bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning of a new gene encoding an antigen recognized by melanoma-specific HLA-A24-restricted tumor-infiltrating lymphocytes.
Authors: Robbins P F , el-Gamil M , Li Y F , Topalian S L , Rivoltini L , Sakaguchi K , Appella E , Kawakami Y , Rosenberg S A 
Published: December 2022

Abstract
The role of tumor-specific T cells in mediating the regression of metastatic melanoma has been suggested by the clinical response of patients to treatment with tumor-infiltrating lymphocytes (TIL). A number of Ags recognized by class I-restricted melanoma-specific T cells have recently been isolated, raising the hope that this will lead to the development of improved therapies. In this study, we report the cloning of a tumor Ag recognized by T cells from melanoma patient 888. Previously, we reported that TIL 888, grown from the tumor of this patient, recognized tyrosinase in an HLA-A24-restricted fashion. This line, when infused into the autologous patient, resulted in complete regression of multiple metastases. Three years later, a second TIL line, TIL 1290, was isolated from a recurrent pelvic tumor. Infusion of a mixture of TIL 888 and TIL 1290 cell lines into the patient resulted in complete regression of a residual abdominal mass and the patient remains disease-free 2 yr later. The TIL 1290 cell line, which recognized melanoma in an HLA-A24-restricted manner, failed to recognize tyrosinase. TIL 1290 was then used to screen an 888 melanoma cDNA library, and an Ag was isolated that did not correspond to any found in sequence databases. This gene, termed p15, was found to be expressed in a variety of normal tissues, and a peptide epitope recognized by TIL 1290 was found to represent the product of an nonmutated gene. Screening of additional cDNA pools resulted in the isolation of a second clone which stimulated TIL 1290. This clone also appeared to represent a transcript of the p15 gene, indicating that this gene may encode the predominant Ag recognized by TIL 1290.
Fine tuning of peptide binding to HLA-B*3501 molecules by nonanchor residues.
Authors: Schönbach C , Ibe M , Shiga H , Takamiya Y , Miwa K , Nokihara K , Takiguchi M 
Published: December 2022

Abstract
The prerequisites of peptide HLA-B*3501 interactions have been revisited by quantitative peptide binding assays with 190 chemically synthesized peptide possessing two anchor residues corresponding to the HLA-B*3501 peptide motif and a statistical residue-position analysis of binding and nonbinding peptides. According to the peptide motif of HLA-B*3501, aliphatic hydrophobic (Leu, Ile, and Met) or aromatic residues (Tyr and Phe) specify the main anchor at the C terminus, and position 2 renders an auxiliary anchor for proline. The importance of these residues was confirmed as a minimum requirement for peptide binding. Moreover, we demonstrated that high affinity peptide binding requires more than one favorable position of positions 3, 4, and 7. Aliphatic hydrophobic residues and residues that contain -OH or -SH side chains in position 3, 7, and 4 significantly enhance binding. Positions 1 and 5, or 7 may deteriorate peptide binding if these positions are held by proline and small residues (Ala and Gly) or basic residues carrying positively charged side chains (Arg and Lys), respectively. Positions 6 and 8 were statistically free of constrains. Yet, bulky aromatic residues and basic residues with a positively charged side chain at position 8 decreased the binding affinity. These findings were used to assess the predictability of binding and nonbinding peptides. Our binding predictions of 28 nonamers were verified by experimental data. Taking into account the importance of anchor and nonanchor positions in peptide binding and their practical value in peptide binding prediction, the search for peptide epitopes becomes more efficient.
Early activation of human V gamma 9V delta 2 T cell broad cytotoxicity and TNF production by nonpeptidic mycobacterial ligands.
Authors: Lang F , Peyrat M A , Constant P , Davodeau F , David-Ameline J , Poquet Y , Vié H , Fournié J J , Bonneville M 
Published: December 2022

Abstract
Human V gamma 9V delta 2 T cells were shown recently to respond to nonpeptidic phosphorylated molecules of mycobacterial origin (previously referred to as TUBag). To investigate the early events of V gamma 9V delta 2 T cell activation, we have analyzed induction of cytotoxicity and TNF production of T cell clones by these molecules. We showed that within minutes after exposure, TUBag induced cytotoxicity of V gamma 9V delta 2 CTL (but not of CTL expressing other TCR V gamma/V delta or V alpha/V beta regions) against a broad set of target cells, including effector cells themselves. Induction of V gamma 9V delta 2 cytotoxicity by TUBag was blocked by anti-TCR mAbs and was abrogated after dephosphorylation of TUBag. Similarly, TUBag, but not dephosphorylated TUBag, induced massive TNF production by V gamma 9V delta 2 T cell clones only, which already was significant 20 min after exposure. Of note, only basal amounts of TNF were produced when cells were maintained in suspension in the presence of TUBag, indicating that efficient activation of TNF production induced by these compounds required a cell-to-cell contact. Finally, preincubation experiments allowed us to demonstrate that activation of V gamma 9V delta 2 T cells was strictly dependent on the presence of TUBag because preincubation of the targets with TUBag followed by a single wash abrogated the activation. Taken together, these results strongly suggest that activation of V gamma 9V delta 2 cells by TUBag occurs after binding of these compounds to (a) yet unidentified, highly conserved, and broadly distributed molecule(s). The results also suggest either that TUBag induces a very rapid and transient expression of a V gamma 9V delta 2 TCR ligand or, more likely, that TUBag is a low affinity component of a complex recognized by the V gamma 9V delta 2 TCR.
Identification of T and B cell epitopes recognized by humans in the C-terminal 42-kDa domain of the Plasmodium falciparum merozoite surface protein (MSP)-1.
Authors: Udhayakumar V , Anyona D , Kariuki S , Shi Y P , Bloland P B , Branch O H , Weiss W , Nahlen B L , Kaslow D C , Lal A A 
Published: December 2022

Abstract
The 42-kDa, C-terminal region of the merozoite surface protein-1 (MSP-1) of Plasmodium falciparum is a putative malaria vaccine candidate Ag. Nine synthetic peptides corresponding to predicted T cell sites of MSP-1 in blocks 15 and 16 and eight overlapping peptides representing the conserved block 17 were used to identify naturally immunogenic epitopes. These peptides were tested for their ability to induce proliferation of PBMC from residents in western Kenya, where malaria transmission is holoendemic. Six peptides (PL145, PL146, PL147, PL148, PL149, and PL150) from blocks 15 and 16 induced a positive proliferative response in &gt; 30% of the individuals tested, and three peptides (PL151, PL152, and PL153) induced a proliferative response in &lt; 25% of the donors. Among these peptides, PL146 was from the highly conserved region, PL150 was from a polymorphic region, and all other peptides were from a dimorphic region of blocks 15 and 16. In block 17, only three peptides, PL99, PL100, and PL103, induced proliferation in 30 to 37% of the volunteers. The rest of the peptides induced a proliferative response in approximately 13 to 25% of the donors. The plasma from these donors widely reacted with different allelic forms of 19-kDa recombinant proteins representing block 17 and recognized at least two linear B epitopes, PL104 and PL97. In summary, this study revealed that a majority of immunodominant T and B epitopes are localized in the conserved or dimorphic regions that are nonpolymorphic in the 42-kDa protein of MSP-1. This study suggests that incorporation of T epitopes from the dimorphic blocks 15 and 16 in a vaccine construct may be useful to ensure Ag-specific memory responses.
Catalytic role of a surface loop of the complement serine protease factor D.
Authors: Kim S , Narayana S V , Volanakis J E 
Published: December 2022

Abstract
We have investigated the structural determinants of the unique functional properties of complement factor D by constructing and testing a series of trypsin-like mutants of the enzyme. Mutational replacement of the primary substrate-binding pocket of factor D with that of trypsin resulted in a mutant (M1) with greatly reduced proteolytic activity and slightly reduced reactivity toward small thioester substrates. Combining the M1 mutations with substitution of Tyr for Ser94, previously shown to enhance substantially both the proteolytic and esterolytic activities of factor D, produced a mutant (M2) with reactivities similar to M1. Replacement of the surface loop formed by residues 184-188 of M1 and M2 with the corresponding loop of trypsin produced mutants exhibiting one and two orders of magnitude higher esterolytic activity, respectively, than native factor D. However, the proteolytic activity of both mutants was similar to that of M1 and M2. We conclude that loop184-188 is an important determinant of the geometry of the primary specificity pocket of factor D. The low proteolytic activity of these mutants supports the proposal that the proteolytically active conformation of factor D is induced by its natural substrate, C3bB.
The high affinity IgE receptor (Fc epsilon RI) mediates IgE-dependent allergen presentation.
Authors: Maurer D , Ebner C , Reininger B , Fiebiger E , Kraft D , Kinet J P , Stingl G 
Published: December 2022

Abstract
The discovery that the high affinity IgE receptor (Fc epsilon RI) is expressed on APCs of patients with atopic diseases raised the possibility that the functional importance of Fc epsilon RI in the pathogenesis of atopy may extend beyond its role in type I allergic reactions. Here we show that, following removal of in vivo-bound IgE by lactic acid treatment, targeting of allergens to monocytes by Ag-specific IgE critically depends on Fc epsilon RI expression. Even more importantly, lactic acid-treated, monocyte-enriched PBMCs present allergen to T cells 100- to 1000-fold more effectively if the allergen has been targeted to Fc epsilon RI on these cells via allergen-specific IgE. This mechanism may critically lower the atopic individual's threshold to mount allergen-specific T cell responses capable of promoting IgE production and delayed-type hypersensitivity reactions.
Evidence for the overexpression of the VH4-34 (VH4.21) Ig gene segment in the normal adult human peripheral blood B cell repertoire.
Authors: Kraj P , Friedman D F , Stevenson F , Silberstein L E 
Published: December 2022

Abstract
The VH4-34 (VH4.21) gene has been repeatedly found to encode monoclonal anti-i/l cold agglutinins and is occasionally used by other autoantibodies with anti-DNA and rheumatoid factor specificity. To understand the basis for the frequent expression of the VH4-34 gene in autoimmunity, we prepared linker-based, amplified C mu and C gamma V gene (cDNA) libraries from the peripheral blood of two healthy adults (PBL-3 and PBL-4). The frequency of VH4 family gene-containing clones was determined with VH family-specific oligonucleotide probes, and by random sequencing we examined the frequency of VH4-34 gene expression among the VH4+ C mu clones. Collectively, these studies suggested that VH4-34 gene expression accounted for 7.8 and 10.3% of all IgM clones in the cDNA libraries of PBL-3 and PBL-4, respectively. In VH4 family-specific libraries prepared from genomic rearranged Ig DNA, the VH4-34 gene was also overrepresented relative to other VH4 family genes. In both the mu-cDNA as well as the rearranged Ig DNA libraries, the VH4-34-expressing clones were 95 to 100% homologous to the germline sequence and contained different CDR3 sequences. By contrast, the VH4-34-expressing C gamma clones showed somatic diversification from germline; in addition, the C gamma clones often had the same CDR3 sequences, suggesting that these clones were derived from either activated B cells or expanded, clonally related B cells. Multiparameter flow cytometric analysis of peripheral blood lymphocytes indicated that 3.2 to 6.2% of mu+CD20+ cells express the VH4-34-related Id 9G4. These current findings are relevant to the interpretation of restricted Ig gene usage reported in monoclonal cold agglutinin disease and other autoimmune disorders.
Chimpanzee MHC class I A locus alleles are related to only one of the six families of human A locus alleles.
Authors: McAdam S N , Boyson J E , Liu X , Garber T L , Hughes A L , Bontrop R E , Watkins D I 
Published: December 2022

Abstract
There are nearly 50 alleles at the highly polymorphic HLA-A class I locus that fall into six distinct families. To determine the allelic repertoire and the mechanism of generation of diversity of the A locus in primates we have analyzed A locus alleles from 28 apparently unrelated chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). We have, therefore, compared the sequences of 19 HLA-A homologues from chimpanzees and bonobos to 42 HLA-A sequences. HLA-A homologues were well preserved in chimpanzees and bonobos with very few new substitutions present in the A locus alleles of both species of chimpanzee. Surprisingly, all chimpanzees and bonobos expressed A locus alleles related to only one of the six families of human HLA-A alleles. This suggests that the common ancestor of these two species either passed through a genetic bottleneck or that selection has favored the maintenance of the HLA-A1, -A3, -A11 family in chimpanzees.
Pathogenesis of post-thymectomy autoimmunity. Role of syngeneic MLR-reactive T cells.
Authors: Bonomo A , Kehn P J , Payer E , Rizzo L , Cheever A W , Shevach E M 
Published: December 2022

Abstract
Thymectomy of 3-day-old mice results in the development of multi-organ-specific autoimmune diseases. The disease process is mediated by CD4+ T cells and is characterized by an inflammatory infiltrate in the affected organ(s) and the presence of autoantibodies. Our analysis of the phenotype of the CD4+ T cells that remain in the 3-day thymectomized animal revealed that the majority (approximately 80%) of the CD4+ lymph node cells express an activated (MEL-14low) phenotype and a smaller percentage expressed the T cell activation Ag CD69 and IL-2R alpha-chain. Thymectomized animals also had an increase in the frequency of mitogen-induced CD4+ IL-4 producers and significantly higher levels of total serum IgG. Functional studies demonstrated that lymph node T cells from 3-day thymectomized mice had an enhanced response in the syngeneic MLR and appeared to preferentially respond to syngeneic dendritic cells. To determine whether the syngeneic MLR-reactive T cells were involved in the pathogenesis of the organ-specific disease, we developed a model that mimicked the 3dTx model by grafting neonatal thymi to adult nu/nu recipients followed by removal of the thymus graft on day 3 or 4. When compared with mice transplanted with an untreated thymus, nu/nu mice transplanted with adult APC-containing thymi demonstrated a decrease in the incidence and severity of gastritis, a marked decrease in the titer of anti-parietal cell Ab, and a decrease in total serum IgG. Thus, intrathymic tolerization to complexes of self-peptides and MHC class II on adult APC prevents organ-specific autoimmune disease.
Immunohistologic analysis of ineffective CD40-CD40 ligand interaction in lymphoid tissues from patients with X-linked immunodeficiency with hyper-IgM. Abortive germinal center cell reaction and severe depletion of follicular dendritic cells.
Authors: Facchetti F , Appiani C , Salvi L , Levy J , Notarangelo L D 
Published: December 2022

Abstract
The CD40 ligand (CD40L) is an activation-induced surface membrane protein expressed by CD4+ T helper cells in lymphoid follicles, and is involved in the contact-dependent signaling-mediated activation, proliferation, and differentiation of CD40+ B cells. Using immunohistochemistry, the present study analyzes the cell microenvironment of lymphoid tissues in two cases of X-linked hyper-IgM syndrome, a congenital immunodeficiency caused by mutations of the CD40L gene, and which represents a unique model to dissect the functional and morphologic consequences of disrupted CD40/CD40L interactions. Prominent primary B follicles are identified in the lymph nodes and in the extranodal lymphoid tissues from both cases, but tiny collections of Bcl-2-, MIB1/Ki67+ centroblasts are also found in one case. Despite the CD40L defect, intrafollicular CD4+CD57+ T helper cells, identified by anti-parvalbumin mAb, are normally present. However, a severe depletion of follicular dendritic cells, recognized by Abs against NGFR, CD21 and CD23, and lack of expression of the Ag recognized by KiM4p on these cells, are noticed. Finally, no major alterations of the architecture and cellular composition of the paracortical T cell area are found. A large number of plasma cells exclusively expressing IgM were detected in the colon lamina propria in one of the patients, who also had extremely elevated IgM serum levels. Taken together, these data support the idea that ineffective CD40/CD40L interactions determine both abortive germinal center cell reaction as well as severe depletion and phenotypical abnormalities of follicular dendritic cells, thus impairing the functional development of B follicles. Recurrent or persisting antigenic stimulation in mucosal tissues is likely to play a major role in determining and maintaining elevated IgM serum levels.
IL-15 has stimulatory activity for the induction of B cell proliferation and differentiation.
Authors: Armitage R J , Macduff B M , Eisenman J , Paxton R , Grabstein K H 
Published: December 2022

Abstract
The identification and cloning of the novel cytokine IL-15 were recently described. IL-15 is produced by a wide range of cell types, with the highest levels of IL-15 mRNA being detected in epithelial lines, monocytes, muscle, and placenta. Although it has no sequence identity with IL-2, IL-15 shares many of the T cell-stimulatory activities described for IL-2. We have examined IL-15 for its ability to stimulate B cells and have compared its activity with that of IL-2. IL-15 costimulates proliferation of B cells activated with immobilized anti-human IgM or phorbol ester, but has no stimulatory effect on resting B cells. In combination with recombinant CD40L, IL-15 is a potent inducer of polyclonal IgM, IgG1, and IgA secretion, but does not cause production of IgG4 or IgE. The activity of IL-15 in B cell proliferation and differentiation assays is comparable with that of IL-2. Studies that used neutralizing Abs have demonstrated that, for signal transduction in B cells, IL-15 uses the beta-chain of the IL-2R complex but, unlike IL-2, does not require the alpha-chain. IL-2 is required for the generation of a human primary Ag-specific in vitro response using sheep erythrocytes as Ag. Of all cytokines examined, only IL-15 has the capacity to replace IL-2 in this system, although only partially. In summary, IL-15 has comparable activity with IL-2 for the induction of B cell proliferation and differentiation and uses at least some of the components of the IL-2R complex to mediate its effects.
Alpha 3 beta 1 and alpha 6 beta 1 integrins mediate laminin/merosin binding and function as costimulatory molecules for human thymocyte proliferation.
Authors: Chang A C , Salomon D R , Wadsworth S , Hong M J , Mojcik C F , Otto S , Shevach E M , Coligan J E 
Published: December 2022

Abstract
Integrins comprise a superfamily of alpha beta heterodimers that serve as cell signaling as well as adhesion molecules. We demonstrate that the alpha 3 beta 1 and alpha 6 beta 1 integrins are laminin/merosin receptors expressed in human thymocytes. By reverse transcriptase-PCR analysis, we determined that the alpha 3A beta 1, but not the alpha 3B beta 1, cytoplasmic structural variant of alpha 3 beta 1 is expressed in thymocytes. In contrast, both alpha 6A beta 1 and alpha 6B beta 1 cytoplasmic structural variants of alpha 6 beta 1 are expressed. A small percentage (10 to 15%) of human thymocytes bind to immobilized laminin, and even fewer (3 to 5%) bind to merosin, the laminin isoform normally present in the thymus. This binding, however, can be increased to 39 to 41% after activation of thymocytes with Mn2+ (or PMA). Binding to either laminin or merosin is completely inhibited by anti-beta 1 mAb or by a mixture of anti-alpha 3 and anti-alpha 6 mAbs, indicating that both alpha 3 beta 1 and alpha 6 beta 1 participate in thymocyte adhesion to the laminin family of extracellular matrix proteins. The protein kinase C inhibitors, calphostin C and staurosporine, inhibit Mn(2+)-enhanced thymocyte binding, suggesting that protein kinase C activity is crucial for the binding. Furthermore, the data indicate that at least two divalent cation binding sites serve to regulate integrin binding activity. Finally, we show that both immobilized laminin and merosin have costimulatory function for anti-CD3-induced thymocyte proliferation, and both anti-alpha 3 and anti-alpha 6 mAbs can block this proliferative response. The cooperative function of alpha 3 beta 1 and alpha 6 beta 1 evidenced in the laminin/merosin binding and proliferation assays suggests that thymocyte-merosin interactions may play an important role in thymic T cell development.
Limited restriction in the TCR-alpha beta V region usage of antigen-specific clones. Recognition of myelin basic protein (amino acids 84-102) and Mycobacterium bovis 65-kDa heat shock protein (amino acids 3-13) by T cell clones established from peripheral blood mononuclear cells of monozygotic twins and HLA-identical individuals.
Authors: Hawes G E , Struyk L , Godthelp B C , van den Elsen P J 
Published: December 2022

Abstract
We have analyzed the TCR-alpha beta repertoire specific for a given peptide/MHC complex by using pairs of HLA-identical individuals ranging from monozygotic twins to unrelated individuals to examine the contribution of genetic background and HLA expression in shaping the potential response to a single antigenic epitope. This panel has been previously defined, demonstrating that the concordance of the peripheral TCR-alpha beta repertoires directly correlates to the level of relation and HLA identity. We have analyzed peptide-specific T cell clones derived from T cell lines from these individuals specific for MHC class II-restricted peptides: Mycobacterium bovis 65-kDa heat shock protein (65-kDa hsp) amino acids (aa) 3-13 (DR3-restricted), and myelin basic protein aa 84-102 (DR2-restricted). DNA sequence analysis was used to determine the composition of the TCR-alpha beta V regions. Although the overall TCR-alpha beta repertoires between individuals were diverse, an intra-individual limited restriction was evident. There was also a limited conservation in the response to the different peptides: high frequencies of V beta 2, 4, 7, 19, V alpha 21, and J alpha 17 responded to the MBP aa84-102, whereas these V/J regions were limited or absent in the 65-kDa hsp aa3-13 repertoire. Similarly, V beta 5.1 and J alpha 9 were increased in the 65-kDa hsp aa3-13 repertoire. Within the CDR3s, motifs could be identified that were similar between twins. Furthermore, one of these motifs resembled CDR3s previously found in corresponding animal models. Similarities could also be seen in the CDR3s of T cell clones sharing V gene usage and peptide specificity. Thus, the in vitro response to antigenic peptides seems to be quite heterogeneous overall and individual specific.