Next generation sequencing and copy number analysis provide insights into the complexity of the CLL coding genome, and reveal an association between NOTCH1 mutational activation and poor prognosis.

The genetic lesions identified in chronic lymphocytic leukemia (CLL) do not entirely recapitulate the disease pathogenesis and the development of serious complications, such as chemorefractoriness. While investigating the coding genome of fludarabine-refractory CLL, we observed that mutations of SF3B1, encoding a splicing factor and representing a critical component of the cell spliceosome, were recurrent in 10 of 59 (17%) fludarabinerefractory cases, with a frequency significantly greater than that observed in a consecutive CLL cohort sampled at diagnosis (17/301, 5%; P ‫؍‬ .002). Mutations were somatically acquired, were generally represented by missense nucleotide changes, clustered in selected HEAT repeats of the SF3B1 protein, recurrently targeted 3 hotspots (codons 662, 666, and 700), and were predictive of a poor prognosis. In fludarabine-refractory CLL, SF3B1 mutations and TP53 disruption distributed in a mutually exclusive fashion (P ‫؍‬ . IntroductionThe clinical course of chronic lymphocytic leukemia (CLL) ranges from a very indolent disorder with a normal lifespan for the patient to a rapidly progressive disease that leads to death. Occasionally, CLL undergoes a transformation to Richter syndrome (RS). [1][2][3] The variable clinical course of CLL is driven, at least in part, by the disease's immunogenetic and molecular heterogeneity. 4 Despite recent advances, the genetic lesions identified to date do not fully recapitulate the molecular pathogenesis of CLL and do not entirely explain the development of severe complications, such as chemorefractoriness, which still represent unmet clinical needs. 5 In approximately 40% of cases, refractoriness to fludarabine is attributable to the disruption of TP53, but in a sizeable fraction of patients, the molecular basis of this aggressive phenotype remains unclear. 6 Recently, 2 independent studies of the CLL coding genome investigated at disease presentation have revealed a restricted number of mutated genes, including NOTCH1. 7,8 These studies have provided a proof of concept that, similar to other malignancies, genome-wide mutational analysis might identify novel lesions of biologic and clinical relevance in CLL. On these grounds, we have embarked on the investigation of the coding genome of fludarabine-refractory CLL to identify genetic lesions associated with chemorefractoriness. The initial phases of this analysis have revealed recurrent mutations of SF3B1, a critical component of the cell spliceosome, pointing to the potential involvement of splicing regulation in CLL pathogenesis and chemorefractoriness. Methods PatientsThe study population comprised 3 cohorts representative of different disease phases: (1) fludarabine-refractory CLL (n ϭ 59), including cases (n ϭ 11) subjected to whole-exome sequencing (supplemental Table 1, available on the Blood Web site; see the Supplemental Materials link at the top of the online article); (2) a consecutive series of newly diagnosed and previously untreated patients with CLL (n ϭ 301; supplemental Table 2 For pers...

464 Fludarabine-refractoriness of chronic lymphocytic leukemia (CLL) is due to TP53 disruption in ∼40% of refractory cases, but in a sizeable fraction of patients the molecular basis of this aggressive clinical phenotype remains unclear. Our initial findings from whole exome sequencing of fludarabine-refractory CLL led to the identification of recurrent mutations of SF3B1, a critical component of the cell spliceosome, prompting further investigations of these alterations in a large CLL panel. The study population comprised 3 clinical cohorts representative of: i) fludarabine-refractory CLL (n=59), including cases (n=11) subjected to whole exome sequencing; ii) newly diagnosed and previously untreated CLL (n=301); and iii) clonally related RS (n=33). Tumor samples were obtained: i) for fludarabine-refractory CLL, immediately before starting the treatment to which the patient eventually failed to respond; ii) for newly diagnosed and previously untreated CLL, at disease presentation. All RS studies were performed on RS diagnostic biopsies. Mutation analysis of SF3B1 was performed on genomic DNA by a combination of Sanger sequencing and targeted next generation sequencing. SF3B1 was altered in 10/59 (17%) fludarabine-refractory CLL by missense mutations (n=9) or in-frame deletions (n=1) clustering in the HEAT3, HEAT4 and HEAT5 repeats of the SF3B1 protein. Two sites that are highly conserved inter-species (codon 662 and codon 700) were recurrently mutated in 3 and 5 cases, respectively. SF3B1 mutations were monoallelic, and were predicted to be functionally significant according to the PolyPhen-2 algorithm. Mutations occurred irrespective of IGHV mutation status, CD38 expression and ZAP70 expression. At the time of fludarabine-refractoriness, SF3B1 mutations were enriched in cases harboring a normal FISH karyotype (p=.008) and distributed in a mutually exclusive fashion with TP53 disruption (mutual information I =0.0609; p=.046). By combining SF3B1 mutations with other genetic lesions enriched in chemorefractory cases (TP53 disruption, NOTCH1 mutations, ATM deletion), fludarabine-refractory CLL appeared to be characterized by multiple molecular alterations that, to some extent, are mutually exclusive. We then compared the prevalence of mutations observed at the time of fludarabine-refractoriness to that observed in other disease phases. At diagnosis, SF3B1 mutations were rare (17/301; 5%), and showed a crude association with short treatment free survival (p<.001) and overall survival (p=.011). Remarkably, 5/17 (29%) CLL mutated at diagnosis were primary fludarabine-refractory patients. In CLL investigated at diagnosis, the hotspot distribution and molecular spectrum of SF3B1 mutations, as well as their mutual relationship with other genetic lesions, were similar to those observed in fludarabine-refractory CLL. SF3B1 mutations were restricted to 2/33 (6.0%) clonally-related RS. Across the different disease phases investigated, mutations were somatically acquired in all cases (n=18) for which germline DNA was available. These data document that mutations of SF3B1, a splicing factor that is a critical component of the spliceosome; i) recurrently associate with fludarabine-refractory CLL; ii) occur at a low rate at CLL presentation; iii) play a minor role in RS transformation, corroborating the notion that CLL histologic shift is molecularly distinct from chemorefractory progression without RS transformation. The identification of SF3B1 mutations points to the involvement of splicing regulation as a novel pathogenetic mechanism in CLL. The pathogenicity of SF3B1 mutations in CLL is strongly supported by clustering of these mutations in evolutionarily conserved hotspots localized within HEAT domains, which are tandemly arranged curlicue-like structures serving as flexible scaffolding on which other components can assemble. Also, the observation that SF3B1 regulates the alternative splicing program of genes controlling cell cycle progression and apoptosis points to a potential contribution of SF3B1 mutations in modulating tumor cell proliferation and survival. In addition to pathogenetic implications, SF3B1 mutations might also provide a therapeutic target for SF3B1 inhibitors, that are currently under pre-clinical development as anti-cancer drugs. Disclosures: No relevant conflicts of interest to declare.

Small extracellular vesicles (small EVs) are commonly released by all cells, and are found in all body fluids. They are implicated in cell to cell short- and long-distance communication through the transfer of genetic material and proteins, as well as interactions between target cell membrane receptors and ligands anchored on small EV membrane. Beyond their canonical functions in healthy tissues, small EVs are strategically used by tumors to communicate with the cellular microenvironment and to establish a proper niche which would ultimately allow cancer cell proliferation, escape from the immune surveillance, and metastasis formation. In this review, we highlight the effects of hematological malignancy-derived small EVs on immune and stromal cells in the tumor microenvironment.

Extracellular vesicles (EV), comprising microvesicles and exosomes, are particles released by every cell of an organism, found in all biological fluids, and commonly involved in cell-to-cell communication through the transfer of cargo materials such as miRNA, proteins, and immune-related ligands (e.g., FasL and PD-L1). An important characteristic of EV is that their composition, abundance, and roles are tightly related to the parental cells. This translates into a higher release of characteristic pro-tumor EV by cancer cells that leads to harming signals toward healthy microenvironment cells. In line with this, the key role of tumor-derived EV in cancer progression was demonstrated in multiple studies and is considered a hot topic in the field of oncology. Given their characteristics, tumor-derived EV carry important information concerning the state of tumor cells. This can be used to follow the outset, development, and progression of the neoplasia and to evaluate the design of appropriate therapeutic strategies. In keeping with this, the present brief review will focus on B-cell malignancies and how EV can be used as potential biomarkers to follow disease progression and stage. Furthermore, we will explore several proposed strategies aimed at using biologically engineered EV for treatment (e.g., drug delivery mechanisms) as well as for impairing the biogenesis, release, and internalization of cancer-derived EV, with the final objective to disrupt tumor-microenvironment communication.

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Small extracellular vesicles (sEV, or exosomes) communication among cells in the tumor microenvironment has been modeled mainly in cell culture, while their relevance in cancer pathogenesis and progression in vivo is less characterized. Here we investigated cancer-microenvironment interactions in vivo using mouse models of chronic lymphocytic leukemia (CLL). sEV isolated directly from CLL tissue were enriched in specific miRNA and immune checkpoint ligands. Distinct molecular components of tumor-derived sEV altered CD8+ T-cell transcriptome, proteome and metabolome leading to decreased functions and cell exhaustion ex vivo and in vivo. Using antagomiRs and blocking antibodies, we defined specific cargo-mediated alterations on CD8+ T-cells. Abrogating sEV biogenesis by Rab27a/b knockout dramatically delayed CLL pathogenesis. This phenotype was rescued by exogenous leukemic sEV or CD8+ T-cell depletion. Finally, high expression of sEV-related genes correlated with poor outcomes in CLL patients, suggesting sEV profiling as prognostic tool. In conclusion, sEV shape the immune microenvironment during CLL progression.

Current standard treatment of patients with hairy cell leukemia (HCL), a chronic B-cell neoplasia of low incidence that affects the elderly, is based on the administration of purine analogs such as cladribine. This chemotherapy approach shows satisfactory responses, but the disease relapses, often repeatedly. Venetoclax (ABT-199) is a Bcl-2 inhibitor currently approved for the treatment of chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML) in adult patients ineligible for intensive chemotherapy. Given that HCL cells express Bcl-2, our aim was to evaluate venetoclax as a potential therapy for HCL. We found that clinically relevant concentrations of venetoclax (0.1 and 1 µM) induced primary HCL cell apoptosis in vitro as measured by flow cytometry using Annexin V staining. As microenvironment induces resistance to venetoclax in CLL, we also evaluated its effect in HCL by testing the following stimuli: activated T lymphocytes, stromal cells, TLR-9 agonist CpG, and TLR-2 agonist PAM3. We found decreased levels of venetoclax-induced cytotoxicity in HCL cells exposed for 48 h to any of these stimuli, suggesting that leukemic B cells from HCL patients are sensitive to venetoclax, but this sensitivity can be overcome by signals from the microenvironment. We propose that the combination of venetoclax with drugs that target the microenvironment might improve its efficacy in HCL.