Mireia Camós

Background: B-cell Acute Lymphoblastic Leukemia (B-ALL) remains an important cause of cancer-related death in children. Therefore, accurate identification at diagnosis of patients at high risk of relapse is crucial. In this context, long non-coding RNAs (lncRNAs) could be novel candidates with great potential. Hence, the aim of this study was to identify new prognostic biomarkers in pediatric B-ALL through an RNA sequencing (RNA-seq) approach that allows the detailed exploration of a wide range of lncRNAs. Methods: Total RNA from two cohorts of B-ALL patients (C1 with 50 Spanish patients, and C2 with 72 Canadian patients) was sequenced with a depth of approximately 150 million paired-reads using Illumina technology. All protein coding and non-coding genes included in lncRNAKB annotation were studied to develop a gene expression-based 5-year Event Free Survival (EFS) prediction model. Results: First, univariate Cox proportional hazards analyses identified 48 genes significantly associated with higher EFS risk in both cohorts. From these, ALASSO regression selected five genes, all of which are lncRNAs, as the most informative to develop the prediction model, which we have called surviBALL. Stratification of patients into three risk groups according to the surviBALL model revealed significantly poorer EFS in high-risk patients across C1, C2, and the integrated C1 + C2 cohort ( P < 0.001). Validation in an independent cohort of 177 publicly available B-ALL samples confirmed surviBALL’s prediction capacity ( P = 2.80 × 10 ^− 4 ) and its independence of both subtype and MRD. Conclusions: These findings suggest that surviBALL has the potential to complement current risk stratification approaches, particularly by identifying patients at high risk of relapse at diagnosis. As a hypothesis-generating proof of concept, this study highlights the promise of more personalized treatment strategies and warrants further validation in independent cohorts.

Relapsed or refractory (R/R) B-cell acute lymphoblastic leukemia (B-ALL) remains a challenging disease with dismal prognosis. Despite the revolutionary impact of CD19-directed chimeric antigen receptor (CAR19) T-cell therapy, >50% of patients relapse within a year. Both leukemia cell–intrinsic factors favoring immune escape and poor CAR T-cell persistence contribute to clinical failure. Moreover, the expression of immune checkpoint receptors (ICRs) and their ligands within the bone marrow (BM) microenvironment may contribute to leukemia progression and therapy resistance. Here, we characterized the expression of ICRs and their ligands in leukemic blasts, T cells, and mesenchymal stromal cells (MSCs) from B-ALL BM samples at diagnosis and relapse, comparing them with age-matched healthy BM controls. Our findings reveal a significantly upregulated expression of TIM-3 in T cells and its ligand, galectin-9, in both blasts and MSCs throughout disease progression. The expression of galectin-9 in B-ALL blasts and TIM-3 in CAR19 T cells negatively correlates with clinical outcome. Furthermore, we demonstrate that galectin-9 impairs CAR19 T-cell homeostasis and cytotoxicity. Notably, an engineered TIM-3–Fc decoy receptor, delivered either by primary T cells coadministered with CAR19 T cells or via a bicistronic all-in-one CAR19–TIM-3–Fc construct, improved the antileukemia efficacy and persistence of CAR19 T cells in B-ALL xenograft models. Mechanistically, CAR19–TIM-3–Fc T-cell treatment promotes the in vivo expansion of transduced and bystander effector and memory T cells, as determined by spectral flow cytometry. Collectively, these TIM-3–Fc decoy–armored CAR19 T cells offer a promising therapeutic strategy for patients with R/R B-ALL.

Summary: B‐cell precursor acute lymphoblastic leukaemia (BCP‐ALL) comprises multiple subtypes characterized by different genetic alterations. With the use of current standard‐of‐care tests used in clinical practice, 20%–30% of the cases may not be classified into the main genetic subtypes and additional approaches are needed. These patients are grouped in the heterogeneous category B‐other ALL. Transcriptome sequencing (RNA‐seq) has allowed the identification of novel fusion genes and gene expression profiles that define new molecular subtypes. We present RNA‐seq results integrated, in a real‐world scenario, with clinical routine diagnostic data to identify new biomarkers and reclassify a cohort of 60 B‐other ALL patients in the newly described genetic subtypes. Overall, 49 rearrangements were identified, including 32 different fusion genes in 41 B‐other patients (68%). Moreover, we reported six novel rearrangements ( IGK::PAX5 , PAX5::IL1RAPL1 , ETV6::KRT78 , IGH::HIC1 , IGH::MIR100HG and NKAIN4::PNPLA7 ). The integration of RNA‐seq results with standard‐of‐care data allowed us to classify 72% of the patients (43/60) in 11 different subtypes, being DUX4 rearranged and PAX5 alt the most represented subtypes. In summary, RNA‐seq is a reliable tool for the identification of new emerging genetic subtypes contributing to a better genetic risk stratification of BCP‐ALL paediatric patients on the path towards a more personalized medicine.

Summary: The use of CAR‐T is becoming more widespread in the treatment of haematological malignancies. In adults, secondary myelodysplastic syndromes (MDS) after CAR‐T have been described. However, there are currently no data on the risk of MDS following CAR‐T in children treated for acute lymphoblastic leukaemia (ALL). We studied all children treated with CAR‐T cells at Hospital Sant Joan de Déu in Barcelona and those with persistent cytopenias were evaluated at the cytological, cytogenetic, and molecular levels to look for MDS. A total of 106 patients received CAR‐T for ALL. Among 40 patients without early relapse or subsequent therapy after CAR‐T, four fulfilled the WHO criteria for myelodysplasia. These four patients had received a haematopoietic stem cell transplantation (HSCT) prior to CAR‐T and presented cytopenias with severe dysplastic changes in bone marrow after CAR‐T. One patient had clonal MDS with high‐risk cytogenetics arising from the host cells requiring a HSCT. Three patients had non‐progressive dysplasia arising from the donor cells. Two are alive in complete remission with stable cytopenias and one succumbed to ALL relapse. This is the first description of post‐CAR‐T MDS and haematological dysplasia in children and highlights the need to monitor children with persistent post‐CAR‐T cytopenias.

Summary: Clinical and biological variables like genetic aberrations at diagnosis and the levels of measurable residual disease (MRD) are the most powerful biomarkers to predict the outcome of paediatric leukaemia. Recently, a model integrating the genetic abnormalities, transcriptional identity, and leukaemia stemness measured as leukaemic stem cell score (pLSC6) has been proposed to identify high‐risk paediatric acute myeloid leukaemia (AML) patients. However, the role of epigenetics in defining prognosis still needs to be established. We evaluated the role of 89 miRNAs regulating stemness and their contribution to predicting outcomes in 110 paediatric patients with acute leukaemia. We identified a 24‐miRNA signature capable of distinguishing paediatric AML patients with excellent or poor outcomes. We validated these results in an independent cohort using public repository‐based data. The 24‐miRNA signature was significantly associated with the leukaemic stemness scores and the underlying genetics of patients. Notably, the combination of classical prognostic factors (MRD and genetics), the pLSC6 score and the 24‐miRNA signature had a higher capacity to predict the overall and event‐free survival than each variable individually. Our 24‐miRNA signature provides epigenetic data to integrate into genetics, MRD and stemness‐related leukaemic scores to refine risk stratification in paediatric AML patients.

Background Although adoptive transfer of CD19-directed chimeric antigen receptor (CAR) T-cells (CD19-CAR T-cells) achieves high rates of complete response in patients with B-cell acute lymphoblastic leukemia (B-ALL), relapse is common. Bone marrow (BM) mesenchymal stem/stromal cells (BM-MSC) are key components of the hematopoietic niche and are implicated in B-ALL pathogenesis and therapy resistance. MSC exert an immunosuppressive effect on T-cells; however, their impact on CD19-CAR T-cell activity is understudied. Methods We performed a detailed characterization of BM-MSC from pediatric patients with B-ALL (B-ALL BM-MSC), evaluated their immunomodulatory properties and their impact on CD19-CAR T-cell activity in vitro using microscopy, qRT-PCR, ELISA, flow cytometry analysis and in vivo using a preclinical model of severe colitis and a B-ALL xenograft model. Results While B-ALL BM-MSC were less proliferative than those from age-matched healthy donors (HD), the morphology, immunophenotype, differentiation potential and chemoprotection was very similar. Likewise, both BM-MSC populations were equally immunosuppressive in vitro and anti-inflammatory in an in vivo model of severe colitis. Interestingly, BM-MSC failed to impair CD19-CAR T-cell cytotoxicity or cytokine production in vitro using B-ALL cell lines and primary B-ALL cells. Finally, the growth of NALM6 cells was controlled in vivo by CD19-CAR T-cells irrespective of the absence/presence of BM-MSC. Conclusions Collectively, our data demonstrate that pediatric B-ALL and HD BM-MSC equally immunosuppress T-cell responses but do not compromise CD19-CAR T-cell activity.

B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric cancer, and high-hyperdiploidy (HyperD) identifies the most common subtype of pediatric B-ALL. Despite HyperD is an initiating oncogenic event affiliated to childhood B-ALL, the mitotic and chromosomal defects associated to HyperD B-ALL (HyperD-ALL) remain poorly characterized. Here, we have used 54 primary pediatric B-ALL samples to characterize the cellular-molecular mechanisms underlying the mitotic/chromosome defects predicated to be early pathogenic contributors in HyperD-ALL. We report that HyperD-ALL blasts are low proliferative and show a delay in early mitosis at prometaphase, associated to chromosome alignment defects at the metaphase plate leading to robust chromosome segregation defects and non-modal karyotypes. Mechanistically, biochemical, functional and mass-spectrometry assays revealed that condensin complex is impaired in HyperD-ALL cells, leading to chromosome hypocondensation, loss of centromere stiffness and mis-localization of the chromosome passenger complex proteins Aurora B Kinase (AURKB) and Survivin in early mitosis. HyperD-ALL cells show chromatid cohesion defects and impaired spindle assembly checkpoint (SAC) thus undergoing mitotic slippage due to defective AURKB and impaired SAC activity, downstream of condensin complex defects. Chromosome structure/condensation defects and hyperdiploidy were reproduced in healthy CD34+ stem/progenitor cells upon inhibition of AURKB and/or SAC. Collectively, hyperdiploid B-ALL is associated to defective condensin complex, AURKB and SAC.

In intermediate-risk cytogenetic acute myeloid leukemia (IRC-AML) patients, novel biomarkers to guide post-remission therapy are needed. We analyzed with high-density arrays 40 IRC-AML patients who received a non-allogeneic hematopoietic stem-cell transplantation-based post-remission therapy, and identified a signature that correlated with early relapse. Subsequently, we analyzed selected 187 genes in 49 additional IRC-AML patients by RT-PCR. BAALC, MN1, SPARC and HOPX overexpression correlated to refractoriness. BAALC or ALDH2 overexpression correlated to shorter overall survival (OS) (5-year OS: 33 ± 8.6% vs. 73.7 ± 10.1%, p = .006; 32 ± 9.3% vs. 66.4 ± 9.7%, p = .016), whereas GPR44 or TP53INP1 overexpression correlated to longer survival (5-year OS: 66.7 ± 10.3% vs. 35.4 ± 9.1%, p = .04; 58.3 ± 8.2% vs. 23.1 ± 11.7%, p = .029). A risk-score combining these four genes expression distinguished low-risk and high-risk patients (5-year OS: 79 ± 9% vs. 30 ± 8%, respectively; p = .001) in our cohort and in an independent set of patients from a public repository. Our 4-gene signature may add prognostic information and guide post-remission treatment in IRC-AML patients.

In B-cell precursor acute lymphoblastic leukaemia (B-ALL), the identification of additional genetic alterations associated with poor prognosis is still of importance. We determined the frequency and prognostic impact of somatic mutations in children and adult cases with B-ALL treated with Spanish PETHEMA and SEHOP protocols. Mutational status of hotspot regions of TP53, JAK2, PAX5, LEF1, CRLF2 and IL7R genes was determined by next-generation deep sequencing in 340 B-ALL patients (211 children and 129 adults). The associations between mutation status and clinicopathological features at the time of diagnosis, treatment outcome and survival were assessed. Univariate and multivariate survival analyses were performed to identify independent prognostic factors associated with overall survival (OS), event-free survival (EFS) and relapse rate (RR). A mutation rate of 12.4% was identified. The frequency of adult mutations was higher (20.2% vs 7.6%, P=0.001). TP53 was the most frequently mutated gene (4.1%), followed by JAK2 (3.8%), CRLF2 (2.9%), PAX5 (2.4%), LEF1 (0.6%) and IL7R (0.3%). All mutations were observed in B-ALL without ETV6-RUNX1 (P=0.047) or BCR-ABL1 fusions (P<0.0001). In children, TP53mut was associated with lower OS (5-year OS: 50% vs 86%, P=0.002) and EFS rates (5-year EFS: 50% vs 78.3%, P=0.009) and higher RR (5-year RR: 33.3% vs 18.6% P=0.037), and was independently associated with higher RR (hazard ratio (HR)=4.5; P=0.04). In adults, TP53mut was associated with a lower OS (5-year OS: 0% vs 43.3%, P=0.019) and a higher RR (5-year RR: 100% vs 61.4%, P=0.029), whereas JAK2mut was associated with a lower EFS (5-year EFS: 0% vs 30.6%, P=0.035) and a higher RR (5-year RR: 100% vs 60.4%, P=0.002). TP53mut was an independent risk factor for shorter OS (HR=2.3; P=0.035) and, together with JAK2mut, also were independent markers of poor prognosis for RR (TP53mut: HR=5.9; P=0.027 and JAK2mut: HR=5.6; P=0.036). TP53mut and JAK2mut are potential biomarkers associated with poor prognosis in B-ALL patients.