The extent of clonal structure in different lymphoid organs

Reconstructing and mining the B cell repertoire with ImmunediveRsity

The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/

How oligoclonal are germinal centers? A new method for estimating clonal diversity from immunohistological sections

Background

The germinal center (GC) reaction leads to antibody affinity maturation and generation of memory B cells, but its underlying mechanisms are poorly understood. To assemble this puzzle, several key pieces of information are needed, one in particular being the number of participating B cell clones. Since this clonal diversity cannot be observed directly, earlier studies resorted to interpreting two types of available experimental data: Immunohistology of GCs containing two phenotypically distinct B-cell populations, and antibody gene sequences of small B-cell samples from GCs. Based on a simple model, investigators concluded that a typical GC was seeded by 2-8 B cells, endorsing the current notion that GCs are oligoclonal from the onset.

Results

A re-evaluation of these data showed that the used simple model is not statistically consistent with the original data. From an analysis of the experimental system, we propose a new model for estimating GC clonal diversity, including the initially neglected sampling and measurement errors, and making more general assumptions. Consistency analysis with the new model yielded an estimation of sampling and measurement errors in the experimental data of 10-11% for one B-cell population and 62-64% for the other population, and an average number of 19-23 seeder B cells. An independent analysis of antibody gene sequences of small B-cell samples from GCs, using an adapted Yule estimator of diversity, yielded a minimum estimation of 20-30 GC founder B cells, confirming the previous results.

Conclusions

Our new experimental-based model provides a highly improved method to estimate the clonal diversity of GCs from inmunohistochemistry data of chimeric animals. Calculations based on this model, and validated by an independent approach, indicate that GCs most likely contain broadly varying numbers of different B cell clones, averaging 5- to 10-fold more clones than previously estimated. These findings, in line with recent results showing that GC sizes and life times are also subject to high variability, dramatically change the picture of GC dynamics.

Modelling Two Possible Mechanisms for the Regulation of the Germinal Center Dynamics

Research on the germinal center has tried to unravel the mechanisms that control its dynamics. In this study we focus on the termination of the germinal center reaction, which is still an open problem. We propose two hypothetical biological mechanisms that may be responsible for the control of germinal center dynamics and analyze them through mathematical models. The first one is based on the differentiation of follicular dendritic cells and/or T cells. Interaction of these cells in the differentiated state with germinal center B cells would promote B cell differentiation into memory B cells and Ab-forming cells, ending the germinal center reaction. The second mechanism applies only to a scenario without recycling and consists of the decay of a hypothetical proliferation signal for centroblasts that limits the number of cell divisions. Each of the models makes predictions that can be experimentally tested.

Experimentally induced unilateral tooth loss: expression of type II collagen in temporomandibular joint cartilage

PURPOSE

We sought to examine possible changes in pattern and concentration of type II collagen in the condylar cartilage and articular disc of the temporomandibular joint (TMJ) in response to unilateral extraction of mandibular teeth in a rabbit model as a means of elucidating the effects of unilateral mastication on the TMJ.

METHODS

A total of 12 experimental rabbits were killed either 3 or 6 weeks after the extractions, and 3 additional rabbits without extractions were used as controls. TMJ blocks from both sides of each of the 15 animals were examined for type II collagen via an immunoperoxidase procedure.

RESULTS

Anti-type II collagen antibody (Ab) binding was detected mainly in the hypertrophic chondroblast layer of the condylar cartilage of normal rabbits. At 3 weeks after unilateral extraction of teeth, anti-type II collagen Ab binding to the territorial matrix of the hypertrophic chondroblast layer of the condylar cartilage and to the disc was stronger than normal. The increase in Ab binding appeared more dramatic on the nonfunctional side than on the functional side of TMJ. Variations from the normal pattern of anti-type II collagen Ab binding in terms of distribution through the extracellular matrix and fibrillar appearance were also observed.

CONCLUSION

The findings suggest that the condylar cartilage and disc adapt to the imbalance induced by unilateral extraction of teeth through chondrocyte repair responses involving collagen II expression that appear to differ between the functional and nonfunctional sides of the TMJ.

Population Size and Radiosensitivity of Murine Hematopoietic Endogenous Long-Term Repopulating Cells

A new assay is described that measures the numbers (n) of endogenous long-term repopulating cells (eLTRC) surviving sublethal irradiation. The assay is based on analysis of variances of Pgk-1a phenotypes within groups of sublethally irradiated Pgk-1a/b mice. When ln n is plotted as a function of dose, the radiosensitivity (D0) is the negative reciprocal of the slope and the y-intercept is N or total numbers of eLTRC per mouse. The assay is unique in that N is an absolute value not requiring correction for seeding efficiency, or f. From two independent estimates, total numbers of eLTRC were determined to be 8,700 or 11,900 cells per mouse and D0 was found to be 0.82 or 0.83 Gy. If eLTRC are, in fact, the long-term repopulating cells (LTRC) defined by classical transfer assay, then LTRC can home to the marrow with nearly unit efficiency, only one to two LTRC are required for a mouse to survive a radiation LD50/30, and LTRC possess nearly unlimited self-renewal potential.

Analysis of somatic hypermutation in mouse Peyer's patches using immunoglobulin kappa light-chain transgenes

We have exploited mice transgenic for an immunoglobulin kappa light chain in order to show that immunoglobulin genes in the B cells of Peyer's patches in unimmunized mice carry a high level of somatic mutations. Most of the mutations are found in the subpopulation of B cells which, based on peanut agglutinin binding, derive from the germinal centers. The number of mutations per clone and their distribution along the variable gene segment (indicative of untemplated point mutations) are very similar to those found in antigen-specific splenic B cells of normal mice after secondary immunization. The mutations accumulate mainly in complementarity-determining region 1, in particular in some specific codons (Ser-26, Ser-31, and Ser-77) which have been previously recognized as intrinsic hypermutational hotspots. These results suggest that, as in the spleen, somatic mutation occurs in B cells which have migrated to the germinal centers, probably as a consequence of stimulation by antigens present in the gut environment. Transgenic animals are increasingly being used to define the signals involved in hypermutation. However, their subsequent study is very time-consuming because it is based on immunization and analysis of hybridomas or antigen-selected cells. We propose that the use of Peyer's patches of unimmunized adult mice offers a reliable and simple approach to analyze hypermutation of transgenes.