Molecular Profiling of MALT lymphoma at different anatomical sites

PhD project strategic theme: Bioscience for an integrated understanding of health

Mucosa-associated lymphoid tissue (MALT) lymphoma is the most common subtype of Marginal Zone B cell lymphoma, and the third most frequent B cell lymphoma. It arises in diverse anatomic sites including the stomach, thyroid, lung, ocular adnexa and small intestine.

Whole exome sequencing (WES) has been carried out only on a small number of MALT lymphoma subtypes. This mutation profiling together with targeted panel sequencing has identified a large number of distinct genetic changes which occur at variable frequency at different anatomic sites. One of these genetic findings is Programmed death-ligand 1 (PD-L1 or CD274) which preferentially occurs in thyroid MALT lymphoma, with a large percentage of the mutations being deleterious.

To further characterise the role of these PD-L1 mutations in thyroid MALT in my 3-month rotation project I sought to investigate whether PD-L1 is also targeted by chromosomal deletions in thyroid MALT using an MLPA assay to assess the potential copy number variation of PD-L1. I investigated 35 thyroid MALT cases and identified frequent deletions of PD-L1 and JAK2 in thyroid MALT. These findings will allow me to correlate the deletions identified in the samples with already existing next generation sequencing (NGS) data as well as clinical data from the patients.

To further investigate the role of PD-L1 it would be vital to establish the expression levels of PD-L1 and PD-1, and the level at which the two proteins and the different immune cells present interact in the tumour micro-environment of thyroid MALT lymphoma. This can be undertaken through immunofluorescent staining of B cell and T cell markers as well as PD-1 and PD-L1 of thyroid MALT sections with and without identified PD-L1 one deletions or deleterious mutations, providing us with further insight into the tumour microenvironment of MALT lymphoma and the potential significance of the PD-L1 inactivation.

The Du laboratory has recently published a study where the group have successfully undertaken NGS on a relatively large number of MALT lymphoma cases, although due to the limited samples they had at the time they could only undertake WES of 13 samples of thyroid MALT.

Currently the Du laboratory has 76 thyroid MALT samples which have been sequenced using a 93-gene panel, although gene panels can provide a vast amount of information they will only cover a part of the mutational profile of the disease due to the reduced area of the genome being analysed in antithesis to WES. Thus, to further elucidate the different genetic mutations in MALT lymphoma, I will firstly undertake WES of thyroid MALT lymphomas which have already been analysed using a targeted sequencing panel, focusing on thyroid MALT lymphomas which do not have PD-L1 mutations, in order to further characterise the genetic landscape of thyroid MALT lymphoma. Moreover, upon analysis of the WES results, a gene panel which can be used to analyse different anatomic sites of MALT lymphoma can be created focusing on recurrent and potentially pathogenic mutations identified in the WES undertaken on the thyroid MALT samples.