Molecular Investigations of high-risk Mantle Cell Lymphoma : Genetic factors and the impact of the microenvironment

Sammanfattning: Mantle cell lymphoma (MCL) is an aggressive disease, with variable clinical course and heterogenous molecular characteristics. In this thesis, which is based upon six original papers, we aimed to understand MCL deregulations, both at intrinsic and extrinsic levels, to identify companion biomarkers that would allow patient stratification. With the aim to bridge the gap between research and clinical application, the current work took advantage of major technological breakthroughs to advance the biological understanding of MCL. Paper I showed the applicability to apply next-generation sequencing to formalin-fixed paraffin-embedded (FFPE) MCL tumor samples, enabling clinical implementation. The workflow allowed for the identification of recurrent and new mutations that can be used to guide treatment and to investigate the efficacy of new compounds in MCL. Despite major clinical benefits, the current standard of care shows varying treatment responses, with most patients eventually relapsing. In paper II we explored the transcriptomic profile of patients submitted to this regimen and identified metabolic changes in patients with worse treatment outcome. We focused on CPT1A, a rate-limiting enzyme in fatty acid oxidation, as a biomarker for MCL, and showed that is has a negative prognostic impact. TP53 mutations have been accepted as markers of poor prognosis in MCL, but genetic evaluation remains a challenge in many clinical facilities. Thus, in paper III we explored the possibility of using p53, evaluated by immunohistochemistry, as a surrogate marker for TP53 missense mutation. We showed a high concordance between p53 overexpression and TP53 missense mutation. In paper IV we intended to understand the role of c-Myc in MCL. We concluded that overexpression of c-Myc at protein and mRNA level was associated with poor clinical outcomes and, contrary to other B-cell lymphomas, MYC was not often translocated nor showed amplifications in MCL. Further, we describe a synergistic negative effect of dual aberrations in MYC and TP53. Paper III and paper IV findings strengthened the need for patient stratification in MCL for effective clinical management of the disease. Paper V and paper VI focused on the tumor-extrinsic factors in MCL. In paper V, we characterized the immune composition of MCL, particularly the presence of T-cell subtypes and the M2-like macrophages (CD163+ cells). We concluded that FoxP3+ cells were associated with shorter time to progression in patients treated with standard of care and that the presence of CD163+ cells was a negative prognostic marker, irrespective of treatment. In paper VI we were interested in understanding the crosstalk between tumor cells, T-cells and CD163+ cells in MCL in a spatial context. We showed that CD163+ cells are affected by their distance to tumor cells and that tumor microenvironments with presence of CD163+ cells show higher levels of MAPK activation. In summary, this work provided a comprehensive analysis of the contribution of molecular and tumor-extrinsic factors to treatment outcome in MCL and advanced the current knowledge of the disease, by highlighting additional therapeutic targets.