Pan-cancer multi-omics analyses reveal crosstalk between the Hippo and immune signaling pathways in the tumor microenvironment.

The Hippo signaling pathway is critical for carcinogenesis. However, the roles of the Hippo signaling pathway in the tumor immune microenvironment have been rarely investigated. This study systematically analyzed the relationship between the Hippo signaling pathway and immune cell infiltration across 32 cancer types. Both bioinformatics analyses and biological experiments revealed that the downstream effector of Hippo signaling YAP1 might inhibit CD8+ T cell infiltration by upregulating the expression of the transcription factor CREB1 in uterine corpus endometrial carcinoma. In addition, esophageal carcinoma (ESCA) patients were classified into three subtypes based on the Hippo-immune gene panel. The subtypes of ESCA had distinct characteristics in immune cell infiltration, immune pathways, and prognosis. Thus, this study also reveals a new classification of the immune subtypes with prognostic characteristics in ESCA.

Estimate of within population incremental selection through branch imbalance in lineage trees.

Incremental selection within a population, defined as limited fitness changes following mutation, is an important aspect of many evolutionary processes. Strongly advantageous or deleterious mutations are detected using the synonymous to non-synonymous mutations ratio. However, there are currently no precise methods to estimate incremental selection. We here provide for the first time such a detailed method and show its precision in multiple cases of micro-evolution. The proposed method is a novel mixed lineage tree/sequence based method to detect within population selection as defined by the effect of mutations on the average number of offspring. Specifically, we propose to measure the log of the ratio between the number of leaves in lineage trees branches following synonymous and non-synonymous mutations. The method requires a high enough number of sequences, and a large enough number of independent mutations. It assumes that all mutations are independent events. It does not require of a baseline model and is practically not affected by sampling biases. We show the method's wide applicability by testing it on multiple cases of micro-evolution. We show that it can detect genes and inter-genic regions using the selection rate and detect selection pressures in viral proteins and in the immune response to pathogens.

The role of BCR isotype in B-cell development and activation.

The development and function of B lymphocytes critically depend on the non-germline B-cell antigen receptor (BCR). In addition to the diverse antigen-recognition regions, whose coding sequences are generated by the somatic DNA rearrangement, the variety of the constant domains of the Heavy Chain (HC) portion contributes to the multiplicity of the BCR types. The functions of particular classes of the HC, particularly in the context of the membrane BCR, are not completely understood. The expression of the various classes of the HC correlates with the distinct stages of B-cell development, types of B-cell subsets, and their effector functions. In this chapter, we summarize and discuss the accumulated knowledge on the role of the µ, δ, and γ HC isotypes of the conventional and precursor BCR in B-cell differentiation, selection, and engagement with (auto)antigens.

Qualifying high-throughput immune repertoire sequencing.

Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.

IgG-switched CLL has a distinct immunogenetic signature from the common MD variant: ontogenetic implications.

PURPOSE: Immunoglobulin G-switched chronic lymphocytic leukemia (G-CLL) is a rare variant of CLL, whose origin and ontogenetic relationship to the common IgM/IgD (MD-CLL) variant remains undefined. Here, we sought for clues about the ontogeny of G-CLL versus MD-CLL by profiling the relevant IG gene repertoires. EXPERIMENTAL DESIGN: Using purpose-built bioinformatics methods, we performed detailed immunogenetic profiling of a multinational CLL cohort comprising 1,256 cases, of which 1,087 and 169 expressed IG mu/delta and gamma heavy chains, respectively. RESULTS: G-CLL has a highly skewed IG gene repertoire that is distinct from MD-CLL, especially in terms of (i) overuse of the IGHV4-34 and IGHV4-39 genes and (ii) differential somatic hypermutation (SHM) load. Repertoire differences were also found when comparing subgroups with similar SHM status and were mainly attributed to the exclusive representation in G-CLL of two major subsets with quasi-identical (stereotyped) B-cell receptors. These subsets, namely #4 (IGHV4-34/IGKV2-30) and #8 (IGHV4-39/IGKV1(D)-39), were found to display sharply contrasting SHM and clinical behavior. CONCLUSIONS: G-CLL exhibits an overall distinct immunogenetic signature from MD-CLL, prompting speculations about distinct ontogenetic derivation and/or immune triggering. The reasons underlying the differential regulation of SHM among G-CLL cases remain to be elucidated.

Using synthetic templates to design an unbiased multiplex PCR assay.

T and B cell receptor loci undergo combinatorial rearrangement, generating a diverse immune receptor repertoire, which is vital for recognition of potential antigens. Here we use a multiplex PCR with a mixture of primers targeting the rearranged variable and joining segments to capture receptor diversity. Differential hybridization kinetics can introduce significant amplification biases that alter the composition of sequence libraries prepared by multiplex PCR. Using a synthetic immune receptor repertoire, we identify and minimize such biases and computationally remove residual bias after sequencing. We apply this method to a multiplex T cell receptor gamma sequencing assay. To demonstrate accuracy in a biological setting, we apply the method to monitor minimal residual disease in acute lymphoblastic leukaemia patients. A similar methodology can be extended to any adaptive immune locus.

Association of protein kinase C-delta with the B cell antigen receptor complex.

Protein kinase C (PKC)-delta is a diacylglycerol-dependent, calcium-independent novel PKC isoform and has been demonstrated to exert negative regulatory functions in B lymphocytes as well as in mast cells. Whereas in mast cells PKC-delta functionally interacts with the high-affinity receptor for IgE, FcepsilonR1, no such association has been described for the B cell antigen receptor (BCR). In this report, for the first time, we demonstrate the interaction of PKC-delta with different classes of BCR by means of affinity purification and native protein complex analysis. Using a C-terminally truncated Ig-alpha as well as non-phosphorylated and phosphorylated peptides representing C-terminal regions of Ig-alpha, the dependence of this BCR/PKC-delta interaction on tyrosine-phosphorylated Ig-alpha is shown. Finally, splenocytes from PKC-delta-deficient mice are found to exert reduced phosphorylation of PKD (a.k.a. PKC-mu) in response to BCR engagement, suggesting the early, membrane-proximal activation of an attenuating kinase complex including PKC-delta and PKD.

Function of B-cell antigen receptor of different classes.

Most mature B lymphocytes co-express two classes of antigen receptor, IgM and IgD. The differences in the signal transduction from the 2 receptors are still a matter of controversy. We have analysed B-cell lines expressing IgM or IgD antigen receptors with the same antigen specificity. Cross-linking of these receptors with either antigen or class-specific antibodies results in the activation of protein tyrosine kinases and the phosphorylation of the same substrate proteins. The kinetics and intensity of phosphorylation, however, were quite different between the 2 receptors when they were cross-linked by antigen. In membrane IgM-expressing cells, the substrate phosphorylation reached a maximum already after 1 min and diminished after 60 min whereas in the membrane IgD-expressing cells, the substrate phosphorylation increases further over time, reached its maximum at 60 min and persisted longer than 240 min after exposure to antigen. Recently prolonged signaling has been found to be responsible for signaling differences between tyrosine kinase receptors using otherwise similar signaling routes. Thus, the duration of a signal may be an important biological feature of signal transducing cascades.

[Immunoglobulin G subclass distribution of anti-intercellular substance antibodies in pemphigus]. / Distribution en sous-classes d'immunoglobulines G des anticorps anti-substance intercellulaire du pemphigus.

INTRODUCTION: The purpose of this study was to analyze the IgG subclass distribution of pemphigus anti-epithelial cell surface (ECS) antibodies and to determine whether it differs according to clinical features. MATERIALS AND METHODS: 25 skin biopsies and 16 serum samples, obtained from 27 cases of pemphigus, were analyzed by direct and indirect IF staining, with mice anti-human IgG subclasses monoclonal antibodies. RESULTS: IgG1 deposits were observed in 21 of 25, IgG2 in 2, IgG3 in 0, and IgG4 in the 25 biopsies. IgG1 anti-ECS anti-ECS antibodies were detected in all 16 sera, IgG2 in 1, IgG3 in 1, and IgG4 in 15 sera. The anti-ECS IgG subclass distribution does not differ according to the clinical parameters studied. DISCUSSION: The isotypic restriction to IgG1 and IgG4 subclasses, observed in this study, is similar to previously reported results. The heterogenous distribution and the small number of the studied samples did not allow to put in evidence a correlation with the clinical parameters.

IgG+, CD5+ human chronic lymphocytic leukemia B cells. Production of IgG antibodies that exhibit diminished autoreactivity and IgG subclass skewing.

Several questions exist regarding CD5+ B cells. These include the ability of these cells, as compared to CD5- B cells, to undergo an Ig isotype class switch, the subclasses utilized, and the effects that switching may have on antigen binding. To address these issues, ten patients with chronic lymphocytic leukemia (CLL) whose CD5+ leukemic B cell clones produced IgG were studied. Monoclonal IgG was collected from PMA-stimulated CLL cells and from heterohybridomas constructed with these cells, and then analyzed for IgG subclass utilization, autoreactivity, and DNA idiotype expression. The monoclonal B cells from 80% of the CLL patients produced IgG1 and those from 20% produced IgG3. None produced IgG2. In contrast to the known autoreactivity of IgM-producing CD5+ CLL cells (> 50% autoreactive), none of these IgG antibodies reacted significantly with the autoantigens tested. However, three did react significantly with autoantigen after artificially increasing antibody valency by crosslinking. Whereas five of the IgG molecules expressed a cross reactive idiotypic (CRI) marker characteristic of non-mutated kappa anti-DNA antibodies, three expressed a CRI displayed primarily on mutated IgG anti-DNA antibodies. Thus, some CD5+ human B cells can undergo an isotype class switch that for these CLL cells is biased against IgG2 and in favor of the IgG1 and IgG3. In their native state the IgG molecules secreted by these isotype-switched CD5+ cells have diminished autoreactivity, as compared to IgM-producing CLL cells. Since some of the IgG antibodies could be made auto- and poly-reactive by increasing antigen-binding valency, while others expressed idiotypic markers of mutated antibodies, certain of these CD5+ B cells probably utilize non-mutated Ig V genes coding for polyreactive antibodies, whereas others may use genes that have undergone somatic mutation and that code for more restricted specificities. Therefore, both valency and VH gene mutation may account for the diminished autoreactivity of these CD5+ B cell-derived IgG antibodies.

Blood lymphocyte characteristics as predictors of prognosis in chronic lymphocytic leukemia of B-cell type.

The prognostic information of blood lymphocyte characteristics and clinical findings was assessed in 62 patients with chronic lymphocytic leukemia of B cell type. Bivariate and multivariate survival analyses were performed using age, Rai stage, surface membrane immunoglobulin (smIg) isotype pattern of the leukemic clone, total lymphocyte counts, numbers of proliferating lymphocytes and T cell subpopulations. Rai stages III and IV, high numbers of blood lymphocytes in S-phase (S+) and sm mu isotype were found to be partly independent factors predicting short therapy-free survival. Patients with a sm mu+ leukemic cell clone had a shorter therapy-free and total survival compared to those with sm mu+/delta+ and sm delta+ leukemic cells. Moreover, patients with high numbers of blood S+ lymphocytes had a shorter therapy-free and total survival compared to those with few S+ cells. These prognostic variables were valid also in patients with a low tumour burden (Rai stages 0, I and II) and may thus be of clinical importance as a guideline for therapeutic intervention.

Prognostic significance of immunologic phenotype in hairy cell leukemia: does it exist?

Of 94 hairy cell leukemia (HCL) patients studied for immunologic phenotype of their hairy cells, 89 patients had B cell markers and five patients were both surface immunoglobulin (slg) negative and E rosette negative. Forty of the 77 cases that had the heavy chains individually determined had IgG only (52.0%); 23 others had IgG in addition to other Ig heavy chains. Seventy-nine patients had monoclonal light chains; 65 with kappa chain and 14 with lambda chain. The only significant difference with respect to survival among the various slg groups occurred between the kappa chain and the lambda chain groups. Within the first 46 months after diagnosis of HCL, 20 deaths occurred among the 65 kappa chain patients, whereas the first and only death among the lambda chain patients occurred at 68 months after diagnosis. The only clinical or laboratory parameter that was significantly different between these two immunologic subgroups was the incidence of infections. Among the lambda chain patients, an infectious complication rate of 28.6% was observed subsequent to the diagnosis of HCL, whereas this rate was 68.8% in kappa chain patients (P = .005). The survival of lambda patients was found to exceed that of the kappa patients by the generalized Wilcoxon test (P = .03). However, when the log rank test was used, no significant difference was detected (P = .13).

The use of haptenated-immunoglobulin molecules to induce tolerance in B cells from neonatal mice.

The role of the Fc region of trinitrophenylated (TNP)-immunoglobulins (Ig) in their ability to induce tolerance in immature B cells was examined. With the use of B cells from neonatal mice, tolerogens that could or could not bind to Fc receptors were assessed for their ability to induce tolerance. This was accomplished by tolerizing spleen cells in bulk culture and assessing the degree of tolerance by challenging the cells with the thymus-independent antigen TNP-Brucella abortus (TNP-BA) in limiting dilution cultures. It was found that by using tolerogens containing 10 to 11 haptens per Ig molecule, immature B cells were very susceptible to tolerance induction. Mature B cells were not as susceptible. This increased susceptibility was independent of the Fc portion of the tolerogen, because TNP11-HGG and a TNP10-F(ab')2 induced equivalent degrees of unresponsiveness. When the TNP density was lowered to approximately five haptens per Ig molecule, those Ig molecules that contained Fc portions were superior tolerogens with the use of B cells from 6-day-old mice. Thus, a TNP4-HGG, TNP7-mouse IgG1, and TNP6-mouse IgG2a were more effective tolerogens than either TNP5-F(ab')2 or TNP6-mouse IgG3. These results confirm previous findings that immature B cells are inherently more susceptible to tolerance induction than mature B cells. They also suggest that very lightly haptenated Ig molecules may depend on Fc receptor-binding for effective tolerance induction. Finally, by means of a cytofluorograph, the surface IgD (sIgD) and sIgM phenotypes of splenic B cells from neonates of increasing age were determined. When comparing the phenotype of maturing cells with their tolerance susceptibilities, a correlation between the appearance of sIgD and the acquisition of resistance to tolerance was observed.

Lymphoma models for B cell activation and tolerance. I. Conditions for the anti-mu-dependent stimulation of growth in NBL, a nude B cell lymphoma.

NBL is a spontaneous B cell lymphoma that originated in NIH Swiss nude mouse, and has been maintained as an in vitro line for 4 yr in our laboratory. It is surface IgM positive and expresses several B cell markers including Fc receptors, as well as Ly-1. Although clones of NBL will grow in serum-containing medium, this cell line enters a quiescent state in serum-free culture. However, in the presence of affinity-purified or monoclonal anti-mu reagents, NBL increases its rate of proliferation as measured by thymidine incorporation or in absolute cell numbers. This stimulation is specific for mu-chain, because it does not occur with anti-beta 2 microglobulin, irrelevant nonbinding antibodies, or with monoclonal anti-B cell lineage markers. Bivalent anti-mu is required, and no consistent Fc-mediated inhibition of growth has been detected. Stimulation of NBL occurs optimally at critical cell densities (greater than 3 X 10(3)/well) in the absence of serum. Therefore, we reasoned that NBL either produced or was receptive to known B cell growth factors. Although no classic IL 1 was detected in NBL supernatants, some BCGF-I-like activity was found. Finally, in the presence of LPS, both spontaneous and anti-mu-stimulated NBL growth was inhibited, a result suggesting maturation of this lymphoma. These results suggest that NBL represents an excellent model to study the growth and differentiation of B cell subsets.

Increased numbers of lymphocytes with single class surface immunoglobulins in Hodgkin's disease.

Lymphocyte populations with abnormal kappa/lambda ratios have been described previously in B-cell non-Hodgkin's lymphomas and in lymphoid hyperplasia. The authors studied 12 patients in whom lymph nodes diagnostic of Hodgkin's disease contained evidence of monoclonal lymphocyte proliferation. One patient subsequently was found to have a B-cell lymphoma. The others have not been found to differ in any important characteristic from 25 Hodgkin's disease patients with normal ratios studied for comparison.

Surface IgG subclasses in human B cell lymphomas as revealed by monoclonal antibodies.

IgG subclass expression on cells from lymph node biopsies of 17 sIgG positive B cell lymphomas has been studied. Subclass specific monoclonal antibodies were used in an immunoradiometric assay. Ten were also tested by immunofluorescence using a biotin-avidin system. Thirteen of the lymphomas expressed IgG only, while four co-expressed other Ig isotypes. Morphological investigations revealed that 14 lymphomas originated from germinal centre cells. IgG1 was found to be dominant subclass in 10 lymphomas, IgG3 in seven, IgG2 in one, while none expressed IgG4. Multiple IgG subclasses could not be detected in any of the lymphomas tested.

Reactive lymphoid hyperplasia with single class (monoclonal) surface immunoglobulin.

Lymphoid tissues from 12 patients were diagnosed as reactive lymphoid hyperplasia, but surface immunoglobulin studies revealed monoclonal (single class) immunoglobulin staining patterns. Infectious, autoimmune, and immunodeficient conditions were diagnosed on the basis of histology and clinical features. Such surface immunoglobulin restriction has been used as an indicator of a neoplastic lymphoid proliferation, but the cases of these patients, in whom the histologic diagnosis was benign, emphasize the importance of a multiparameter approach to diagnosis. Although at the time of this report none of the patients still available to follow-up study have developed known lymphoid neoplasms, the possibility that monoclonal SIg patterns are a harbinger of neoplastic disease makes continuing follow-up of such patients important.

Cellular mechanisms of restricted immunoglobulin formation in the human neonate.

The functional capacity of human neonatal B lymphocytes has been investigated by in vitro methods using T lymphocyte-dependent (pokeweek mitogen, PWM) and -independent (Epstein-Barr virus, EBV) polyclonal B cell activators. B cell activation of single cells was detected by class-specific immunoglobulin (Ig) secretion using a reversed hemolytic plaque assay. It was found that neonatal B cells were triggered to secretion of IgM by EBV, with a magnitude comparable to adult levels, but that, in contrast to B cells from adults, they did not secret IgG. Cord lymphocytes did not secret Ig although they displayed a sizable DNA synthetic response to PWM. Using cell separation and culture experiments, it was shown that (allogeneic) adult T lymphocytes could restore cord B cell responsiveness to PWM and that cord T lymphocytes could not cooperate with adult B cells. In addition to this immaturity of cord T helper function for antibody synthesis, we found cells in the cord T cell-enriched fraction which inhibited the polyclonal response of adult lymphocytes to both PWM and EBV. These lymphocytes suppressed adult B lymphocytes directly but appeared ineffective against neonatal B lymphocytes themselves. The nature of these suppressing cells and their possible role in the fetal/maternal relationship are a matter of speculation.