Role In Chronic Lymphocytic Leukemia Research Articles

Antigen-independent, autonomous B cell receptor signaling drives activated B cell DLBCL.

Diffuse large B cell lymphoma of activated B cell type (ABC-DLBCL), a major cell-of-origin DLBCL subtype, is characterized by chronic active B cell receptor (BCR) signaling and NF-κB activation, which can be explained by activating mutations of the BCR signaling cascade in a minority of cases. We demonstrate that autonomous BCR signaling, akin to its essential pathogenetic role in chronic lymphocytic leukemia (CLL), can explain chronic active BCR signaling in ABC-DLBCL. 13 of 18 tested DLBCL-derived BCR, including 12 cases selected for expression of IgM, induced spontaneous calcium flux and increased phosphorylation of the BCR signaling cascade in murine triple knockout pre-B cells without antigenic stimulation or external BCR crosslinking. Autonomous BCR signaling was associated with IgM isotype, dependent on somatic BCR mutations and individual HCDR3 sequences, and largely restricted to non-GCB DLBCL. Autonomous BCR signaling represents a novel immunological oncogenic driver mechanism in DLBCL originating from individual BCR sequences and adds a new dimension to currently proposed genetics- and transcriptomics-based DLBCL classifications.

Evaluation the -174G>C Genetic Polymorphism of Interleukin-6 in Iranian Patients with Chronic Lymphocytic Leukemia.

Interleukin-6 (IL-6) is involved in inflammation and has a significant role in chronic lymphocytic leukemia (CLL) progression. Accordingly, IL-6 level may increase in CLL-affected patients compared to healthy individuals. The -174G>C single nucleotide polymorphism (SNP) in IL-6 promoter region has been related to differences in IL-6 transcription. Therefore, we investigated the possible association of IL-6 polymorphism with CLL. We examined the -174G>C SNP in IL-6 gene and studied its possible relationship with CLL in affected patients and in healthy controls using Amplification Refractory Mutation System- polymerase chain reaction genotyping method. IL-6 plasma level was measured in both studied groups. According to the results, IL-6 mean plasma concentration was increased significantly in the CLL patients compared to the controls. However, 174G>C genotype of the IL-6 gene was not associated with CLL. Furthermore, there were no significant differences in the distribution of allele and genotype frequencies between the CLL-affected patients and the controls (P>0.05). Our study showed that -174G>C SNP in promotor of IL-6 gene could not be considered a risk factor for CLL. Larger prospective studies should be performed to confirm our results.

Novel circular RNAs of the apoptosis-related BAX and BCL2L12 genes identified in a chronic lymphocytic leukemia cell line using nanopore sequencing.

Circular RNAs (circRNAs), a novel RNA type generated by back-splicing, are key regulators of gene expression, with deregulated expression and established involvement in leukemia. The products of BCL2 and its homologs, including BAX and BCL2L12, are implicated in chronic lymphocytic leukemia (CLL). However, to the best of our knowledge, nothing is known about circRNAs produced by these two genes and their role in CLL. We sought to further elucidate the contribution of BAX and BCL2L12 in CLL by unraveling the identity, localization, and potential role of their circRNAs. Therefore, total RNA from the EHEB cell line and peripheral blood mononuclear cells (PBMCs) of CLL patients and non-leukemic blood donors was extracted and reverse-transcribed using random hexamers. Next, nested PCRs with divergent primers were performed and the purified PCR products were subjected to 3rd generation nanopore sequencing. Nested PCRs were also applied to first-strand cDNAs synthesized from total RNA extracts of PBMCs from CLL patients and non-leukemic blood donors. Lastly, a single-molecule resolution fluorescent in situ hybridization (smFISH) method called circFISH was used to visualize the circRNA distribution in EHEB cells. We discovered several novel circRNAs produced by BAX and BCL2L12, which were characterized by great exon structure diversity. In addition, intriguing findings regarding their formation emerged. Interestingly, visualization of the most abundant circRNAs showed distinct intracellular localization. Moreover, a complex BAX and BCL2L12 circRNA expression pattern was revealed in CLL patients and non-leukemic blood donors. Our data suggest a multifaceted role of BAX and BCL2L12 circRNAs in B-cell CLL.

Interleukin-27 potentiates CD8+ T-cell-mediated anti-tumor immunity in chronic lymphocytic leukemia.

Chronic Lymphocytic Leukemia (CLL) cells are highly dependent on interactions with the immunosuppressive tumor microenvironment (TME) for survival and proliferation. In the search for novel treatments, pro-inflammatory cytokines have emerged as candidates to reactivate the immune system. Among those, IL-27 has recently gained attention, but its effects differ among malignancies. Here, we utilized the Eμ-TCL1 and EBI3 knock-out mouse models as well as clinical samples from patients to investigate the role of IL-27 in CLL. Characterization of murine leukemic spleens revealed that the absence of IL-27 leads to enhanced CLL development and a more immunosuppressive TME in transgenic mice. Gene-profiling of T-cell subsets from EBI3 knock-out highlighted transcriptional changes in the CD8+ T-cell population associated with T-cell activation, proliferation, and cytotoxicity. We also observed an increased anti-tumor activity of CD8+ T cells in presence of IL-27 ex vivo with murine and clinical samples. Notably, IL-27 treatment led to the reactivation of autologous T cells from CLL patients. Finally, we detected a decrease in IL-27 serum levels during CLL development in both pre-clinical and patient samples. Altogether, we demonstrated that IL-27 has a strong antitumorigenic role in CLL and postulate this cytokine as a promising treatment or adjuvant for this malignancy.

Measurable residual disease in chronic lymphocytic leukemia.

Measurable residual disease (MRD) is defined as the presence of residual cancer cells after treatment in patients with clinically undetectable disease, who would otherwise be considered in complete remission. It is a highly sensitive parameter which indicates the disease burden and predicts survival in this setting of patients. In recent years, MRD has gained a role in many hematological malignancies as a surrogate endpoint for clinical trials: undetectable MRD has been correlated to longer progression free survival (PFS) and overall survival (OS). New drugs and combinations have been developed with the aim to achieve MRD negativity, which would indicate favorable prognosis. Different methods to measure MRD have also been devised, which include flow cytometry, polymerase chain reaction (PCR) and next generation sequencing (NGS), with different sensitivity and accuracy in evaluating deep remission after treatment. In this review, we will analyze the current recommendations for the detection of MRD, with particular focus on its role in Chronic Lymphocytic Leukemia (CLL), as well as the different detection methods. Moreover, we will discuss the results of clinical trials and the role of MRD in new therapeutic schemes with inhibitors and monoclonal antibodies. MRD is not currently used in the clinical practice to evaluate response to treatment, due to technical and economical limitations, but it's gaining more and more interest in trials settings, especially since the introduction of venetoclax. The use of MRD in trials will likely be followed by a broader practical application in the future. The aim of this work is to provide a reader-friendly summary of the state of art in the field, as MRD will soon become an accessible tool to evaluate our patients, predict their survival and guide physician's therapeutic choices and preferences.

Dysregulation of PRMT5 in chronic lymphocytic leukemia promotes progression with high risk of Richter’s transformation

Richter’s Transformation (RT) is a poorly understood and fatal progression of chronic lymphocytic leukemia (CLL) manifesting histologically as diffuse large B-cell lymphoma. Protein arginine methyltransferase 5 (PRMT5) is implicated in lymphomagenesis, but its role in CLL or RT progression is unknown. We demonstrate herein that tumors uniformly overexpress PRMT5 in patients with progression to RT. Furthermore, mice with B-specific overexpression of hPRMT5 develop a B-lymphoid expansion with increased risk of death, and Eµ-PRMT5/TCL1 double transgenic mice develop a highly aggressive disease with transformation that histologically resembles RT; where large-scale transcriptional profiling identifies oncogenic pathways mediating PRMT5-driven disease progression. Lastly, we report the development of a SAM-competitive PRMT5 inhibitor, PRT382, with exclusive selectivity and optimal in vitro and in vivo activity compared to available PRMT5 inhibitors. Taken together, the discovery that PRMT5 drives oncogenic pathways promoting RT provides a compelling rationale for clinical investigation of PRMT5 inhibitors such as PRT382 in aggressive CLL/RT cases.

Dysregulation of PRMT5 in Chronic Lymphocytic Leukemia Supports Transformation to Diffuse Large B-Cell Lymphoma

Background: Richter's transformation (RT) is the progression of chronic lymphocytic leukemia (CLL) to a high-grade lymphoma, most commonly resembling a diffuse large B-cell-like lymphoma, that has a bleak prognosis of 6-12 months. Many of the recurrent somatic alterations identified in RT are also associated with the CLL-phase of disease, suggesting additional unidentified genetic, epigenetic, or molecular events underlie transformation. Aberrant PRMT5 expression is known to promote and maintain oncogenic signaling in non-Hodgkin's lymphomas but its role in CLL and RT remains unclear. Methods: Tissue microarrays and western blots were used to evaluate PRMT5 expression in CLL/SLL and RT lymph nodes (LN). Differentially expressed genes between patient-matched RT LNs and CLL PBMCs were identified with scRNA-seq & scV(D)J-seq. ScRNA-seq was utilized to identify transcriptional changes between Eμ-PRMT5/TCL1 & Eμ-TCL1 mice. Tumor allografts were generated by administering 5 x 10^6 CD19+CD5+ spleen cells from Eμ-PRMT5/TCL1 mice intravenously to C57/BL6J mice. One week post-engraftment mice were enrolled in treatment groups (PRT382 10mg/kg, n=10; vehicle, n=7) with all treatments administered for 4 contiguous days per week by oral gavage. Results: Tissue microarray analysis on 70 CLL and 15 RT LN cases showed robust PRMT5 staining in RT LNs and minimal staining in CLL tissues. Immunoblot analysis revealed that CLL cells from patients that eventually undergo transformation displayed significant increase in PRMT5 expression months prior to transformation, whereas CLL patients maintained variable to minimal PRMT5 expression. ScRNA-seq & scV(D)J-seq on RT LN biopsies and CLL PBMCs from two patients revealed that PRMT5 expression was restricted to distinct nodal B cell subpopulations co-expressing MYC, BIRC5, CD83, and CD69. One PRMT5+ cluster displayed overlapping expression of proliferative markers (Mki67, TOP2A, PCNA, CALM2/3, and HMGB1/2) with enriched EIF4 signaling. Anti-apoptotic and immune modulating genes (BCL21A, IL4I1, TCL1A, and CCL3/4) were enriched in the second PRMT5+ nodal cluster. Interestingly, transcriptional diversity was enhanced in clonally related RT B cell populations with an increased proportion of cells expressing PRMT5 when compared to the CLL-phase of disease. To further evaluate the role of PRMT5 in CLL disease progression, we conducted histopathologic analysis on the spleen and lymph nodes of 6 month old animals from Eµ-PRMT5/TCL1 & Eµ-TCL1 mouse models, revealing a RT-like histology with loss of germinal centers and effacement of normal architecture exclusively in Eµ-PRMT5/TCL1 animals. Transcriptional changes underlying phenotypic differences between Eµ-PRMT5/TCL1 & Eµ-TCL1 mice were also assessed by scRNA-seq, where splenic B cells of the Eµ-PRMT5/TCL1 exhibited increased expression of oncogenic and immune regulating genes (Myc, Mki67, Egr1, Cxcr5, Ccr7, Il-10, Ctla4, and Pd-L1). Interestingly, the dominant B-cell clusters enriched in Eµ-PRMT5/TCL1 spleen and LNs showed significant transcriptional overlap with human RT PRMT5 expressing LN clusters (e.g., Myc, Cd83, and Cd69). With the observation that PRMT5 may play a significant role in CLL-to-RT evolution, we then aimed to evaluate the use of targeted PRMT5 inhibition against murine RT-like tumors in vivo. Using the selective SAM-competitive PRMT5 inhibitor, PRT382, in Eµ-PRMT5/TCL1 allografts, we observed PRT382 treatment delayed leukemic expansion, increased median survival (p<0.0001), and reduced spleen mass compared to vehicle treated mice. Conclusion: We show that PRMT5 is upregulated in the lymph nodes of CLL patients prior to and after transformation, suggesting a role for PRMT5 in CLL transformation to RT. Likewise, the Eμ-PRMT5/TCL1 mouse model develops a RT-like histology and shows significant overlap in the transcriptional profile to human RT tumors. And further, inhibition of PRMT5 with PRT382 provides significant improvement in median overall survival and slows disease progression in Eμ-PRMT5/TCL1 adoptive transfer models. Our preclinical data identifies PRMT5 as a high-risk marker in CLL and provides rationale for the clinical evaluation of PRMT5 inhibition in the treatment of high-risk CLL/RT.

Antigen-Independent, Autonomous B-Cell Receptor Signaling in Diffuse Large B-Cell Lymphoma

Gene expression profiling of diffuse large B-cell lymphoma (DLBCL) defines the Cell-of-origin (CoO) classification with two major subtypes, germinal center B-cell (GCB) and the more aggressive activated B-cell (ABC) type. Chronic activation of B-cell receptor (BCR) signaling with constitutive activation of the NF-κB pathway is an essential oncogenic mechanism in ABC DLBCL. BCR pathway activation with increased NF-κB activation can be caused by gain-of-function mutations of the BCR signaling cascade. We investigated whether antigen-independent, i.e. autonomous BCR signaling, akin to its essential pathogenetic role in chronic lymphocytic leukemia, acts as a functional driver mechanism in DLBCL without such gain-of-function mutations. DNA and RNA were extracted from ABC DLBCL cell lines TMD8 and OCI-Ly3 and from fresh-frozen biopsies of 18 histologically confirmed DLBCL cases. Functional BCR transcripts were identified by ARTISAN PCR and transduced into murine triple knock out (TKO) cells. TKO cells lack the recombination activation gene 2 (Rag2) and lambda 5 gene (λ5) and are therefore incapable of expressing an endogenous BCR. In addition, the BCR signal transduction molecule SLP65 is replaced with a tamoxifen-inducible estrogen receptor (ERT2) - SLP65 fusion gene. Upon transduction of both heavy and light BCR chains and staining with Indo-1, background calcium flux can be measured as Indo-1 signal intensity ratio (SIR) by flow cytometry. After restoring functionality of the BCR signaling cascade by tamoxifen, antigen-independent BCR signaling is measured as SIR, followed by maximum BCR stimulation with an isotype-specific crosslinking antibody. Autonomous BCR signaling strength (SSBCR) is quantified by an arithmetic product based on the relative Indo-1 SIR and the relative number of cells with SIR above background in the presence of tamoxifen and calibrated on crosslinking-induced maximum SIR. According to the primary hypothesis, the BCR of CARD11 wild-type, IgM-expressing TMD8 cells demonstrated strong autonomous BCR signaling (SSBCR=0.243), whereas the BCR of CARD11 mutated, IgG-expressing OCI-Ly3 cells completely lacked autonomous signaling (SSBCR=0.022). BCR from 13 primary DLBCL signaled autonomously (SSBCR=0.125-0.619), where 5 samples were negative (SSBCR=0.004-0.023) Autonomous BCR signaling was absolutely dependent on IgM isotype (Fisher's exact test: p=0.0016). CoO classification by digital gene expression (Nanostring) analyses or immunohistochemistry demonstrated autonomous BCR signaling in 8/9 ABC (non-GCB) DLBCL, 2/6 GCB DLBCL, and 2 unclassifiable DLBCL, and a transformed follicular lymphoma DLBCL. Independent of CoO, DLBCL can be assigned to 6-7 clusters based on their genetic aberrations (Chapuy 2018, Wright 2020). Fifteen DLBCL were suited for WES and targeted panel sequencing. Four cases were assigned by a probabilistic calculation to Chapuy cluster C5, 2 cases to C2, and one case to C1, while 8 cases remained unclassifiable. Clustering by the LymphGen tool assigned 3 cases to cluster ST2, one case each into MCD, EZB, and N1, 4 cases into various clusters, and 5 cases unclassified. DLBCL with autonomous BCR signaling fell into clusters C1/unclassified, C2/unclassified, C5/unclassified (n=3), unclassified/EZB, unclassified/ST2, unclassified/N1 and unclassified/unclassified (n=2). Cases lacking autonomous BCR signaling were assigned to unclassified/ST2 (n=2), C5/MCD, and unclassified/unclassified. Eleven of 13 cases with an autonomous signaling BCR lacked activating CARD11 mutations. In conclusion, autonomous BCR signaling is a potential immunological oncogenic driver in DLBCL that cannot be detected by sequencing studies, is independent of external antigen stimulation, and originates from a self-organizing conformation of the surface BCR (Minici 2017). Autonomous BCR signaling is present predominantly in ABC DLBCL and dependent on IgM isotype. Autonomous BCR signaling offers a convincing explanation for oncogenic NF-κB activation in DLBCL. Limited data suggest that the majority of DLBCL with autonomous BCR signaling fall into the ABC-dominated genetic clusters C1/C5, and MCD/N1, respectively. In summary, genetic aberrations, BCR function, and gene expression profile form 3 independent layers of DLBCL pathophysiology that need to be analyzed separately and offer independent targets for therapy.

The miR-15a/16-1 and miR-15b/16-2 clusters regulate early B cell development by limiting IL-7 receptor expression.

MicroRNAs are small non-coding RNAs that have emerged as post-transcriptional regulators involved in development and function of different types of immune cells, and aberrant miRNA expression has often been linked to cancer. One prominent miRNA family in the latter setting is the miR-15 family, consisting of the three clusters miR-15a/16-1, miR-15b/16-2 and miR-497/195, which is best known for its prominent tumor suppressive role in chronic lymphocytic leukemia (CLL). However, little is known about the physiological role of the miR-15 family. In this study, we provide a comprehensive in vivo analysis of the physiological functions of miR-15a/16-1 and miR-15b/16-2, both of which are highly expressed in immune cells, in early B cell development. In particular, we report a previously unrecognized physiological function of the miR-15 family in restraining progenitor B cell expansion, as loss of both clusters induces an increase of the pro-B as well as pre-B cell compartments. Mechanistically, we find that the miR-15 family mediates its function through repression of at least two different types of target genes: First, we confirm that the miR-15 family suppresses several prominent cell cycle regulators such as Ccne1, Ccnd3 and Cdc25a also in vivo, thereby limiting the proliferation of progenitor B cells. Second, this is complemented by direct repression of the Il7r gene, which encodes the alpha chain of the IL-7 receptor (IL7R), one of the most critical growth factor receptors for early B cell development. In consequence, deletion of the miR-15a/16-1 and miR-15b/16-2 clusters stabilizes Il7r transcripts, resulting in enhanced IL7R surface expression. Consistently, our data show an increased activation of PI3K/AKT, a key signaling pathway downstream of the IL7R, which likely drives the progenitor B cell expansion we describe here. Thus, by deregulating a target gene network of cell cycle and signaling mediators, loss of the miR-15 family establishes a pro-proliferative milieu that manifests in an enlarged progenitor B cell pool.

Exploring the significance of PAK1 through chromosome conformation signatures in ibrutinib-resistant chronic lymphocytic leukaemia.

Ibrutinib exerts promising anticancer effects in chronic lymphocytic leukaemia (CLL). However, acquired resistance occurs during treatment, necessitating the exploration of underlying mechanisms. Although three‐dimensional genome organization has been identified as a major player in the development and progression of cancer, including drug resistance, little is known regarding its role in CLL. Therefore, we investigated the molecular mechanisms underlying ibrutinib resistance through multi‐omics analysis, including high‐throughput chromosome conformation capture (Hi‐C) technology. We demonstrated that the therapeutic response to ibrutinib is associated with the expression of p21‐activated kinase 1 (PAK1). PAK1, which was up‐regulated in CLL and associated with patients' survival, was involved in cell proliferation, glycolysis and oxidative phosphorylation. Furthermore, the PAK1 inhibitor IPA‐3 exerted an anti‐tumour effect and its combination with ibrutinib exhibited a synergistic effect in ibrutinib‐sensitive and ‐resistant cells. These findings suggest the oncogenic role of PAK1 in CLL progression and drug resistance, highlighting PAK1 as a potential diagnostic marker and therapeutic target in CLL including ibrutinib‐resistant CLL.

P595: DISCOVERY OF NOVEL CIRCULAR RNAS (CIRCRNAS) OF THE APOPTOSIS-RELATED BAX AND BCL2L12 GENES WITH A MULTIFACETED ROLE IN CHRONIC LYMPHOCYTIC LEUKEMIA, USING CUTTING-EDGE NANOPORE SEQUENCING TECHNOLOGY

Background: Circular RNAs (circRNAs), a novel RNA type generated by back-splicing, are key indirect regulators of gene expression, with deregulated expression and established involvement in several human malignancies. Many circRNAs have been shown to bind microRNAs (miRNAs), thus making miRNAs unavailable to regulate protein-coding gene expression. Moreover, some of them have been described to interact with chromatin and affecting its structure. Despite their pivotal roles in the development and progression of cancer, only three studies have investigated their expression and role(s) in chronic lymphocytic leukemia (CLL), so far. The products of BCL2 and its homologues, including BAX and BCL2-like 12 (BCL2L12), are implicated in CLL, as apoptosis regulators. Moreover, expression levels of both BAX and BCL2L12 mRNAs are deregulated in CLL and are associated with patients’ response to therapy and overall survival. However, to the best of our knowledge, nothing is known about circRNAs produced by these two genes and their regulatory potential. Aims: We sought to further elucidate the contribution of both BAX and BCL2L12 in CLL by unraveling the identity of their circRNAs in a B-cell leukemic cell line (EHEB) and by studying in silico their potential interactions with miRNAs having an already established role in CLL. Methods: EHEB cells were propagated according to ATCC instructions. After total RNA extraction, 2μg of total RNA were reverse-transcribed using random hexamers. Next, nested PCR with divergent primers was performed, starting from each exon of BAX and BCL2L12 genes; thus, only cDNAs from BAX and BCL2L12 circRNAs were amplified, respectively. After having mixed and purified all nested-PCR products, nanopore sequencing libraries were built according to an optimized protocol. Following nanopore sequencing and basecalling in a MinION Mk1C 3rd-generation sequencer, sequencing reads were aligned and corrected using Minimap2 and TranscriptClean, respectively. circRNA sequences were identified using an in-house–built, PERL-based algorithm. A single-molecule resolution fluorescent in situ hybridization (FISH) method called circFISH was used to visualize the circRNA distribution in the cells. Lastly, miRDB was used to predict interactions of the most abundant BAX and BCL2L12 circRNAs with miRNAs. Results: We discovered 18 and 21 novel circRNAs produced by BAX and BCL2L12 genes, respectively, in this leukemic cell line. The exon structure of these novel circRNAs showed remarkable diversity, also comprising genomic regions that have previously been considered as intronic, as they are not included in messenger RNAs (mRNAs). Interestingly, one of the two most abundant BAX circRNAs is composed of a single exon, also spanning two introns. Similar intron retentions have been observed in a few BCL2L12 circRNAs. The gamut of miRNAs predicted to be bound by novel circRNAs includes miR-484, miR-181a-2-3p and miR-214-3p. Particularly, the inhibition of miR-214-3p is associated with elevated apoptosis in leukemic B-cells. Summary/Conclusion: Alternative splicing and back-splicing mechanisms of the primary BAX and BCL2L12 transcripts produce multiple distinct circRNAs in this B-cell CLL cell line. Interestingly, one of the two most abundant circular transcripts of BAX is a circRNA spanning three exons and two intervening introns of this gene. Lastly, several miRNAs are predicted to be sequestered by circRNAs of either of these apoptosis-related genes, including miR-181 family members that have been associated with chemosensitivity. Our data suggest a multifaceted role of BAX and BCL2L12 circRNAs in B-cell CLL.

P623: IBRUTINIB REGULATES MIR-181A/B VIA C-FOS IN CHRONIC LYMPHOCYTIC LEUKEMIA

Background: B-cell receptor (BCR) signalling controls B-cell survival and proliferation, and its deregulation has a pathogenic role in Chronic Lymphocytic Leukemia (CLL), a B-cell malignancy. Currently, several BCR signalling inhibitors are used in therapy, among them the Ibrutinib. We previously reported that the BCR-signalling inhibition mediated by Ibrutinib leads to miR-181a/b activation; those miRNAs are significant biomarkers of CLL progression, and their downregulation is associated to a poor prognosis; furthermore, low levels of miR-181a/b impair several anti-apoptotic proteins, contributing to cell survival. BCR signalling also controls c-Fos/AP-1 pathway in pre-B cells. Recently, we suggested the involvement of c-Fos in miR-181b expression, however the mechanism by which this regulation is exerted is still not explored. Moreover, the involvement of c-Fos in miR-181a/b transcription during Ibrutinib is still not clear. Aims: Assess the impact of Ibrutinib on c-Fos expression; assess the involvement of the transcription factor c-Fos in miR-181a/b transcription; assess the impact of miR-181a/b in CLL cells survival during Ibrutinib treatment. Methods: To assess the impact of Ibrutinb on c-Fos transcription, we evaluated its expression in CLL cells treated with Ibrutinib or vehicle. To assess the involvement of c-Fos in miR-181a/b transcription, we evaluated i) the expression of the miRs and of their primary transcripts in CLL cells overexpressing c-Fos, and ii) the ability of c-Fos to bind miR-181a/b host gene promoter by luciferase, ChIP and EMSA assays. To assess the impact of the miRs on CLL cells survival during Ibrutinib treatment, we performed MTT assay in CLL cells after miR-181a/b silencing and Ibrutinib treatment. Results: Considering that c-Fos was found to be controlled by BCR signalling in pre-B cells, we evaluated whether BCR signalling affect c-Fos also in CLL cells: we found that c-Fos expression increases in primary CLL cells after Ibrutinib treatment. Since miR-181a/b was up-regulated after Ibrutinib treatment in vitro and in vivo in CLL cells, and considering that a possible involvement of c-Fos in miR-181b expression was already suggested, we sought to identify if c-Fos was a direct regulator of miR-181a/b expression. We confirmed that c-Fos overexpression affects miR-181b levels in CLL patients, but not miR-181a; however, the dysregulation of the miR shows heterogeneity among patients. Indeed miR-181b expression increases in 3 and decreases in 2 of 7 patients. To better understand how c-Fos impact on miRs expression, we analysed both miR-181a and miR-181b at the transcriptional level in CLL and lymphoblastoid cell lines, finding that c-Fos negatively regulates the pri-miR-181a/b. To clarify the mechanism by which c-Fos regulates miR-181a/b transcription, we analysed the miRs host gene (MIR181A2HG) promoter. Since MIR181A2HG promoter shows two consensus sequences for the transcription factor c-Fos, we studied whether c-Fos binds these regions. We found that c-Fos binds at MIR181A2HG promoter by recognizing the two consensus sequences. Accordingly, after their deletion, the ability of c-Fos to recognize the promoter was overcome. Finally, since miR-181a and miR-181b are involved in cell death, we assessed whether those miRNAs participate in CLL cells death induced by Ibrutinib: we found that the silencing of both miRNAs improves CLL cell survival during Ibrutinib treatment. Summary/Conclusion: c-Fos is a downstream target of BCR signalling and a direct regulator of miR-181a/b transcription in CLL. MiR-181a/b are effectors of Ibrutinib-induced CLL cells death.

Chronic Lymphocytic Leukemia: Chemotherapy Free and Other Novel Therapies Including CAR T.

Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. Most individuals diagnosed with CLL will not need treatment immediately but over time the clonal B cells infiltrate the bone marrow, lymph nodes, liver, and spleen, causing anemia, thrombocytopenia, systemic symptoms, and increased risk for infections. When clonal B cells begin adversely affecting other organs, treatment is warranted. Therapy for CLL has undergone a paradigm shift away from chemotherapy-based regimens to targeted therapy with small-molecule inhibitors. B-cell receptor (BCR) signaling plays a key role in CLL. BCR signaling occurs via many factors including Bruton's tyrosine kinase (BTK), phosphatidylinositol 3-kinase (PI3K), phosphatidylinositol-4,5-bisphosphonate phosphodiesterase gamma-2 (PLCγ2), and CD19. CLL cells also express high levels of B-cell lymphoma or leukemia 2 (BCL2). Drugs that interfere with these pathways, such as ibrutinib, venetoclax, and idelalisib, have improved clinical outcomes. For any CLL patient that meets criteria for treatment, after evaluating for prognostic cytogenetic abnormalities, oral BTK inhibitors or venetoclax in combination with anti-CD20 therapy are considered first-line therapy. It is important to note that these novel therapies are particularly preferred for patients with TP53 mutations or deletion of the small arm of chromosome 17 (del(17p)), as those patients usually are chemotherapy refractory or display short remissions to chemotherapy. Nevertheless, patients without high-risk features such as TP53 abnormalities also benefit from novel agents. Following relapse, depending on the primary oral agent used, BTK inhibitors, venetoclax in combination with anti-CD20 antibodies, or PI3K inhibitors are preferred.

Awareness, Knowledge, and Preferences of United States (US) Patients with Chronic Lymphocytic Leukemia (CLL) and Their Caregivers Related to Finite Duration (FD) Therapy and Minimal (Measurable) Residual Disease (MRD)

Awareness, Knowledge, and Preferences of United States (US) Patients with Chronic Lymphocytic Leukemia (CLL) and Their Caregivers Related to Finite Duration (FD) Therapy and Minimal (Measurable) Residual Disease (MRD)

Clonal hematopoiesis, myeloid disorders and BAX-mutated myelopoiesis in patients receiving venetoclax for CLL

The BCL2 inhibitor venetoclax has established therapeutic roles in chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML). As BCL2 is an important determinant of survival of both myeloid progenitor and B cells, we investigated whether clinical and molecular abnormalities arise in the myeloid compartment during long-term continuous venetoclax treatment of CLL in 89 patients (87 with relapsed/refractory CLL). Over a median follow-up of 75 (range 21-98) months, persistent cytopenias (≥1 of neutropenia, thrombocytopenia, anemia) lasting ≥4 months and unrelated to CLL occurred in 25 patients (28%). Of these patients, 20 (80%) displayed clonal hematopoiesis, including 10 with therapy-related myeloid neoplasms (t-MNs). t-MNs occurred exclusively in patients previously exposed to fludarabine-alkylator combination therapy with a cumulative 5-year incidence of 10.4% after venetoclax initiation, consistent with rates reported for patients exposed to fludarabine-alkylator combination therapy without venetoclax. To determine whether the altered myelopoiesis reflected the acquisition of mutations, we analyzed samples from patients with no or minimal bone marrow CLL burden (n = 41). Mutations in the apoptosis effector BAX were identified in 32% (13/41). In cellular assays, C-terminal BAX mutants abrogated outer mitochondrial membrane localization of BAX and engendered resistance to venetoclax killing. BAX-mutated clonal hematopoiesis occurred independently of prior fludarabine-alkylator combination therapy exposure and was not associated with t-MNs. Single-cell sequencing revealed clonal co-occurrence of mutations in BAX with DNMT3A or ASXL1. We also observed simultaneous BCL2 mutations within CLL cells and BAX mutations in the myeloid compartment of the same patients, indicating lineage-specific adaptation to venetoclax therapy.

Rare Germline Variant in NFATC4 Associated with Familial Chronic Lymphocytic Leukemia

Chronic lymphocytic leukemia (CLL) has one of the highest familial risks of any cancer, with up to eightfold increased risk in first degree relatives of CLL patients. Genome-wide association studies (GWAS) have identified multiple common single nucleotide polymorphisms (SNPs) associated with risk, but these have modest effect. Similarly, identified germline variants associated with disease account for just a small minority of CLL patients, making familial CLL an attractive target for research, that could provide direct insight into pathobiology.We used whole exome sequencing (WES; Illumina) to search for rare germline variants (<1% Minor Allele Frequency) in 36 patients from 17 families with Mendelian-like CLL inheritance, where at least two affected family members were sequenced. Median age at diagnosis was 56.4 (range 41-72), 61% were male, 10/23 (43%) were IGHV -unmutated, and 5/24 (21%) had del17p and/or TP53 mutation. We found 3819 rare variants shared within all affected members of a given family. Of those, 71 non-synonymous variants were shared across at least 2 families, and 39 of these were predicted to be pathogenic by at least two commonly-used phenotype prediction tools. None of these variants are within known somatic CLL driver genes, nor were any found in genes near known CLL GWAS SNPs. In order to prioritize these variants, we assessed whether they were enriched among CLL cases (n = 646) as compared to ethnically matched normal population controls (n=8,920), a dataset we have recently reported (Tiao, Improgo et al, Leukemia). Using Fisher's exact test with Benjamini-Hochberg (BH) correction for multiple tests, we found that 27 of the 71 shared variants across multiple families were also enriched in unrelated CLL patients compared to controls. Among those, a rare variant of nuclear factor of activated T-cells 4 (NFATC4), rs200328372, was the most highly enriched in CLL (OR 20.8, Fisher-q-BH 0.026). This variant affects a splice acceptor site predicted to have a deleterious effect on the protein (FATHMM for non-coding variants). In a pathway analysis (MSigDB, DAVID) of genes carrying shared variants across families, NFATC4 together with SOS1 and PTPN7 were associated with the T-cell receptor, B-cell receptor, and MAP-kinase pathways, suggesting a possible role in CLL pathogenesis.The NFATC4 protein, also known as NFAT3, is part of a DNA-binding transcriptional complex that translocates to the nucleus after activation through dephosphorylation by calcineurin. This complex is involved in the inducible expression of cytokine genes in T cells, including interleukin (IL)-2 and IL-4. While NFATC1 has been implicated in CLL pathogenesis and was associated with more aggressive disease in a mouse model of CLL, the role of NFATC4 has not been elucidated. To further investigate this as well as its association with familial CLL, we compared gene expression profiling (GEP; Affymetrix U133 plus 2.0 array) data between familial and sporadic CLL patients and normal B-cells. While NFATC4 expression did not differ between normal B-cells (n=16) and CLL (n=143), it was significantly down-regulated in familial (n=47) as compared to sporadic (n=96) CLL cases (Mann-Whitney, p=0.005). In the 4 cases that harbor the shared risk variant, GEP results showed additional significant down-regulation of NFATC4 expression (Kruskal-Wallis, p=0.003 for all comparisons) (Figure 1).RNA sequencing (Illumina) demonstrated NFATC4 down-regulation in all CLL samples (not specifically in familial CLL as with GEP; n=100) versus normal B-cells (n=6; Mann-Whitney, p=-0.00024), suggesting a putative role for NFATC4 as a tumor suppressor. Since NFATC4 has over 30 alternatively spliced transcripts potentially affected by the rs200328372 variant, we used Cufflinks software to look at isoform-level RNA sequencing data, available on two relatives who carried this variant, compared to CLL cases and controls. Both relatives had reduced expression of all isoforms (Figure 2), suggesting that this mutation may reduce NFATC4 expression altogether. Studies of protein expression are ongoing.In conclusion, through rare germline variant analysis in familial CLL, we found a potentially deleterious variant of NFATC4 that is enriched in CLL. Subsequently, we used RNA sequencing data to show, for the first time, that NFATC4 expression is decreased in CLL versus normal B-cells, revealing a potential tumor suppressor mechanism in CLL. [Display omitted] DisclosuresBrown:Sun BioPharma: Consultancy, Research Funding; Gilead: Consultancy, Research Funding; Pharmacyclics: Consultancy; Redx: Consultancy; AstraZeneca: Consultancy; Pfizer: Consultancy; Janssen Oncology: Honoraria; AbbVie: Consultancy, Honoraria; Roche/Genentech: Consultancy; Celgene: Consultancy; Janssen: Consultancy; Infinity Pharmaceuticals: Consultancy; Astellas Pharma: Consultancy.

Importance of Mitochondrial Metabolism As a Selective Therapeutic Approach in Chronic Lymphocytic Leukemia Patients

Objective: Chronic lymphocytic leukemia (CLL) is the most common blood cancer among adults in Western countries. Impairments in mitochondrial physiology play a role in CLL. Selectively targeting mitochondrial bioenergetics in leukemia cells may be an effective therapeutic approach for CLL. However, mitochondrial metabolism in CLL remains relatively unexplored. Nicotinamidephospho-robosyltransferase (NAMPT) is a key enzyme in the nitoinamide adenine dinucleotide (NAD) salvage pathway. FK866, a chemical inhibitor of NAMPT depletes cellular NAD and ATP levels and triggers apoptosis, suggesting NAMPT contributes to the prolonged survival of CLL cells. Idelalisib, an inhibitor of phosphatidylinositol-3-kinase-delta (PI3Kδ) is an approved therapy for B-cell malignancies including CLL. Herein, bioenergetics profile in 20 CLL patients have been defined and the effects of these drugs on this profile, cell viability, mitochondrial membrane potential (MMP), reactive oxygen species (ROS) and protein levels of mitochondrial complexes and pPI3Kδ were analyzed. We hypothesize that both inhibitors will alter CLL mitochondrial bioenergetics profiles and function, cell viability, ROS levels and enable lower doses and profound effects for combination therapies rather than single agent therapy.Methods: A high resolution Oroboros Oxygraph 2K (Oroboros Instruments, Innsbruck, Austria), a Clarke-type oxygen electrode is used to measure mitochondrial respiration rates CLL cells at 370C. Freshly isolated CLL cells (5-10 mil./ml) were added to the chamber in 2 ml of RPMI. After the measurement of basal respiration rates (BR), the following chemicals were added: oligomycin (2μM), FCCP: carbonyl cyanide p-trifluoromethoxy phenyhydrazone (2.5-12.5 μM), and antimycin A (2 μM). Oxygen consumption rate is expressed in pmol oxygen/s/mil. cells. Protein levels in CLL cell lysates were determined by Western blotting. Cell viability, MMP, and ROS were assessed by Novocyte flow cytometer.Results: Bioenergetics profile (BR: 14.45 ± 3.40; FCCP-induced MR: 57.48 ± 14.94; reserve respiratory capacity, RRC: 43.03 ± 12.80; respiratory control ratio, RCR: 9.36 ± 3.99; proton leak: 6.77 ± 2.45 and residual respiration: 6.03 ± 1.49; Mean ± SD) of 20 CLL patients was individually illustrated and summarized. Our data show that CLL cells have a high mitochondrial RRC and require a higher concentration of uncoupler, namely FCCP to achieve MR than commonly used. BR was not significantly decreased by 24 hours of treatment with FK866 at 1 nM (FK1) nor idelalisib at 6.25 μM (ID6.25) or the combination. After 48 hours, basal respiration of ID6.25 or ID6.25 + FK1 - treated cells was significantly decreased compared to DMSO vehicle control. However, after 24 or 48 hours MR, RRC, and RCR were significantly decreased by each individual drug or its combination compared to DMSO vehicle control. After 24 hours, combination therapy did not significantly decrease BR, RRC, and RCR compared to the treatment of FK1 (except MR), but MR, RRC, and RCR were decreased significantly compared to ID6.25 (except BR). The combination treatment of these two drugs significantly decreased all bioenergetics parameters compared to each individual drug after 48 hours. Preliminary data with another NAMPT-inhibitor, GMX-1778 at 1nM also showed similar effect to FK866 and in combination with ID6.25. MMP was not affected by these drug treatments, cell viability corresponded to the effect of mitochondrial bioenergetics profile, however, ROS levels were increased. Protein expression of certain subunits of mitochondrial complexes I, III and V and pPI3Kδ were decreased after the combined treatment.Conclusion:Bioenergetics profile can be directly evaluated by high resolution Oroboros oxygraph in CLL cells without any excess manipulation. CLL cells have immense mitochondrial RRC and highly sensitive to an uncoupler. Both FK866 and idelalisib affected bioenergetics profile in CLL cells at doses as low as 1 nM or 6.25 µM, respectively. The combined effect of these drugs is more profound than each agent alone on mitochondrial bioenergetics profile, cell viability, ROS and protein levels of mitochondrial complexes and pPI3Kδ. These novel data derived from the combined treatment with lower doses targeting mitochondrial metabolism provide rational therapeutic combination that may lead to reduce toxicity and increased drug efficacy in CLL. DisclosuresNo relevant conflicts of interest to declare.

Neutrophil to T-Lymphocyte Ratio (NLR) and Neutrophil to Monocyte Ratio (NMR) Are Promising Biomarkers in Chronic Lymphocytic Leukemia Prognostic Assessment

Development of targeted drugs produced a significant changes in the management of patients with Chronic Lymphocytic Leukemia (CLL). The recent advances in molecular diagnostic techniques has provided a better prediction of disease progression but they are not easily accessible to all Institutions.CLL cells proliferation and survival are sustained by a complex microenvironmental network of cells interactions that are at least partially mediated through B cell receptor signaling.An increased number of studies describe the role of neutrophils and monocytes as markers of the inflammation and antitumor immunity that support tumorigenesis. Recently, authors published the increased NLR is associated to a prognosis in different cancer type.In our study we retrospectively evaluated the prognostic significance of peripheral blood neutrophils, monocytes and non-neoplastic lymphocytes in a unicentric, unselected, CLL cohort of 400 CLL patients at diagnosis (median age 64; stage Binet A 76%,B 18%,C 6%).Using blood count and the flow cytometric analysis reports, absolute neutrophil count (ANC), absolute monocyte count (AMC) and absolute T-lymphocyte count (ALC-CD3+) were evaluated and the neutrophil to T-lymphocyte ratio (NLR), the monocyte to T-lymphocyte ratio (MLR) and the neutrophil to monocyte ratio (NMR) were calculated at diagnosis, follow up and at relapse. Clinical and biological data from all patients were also retrieved to make a better comparison with the major clinical and prognostic markers commonly used.Compared to normal controls, CLL patients showed an increase AMC value (788±65 vs 469±51 cells/μL, p=0.005) and a slightly increased in the ALC-CD3+ value (2514±63 vs 2189±45 cells/μL, p=0.04). No difference in the ANC. The median NLR ratio was higher in CLL patients compared to healthy individuals (2.32 vs 1.7, p=0.02) and appeared more increased in early stage (2.65, 2.14, 1.95 mean value in Binet A, B, C respectively, p=0.0015). NMR median value was also significantly higher in early stage compared to advanced stage (8.0, 6.7, 5.1 in Binet A, B, C, p=0.0008).Conversely, MLR showed the opposite trend resulting more elevated in advanced stage at diagnosis, although with a low statistical significance.We did not found any correlation between these ratio and the IGVH status or genetic abnormalities.NLR and NMR higher level are associated with the absence of serum prognostic markers, such as CD38, and CD49d (p=0.002).160 out of 400 patients of our CLL cohort received a treatment during the course of disease. In our analysis, NLR and NMR are significantly higher in untreated patients than treated ones (median NLR 2.42 vs 1.95, p=0.0021; NMR 8.0 vs 7.0, p=0.0002). Among treated patients NLR and NMR significantly correlate with the time to treatment initiation (TTFT): lower NLR and NMR ratio correspond to a shorter TTFT (NLR p=0.03; NMR p=0.0035). For MLR the trend is opposite.A subgroup analysis conducted only on Rai 0/Binet A patients (n 219, 55%) showed that NLR and specially NMR are significantly associated with the risk of progression: lower NLR and NMR ratio correspond to an increased risk to symptomatic progression (p=0.0017), strengthening the hypothesis that high ratios are associated with a more indolent form of disease.In the 0/A population, analysis showed that a higher AMC and at a lesser extend a high ALC-CD3+ correlate with the progression rate and treatment initiation (Kaplan-Meier survival curve, p= 0.0001).Univariate analysis suggested that NLR ≥ 3.0, NMR ≥ 8.0 and AMC <900/mmc predicted a good prognosis in CLL patients. However, only NMR and AMC appeared as independent prognostic factors in multivariable analysis in Rai 0/Binet A patients.Our in vitro experiments supported these finding confirming: the non “immunosuppressive” role for neutrophils in CLL and the increased ability for monocytes to suppress T-lymphocytes activation and expand T-regulatory cell.In our study NLR ratio showed a positive prognostic role in CLL. A strongest protective meaning is displayed by NMR value. These combined value and AMC count provide more prognostic information at diagnosis and are associated with clinical outcome in CLL patients.These simple, cheap and reliable markers could be easily integrated into clinical practice reflecting both inflammatory status, immune response and microenviroment that contribute to disease progression. DisclosuresNo relevant conflicts of interest to declare.

MiR-29 modulates CD40 signaling in chronic lymphocytic leukemia by targeting TRAF4: an axis affected by BCR inhibitors

B-cell receptor (BCR) signaling and T-cell interactions play a pivotal role in chronic lymphocytic leukemia (CLL) pathogenesis and disease aggressiveness. CLL cells can use microRNAs (miRNAs) and their targets to modulate microenvironmental interactions in the lymph node niches. To identify miRNA expression changes in the CLL microenvironment, we performed complex profiling of short noncoding RNAs in this context by comparing CXCR4/CD5 intraclonal cell subpopulations (CXCR4dimCD5bright vs CXCR4brightCD5dim cells). This identified dozens of differentially expressed miRNAs, including several that have previously been shown to modulate BCR signaling (miR-155, miR-150, and miR-22) but also other candidates for a role in microenvironmental interactions. Notably, all 3 miR-29 family members (miR-29a, miR-29b, miR-29c) were consistently down-modulated in the immune niches, and lower miR-29(a/b/c) levels associated with an increased relative responsiveness of CLL cells to BCR ligation and significantly shorter overall survival of CLL patients. We identified tumor necrosis factor receptor–associated factor 4 (TRAF4) as a novel direct target of miR-29s and revealed that higher TRAF4 levels increase CLL responsiveness to CD40 activation and downstream nuclear factor-κB (NF-κB) signaling. In CLL, BCR represses miR-29 expression via MYC, allowing for concurrent TRAF4 upregulation and stronger CD40–NF-κB signaling. This regulatory loop is disrupted by BCR inhibitors (bruton tyrosine kinase [BTK] inhibitor ibrutinib or phosphatidylinositol 3-kinase [PI3K] inhibitor idelalisib). In summary, we showed for the first time that a miRNA-dependent mechanism acts to activate CD40 signaling/T-cell interactions in a CLL microenvironment and described a novel miR-29–TRAF4–CD40 signaling axis modulated by BCR activity.

Altered T Follicular Helper Cell Subsets and Function in Chronic Lymphocytic Leukemia.

Follicular helper T cells (TFH) have specialized properties in promoting normal B cell activation but their role in chronic lymphocytic leukemia (CLL) is unknown. We find that TFH cells are elevated in CLL patients and are phenotypically abnormal, expressing higher levels of PD-1, TIGIT, CD40L, IFNγ and IL-21, and exhibiting abnormal composition of TFH1, TFH2 and TFH17 subsets. Frequencies of CD4-positive T cells expressing TFH1 markers and IL-21 were positively correlated with patient lymphocyte counts and RAI stage, suggesting that accumulation of abnormal TFH cells is concomitant with expansion of the leukemic B cell clone. Treatment with ibrutinib led to normalization of TFH frequencies and phenotype. TFH cells identified in CLL bone marrow display elevated expression of several functional markers compared to blood TFH cells. CLL T cell-B cell co-culture experiments revealed a correlation of patient TFH frequencies with functional ability of their CD4-positive T cells to promote CLL proliferation. Conversely, CLL cells can preferentially activate the TFH cell subset in co-culture. Together our results indicate that CLL development is associated with expansion of abnormal TFH populations that produce elevated levels of cytokines and costimulatory molecules which may help support CLL proliferation.