Research

ALL is a hematological cancer consequence of an uncontrolled proliferation of both subtypes of immature lymphocytes (B and T cell precursors), which prevent a healthy hematopoiesis capable of sustaining vital functions. While ALL is a curable disease in the pediatric population (cure rate> 90%), only half of adult patients survive the disease. Since 2012, our group analyzes biologic samples from adult ALL patients in order to deepen our knowledge about the origin, development and response to the treatment of this disease. During this time, we have found that each ALL is unique genetically, a fact that explains, in part, why not all patients respond equally to the same treatment.

Given this heterogeneous genetic landscape, it is necessary to analyze samples from a large number of patients in order to find genetic alterations with prognostic significance. To this end, our research group actively participates with the Spanish cooperative group PETHEMA (Programa Español de Tratamientos en Hematología), which is the reference cooperative group in the treatment of ALL in Spain and in several countries from South America, such as Argentina, Colombia or Paraguay. This allows us to correlate the genetic information with the clinical data of each patient and thus identify which genetic markers carry a higher risk of disease relapse.

The current research of the group is divided in two main areas, according to the two main subtypes distinguish in of ALL: 

1. B cell Precursor Acute Lymphoblastic Leukemia (BCP ALL):

Jordi Ribera (jribera@carrerasresearch.org), postdoctoral researcher.

BCP ALL is the most prevalent ALL subtype accounting for 75%-85% of ALL cases. Although it is a genetically heterogeneous disease, different cytogenetic subtypes have been identified so far and, more importantly, their prognosis has been clearly established in many clinical trials. This has allowed clinicians to stratify patients according to their genetic profile to schedule intensive or less intensive treatments, and more recently, targeted therapies and/or immunotherapy. However, not all patients within the same cytogenetic subtype show the same degree of response when receiving the same treatment, suggesting that additional genetic alterations may modulate the intrinsic prognosis of each cytogenetic subtype. In this sense, we are interested in characterizing the genetic alterations leading to treatment resistance and disease recurrence. To achieve this objective, we work at both clinical and translational level.

1.1  Genetic analysis for risk stratification for ongoing clinical trials of the PETHEMA Group

Previous research of our group has identified different genetic alterations in adult BCP ALL conferring a very high-risk of relapse that have been used to design the new national treatment protocol of PETHEMA for adult ALL (PETHEMA LAL19). This is allowing a more personalized treatment for each patient depending on the genetics of each ALL. For instance, Ph-negative patients with concomitant deletions of IKZF1 (Ikaros) and CDKN2A/B (Figure 1) have 90% of relapse probability and are receiving stem cell transplantation, instead of maintenance chemotherapy. The analysis of the results of LAL19 trial will be crucial to assess if these specific therapeutic interventions have improved patients’ survival and quality of life. We are currently analyzing samples from patients of this protocol to detect poor prognosis markers to be incorporated in the subsequent PETHEMA protocol. This is a continuous process of improvement performed in each protocol aiming to elaborate a confident gene alteration catalogue applicable in subsequent protocols of the group.

Figure 1. BCP ALL with concomitant IKZF1 and CDKN2A/B gene deletions.

1.2  Genomic analysis for new biomarker discovery

In addition to give support for ALL diagnosis, we also analyze samples with “OMIC techniques”, which give us information about the whole genome of each ALL. By this, we can get additional information relevant for patients’ clinical care. For example, we have previously observed that not all patients with IKZF1 deletion show poor prognosis. By using RNAseq (Figure 2) we have identified different transcriptional programs depending on the type of IKZF1 deletion, which may behind the different patients’ response and may be molecular targets for therapeutic intervention. This has prompted us to lead a European study for the HARMONY Alliance (Project reference: ALL2) to get more insights into which is the best treatment for each patient with IKZF1 loss (personalized medicine).

Figure 2. Downregulated and upregulated genes of one subtype of IKZF1 deletions compared to patients without IKZF1 loss.

2. T-cell Acute Lymphoblastic Leukemia (T-ALL):

Eulàlia Genescà (egenesca@carrerasresearch.org), senior researcher. 

T-ALL is the less common and the most complex and heterogeneous at the genetic level ALL subtype with dismal prognosis. Traditionally, the therapeutic protocols for ALL do not consider the differences in the molecular background of the two main ALL subtypes, and few new alternative therapies are only available in refractory or resistant ALL, especially in T-ALL. In such scenario, we believe that to improve the survival of patients with T-ALL we need firstly to obtain detailed and relevant molecular information to accurately define the risk and decide on the treatment. Secondly, we need to have specific therapeutic alternatives available to apply to these new oncogenetic T-ALL subgroups. Therefore, two main lines of research are established in this area:

2.1. Improvement of stratification of adult T-ALL patients in the context of PETHEMA trials: we are using OMICs techniques (SNPa; TDS; digital karyotype) (Figure 3) to dissect the mutational landscape of T-ALL patients included in the PETHEMA treatment protocols to refine their stratification and improve their survival. The results obtained until now, are currently been applied in the ALL-2019 (NCT04179929) treatment protocol and research currently been performed in the group will be applied in future PETHEMA trials.

Figure 3. Mutational spectrum of ≥3 CK

2.2 Development of new therapeutic alternatives: focused on the study of the mechanisms of relapse and the identification of the cells responsible for clonal resistance to treatment, we want to identify new ways to treat T-ALL patients to overcome resistance, which is responsible of treatment failure in 60% of T-ALL cases. In addition, we are using the genomic information obtained at time of diagnosis to explore new chemotherapeutic schedules in combination or not with new target therapies to improve treatment of these patients. For that, our lab has developed a primary co-culture system to grow leukemias in vitro and a PDX mouse model to assess these new anti-leukemic therapies in vivo (Figure 4).

Figure 4. Engraftment of primary in the bone marrow of an immunodeficient mouse. 

We are convinced that the new treatments for ALL patients can only be obtained through basic research. The valuable information about the genome and epigenome extracted from patient samples will allow detecting genetic lesions involving critical pathways for proliferation of ALL cells that could be targetable with new drugs. This research is changing the treatment paradigm of ALL and will contribute significantly to improve the patients’ survival.