a.collins@unsw.edu.au

Project 1:  A bioinformatic study of immunoglobulin lambda genes

Project available for 1 student

Over the last few years, we have conducted bioinformatics studies of immunoglobulin heavy chain genes, and kappa light chain genes. We wish to conclude this series of studies by evaluating the reported lambda light china genes. This project will involve the development of a database of rearranged genes, and their partitioning into IGLV and IGLJ components. This will then allow gene usage, as well as gene processing (exonuclease removals and N nucleotide addition), to be quantified. Detailed analysis of gene usage should allow us to identify allele sequences that include sequencing errors, as well as identifying the existence of likely unreported polymorphisms. If any such polymorphisms are identified, and if the student was willing and able, the honours project could be modified to include genome screening for these polymorphisms. This would involve PCR, cloning and sequencing.

Selected References (Available on request)

• Lee, C.E.H. et al. Reconsidering the human immunoglobulin heavy chain locus. 1. An evaluation of the expressed human IGHD gene repertoire. Immunogenetics 57, 917-925 (2006).

• Lee, C.E.H., Jackson, K.J.L., Sewell, W.A. & Collins, A.M. Use of IGHJ and IGHD gene mutations in analysis of immunoglobulin sequences for the prognosis of chronic lymphocytic leukemia. Leukemia Research 31, 1247-1252 (2007).

• Wang Y, Jackson^, K.J.L., Sewell W. A. and Collins A. M. The human immunoglobulin heavy chain gene repertoire contains relatively few IGHV gene polymorphisms. (Submitted for publication, and available on request.)

Project 2: The study of IgG subclasses by mutation analysis of rearrangedVDJ genes

IgG subclasses have been known of for several decades, and subclass responses to specific antigens are routinely reported in the scientific literature. There is some knowledge of how subclass responses are regulated, and there have been many reports that have identified particular subclasses with the response to specific antigens. For example, it is often said that IgG3 antibodies are directed against polysaccharide antigens. Our overall understanding of IgG subclass functions, however, is poor. We have recently revealed unexpected characteristics of the IgE response, by sequencing IgE genes and by studying the patterns of somatic point mutations seen in these genes. We now wish to use this approach to study IgG subclasses. We are particularly interested to study the mutational patterns of IgG3 and IgG4 antibodies.

This project will involve the development of RT-PCR for the amplification rearranged VDJ genes from cells that have class switched to different IgG subclass. Particularly for IgG4 sequences, this may require the development of nested PCRs to amplify the very few transcripts that are likely to be present in samples. PCR products will then be cloned and sequences. Patterns of mutation will then be determined using bioinformatic tools developed in our laboratory.

Selected References (Available on request)

• Dahlke, I., Nott, D.J., Ruhno, J., Sewell, W.A. & Collins, A.M. Antigen selection in the IgE response of allergic and non-allergic individuals. Journal of Allergy and Clinical Immunology 117, 1477-1483 (2006).