Genomic determinants of chronic lymphocytic leukemia progression: from individual drivers to a heterogeneous genetic makeup

Ferran Nadeu Prat

Dr. Elias Campo

Chronic lymphocytic leukemia (CLL) is the most common form of leukemia in adults in Western countries. Although the disease can follow an indolent clinical course, it can progress rapidly in a fraction of cases, become resistant to treatment and even transform into a more aggressive B-cell lymphoma, a phenomenon known as Richter's syndrome. During my doctoral thesis, we delved into the characterization of the genomic determinants that influence the progression of CLL, providing tools that would facilitate and improve the characterization of patients in clinical practice. During the first part of the thesis, we 1) characterized a novel non-coding mutation affecting the small nuclear RNA U1, a component of the spliceosome involved in the recognition of the 5' splice site; 2) to delve deeper into the subclonal architecture of CLL by identifying mutations present in small subpopulations associated with disease progression, and 3) to analyze the complete genome of CLL patients who developed Richter syndrome and identify a new mutational process causing the mutational and genomic complexity associated with this syndrome. Despite the great genomic and epigenetic knowledge of this disease generated in recent years, only two biomarkers are studied in the diagnosis of patients. These two biomarkers, which are associated with the prognosis of patients and their response to treatment, are the mutational status of immunoglobulins and TP53 mutations. The complexity of the immunoglobulin gene prevents its characterization using next-generation sequencing data with available analysis programs and, as a result, its study continues to be carried out using specific assays. To facilitate their characterization both in research and clinical practice, in the second part of my doctoral thesis we developed a bioinformatics algorithm called IgCaller aimed at reconstructing the rearrangements and mutational status of immunoglobulins in lymphoid neoplasms from whole genome or exome sequencing. Using IgCaller we also characterized a recurrent mutation in the immunoglobulin gene IGLV3-21 associated with an aggressive form of CLL and with a strong influence on the current stratification of patients. The use of IgCaller allows, for the first time, the analysis of the mutational status of immunoglobulins and the identification of this new mutation in a simple and economical way from next-generation sequencing data, a methodology currently used to study TP53 mutations. Thus, a single diagnostic kit will allow the determination of the different biomarkers studied during the diagnosis of patients with CLL. IgCaller has aroused the interest of the Hospital Clínic de Barcelona and biotechnology companies with extensive experience in the sector (SOPHiA GENETICS, Aniling and Illumina). Based on this interest, we have started several collaborations to introduce IgCaller into their diagnostic kits already used in several national and international hospitals. Here I propose the development and translation of IgCaller into clinical practice by top national and international hospitals and companies in the PIONER 2020 Award.

- Originality: IgCaller is the first bioinformatics algorithm that allows the analysis of immunoglobulins from next-generation sequencing data (genome sequencing, exome and gene panels), facilitating the use of a single diagnostic kit that characterizes the different biomarkers studied in the clinical routine of CLL. - Feasibility: we have demonstrated in the two publications mentioned above that IgCaller works correctly to be used in clinical practice. Together with companies with extensive experience in the sector, we will bring IgCaller to clinical routine - Expected impact: it is expected that different national and international hospitals, such as the Hospital Clínic de Barcelona, ​​will adopt the use of IgCaller for the characterization of immunoglobulins in the diagnosis of CLL, thus reducing costs and time. - Expected time to application: the first diagnostic kit from SOPHiA GENETICS analyzing immunoglobulins with the IgCaller is expected to be available in mid-2021. The collaboration with Aniling and Illumina is expected to be carried out during 2021.

Chronic Lymphocytic Leukemia (CLL); Adult Leukemia; Indolent Clinical Course; Rapid Progression; Treatment Resistance; Richter's Syndrome; Genomic Determinants; Disease Progression; Patient Characterization; Clinical Practice; Non-coding Mutation; Small Nuclear RNA U1; Spliceosome; 5' Splice Site Recognition; Subclonal Architecture; Small Subpopulations; Mutational Process; Genomic Complexity; Epigenetic Knowledge; Biomarkers; Diagnosis; Prognosis; Treatment Response; Immunoglobulin Mutational Status; TP53 Mutations; Next-Generation Sequencing Data; Bioinformatics Algorithm; IgCaller; Reconstruct Rearrangements; Lymphoid Neoplasms; Whole Genome Sequencing; Exome Sequencing; Recurrent Mutation; Immunoglobulin Gene IGLV3-21; Aggressive CLL; Patient Stratification; Simple Analysis; Economical Analysis; Diagnostic Kit; Hospital Clínic de Barcelona; Biotechnology Companies; SOPHiA GENETICS; Aniling; Illumina; Collaborations; Diagnostic Kits; National Hospitals; International Hospitals; PIONER 2020 Award.