Genetics of diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is one the most common forms of non-Hodgkin lymphoma and one of the most aggressive B-cell neoplasms. Although most patients respond to current standard treatments, a significant number of them relapse and become refractory to treatment. Hence, there is a need for new approaches in the management of DLBCL. In recent years, a number of studies using next-generation sequencing (NGS) have contributed to the characterization of the disease and have revealed a set of deregulated cellular mechanisms in DLBCL. However, DLBCL is a very heterogeneous disease and additional work is required in order to achieve a comprehensive understanding of the mechanisms underlying its lymphomagenesis.

The work described in this thesis aimed to further characterize the genome of DLBCL and identify novel genomic alterations by employing a number of NGS methods. Furthermore, this thesis sought to functionally describe the effect of some of these alterations and explore how they could be meaningful from a therapeutic perspective.

We first embarked on a targeted sequencing approach in order to assess the impact of mutations in a set of key DNA repair genes. DNA repair is critical in B-cell development as it ensures the regulation of antibody diversification processes. The results showed that half of the tumors analyzed carry mutations in DNA repair genes and the most frequently targeted mechanisms are mismatch repair, DNA damage response, homologous recombination and non-homologous end-joining. Moreover, functional analysis enabled the association of a number of those mutations to specific phenotypes.

Whole exome sequencing identified a number or previously unreported somatic mutation targets in DLBCL. In addition, it revealed that some genes known to be involved in DLBCL were mutated at a much higher frequency in Chinese patients as compared to patients from Western populations. The impact of mutations in DTX1, a gene encoding for a negative regulator of Notch signaling, was functionally assessed and a number of mutations were found to be deleterious.

Finally, whole genome sequencing enabled the identification of structural variations such as translocations in the genome of DLBCL. IGH translocations are a hallmark of DLBCL and the locus is often found juxtaposed to proto-oncogenes which leads to their upregulation. We identified PD-L1, a common culprit of immune suppression in cancer, as a novel IGH translocation partner in DLBCL. Translocations involving the PD-L1 locus were found to impact patient survival and were associated with the more aggressive non-germinal center-like subtype of the disease

List of scientific papers

I. de Miranda NF, Peng R, Georgiou K, Wu C, Falk Sörqvist E, Berglund M, Chen L, Gao Z, Lagerstedt K, Lisboa S, Roos F, van Wezel T, Teixeira MR, Rosenquist R, Sundström C, Enblad G, Nilsson M, Zeng Y, Kipling D, Pan-Hammarström Q. DNA repair genes are selectively mutated in diffuse large B-cell lymphomas. J Exp Med. 2013 Aug 26;210(9):1729-42.
https://doi.org/10.1084/jem.20122842

II. de Miranda NF, Georgiou K, Chen L, Wu C, Gao Z, Zaravinos A, Lisboa S, Enblad G, Teixeira MR, Zeng Y, Peng R, Pan-Hammarström Q. Exome sequencing reveals novel mutation targets in diffuse large B-cell lymphomas derived from Chinese patients. Blood. 2014 Oct 16;124(16):2544-53.
https://doi.org/10.1182/blood-2013-12-546309

III. Georgiou K, Chen L, Berglund M, de Miranda NF, Lisboa S, Fangazio M, Ren W, Zhu S, Hou Y, Wu K, Fang W, Wang X, Zhang H, Zhang L, Zeng Y, Bhagat G, Nordenskjöld M, Sundström C, Dalla-Favera R, Enblad G, Teixeira MR, Pasqualucci L, Peng R, Pan-Hammarström Q. Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas. [Submitted]