire of viral immunomodulator homologs expanded as a result of sequencing the complete genome of another six, large DNA viruses, but also new concepts of how they work have been proposed and in some cases supported by in vivo evidence. Recent developments have been made in understanding a spectrum of host-related viral modulators, including complement control proteins, TNF-receptor homologs, IL-18 binding proteins, viral interleukins (vIL-6 and vIL-10), chemokine mimics and chemokine receptor homologs.     

Induction of helper and suppressor T cells by nonoverlapping determinants on the large protein antigen, beta-galactosidase

The fine specificity of the T cell repertoire directed against T helper (Th)-inducing and T suppressor (Ts)-inducing determinants was examined with cyanogen bromide and tryptic peptides of Escherichia coli beta-galactosidase (GZ), a large tetrameric protein (monomer molecular weight = 116 kDa). Immunization with cyanogen bromide fragment 2 [CB-2, amino acids (a.a.) 3-92] induced both specific Th and Ts cells. Study of the induction of these functionally opposite T cell subpopulations with tryptic peptides of CB-2 indicated that Th and Ts were activated by separate, nonoverlapping determinants. Th-inducing activity resided in a nonapeptide, T6 (a.a. 44-52), whereas T4 (a.a. 27-37) induced Ts cells. The presence of distinct helper and suppressor determinants suggests that the specificity repertoire in these T cell subpopulations may differ, perhaps owing to the expression of antigen-recognizing receptors that are coded by unique gene families. Alternatively, antigen presentation structures may be physicochemically quite different, and bind to distinct parts of the peptide antigen.     

POFs: what we don't know can hurt us

Over a quarter of all eukaryotic genes encode proteins with obscure features that lack currently defined motifs or domains (POFs). Interestingly, most of the differences in gene repertoire among species were recently found to be attributed to POFs. A comparison of the Arabidopsis, rice and poplar genomes reveals that Arabidopsis contains 5069 POFs, of which 2045 have no obvious homologs in rice or poplar and are likely to be involved in species- or phylogenetic-specific functions in Arabidopsis. The study of POFs is an important endeavor that will shed much needed light on the genetic properties that make any given plant species unique. Furthermore, with respect to many species-specific features, such studies show that we seem to be limited in what we can expect to learn from a model plant such as Arabidopsis.     

Song Differentiation and Population Structure: the Example of the Whistled Songs in an Introduced Population of European Starlings Sturnus vulgaris in Australia

Whistled songs of male starlings were studied in Australia and results compared with previous ones in Europe. Starling whistle sonograms can be divided into general classes according to certain criteria. All or most males sing five whistled types (“species-specific” themes), plus other (“individual”) themes. The basic repertoire of species-specific themes is almost the same in Europe and Australia with the same characteristics and similar variation ranges. In both continents each male has a certain number of individual themes, but Australian repertoires tend to be smaller, with two species-specific themes less and fewer individual themes. In all study areas dialects were based on local variations in species-specific theme structure, but the Australian dialectal system is simpler than in Europe. Therefore basic characteristics seem to have been similarly transmitted across generations in both continents. But some of the differences (individual characteristics, repertoire size, frequencies) may stem from different habitat characteristics and also social structure, which could have greatly affected song differentiation.     

B cells

B cells are an important component of adaptive immunity. They produce and secrete millions of different antibody molecules, each of which recognizes a different (foreign) antigen. The fact that humans express a very large repertoire of antibodies is due to the complex mechanism of V(D)J recombination of immunoglobulin (Ig) genes as well as other processes including somatic hypermutation, gene conversion and class switching. The B cell receptor (BCR) is an integral membrane protein complex that is composed of two Ig heavy chains, two Ig light chains and two heterodimers of Igalpha and Igbeta. To eliminate foreign antigens, B cells cooperate with other cells of the immune system including macrophages, dendritic cells and T cells. B cell development is a tightly controlled process in which over 75% of the developing cells become apoptotic because of inappropriate immunoglobulin gene rearrangements or recognition of self antigens by Igs. Hence, the majority of B cell-associated disorders are caused by the incorrect function of genes/proteins involved in B cell development.     

Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus

The plant cell wall, which consists of a highly complex array of interconnecting polysaccharides, is the most abundant source of organic carbon in the biosphere. Microorganisms that degrade the plant cell wall synthesize an extensive portfolio of hydrolytic enzymes that display highly complex molecular architectures. To unravel the intricate repertoire of plant cell wall-degrading enzymes synthesized by the saprophytic soil bacterium Cellvibrio japonicus, we sequenced and analyzed its genome, which predicts that the bacterium contains the complete repertoire of enzymes required to degrade plant cell wall and storage polysaccharides. Approximately one-third of these putative proteins (57) are predicted to contain carbohydrate binding modules derived from 13 of the 49 known families. Sequence analysis reveals approximately 130 predicted glycoside hydrolases that target the major structural and storage plant polysaccharides. In common with that of the colonic prokaryote Bacteroides thetaiotaomicron, the genome of C. japonicus is predicted to encode a large number of GH43 enzymes, suggesting that the extensive arabinose decorations appended to pectins and xylans may represent a major nutrient source, not just for intestinal bacteria but also for microorganisms that occupy terrestrial ecosystems. The results presented here predict that C. japonicus possesses an extensive range of glycoside hydrolases, lyases, and esterases. Most importantly, the genome of C. japonicus is remarkably similar to that of the gram-negative marine bacterium, Saccharophagus degradans 2-40(T). Approximately 50% of the predicted C. japonicus plant-degradative apparatus appears to be shared with S. degradans, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms.     

Relationship between number of muscles,behavioral repertoire size,and encephalization in mammals

Behavior for mammals is built out of multiple muscles acting in a coordinated fashion. Prima facie, there are three principal ways to increase an animal's behavioral repertoire size. The first is to, for each new behavior type, create a set of new muscle types (e.g. triceps, sartorius, etc.) with new functions specifically devoted to the implementation of that behavior type. If this were the case, then although each behavior is built out of many muscles, behavior is not built in a combinatorial fashion out of muscles. The second is similar to the first in that new behavior types are implemented via new muscle types, but, instead, muscles are used in a combinatorial fashion, so that it is the combination of the new muscle type with existing muscle types that makes the new behavior type possible. This is analogous to the addition of new words in a language. The third way behavioral complexity may be scaled up is to increase the complexity of behavioral expressions themselves (rather than increasing the number of muscles types), namely by having more muscles involved in an average behavior. This is analogous to uttering longer sentences in a language. My main task in this paper is to examine which of these ways underlies the increase of behavioral complexity among mammals. Behavioral repertoire sizes from the ethology literature were accumulated for mammals from two dozen species across eight orders, and the number of muscle types was estimated from atlases of anatomy across eight mammalian orders. The manner in which behavioral complexity actually increases among mammals appears to favor the second possibility mentioned above: greater behavioral complexity is achieved primarily by increasing the number of muscle types, and by using muscles in a combinatorial fashion. The theoretical framework I describe allows us to interpret the manner in which the number of muscle types scales with behavioral repertoire size, and I conclude that the number of degrees of freedom in the construction of behavioral expressions is on the order of three, which is probably due to neurobiological limitations in forming behaviors. The ontogeny of behavior in rat is also discussed within this framework. Finally, I show that there is a strong positive relationship between behavioral repertoire size and encephalization among mammals.     

Mycobacterium tuberculosis lipoarabinomannan-mediated IRAK-M induction negatively regulates Toll-like receptor-dependent interleukin-12 p40 production in macrophages

Mannose-capped lipoarabinomannans (Man-LAMs) are members of the repertoire of Mycobacterium tuberculosis modulins that the bacillus uses to subvert the host innate immune response. Interleukin-12 (IL-12) production is critical for mounting an effective immune response by the host against M. tuberculosis. We demonstrate that Man-LAM inhibits IL-12 p40 production mediated by subsequent challenge with lipopolysaccharide (LPS). Man-LAM inhibits LPS-induced IL-12 p40 expression in an IL-10-independent manner. It attenuates LPS-induced NF-kappaB-driven luciferase gene expression, suggesting that its effects are likely directly related to inhibition of NF-kappaB. This is probably because of dampening of the Toll-like receptor signaling. Man-LAM inhibits IL-1 receptor-associated kinase (IRAK)-TRAF6 interaction as well as IkappaB-alpha phosphorylation. It directly attenuates nuclear translocation and DNA binding of c-Rel and p50. Man-LAM exerts these effects by inducing the expression of Irak-M, a negative regulator of TLR signaling. Knockdown of Irak-M expression by RNA interference reinstates LPS-induced IL-12 production in Man-LAM-pretreated cells. The fact that Irak-M expression could be elicited by yeast mannan suggested that ligation of the mannose receptor by the mannooligosaccharide caps of LAM was the probable trigger for IRAK-M induction.     

Lambda light chain revision in the human intestinal IgA response

Revision of Ab L chains by secondary rearrangement in mature B cells has the potential to change the specific target of the immune response. In this study, we show for the first time that L chain revision is normal and widespread in the largest Ab producing population in man: intestinal IgA plasma cells (PC). Biases in the productive and non-productive repertoire of lambda L chains, identification of the circular products of rearrangement that have the characteristic biases of revision, and identification of RAG genes and protein all reflect revision during normal intestinal IgA PC development. We saw no evidence of IgH revision, probably due to inappropriately orientated recombination signal sequences, and little evidence of kappa-chain revision, probably due to locus inactivation by the kappa-deleting element. We propose that the lambda L chain locus is available and a principal modifier and diversifier of Ab specificity in intestinal IgA PCs.     

The glycan-binding properties of the cation-independent mannose 6-phosphate receptor are evolutionary conserved in vertebrates

The 300-kDa cation-independent mannose 6-phosphate receptor (CI-MPR) plays an essential role in the biogenesis of lysosomes by delivering newly synthesized lysosomal enzymes from the trans Golgi network to the endosomal system. The CI-MPR is expressed in most eukaryotes, with Saccharomyces cerevisiae and Caenorhabditis elegans being notable exceptions. Although the repertoire of glycans recognized by the bovine receptor has been studied extensively, little is known concerning the ligand-binding properties of the CI-MPR from non-mammalian species. To assess the evolutionary conservation of the CI-MPR, surface plasmon resonance analyses using lysosomal enzymes with defined N-glycans were carried out to probe the glycan-binding specificity of the Danio rerio CI-MPR. The results demonstrate that the D. rerio CI-MPR harbors three glycan-binding sites that, like the bovine CI-MPR, map to domains 3, 5 and 9 of its 15-domain-containing extracytoplasmic region. Analyses on a phosphorylated glycan microarray further demonstrated the unique binding properties of each of the three sites and showed that, similar to the bovine CI-MPR, only domain 5 of the D. rerio CI-MPR is capable of recognizing Man-P-GlcNAc-containing glycans.