Molecular and functional characterization of the interplay between malignant and stromal cells in acute myeloid leukemia and myelodysplastic syndrome

In this thesis, we studied the cross-talk between malignant cells and stromal cells, with the aim to elucidate the respective contribution to myeloid neoplasm onset and progression. First, we characterized and compared mesenchymal stromal cells (MSCs) isolated from myelodysplastic syndrome (MDS-MSCs) and acute myeloid leukemia (AML-MSCs) patients. We demonstrated that, despite some unaltered functions, patient-derived MSCs show also intrinsic, distinct functional abnormalities, which could all potentially favor a leukemia-protective bone marrow (BM) niche in vivo. Second, we investigated the ability of AML cells to modulate the AML-MSC functions. In a GEP-screening, we found that 40% of BM-derived AML samples show a higher IFN-γ expression, compared to the mean IFN-γ expression in healthy BM-derived cells. We demonstrated that in co-culture experiments, IFN-γ+ AML cells modify AML-MSC gene expression and function, inducing the up-regulation of IDO1, and consequently the generation of T regulatory cells. Finally, we wondered if the transcriptome of stromal cells could be influenced by the hematopoietic-specific alterations, i.e. Dnmt3a and Asxl1 mutations, which occur early in MDS/AML patients. We found that Dnmt3a- and Asxl1-null BM cells, when transplanted in wild-type mice, induce profound and deletion-specific modifications in the transcriptome of wild-type BM stromal cells, suggesting the ability of Dnmt3a- and Asxl1-null BM cells to shape the niche. Furthermore, we compared the transcriptome of wild-type BM stromal cells, obtained from transplantation experiments, with that of MSCs isolated from low-risk MDS patients with DNMT3A and ASXL1 mutations, and we highlighted some common modifications, which could be potentially relevant for human disease and specific for DNMT3A/ASXL1 mutations. In conclusion, this thesis pointed out that there is a bi-directional cross-talk, in which stromal cells can influence malignant cells, and in turn malignant/pre-malignant cells can alter stromal cell gene expression and function. Both mechanisms could potentially contribute to the pathogenesis of myeloid malignancies.

Azacitidine and Lenalidomide Combination Therapy in Myelodysplastic Syndromes: Topography and Translational Relevance of Nuclear Phospholipase C β - dependent Signalling

Nuclear inositide signalling pathways, and particularly those regulated by PI-PLCβ1, are associated with cell proliferation and differentiation. Myelodysplastic syndromes (MDS) are a heterogeneous spectrum of chronic myeloid hemopathies with associated symptomatic cytopenias and substantial potential for evolution to acute myeloid leukemia (AML). MDS patients are currently treated with two main approaches, epigenetic (Azacitidine) and immunomodulatory (Lenalidomide: above all in cell clones bearing a deletion of the long arm of the chromosome 5 [del(5q)]). As Azacitidine and Lenalidomide alone can show adverse effects or patients can be refractory, an experimental current approach is the combination of the two drugs. Clinically, this combination therapy is promising, while its molecular effect has to be clarified. Stemming from these data, in this study the effect of an Azacitidine-Lenalidomide combination therapy was studied, in both MDS patients and hematopoietic cell lines. The specific aims of this study were to evaluate the effect of Azacitidine and Lenalidomide MDS therapy on: cell cycle regulation, hematopoietic differentiation, gene mutation and miR expression. Lenalidomide alone, via PI-PLCβ1/PKC pathway, was able to induce a selective G0/G1 arrest of the cell cycle in del(5q) cells, slowing down their rate proliferation and favouring erythropoiesis activation. In addition, although the mutation profile at baseline was not entirely capable of predicting the clinical effect of Azacitidine and Lenalidomide therapy, the presence of specific point mutations affecting three inositide genes (PI3KCD, AKT3, PLCG2) was correlated to and anticipated a negative clinical outcome. Moreover, the differential miR expression was detectable even from the 4th cycle of therapy in responder patients, as compared to non-responders. In MDS, this is the first evidence that the molecular mutation profiling of inositide genes or a specific mini-cluster of differentially expressed miRs, targeting inositide signaling molecules, can be associated with the clinical response, thus possibly predicting the effect of the therapy.

The human gut microbiome in disease: Role in chemotherapy treatments and relationship with clinical outcomes

The gut microbiome (GM) is a plastic entity, capable of adapting in response to intrinsic and extrinsic factors. However, several circumstances can disrupt this homeostatic balance, forcing the GM to shift from a health-associated mutualistic configuration to a disease-associated profile. Nowadays, a new frontier of microbiome research is understanding the GM role in chemo-immunotherapies and clinical outcomes. Here, the role of the genotoxin‐producing pathogen Salmonella in colorectal carcinogenesis was characterized by in-vitro models. A synergistic effect of Salmonella and the CRC-associated mutation (APC gene) promoted a tumorigenic microenvironment by increasing cellular genomic instability. Subsequently, the GM involvement in anti-cancer therapies was investigated via next-generation sequencing in different patient cohorts. The GM trajectory during treatments was characterized for women with epithelial ovarian cancer and pediatric patients undergoing hematopoietic stem cell transplantation (HSCT). The results highlighted the loss of GM homeostasis, with diversity reduction, decrease in health-associated microorganisms and pathobiont bloom. Interestingly, a distinctive GM profile was identified in ovarian cancer patients with a poor response to chemotherapy compared to patients in remission. Moreover, maintenance of GM homeostasis through enteral feeding in pediatric HSCT patients highlighted a better prognosis, with reduced risk of clinical complications. In this context, the gut resistome – the pattern of GM antibiotic-resistance genes (ARGs) – was evaluated longitudinally in HSCT patients. The results showed new acquisitions and consolidation of ARGs already present in patients developing clinical complications. Antibiotic exposure was also evaluated in infants under low-dose antibiotic prophylaxis for vesico-ureteral reflux showing an impairment of the GM configuration with possible long-term health implications. Dramatic GM dysbiosis was finally observed in critically ill patients with COVID-19 (undergoing multiple drug therapies) and correlated with increased risk of bloodstream infection. All these findings pointed out the importance of maintaining GM homeostasis during chemotherapy treatments for improving patients’ clinical outcomes.

Metilazione del DNA e Trapianto Allogenico di Cellule Staminali Emopoietiche

Il trapianto di cellule staminali emopoietiche rappresenta la terapia di scelta per numerose patologie ematologiche. Tuttavia, la mortalità da trapianto (non relapse mortality-NRM), ha limitato per lungo tempo il suo utilizzo in pazienti di età >65 anni. L’età non può più essere considerata una controindicazione assoluta al trapianto e il suo utilizzo in fasce di età un tempo ritenute non idonee è in sensibile aumento. La NRM è legata a tre ordini di complicanze: immunologiche (malattia del trapianto contro l’ospite, Graft versus-Host Disease -GVHD-), infettive e tossiche. La tossicità d’organo è direttamente correlata alla intensità del condizionamento che quindi viene ridotta in caso di comorbidità e nel paziente anziano. Tuttavia, ridurre l’intensità del condizionamento significa anche aumentare il rischio di ripresa della malattia ematologica di base e quindi tale aggiustamento deve essere fatto in funzione di indici di invecchiamento e di comorbidità, al fine di non ridurre la potenzialità curativa del trapianto. Per valutare le comorbidità abbiamo uno score altamente predittivo (Hematopoietic Cell Transplant-Comorbidity Index, di Sorror), mentre per valutare l’invecchiamento c’è una grande necessità clinica di marcatori innovativi di età biologica. Il presente lavoro ha l’obiettivo di valutare, nei pazienti sottoposti a trapianto allogenico di cellule staminali emopoietiche per tutte le indicazioni ematologiche, lo stato di metilazione del DNA, indice di età biologica. Lo scopo è di correlare l’epigenoma al rischio trapiantologico del singolo individuo.

Outcomes of global coagulation assays in patients with Philadelphia-negative myeloproliferative neoplasms with respect to genetic determinants of clonal progression

Classical myeloproliferative neoplasms (MPNs) are hematopoietic stem cell disorders that manifest with inflammation, promotion of atherosclerosis, hypercoagulability, fibrosis, and clonal evolution. The complex biological background lends itself to multi-omics studies. We have previously shown that reduced platelet fibrinogen receptor (PFR) expression may follow hyperactivation of plasma-dependent mechanisms, such as tissue factor (TF) release, unbalanced thrombin generation, involvement of protease-activated receptors (PARs). Acetylsalicylic acid (ASA) helped to restore the expression of PFRs. In this study, we enrolled 53 MPN patients, subjecting them to advanced genetic testing (panel of 30 genes in NGS), global coagulation testing (Rotational Thromboelastometry - ROTEM) and cytofluorometric determination of PFRs. ROTEM parameters appear to differ considerably depending on the type of pathology under investigation, cell count, and selected mutations. Essential thrombocythemia (ET) and CALR mutation appear to correlate with increased efficiency of both classical coagulation pathways, with significantly more contracted clot formation times (CFTs). In contrast, primary myelofibrosis (PMF) and polycythemia vera (PV) show greater imbalances in the hemostatic system. PV, probably due to its peculiar hematological features, shows a lengthening of the CFT and, at the same time, a selective contraction of parameters in INTEM with the increase of platelets and white blood cells. PMF - in contrast - seems to exploit the extrinsic pathway more to increase cell numbers. The presence of DNMT3A mutations is associated with reduced clotting time (CT) in EXTEM, while ASXL1 causes reduced maximal lysis (ML). EZH2 could be responsible for the elongation of CFT in INTEM assay. In addition, increased PFR expression is associated with history of hemorrhage and sustained CT time in FIBTEM under ASA prophylaxis. Our findings corroborate the existing models on the connection between fibrosis, genetic complexity, clonal progression, and hypercoagulability. Global coagulation assays and PFR expression are potentially useful tools for dynamic evaluation of treatments’ outcomes.

Contribution of cytokines to the etiology and progression of Primary Myelofibrosis

Primary Myelofibrosis (PMF) is the end-stage of Philadelphia-negative myeloproliferative neoplasms (MPN) and is characterized by fibrosis and hematopoietic failure in bone marrow, with a consequential migration of the malignant hematopoietic stem cells (HSC) in the spleen where they induce ineffective haematopoiesis. To date, available therapies for PMF are still palliative and do not halt the progression of this neoplasm. During my PhD years, our laboratory investigated the factors promoting the onset and progression of PMF. In our PMF mice model, Gata1low mouse, we studied the role of the interaction of HSC niche with megakaryocytes and HSC localization in the bone marrow during their division and cycle. We observed the inflammation and the main protagonists (LNC-2, CXCL1, and TGF-β) of this process and how their level changes before and after the onset of the disease. We investigated the different megakaryocyte populations in the fibrotic environment in different organs (lung and bone marrow) to define the megakaryocytes implicated in this process. In human samples, we described different ultrastructural abnormalities of megakaryocytes from the bone marrow and the spleen, identifying a possible different metabolism in those two populations. In conclusion, we highlighted the intricated crosstalk between the megakaryocytes, the niche and HSC in PMF. We identified megakaryocytes-dependent cytokines altering the homeostasis of the niche and HSC. Those cytokines could be used as alternative therapeutic targets. Furthermore, we observed different megakaryocytic populations in different organs, providing new prospective on the role of megakaryocytes in different microenvironments.

Pharmacological targeting of P-selectin to halt the progression of myelofibrosis in the Gata1low mouse model

Primary myelofibrosis is a clonal hematopoietic disorder characterized by marked degrees of systemic inflammation. The release of pro-inflammatory factors by clonal hematopoietic cell populations cause the remodeling of a specialized microenvironment, defined niche, in which the hematopoietic stem cells reside. The main source of pro-inflammatory cytokines is represented by malignant megakaryocytes. The bone marrow and spleen from myelofibrosis patients, as well as those from the Gata1low mouse model of the disease, contain increased number of abnormal megakaryocytes. These cells express on their surface high levels of the adhesion receptor P-selectin that, by triggering a pathological megakaryocyte-neutrophil emperipolesis, lead to increased bioavailability of TGF-β1 in the microenvironment and disease progression. Gata1low mice develop with age a phenotype similar to that of patients with myelofibrosis. We previously demonstrated that deletion of the P-selectin gene in Gata1low mice prevented the development of the myelofibrotic phenotype in these mice. In the current study, we tested the hypothesis that pharmacological inhibition of P-selectin may rescue the fibrotic phenotype of Gata1low mice. To test this hypothesis, we have investigated the phenotype expressed by old Gata1low mice treated with the anti-mouse monoclonal antibody against P-selectin RB40.34, alone or in combination with the JAK2 inhibitor Ruxolitinib. The results showed that the combined therapy normalized the phenotype of Gata1low mice with limited toxicity by reducing fibrosis, TGF-β1 and CXCL1 content in the BM and spleen and by restoring hematopoiesis in the bone marrow and the normal architecture of the spleen. In conclusion, pharmacological inhibition of P-selectin was effective in targeting malignant megakaryocytes and the microenvironmental abnormalities that affect the hematopoietic stem cell compartment in this model. These results suggest that P-selectin and JAK1/2 inhibitors in combination may represent a valid therapeutic option for patients with myelofibrosis.