Biomedical subjects

Ramit Mehr

Publications and source records attributed to Ramit Mehr.

At least 19 recordsLinked to original sources

PubMed2006

Novel analysis of clonal diversification in blood B cell and bone marrow plasma cell clones in immunoglobulin light chain amyloidosis.

Immunoglobulin light chain amyloidosis (AL) is characterized by a limited clonal expansion of plasma cells and amyloid formation. Here, we report restriction in the diversity of VL gene usage with a dominance of clonally related B cells in the peripheral blood (PB) isotype-specific repertoire of AL patients. A rigorous quantification of lineage trees reveals presence of intraclonal variations in the PB clones compared to the bone marrow (BM) clones, which suggests a common precursor that is still subject to somatic mutation. When compared to normal BM and PB B cells, AL clones showed significant but incomplete impairment of antigenic selection, which could not be detected by conventional R and S mutation analysis. Therefore, graphical analysis of B cell lineage trees and mathematical quantification of tree properties provide novel insights into the process of B cell clonal evolution in AL.

Algorithms↗

PubMed2006

Feedback loops, reversals and nonlinearities in lymphocyte development.

Systems of differentiating cells are often regarded by experimental biologists as unidirectional processes, in which cells spend a fixed time at each successive developmental stage. However, mathematical modeling has in several cases revealed that differentiating cell systems are more complex than previously believed. For example, non-linear transitions, feedback effects, and even apparent reversals have been suggested by our studies on models for the development of lymphocytes and their receptor repertoires, and are reviewed in this paper. These studies have shown that cell population growth in developing lymphocyte subsets is usually nonlinear, as it depends on the density of cells in each compartment. Additionally, T cell development has been shown to be subject to feedback regulation by mature T cell subsets, and B cell development has been shown to include a phenotypic reflux from an advanced to an earlier developmental stage. The challenges we face in our efforts to understand how the repertoires of these cells are generated and regulated are also discussed here.

Animals↗

PubMed2006

Quantitative analysis of clonal bone marrow CD19+ B cells: use of B cell lineage trees to delineate their role in the pathogenesis of light chain amyloidosis.

Light chain amyloidosis (AL) is a bone marrow (BM) plasma cell neoplasia with systemic deposition of Ig light chain amyloid fibrils. Here, we report the identification of clonal CD19 B cells in the BM and the use of a novel mathematical algorithm to generate B cell lineage trees of the clonal CD19 B cells and CD138 plasma cells from the BM of AL patients to delineate the relationship between these two clonal populations. The CD19+ clonal B cells in the BM of AL patients related to the clonal plasma cells represent a pre-plasma cell precursor population. The B cell lineage trees from AL patients also show significant differences in clonal diversification and antigenic selection compared to clones from normal, healthy controls. These data provide a robust example of the use of graphical quantification methods in delineating the role of neoplastic precursors in the pathogenesis of hematopoietic malignancies.

Algorithms↗

PubMed2005

B cell development in aging mice: lessons from mathematical modeling.

Previous studies have not completely clarified the precise defect that characterizes B cell development in aged animals. The question of which developmental mechanism is actually deficient in aging remains controversial. The goal of this study was to elucidate the effects of aging on bone marrow B cell population dynamics. We used mathematical modeling to predict the outcome of the different possible effects, and then compared these predictions to experimental data, to find the most plausible effects. Our model shows that the three main differences between B cell development in young and old mice are a decrease in the maximum number of cells in the pre-B compartment and increases in the rate of transition from cycling pre-B cells to resting pre-B cells and in the fractions of static cells included in the immature B cell subset.

Aging↗

PubMed2005

Immunoglobulin variable-region gene mutational lineage tree analysis: application to autoimmune diseases.

Lineage trees have frequently been drawn to illustrate diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. In order to extract more information from IGV sequences, we developed a novel mathematical method for analyzing the graphical properties of IgV gene lineage trees, allowing quantification of the differences between the dynamics of SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we investigated trees generated from published IGV sequence data from B cell clones participating in autoimmune responses in patients with Myasthenia Gravis (MG), Rheumatoid Arthritis (RA), and Sjögren's Syndrome (SS). At present, as no standards exist for cell sampling and sequence extraction methods, data obtained by different research groups from two studies of the same disease often vary considerably. Nevertheless, based on comparisons of data groups within individual studies, we show here that lineage trees from different individual patients are often similar and can be grouped together, as can trees from two different tissues in the same patient, and even from IgG- and IgA-expressing B cell clones. Additionally, lineage trees from most studies reflect the chronic character of autoimmune diseases.

Arthritis, Rheumatoid↗

PubMed2005

Natural killer cell education in mice with single or multiple major histocompatibility complex class I molecules.

The ability of murine NK cells to reject cells lacking self MHC class I expression results from an in vivo education process. To study the impact of individual MHC class I alleles on this process, we generated mice expressing single MHC class I alleles (K(b), D(b), D(d), or L(d)) or combinations of two or more alleles. All single MHC class I mice rejected MHC class I-deficient cells in an NK cell-dependent way. Expression of K(b) or D(d) conveyed strong rejection of MHC class I-deficient cells, whereas the expression of D(b) or L(d) resulted in weaker responses. The educating impact of weak ligands (D(b) and L(d)) was further attenuated by the introduction of additional MHC class I alleles, whereas strong ligands (K(b) and D(d)) maintained their educating impact under such conditions. An analysis of activating and inhibitory receptors in single MHC class I mice suggested that the educating impact of a given MHC class I molecule was controlled both by the number of NK cells affected and by the strength of each MHC class I-Ly49 receptor interaction, indicating that NK cell education may be regulated by a combination of qualitative and quantitative events.

Alleles↗

PubMed2005

Models for the dynamics and order of immunoglobulin isotype switching.

Experiments show that class switch recombination (CSR) depends on the number of divisions that the cell has performed rather than on the time since stimulation. Using computer simulations of CSR dynamics in B cell populations, we addressed the following questions. How does the probability of CSR depend on the number of divisions that a cell has performed? How does the cell decide which isotype to switch to? Does this decision depend on the distance between the genes of the pre-switch and the post-switch isotype? Our results indicate that post-switch isotype choice may be determined indirectly by the probabilities of division (which is fixed) and of switching per division (which increases as a function of the number of divisions that a cell performs), and more directly by a bias in the choice of the post-switch C gene segment towards those proximal to the pre-switch C gene.

Algorithms↗

PubMed2005

Computational modeling of human natural killer cell development suggests a selection process regulating coexpression of KIR with CD94/NKG2A.

Natural killer cells fail to lyse target cells expressing sufficient levels of self MHC class I molecules, providing one mechanism to secure self tolerance. Inhibition of lysis is mediated by inhibitory receptors expressed by NK cells, such as the murine Ly49 receptors, human KIR receptors and CD94/NKG2A, expressed by both species. To ensure that most, if not all, NK cells express at least one inhibitory receptor for self MHC class I, selection processes have been postulated for murine NK cells regulating the number and identity of inhibitory receptors expressed by each cell. The presence of similar selection processes in human NK cells has not been demonstrated. In previous studies using mathematical modeling we have shown that, in the Ly49 system, the sequential model (in which gene expression and selection operate simultaneously) is most likely to explain the observed expression frequencies. We also predicted the parameters (such as receptor-ligand binding affinity levels) under which the models fit with the observed frequencies. This study aims to evaluate whether these models may be valid in the human system. Our data suggest that if selection operates during human NK cell development, it affects the co-expression of CD94/NKG2A and KIR rather than KIR expression alone, and is more likely to be governed by the two-step selection model.

Animals↗

PubMed2004

Screening of alternative models for transitional B cell maturation.

Several functional and phenotypic B cell populations have been described in the spleen. These include the 'transitional' subsets, which are thought to be late differentiation intermediates of marrow-derived, mature follicular B cells. The exact progenitor-successor relationships of these transitional subsets, as well as whether a proliferative step is requisite for follicular B cell maturation, remain controversial. Moreover, whether late B cell differentiation might involve branched or asynchronous maturation pathways, thus allowing some cells to 'skip' one or more of these stages, has not been investigated. Herein we have used mathematical modeling to interrogate these possibilities. Using mathematical models that numerically simulate splenic B cell population dynamics, we have determined which alternative models of differentiation best fit existing in vivo labeling data. Our results indicate that follicular differentiation does not involve a proliferating splenic intermediate. Our results further suggest that some developing cells move directly from the immature marrow pool to more advanced semi-mature peripheral subsets without passing through the least mature subset in the spleen.

Animals↗

PubMed2004

Analysis of mutational lineage trees from sites of primary and secondary Ig gene diversification in rabbits and chickens.

Lineage trees of mutated rearranged Ig V region sequences in B lymphocyte clones often serve to qualitatively illustrate claims concerning the dynamics of affinity maturation. In this study, we use a novel method for analyzing lineage tree shapes, using terms from graph theory to quantify the differences between primary and secondary diversification in rabbits and chickens. In these species, Ig gene diversification starts with rearrangement of a single (in chicken) or a few (in rabbit) V(H) genes. Somatic hypermutation and gene conversion contribute to primary diversification in appendix of young rabbits or in bursa of Fabricius of embryonic and young chickens and to secondary diversification during immune responses in germinal centers (GCs). We find that, at least in rabbits, primary diversification appears to occur at a constant rate in the appendix, and the type of Ag-specific selection seen in splenic GCs is absent. This supports the view that a primary repertoire is being generated within the expanding clonally related B cells in appendix of young rabbits and emphasizes the important role that gut-associated lymphoid tissues may play in early development of mammalian immune repertoires. Additionally, the data indicate a higher rate of hypermutation in rabbit and chicken GCs, such that the balance between hypermutation and selection tends more toward mutation and less toward selection in rabbit and chicken compared with murine GCs.

Algorithms↗

PubMed2003

Models for antigen receptor gene rearrangement. III. Heavy and light chain allelic exclusion.

The extent of allelic exclusion in Ig genes is very high, although not absolute. Thus far, it has not been clearly established whether rapid selection of the developing B cell as soon as it has achieved the first productively rearranged, functional heavy chain is the only mechanism responsible for allelic exclusion. Our computational models of Ag receptor gene rearrangement in B lymphocytes are hereby extended to calculate the expected fractions of heavy chain allelically included newly generated B cells as a function of the probability of heavy chain pairing with the surrogate light chain, and the probability that the cell would test this pairing immediately after the first rearrangement. The expected fractions for most values of these probabilities significantly exceed the levels of allelic inclusion in peripheral B cells, implying that in most cases productive rearrangement and subsequent cell surface expression of one allele of the heavy chain gene probably leads to prevention of rearrangement completion on the other allele, and that additional mechanisms, such as peripheral selection disfavoring cells with two productively rearranged heavy chain genes, may also play a role. Furthermore, we revisit light chain allelic exclusion by utilizing the first (to our knowledge) computational model which addresses and enumerates B cells maturing with two productively rearranged kappa light chain genes. We show that, assuming that there are no selection mechanisms responsible for abolishing cells expressing two light chains, the repertoire of newly generated B lymphocytes exiting the bone marrow must contain a significant fraction of such kappa double-productive B cells.

Alleles↗

PubMed2003

Generation of the natural killer cell repertoire: the sequential vs. the two-step selection model.

Natural killer (NK) cells are lymphocytes which can kill tumor and virus-infected cells, and mediate acute rejection of bone marrow grafts. NK-cell killing is directed primarily at target cells which do not express sufficient levels of self-major histocompatibility complex (MHC) class-I molecules. Inhibition of lysis of self-MHC-expressing target cells is mediated via inhibitory receptors on the NK cell, which bind to MHC molecules. Each NK cell expresses only a subset of all its inhibitory receptor gene repertoire, which may bind to only a subset of the self-MHC molecules expressed by other cells of the organism. Two conceptual models have been proposed to explain the process of NK cell 'education' in which these cells adapt, during their development, to the self-MHC environment: the two-step selection and the sequential models. In this manuscript we develop mathematical and computational models of the process of NK cell development and education, which implement the two conceptual models. We use this theoretical framework to examine the available data on NK cell repertoire compositions, and evaluate the degree these data support either of the two conceptual models. We show that the data published so far on NK cell receptor expression patterns is insufficient to refute either model, since data on NK cell receptor binding affinities to MHC is also needed. However, the models allow us to make predictions on these binding affinities, which can later be tested experimentally.

Animals↗

PubMed2003

Maximum likelihood estimator and likelihood ratio test in complex models: an application to B lymphocyte development.

In this paper we introduce a simple framework which provides a basis for estimating parameters and testing statistical hypotheses in complex models. The only assumption that is made in the model describing the process under study, is that the deviations of the observations from the model have a multivariate normal distribution. The application of the statistical techniques presented in this paper may have considerable utility in the analysis of a wide variety of complex biological and epidemiological models. To our knowledge, the model and methods described here have not previously been published in the area of theoretical immunology.

Animals↗

PubMed2003

Asynchronous differentiation models explain bone marrow labeling kinetics and predict reflux between the pre- and immature B cell pools.

B lymphopoiesis has historically been depicted as a unidirectional process, in which cohorts of developing cells transit through successive differentiative stages in an irreversible, synchronous manner. Here, we examine this view by combining kinetic analysis of developing B cell subsets in the bone marrow with mathematical modeling. Our bromo-deoxyuridine (BrdU) labeling data are incompatible with B cell development being a synchronous process, because labeling curves are non-linear. Moreover, we show that B cell development may not be completely unidirectional, because our results support the possibility of a phenotypic "reflux" among the immature to the pre-B cell subsets.

Animals↗

PubMed2002

Age- and tissue-specific differences in human germinal center B cell selection revealed by analysis of IgVH gene hypermutation and lineage trees.

The elderly produce increased levels of antibodies to autologous antigens and are less able to make high-affinity antibodies to foreign antigens. Ig gene hypermutation is integral to the affinity maturation process but previous studies of hypermutation with age have yielded conflicting results. The cells studied have represented post-germinal center (GC) populations and, therefore, the results may be complicated by possible differences in activation history. We studied Ig genes from GC B cells to elucidate which factors in the affinity maturation process change with age. Age-related changes in the pattern of hypermutation were seen, although the analysis of variable region heavy chain (VH) genes and their lineage trees shows that an alteration in the mechanism of somatic hypermutation is unlikely. The changes are due to founder cell effects and/or the process of selection. Striking tissue-specific differences were seen. All measurements indicated that selection of Ig genes may decrease in Peyer's patch GC but increase in splenic GC with age. These tissue-specific differences highlight the importance of considering the activation and effector sites when studying immune senescence.

Aging↗

PubMed2002

The dynamics of germinal centre selection as measured by graph-theoretical analysis of mutational lineage trees.

We have developed a rigorous graph-theoretical algorithm for quantifying the shape properties of mutational lineage trees. We show that information about the dynamics of hypermutation and antigen-driven clonal selection during the humoral immune response is contained in the shape of mutational lineage trees deduced from the responding clones. Age and tissue related differences in the selection process can be studied using this method. Thus, tree shape analysis can be used as a means of elucidating humoral immune response dynamics in various situations.

Algorithms↗

PubMed2002

PESI--an intelligent system for prediction of enzyme-substrate interactions based on experimental constraints.

We present a system for predicting protein-protein modifications, and demonstrate its usefulness in the field of signal transduction research. Signal transduction is one of the most important areas of investigation in biological research. One of the major mechanisms frequently employed by cells to regulate signal transduction processes involves protein phosphorylation by various kinases. As many as 1,000 protein kinases and 500 protein phosphatases in the human genome are thought to be involved in phosphorylation processes which regulate all aspects of cell function. The complexity of such interactions stems from the enormous number of factors and interactions, which makes the identification of putative substrates for any given enzyme by straightforward experimentation increasingly difficult. We present here a data mining algorithm, based on the similarity between the modifier proteins and between the modified proteins, and on experimental constraints. The application presented here (PESI) focuses on substrate phosphorylation by various enzymes. This algorithm reduces the number of substrate candidates for experimental study by about two orders of magnitude. Moreover, this algorithm has already yielded predictions for previously unknown substrates of the enzymes PKCdelta and PKCeta, which we have confirmed experimentally.

Algorithms↗

PubMedDate not supplied

Immune system learning and memory quantified by graphical analysis of B-lymphocyte phylogenetic trees.

The immune system learns from its encounters with pathogens and memorizes its experiences. One of the mechanisms it uses for this purpose is the intra-individual evolution of antigen receptors on B lymphocytes, achieved via hypermutation and selection of antigen receptor variable region genes during an immune response. We have developed a novel method for analyzing the graphical properties of phylogenetic trees of receptor genes which have been mutated and selected during an immune response. In the study presented here, we address the artifacts introduced by experimental methods of cell collection for DNA analysis, the meaning of each parameter measured on the tree graphs, and the differences between the dynamics of the humoral immune response in different lymphoid tissues.

Adaptation, Physiological↗