Waldenström Macroglobulinemia (WM) is a B-cell lymphoma characterized by the precursor condition IgM monoclonal gammopathies of undetermined significance (IgM MGUS). We performed a gene expression profiling study to compare the transcriptome signatures of bone marrow (BM) B-cells and plasma cells of 36 WM patients, 13 IgM MGUS cases, and 7 healthy subjects used as controls (CTRLs) by Affymetrix microarray. We determined 2038 differentially expressed genes (DEGs) in CD19+ cells and 29 DEGs genes in CD138+ cells, respectively. The DEGs identified in B-cells were associated with KEGG pathways, mainly involved in hematopoietic cell lineage antigens, cell adhesion/focal adhesion/transmembrane proteins, adherens junctions, Wnt-signaling pathway, BCR-signaling pathway, calcium signaling pathway, complement/coagulation cascade, platelet activation, cytokine-cytokine receptor interactions, and signaling pathways responsible for cell cycle, apoptosis, proliferation and survival. In conclusion, we showed the deregulation of groups of genes belonging to KEGG pathways in the comparison among WM vs. IgM MGUS vs. CTRLs in B-cells. Interestingly, a small set of genes in B-cells displayed a common transcriptome expression profile between WM and IgM MGUS compared to CTRLs, suggesting its possible role in the risk of transformation of IgM MGUS to WM.

Background: Despite recurrent and activating mutations, including MYD88, CXCR4, ARID1A, KMT2D, and CD79B were identified, the genetic basis for Waldenström's Macroglobulinemia (WM) and the risk of progression of IgM MGUS to WM remain to be fully elucidated.Methods: We investigated the mutation status of WM (n = 8), sWM (n = 7), and IgM MGUS (n = 5) patients, by performing high‐throughput targeted AmpliSeq NGS on 117 target genes. Specifically, we analyzed the CD19+ cells from 15 WM/sWM patients and five IgM MGUS patients. We also analyzed the CD138+ cells from four WM/sWM patients and two IgM MGUS patients.Results: We detected the classic mutation MYD88L265P in 93% of WM/sWM and in 60% of IgM MGUS patients. The CXCR4S338Ter mutation was identified in 26% of WM/sWM patients, whereas it was undetectable in IgM MGUS subjects. Interestingly, we identified new mutated genes, including WNK2 somatic mutations affecting 46% of WM/sWM patients, for which a recurrent allelic variant (V1635Ter) was observed in this cohort. Moreover, sequencing evaluation revealed recurrently frameshift or missense mutations involving NFKB2 (L473Afs) in 60% of IgM MGUS and 20% of WM/sWM, PTPN13 (P1546Tfs) in 20% of IgM MGUS and 7% of WM/sWM, CARD11 (S622del) in 20% of IgM MGUS and 20% of WM/sWM, KMT2C (I823T) in all IgM MGUS and 93% of WM/sWM, and ATM in 20% of IgM MGUS and 47% of WM/sWM patients.Conclusion: In conclusion, we uncovered new insights into the mutational landscape of WM, depicting a more complex involvement of the NF‐kB pathway, and providing evidence of the recurrence of some variants (MYD88, IL17RB, NFKB2, ATM, CARD11, PTPN13, and WNK2) also in IgM MGUS.

Wnt/β-catenin signaling is critically required for the development and maintenance of leukemia stem cells (LSCs) in acute myeloid leukemia (AML) by constitutive activation of myeloid regeneration-related pathways. Cell-intrinsic activation of canonical Wnt signaling propagates in the nucleus by β-catenin translocation, where it induces expression of target oncogenes such as JUN, MYC and CCND1. As the Wnt/β−catenin pathway is now well established to be a key oncogenic signaling pathway promoting leukemic myelopoiesis, targeting it would be an effective strategy to impair LSC functionality. Although the effects of the adenosine analogue cordycepin in repressing β-catenins and destabilizing the LSC niche have been highlighted, the cellular and molecular effects on AML–LSC have not been fully clarified. In the present study, we evaluated the potency and efficacy of cordycepin, a selective repressor of Wnt/β-catenin signaling with anti-leukemia properties, on the AC133⁺ LSC fraction. Cordycepin effectively reduces cell viability of the AC133⁺ LSCs in the MUTZ−2 cell model and patient-derived cells through the induction of apoptosis. By Wnt-targeted RNA sequencing panel, we highlighted the re-expression of WIF1 and DKK1 among others, and the consequent downregulation of MYC and PROM1 (CD133) following MUTZ−2 cell exposure to increasing doses of cordycepin. Our results provide new insights into the molecular circuits involved in pharmacological inhibition mediated by cordycepin reinforcing the potential of targeting the Wnt/β-catenin and co-regulatory complexes in AML.

Background and Objectives: This study aimed to investigate the causes of continuous deep fluctuations in the absolute lymphocyte count (ALC) in an untreated patient with Chronic Lymphocytic Leukemia (CLL), who has had a favorable prognosis since the time of diagnosis. Up until now, the patient has voluntarily chosen to adopt a predominantly vegetarian and fruitarian diet, along with prolonged periods of total fasting (ranging from 4 to 39 days) each year. Materials and Methods: For this purpose, we decided to analyze the whole transcriptome profiling of peripheral blood (PB) CD19+ cells from the patient (#1) at different time-points vs. the same cells of five other untreated CLL patients who followed a varied diet. Consequently, the CLL patients were categorized as follows: the 1st group comprised patient #1 at 20 different time-points (16 time-points during nutrition and 4 time-points during fasting), whereas the 2nd group included only one time point for each of the patients (#2, #3, #4, #5, and #6) as they followed a varied diet. We performed microarray experiments using a powerful tool, the Affymetrix Human Clariom™ D Pico Assay, to generate high-fidelity biomarker signatures. Statistical analysis was employed to identify differentially expressed genes and to perform sample clustering. Results: The lymphocytosis trend in patient #1 showed recurring fluctuations since the time of diagnosis. Interestingly, we observed that approximately 4–6 weeks after the conclusion of fasting periods, the absolute lymphocyte count was reduced by about half. The gene expression profiling analysis revealed that nine genes were statistically differently expressed between the 1st group and the 2nd group. Specifically, IGLC3, RPS26, CHPT1, and PCDH9 were under expressed in the 1st group compared to the 2nd group of CLL patients. Conversely, IGHV3-43, IGKV3D-20, PLEKHA1, CYBB, and GABRB2 were over-expressed in the 1st group when compared to the 2nd group of CLL patients. Furthermore, clustering analysis validated that all the samples from patient #1 clustered together, showing clear separation from the samples of the other CLL patients. Conclusions: This study unveiled a small gene expression signature consisting of nine genes that distinguished an untreated CLL patient who followed prolonged periods of total fasting, maintaining a gradual growth trend of lymphocytosis, compared to five untreated CLL patients with a varied diet. Future investigations focusing on patient #1 could potentially shed light on the role of prolonged periodic fasting and the implication of this specific gene signature in sustaining the lymphocytosis trend and the favorable course of the disease.

In the PhilosoPhi34 study (EudraCT: 2012-005062-34) on 87 CP-CML patients, we analyzed the gene expression profiling (GEP) of bone marrow (BM) CD34+/lin- cells of 79 patients with chronic-phase chronic myeloid leukemia (CP-CML) patients at diagnosis and after 12 months of nilotinib treatment (Pungolino et al. AM J Hematol. 2018). FISH analyses identified CD34+/lin- Ph+ cells in all 79 CML-CP patients at diagnosis. 78/79 patients achieved at least a complete cytogenetic response after 12 months of nilotinib whereas 1/79 patients relapsed at 12 months. No Ph+ nuclei were detected in 78/79 patients at 12 months. We have demonstrated that genes involved in the JAK-STAT signaling pathway, the cell cycle, and the ATP-binding cassette (ABC) transporters were significantly over expressed in patients at diagnosis compared to 12 months of nilotinib treatment (Trojani et al, PLoS One. 2019). In this preliminary study, we isolated BM CD34+/lin- cells from 9 healthy donors (CTRLs). We investigated the gene expression profiling of 79 CP-CML patients at diagnosis vs. the same patients after 12 months of nilotinib treatment (12 months) vs. 9 CTRLs using Affymetrix HTA 2.0. Data was preprocessed and normalized using RMA and ComBat. Selection of differentially expressed genes (DEg) was performed at diagnosis vs. 12 months of nilotinib vs. CTRLs, using Statistical Analysis for Microarrays (SAM) on 3 groups and a Benjamini Hochberg false discovey rate threshold of 5%, followed, for significance comparisons, by a pair-wise SAM test. We focused on 34 genes of the cell cycle and mitosis, 6 genes belonging to the JAK-STAT signaling pathway, and the ABC transporter gene ABCD3 which were significantly under expressed at diagnosis vs. 12 months of nilotinib vs. CRTLs (Tab.1). In the cell cycle, we found that ORC2, ORC4, ORC5, MCM6, and HDAC2 (G1 phase) were progressively significantly down regulated at diagnosis vs. 12 months vs. CTRLs. We noticed HDAC2 which showed the high fold changes of 2.89 and 4.29 in the comparison between 12 months vs. CTRLs and between diagnosis vs. CTRLs, respectively. This gene plays a crucial role in CML, as HDAC inhibitors treatment represent an effective strategy to target leukemic stem cells in CP-CML patients receiving tyrosine kinase inhibitors. CCNA2, CDK7, CDC6, DBF4 (S phase), WEE1, PRKDC, ATM, MDM2, CCNB1 (G2 phase), and TTK, MAD2L1, BUB1, BUB3, ANAPC4, CDC27, SMC3, YWHAE, and YWHAZ (M phase) were progressively down regulated at diagnosis vs. 12 months vs. CTRLs. Among them, SMC3, YWHAE and YWHAZ showed the following high fold changes in the comparison between 12 months vs. CTRLs and between diagnosis vs. CTRLs: 2.31 and 3.15, 2.59 and 3.94, 2.75 and 4.15, respectively. Notably, the proto-oncogene MDM2 which promotes the development of tumors by targeting p53, was progressively up regulated in CTRLs vs. 12 months vs. diagnosis. In the mitosis, we detected that 10 genes playing a crucial role in mitotic chromosome organization, were progressively under expressed at diagnosis vs. 12 months vs. CTRLs (Tab.1). Notably, CLAPS2, ZW10 and ANLN (hematopoietic cell differentiation) regulate the exit from mitosis. NDC80, SMC4, ZNF207, and NEK2 take part in the mitotic sister chromatid segregation whereas CENPE and SMC2 are mitotic cell cycle check points. In the JAK-STAT signaling pathway, SOS1, PIK3CA, IL7, JAK2, STAM, and PTPN11 were progressively up regulated in CTRLs vs. 12 months vs. diagnosis (Tab.1). ABCD3, encoding a protein which pumped drugs out of the cells, was progressively under expressed at diagnosis vs. 12 months vs. CRTLs as shown in Tab.1. In conclusion, we found progressive gene expression changes in BM CD34+/lin- cells of 79 CP-CML patients at diagnosis vs. 12 months of nilotinib vs. the normal cell counterparts of 9 CTRLs in the cell cycle, JAK-STAT, and the ABC transporter ABCD3. FISH analyses demonstrated that the BM CD34+/lin- cells of 78/79 patients after 12 months of nilotinib were Ph-negative. Despite, our GEP results suggested that BM CD34+/lin- cells after 12 months of nilotinib treatment and the normal cell counterparts differed mostly in the expression of genes regulating the cell cycle and the JAK-STAT signaling pathway.