Panagiotis Baliakas' research on molecular genetics of hematological malignancies

Stereotyped subsets in CLL

Panagiotis Baliakas, Viktor Ljungström, Mattias Mattsson, Lesley-Ann Sutton, Paolo Ghia, Kostas Stamatopoulos, Richard Rosenquist

One of the strongest pieces of evidence for antigen selection in CLL is the fact that up to 30 % of all patients belong to subgroups defined as stereotyped subsets; where within each subset patients carry quasi-identical B-cell receptors (BcRs). Preliminary evidence suggest that this shared immunogenetic signature extends to similar clinico-biological characteristics.

In a cohort of more than 8500 patients with CLL, we have shown that each stereotyped subset is a distinct clinical entity, overcoming even the classification of CLL based on the somatic hypermutation status of the immunoglobulin heavy variable genes (IGHV), namely unmutated and mutated CLL (U-CLL and M-CLL respectively). We also proposed a novel stratification scheme integrating immunogenetic and genetic data, improving the well-established Döhner hierarchical model.

Moving a step further, we reported that patients belonging to stereotyped subsets #1 and #2 have not benefited from the advances in the chemo(immune)therapy, similar to patients carrying TP53 aberrations, suggesting that alternative treatments should be tested for subset #1 and #2 patients.

The genetics of stereotyped subsets

As mentioned above, patients in each stereotyped subset are characterized by a distinct genomic background. We and others have for example highlighted the striking enrichment for SF3B1 and NOTCH1 mutations in subsets #2 and #8 respectively. We are currently proceeding with whole genome sequencing in more than 200 CLL patients belonging to major stereotyped subsets, with the aim to fully elucidate the genetic landscape of each stereotyped subset.

Genomic complexity in CLL

Panagiotis Baliakas, Alexander C Leeksma, Blanca Espinet, David Oscier, Sarka Pospisilova, Claudia Haferlach, Aron Karter, Paolo Ghia, Kostas Stamatopoulos; on behalf of ERIC (European Research Initiative on CLL)

Recently, chromosome banding analysis (CBA) in CLL has attracted great interest due to reports suggesting that complex karyotype (CK), defined by the presence of three or more numerical and/or structural aberrations, may represent a novel predictive marker for refractoriness to both chemo-based regimens as well as novel targeted therapies, independently of the presence of TP53 aberrations.

However, many challenges towards routine clinical application of CBA still need to be overcome, indicating the need for rigorous definitions, validated methodologies and systematic investigation in large cohorts.

We evaluated CK in a multi-institutional series of more than 5000 patients with CLL and available CBA data. We reported that not all CKs are equivalent and only high complexity, defined by the presence of at least 5 chromosomal aberrations, was prognostically adverse, independently of clinical stage, SHM and TP53 status. Moreover, we propose a novel hierarchical model, incorporating CK, SHM and TP53 status, that is capable of identifying subgroups of patients with markedly distinct clinical outcomes.

Clonal evolution in CLL treated with B-cellreceptor inhibitors

Mattias Mattsson, Tatjana Pandzic, Viktor Ljungström, Lydia Scarfo, Niki Stavroyanni, Paolo Ghia, Panagiotis Baliakas, Kostas Stamatopoulos, Richard Rosenquist

The introduction of B-cellreceptor inhibitors (BCRi) has revolutionized the treatment possibilities of CLL and introduced treatment principles based on the expanded knowledge regarding the basic biology of CLL. Initially, these treatments have been introduced for patients with TP53-aberrations and/or being refractory to chemoimmunotherapy, but are now being more used in other subgroups of CLL-patients.

The treatment with BCRi is carried out as a continuous, oral treatment with good effect regarding the patients’ symptoms and blood counts. However, only a few will reach complete remission (5 % on monotherapy with ibrutinib). After one year of treatment with ibrutinib, 25 % of the patients still have a remaining lymphocytosis in peripheral blood. Consequently, these patients have a high residual tumour burden over time.

Resistance to BCRi is well described and it is accounted for by mutations in BTK (C481S) and several activating mutations in PLCg2. Clonal evolution is also well described in both untreated CLL patients and after treatment with chemoimmunotherapy, with the last group displaying an accelerated clonal evolution with the selection of resistant clones.

The genetic landscape of CLL

With this background we have collected longitudinal blood- and bone marrow samples from CLL patients on fixed time-points from start of treatment and during treatment, up until 39 moths after treatment initiation. We are now performing whole exome sequencing (WES) and array analysis to identify the genetic landscape at the start of treatment, changes due to clonal evolution over time, as well as in-depth studies on potential new findings. In parallel, we have collected detailed clinical data on all patients to be able to correlate genetic findings with the clinical development of their disease.

Myeloid neoplams with germline predisposition

Anna Eriksson, Tatjana Pandzic, Martin Höglund, Lucia Cavelier, Eva Hellström Linberg, Jörg Cammenga, Panagiotis Baliakas

Myeloid neoplasms (MNs) with germline predisposition are a group of rare diseases recently recognized as novel entities in the latest World Health Organization (WHO) classification for MNs. In short, individuals with MNs and germline predisposition exhibit an increased risk for the development of MNs due to a germline pathogenic variant. Setting the diagnosis of an MN due to germline predisposition is of crucial clinical significance, not only for the patient as it affects decisions related to donor choice or conditioning regimen, but also for the patient’s family, similar to all tumor predisposition syndromes.

The main aim of this project is to provide recommendations for the management of patients with suspicion of MN with germline predisposition in the clinical setting, in order to develop a pipeline applied in the everyday routine.

TP53 mutations in lymphoid and myeloid leukemia: from bench to bedside and back

Thierry Soussi, Simone Weström, Tatjana Pandzic, Claes Ladenvall, Panagiotis Baliakas, in collaboration with Adar Yacoov and Shai Rosenberg (Jerusalem), François Delhomeau, Pierre Hirsh and Florence Cymbalista (Paris)

Mutations in TP53 are present in approximately 10 % of patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) and represent a unique subtype with poor outcome. In chronic lymphocytic leukemia (CLL), TP53 defects are a well-established marker for poor prognosis and chemotherapy-resistant disease. Patients with TP53 defects strongly benefit from targeted therapy with BcR pathway or bcl2 inhibitors that are presumed to act independent of the p53 pathway. It is therefore of tremendous importance to develop an accurate method to assess TP53 status in these patients

The main aim of this project is two-fold: improving the sensitivity of TP53 mutation detection in NGS pipeline and developing a novel classification of TP53 variants pathogenicity using specific machine learning algorithms.

Myeloid neoplams in children with tandem duplications in UBTF

Linda Holmfeldt, Simone Weström, Panagiotis Baliakas

Acute myeloid leukemia (AML) characterized by in-frame tandem duplications in the UBTF gene has recently been suggested by us and others to be a novel genetic subtype of AML accounting for approximately 4 % of pediatric de novo AML cases, and that is associated with a poor prognosis.

The main aim of this project is to further characterize the functional role of UBTF tandem duplications within AML for a better understanding of these mutations within leukemia onset, progression and therapy resistance, with the ultimate goal of identifying optimal therapeutic approaches for this difficult-to-treat disease.