Immunogenetic Architecture of Chronic Lymphocytic Leukemia at Early Stage: Insights from the O-CLL1 Cohort Davide Bagnara, Andrea Nicola Mazzarello, Monica Colombo, Ennio Nano, Niccolò Cardente, Fabiana Ferrero, Nadia Bertola, Vanessa Cossu, Fabio Ghiotto, Adalberto Ibatici, Emanuele Angelucci, Antonino Neri, Massimo Gentile, Fortunato Morabito, Manlio Ferrarini, Giovanna Cutrona, Franco Fais Antibodies, 2026 Background/Objectives: The immunoglobulin heavy-chain variable (IGHV) gene repertoire represents a characteristic feature of chronic lymphocytic leukemia (CLL), although its configuration is not well defined at the early disease stages. The IGHV repertoire of a cohort of early CLL patients was analyzed and compared to that of a “real-world” reference cohort. Methods: Patients from the O-CLL1 observational protocol, which enrolled only Binet stage A cases within twelve months from diagnosis, were studied. IGHV/IGHJ rearrangements were sequenced and annotated following ERIC recommendations, and stereotyped subsets were assigned using ARResT/AssignSubsets. The repertoire features were compared with the dataset of a real-world cohort of patients with heterogeneous staging (CTR cohort) and with published early-diagnosis series. Results: IGHV and IGHJ gene distributions and HCDR3-length profiles in O-CLL1 closely mirrored those of CTR, indicating that the BcR IG repertoire at diagnosis is already defined rather than being selected during disease progression. Mutated IGHV (M-CLL) predominated, with a frequency of stereotyped BcR IG comparable to that of other early-diagnosis cohorts. However, within this conserved framework, subset #4 was over-represented among M-CLL from O-CLL without an increased overall IGHV4-34 gene usage, suggestive of a selective expansion rather than a recombinational bias. Subset #4 cases retained canonical HCDR3 motifs and showed time-to-first-treatment like other M-CLL, likely reflecting the younger age structure of O-CLL1. Conclusions: Early-diagnosis CLL displays a biased IGHV repertoire with stereotyped configurations characteristic of CLL, including subsets that are rare in the normal B-cell repertoire. These findings support a central role for antigen-driven selection in shaping CLL evolution.
Intraclonal Enrichment of IL-23 Receptor Complex Expression in the Proliferative Fraction of Chronic Lymphocytic Leukemia Martina Cardillo, Fabiana Ferrero, Nadia Bertola, Ennio Nano, Rosanna Massara, Maria Cristina Capra, Daniele Reverberi, Monica Colombo, Vanessa Cossu, Fabio Ghiotto, Adalberto Ibatici, Emanuele Angelucci, Antonino Neri, Massimo Gentile, Fortunato Morabito, Andrea Nicola Mazzarello, Manlio Ferrarini, Franco Fais, Giovanna Cutrona International Journal of Molecular Sciences, 2026 Chronic lymphocytic leukemia (CLL) is a dynamic malignancy in which intraclonal subfractions differ in activation history and responsiveness to microenvironmental signals. Here, we investigated the expression and inducibility of IL-12 family receptor subunits (IL-23R, IL-12Rβ1, IL-12Rβ2) and the related receptor complexes in recirculating CLL cells, with a focus on CXCR4/CD5-defined fractions: the proliferative fraction (PF; CXCR4dim/CD5bright; most recently divided, tissue-emigrated cells) and the resting fraction (RF; CXCR4bright/CD5dim; older, quiescent cells). At baseline, IL-12Rβ1 was enriched in the PF and was associated with a higher proportion of cells expressing IL-23R and IL-12R receptor complexes. Concomitantly, RT-qPCR disclosed higher IL-12Rβ1 mRNA levels. Following antigen-independent activation with CpG or CpG + IL-15, there was a marked increase in IL-23R and IL-12Rβ1 but not in IL-12Rβ2 surface expression, resulting in preferential upregulation of the IL-23R complex over the IL-12R complex. Fraction-specific analyses showed stronger induction of IL-23R and IL-23R complex expression in PF compared with RF. These findings identify an intraclonal bias toward IL-23 responsiveness in the CLL cells with a phenotype of recently divided, tissue-emigrated cells and suggest the IL-23/IL-23R axis as a potential therapeutic target.
To Treat or Not to Treat: Navigating Early-Stage CLL in the Era of Targeted Therapy Enrica Antonia Martino, Santino Caserta, Ernesto Vigna, Giovanna Cutrona, Antonella Bruzzese, Francesco Mendicino, Maria Eugenia Alvaro, Caterina Labanca, Eugenio Lucia, Virginia Olivito, Nicola Amodio, Franco Fais, Antonino Neri, Manlio Ferrarini, Valter Gattei, Fortunato Morabito, Massimo Gentile European Journal of Haematology, 2026 Chronic lymphocytic leukemia (CLL) is most frequently diagnosed at early, asymptomatic stages (Rai 0/Binet A), in which a watch‐and‐wait strategy remains the standard of care, based on historical trials demonstrating no overall survival benefit from early treatment. Over the past two decades, however, substantial advances in genomic profiling—including immunoglobulin heavy‐chain variable region (IGHV) mutational status, TP53 disruption, recurrent gene mutations, and complex karyotype—have uncovered marked biological heterogeneity among early‐stage patients and substantially improved prediction of disease progression. In parallel, targeted therapies such as Bruton tyrosine kinase (BTK) inhibitors and venetoclax‐based combinations have transformed the management of symptomatic CLL, raising renewed interest in whether early intervention might favorably alter the natural history of biologically high‐risk disease. In this review, we critically examine the evolution of prognostication in early‐stage CLL, integrate contemporary molecular and clinical risk models, and summarize evidence from both historical chemotherapy‐era studies and modern early‐intervention trials. We discuss key unresolved controversies, including reliance on surrogate endpoints, the risks of overtreatment, and the persistent absence of an overall survival benefit across all early‐treatment strategies. Finally, we outline future research priorities, including refined genomic stratification, minimal residual disease‐driven (MRD)‐driven approaches, and combination targeted therapies currently under investigation. Despite renewed interest in preemptive treatment, available evidence supports continued observation for asymptomatic patients outside clinical trials.
Targeting the p53/xCT/GSH Axis with PRIMA-1Met Combined with Sulfasalazine Shows Therapeutic Potential in Chronic Lymphocytic Leukemia Martina Pasino, Andrea Speciale, Silvia Ravera, Giovanna Cutrona, Rosanna Massara, Nadia Bertola, Maurizio Viale, Irena Velkova, Andrea Nicola Mazzarello, Franco Fais, Fabrizio Loiacono, Serena Matis, Giulia Elda Valenti, Nicola Traverso, Cinzia Domenicotti, Barbara Marengo, Bruno Tasso, Adalberto Ibatici, Emanuele Angelucci, Tiziana Vaisitti, Paola Monti, Paola Menichini International Journal of Molecular Sciences, 2025 In Chronic Lymphocytic Leukemia (CLL), mutations at the TP53 tumor suppressor gene are an important hallmark since they may strongly influence the therapeutic decision. PRIMA-1Met (also known as APR-246/Eprenetapopt) is a small molecule able to restore the wild-type (wt) p53 conformation to mutant p53 proteins and to stimulate apoptosis in tumor cells; in addition, it can deplete the glutathione reservoir, increasing reactive oxygen species (ROS) production. In this study, we investigated whether combining PRIMA-1Met with Sulfasalazine (SAS), a SLC7A11/xCT inhibitor, reduces CLL cell viability by targeting mutant p53 and the glutathione pathway. The results demonstrated that, in CLL cells, PRIMA-1Met did not restore the wt functions in the mutant p53 proteins, but it strongly reduced the antioxidant defense and induced cell death. PRIMA-1Met and SAS combination synergistically reduced cell survival regardless of p53 status and further impaired antioxidant capacity, especially in mutant p53 cells, linking their cytotoxic effect to redox imbalance. Thus, the association of PRIMA-1Met with drugs targeting the antioxidant response could represent a valid strategy to kill CLL cells carrying either wt or mutant p53.
MicroRNA Profiling as a Predictive Indicator for Time to First Treatment in Chronic Lymphocytic Leukemia: Insights from the O-CLL1 Prospective Study Ennio Nano, Francesco Reggiani, Adriana Agnese Amaro, Paola Monti, Monica Colombo, Nadia Bertola, Fabiana Ferrero, Franco Fais, Antonella Bruzzese, Enrica Antonia Martino, Ernesto Vigna, Noemi Puccio, Mariaelena Pistoni, Federica Torricelli, Graziella D’Arrigo, Gianluigi Greco, Giovanni Tripepi, Carlo Adornetto, Massimo Gentile, Manlio Ferrarini, Massimo Negrini, Fortunato Morabito, Antonino Neri, Giovanna Cutrona Non Coding RNA, 2024 A “watch and wait” strategy, delaying treatment until active disease manifests, is adopted for most CLL cases; however, prognostic models incorporating biomarkers have shown to be useful to predict treatment requirement. In our prospective O-CLL1 study including 224 patients, we investigated the predictive role of 513 microRNAs (miRNAs) on time to first treatment (TTFT). In the context of this study, six well-established variables (i.e., Rai stage, beta-2-microglobulin levels, IGVH mutational status, del11q, del17p, and NOTCH1 mutations) maintained significant associations with TTFT in a basic multivariable model, collectively yielding a Harrell’s C-index of 75% and explaining 45.4% of the variance in the prediction of TTFT. Concerning miRNAs, 73 out of 513 were significantly associated with TTFT in a univariable model; of these, 16 retained an independent relationship with the outcome in a multivariable analysis. For 8 of these (i.e., miR-582-3p, miR-33a-3p, miR-516a-5p, miR-99a-5p, and miR-296-3p, miR-502-5p, miR-625-5p, and miR-29c-3p), a lower expression correlated with a shorter TTFT, whereas in the remaining eight (i.e., miR-150-5p, miR-148a-3p, miR-28-5p, miR-144-5p, miR-671-5p, miR-1-3p, miR-193a-3p, and miR-124-3p), the higher expression was associated with shorter TTFT. Integrating these miRNAs into the basic model significantly enhanced predictive accuracy, raising the Harrell’s C-index to 81.1% and the explained variation in TTFT to 63.3%. Moreover, the inclusion of the miRNA scores enhanced the integrated discrimination improvement (IDI) and the net reclassification index (NRI), underscoring the potential of miRNAs to refine CLL prognostic models and providing insights for clinical decision-making. In silico analyses on the differently expressed miRNAs revealed their potential regulatory functions of several pathways, including those involved in the therapeutic responses. To add a biological context to the clinical evidence, an miRNA–mRNA correlation analysis revealed at least one significant negative correlation between 15 of the identified miRNAs and a set of 50 artificial intelligence (AI)-selected genes, previously identified by us as relevant for TTFT prediction in the same cohort of CLL patients. In conclusion, the identification of specific miRNAs as predictors of TTFT holds promise for enhancing risk stratification in CLL to predict therapeutic needs. However, further validation studies and in-depth functional analyses are required to confirm the robustness of these observations and to facilitate their translation into meaningful clinical utility.
Unexpected chronic lymphocytic leukemia B cell activation by bisphosphonates Andrea N. Mazzarello, Elena Gugiatti, Vanessa Cossu, Nadia Bertola, Davide Bagnara, Sonia Carta, Silvia Ravera, Chiara Salvetti, Adalberto Ibatici, Fabio Ghiotto, Monica Colombo, Giovanna Cutrona, Cecilia Marini, Gianmario Sambuceti, Franco Fais, Silvia Bruno Cancer Immunology Immunotherapy, 2024 Chronic lymphocytic leukemia (CLL) is a disease of the elderly, often presenting comorbidities like osteoporosis and requiring, in a relevant proportion of cases, treatment with bisphosphonates (BPs). This class of drugs was shown in preclinical investigations to also possess anticancer properties. We started an in vitro study of the effects of BPs on CLL B cells activated by microenvironment-mimicking stimuli and observed that, depending on drug concentration, hormetic effects were induced on the leukemic cells. Higher doses induced cytotoxicity whereas at lower concentrations, more likely occurring in vivo, the drugs generated a protective effect from spontaneous and chemotherapy-induced apoptosis, and augmented CLL B cell activation/proliferation. This CLL-activation effect promoted by the BPs was associated with markers of poor CLL prognosis and required the presence of bystander stromal cells. Functional experiments suggested that this phenomenon involves the release of soluble factors and is increased by cellular contact between stroma and CLL B cells. Since CLL patients often present comorbidities such as osteoporosis and considering the diverse outcomes in both CLL disease progression and CLL response to treatment among patients, illustrating this phenomenon holds potential significance in driving additional investigations.
Unraveling the Bone Tissue Microenvironment in Chronic Lymphocytic Leukemia Paolo Giannoni, Cecilia Marini, Giovanna Cutrona, Gian Mario Sambuceti, Franco Fais, Daniela de Totero Cancers, 2023 Chronic lymphocytic leukemia (CLL) is the most frequent leukemia in Western countries. Although characterized by the progressive expansion and accumulation of leukemic B cells in peripheral blood, CLL cells develop in protective niches mainly located within lymph nodes and bone marrow. Multiple interactions between CLL and microenvironmental cells may favor the expansion of a B cell clone, further driving immune cells toward an immunosuppressive phenotype. Here, we summarize the current understanding of bone tissue alterations in CLL patients, further addressing and suggesting how the multiple interactions between CLL cells and osteoblasts/osteoclasts can be involved in these processes. Recent findings proposing the disruption of the endosteal niche by the expansion of a leukemic B cell clone appear to be a novel field of research to be deeply investigated and potentially relevant to provide new therapeutic approaches.
The time to first treatment is an independent predictor of overall survival in chronic lymphocytic leukemia Fortunato Morabito, Giovanni Tripepi, Francesca Romana Mauro, Luca Laurenti, Gianluigi Reda, Riccardo Moia, Adalgisa Condoluci, Iolanda Vincelli, Annalisa Chiarenza, Ernesto Vigna, Enrica Antonia Martino, Antonella Bruzzese, Sabrina Mezzatesta, Roberta Laureana, Giovanna Cutrona, Francesco Di Raimondo, Gilberto Fronza, Antonella Zucchetto, Riccardo Bomben, Francesca Maria Rossi, Jacopo Olivieri, Francesco Zaja, Davide Rossi, Gianluca Gaidano, Maria Ilaria Del Principe, Fiorella Ilariucci, Giovanni Del Poeta, Manlio Ferrarini, Antonino Neri, Valter Gattei, Massimo Gentile American Journal of Hematology, 2023 Approximately, 80% of chronic lymphocytic leukemia (CLL) patients are diagnosed in the asymptomatic phase and/or at an early stage of the disease. Although the majority of these patients show a low-risk profile and are managed with active observation,1 the time to the first treatment (TTFT) in these CLL patients appears quite heterogeneous. Historical clinical observations suggested that CLL patients experiencing early progression develop a persistent risk of short overall survival (OS).2 Similar findings indicating a correlation between early progression after therapy and short OS have been reported in other hematological malignancies.3-5 Here, we hypothesized that an early need for treatment could inform OS also in the CLL setting. Therefore, we investigated the inclusion of the duration of the therapy-free interval following diagnosis as additional prognosticator to refine the OS prediction of well-recognized risk factors in a wide multicenter cohort of newly diagnosed CLL patients on a watch-and-wait strategy. The REporting recommendations for tumor MARKer prognostic studies (REMARK) criteria were followed throughout this study.6 Further details in Supplementary Appendix. Distribution in the whole cohort of 3860 CLL cases of the clinical and biological variables validated in CLL-IPI7 and Brno-Barcelona8 score systems, including age, Rai staging, β2-microglobulin, immunoglobulin heavy-chain variable (IGHV) gene mutational status, del(11q) and del(17p), all tested at diagnosis/first presentation, are reported in Supplementary Table 1. Distribution of variables is as expected in a cohort of early-stage CLL.9 Sufficient information for evaluation of the CLL-IPI7 and Brno-Barcelona8 score systems were available in 2573 cases, which were included in the final analysis (Supplementary Figure 1). The median follow-up time was 6.8 years (interquartile range: 4.2–9.9 years). At univariate analyses, age ≥65 years, Rai stages I–II, abnormal β2M serum levels, del(11q), IGHVunmut status and del(17p) were all OS predictors both in univariable and multivariable analysis; this basic model provided an explained variation in mortality (R2) and a Harrell's C index of 37.7% and 72.6%, respectively (Supplementary Table 2). Patients experiencing therapy need within 6, 12, 18, 24, 30, 36, 42, 48, 54, and 60 months from diagnosis were defined as TTFT6-60 failures (TTFT6-60Fail). Cases remaining therapy-free within 6–60 months were categorized as TTFT6-60 achievers (TTFT6-60Achieve). OS for TTFT6-60Fail cases was defined as the time from TTFT6-60 failure to death or last follow-up. OS for patients with TTFT6-60Achieve was defined as the survival time from achieving TTFT6-60 until death or last follow-up. In each TTFT6-60 category, patients died before 6–60 months or with <6–60 months of follow-up were excluded from the analysis (Supplementary Figure 1). Cases requiring therapy within 6–60 months (TTFT6-60Fail) experienced a roughly three-time higher risk of dying (Hazard ratios (HRs) ranging from 2.6 to 3.2) as compared to patients with a longer therapy-free interval (TTFT6-60Achieve; reference group, HR = 1) in univariate Cox analyses (Supplementary Table 3). All the investigated cut-offs of TTFT, except the TTFT6 (p = .083), independently predicted the mortality incidence rate (HR ranging from 1.45 to 2.04) in a sequence of multivariable models including all the variables of the CLL-IPI and the Brno-Barcelona scores as potential confounders (Supplementary Table 4). In addition, the inclusion of the biomarker TTFT in the range from TTFT12 to TTFT42 significantly improved the prognostic accuracy of this risk stratification model compared to a model including the CLL-IPI and Brno-Barcelona scores variables alone (Supplementary Table 2), as witnessed by higher values for both R2 and Harrell's indices (values ranging from 38.6% to 40.4%, and from 72.9% to 73.8%, respectively; Supplementary Table 4) in models that include TTFT values. Conversely, TTFT at time points ranging from 48 to 60 months failed to add prognostic accuracy to the same model in terms of R2 and Harrel's indices (Supplementary Table 4). Remarkably, the zenith of the prognostic accuracy of TTFT was found at a cut-off value of 18 months (TTFT18; HR 2.04, 95% CI 1.52–2.75; R2 40.4%; Harrell's C index 73.8%), while at values of TTFT ranging from 24 to 60 months, a gradual reduction of both R2 (from 39.8% to 36.3%) and Harrell's C index (from 73.3% to 70.9%) was observed (Supplementary Figure 2). To establish whether the prognostic power of TTFT18Fail was dependent not only on the time of the therapy (i.e., less than 18 months) but also on treatment (i.e., treated/untreated), we performed univariate and multivariable Cox analyses by splitting cases of our cohort in those never-treated (never-treated TTFT18Achieve) from those treated but after 18 months (TTFT18Achieve) and comparing them with TTFT18Fail cases. A significantly shorter OS was accounted for in cases with TTFT18Fail (median 8 years) compared with treated TTFT18Achieve (median 13 years) and with never-treated TTFT18Achieve cases (median 22 years; Supplementary Figure 3). In this context, however, when tested by multivariable analysis (n = 2336), the treated TTFT18Achieve group lost its independent prognostic role with respect to the never-treated TTFT18Achieve group, while TTFT18Fail remained an independent prognostic factor of OS together with del(17p), del(11q), abnormal β2M serum level, IGHVunmut status, and age, but not Rai stage (Supplementary Table 5; R2, 42%; C index, 75%). In an additional multivariable model utilizing the same variables but combining the treated and never-treated TTFT18Achieve groups in a single group, TTFT18 remained again independent predictor of OS along with β2M, del(11q), del(17p), IGHV gene status and age, while the Rai stage lost its prognostic value (Supplementary Table 6). According to this multivariable model, we derived a novel survival risk score (SRS), which included TTFT18 as a new prognostic factor (SRSTTFT18), which utilizes the regression coefficients in predicting mortality to assign weights to the various variables independently associated with death (Supplementary Table 6). After calculating the assigned risk scores on an individual basis, patients were first grouped into four risk categories by quartile (Supplementary Figure 4); then, since the second quartile did not significantly differ from the third quartile, the two curves were collapsed together (Figure 1). Based on such stratification, 622 (26.6%) cases of the cohort were allocated in the low-risk group, 930 (39.8%) in the intermediate-risk group, and 784 (33.6%) in the high-risk group (SRSTTFT18 0 = low risk; score >0–37.8 = intermediate risk; score > 37.8 = high risk; Supplementary Table 6). The 5-year probability was respectively 97.5% for low-risk group (HR = 1, reference category), 91.8% (HR = 3.2, 95% CI 2.2–4.7, p < .001) for intermediate-risk group, and 77.7% (HR = 10.3, 95% CI 7.2–14.7, p < 0.001) for high-risk group (Figure 1). Notably, differently from the low-risk group, which did not cross the median timeline, the estimated median OS was 16 years (95%CI 10.7–21.6 years) and 9.9 years (95%CI 8.1–10.1 years) for intermediate- and high-risk cases, respectively (Figure 1). The Harrell's C index and the explained variation in mortality were consistently higher for scores including TTFT18 than those excluding this variable (72.6% vs. 73.8% and 37.7% vs. 40.4% for HC and R2, respectively). The significant improvement in the goodness of fit (expanded vs. reduced model, χ2 = 22.14 [1 df], p < .001) indicated that the inclusion of TTFT18 into the reduced model significantly increased the prognostic accuracy of the same model for predicting mortality. Herein, we demonstrated for the first time the independent prognostic value on mortality of the duration of TTFT ranging from 12 to 60 months in a sizeable cohort of newly diagnosed CLL patients, initially followed by a watch-and-wait strategy. We showed that patients who experienced an early therapy need within 6–60 months (TTFT6-60Fail) experienced roughly three-time higher risk of dying than those with a longer therapy-free interval (TTFT6-60Achieve). When risk factors included in the CLL-IPI2 and Brno-Barcelona score systems3 were jointly introduced into the same multivariable model with several TTFT thresholds, cases experiencing therapy need within 12 through 60 months, i.e., those labeled as TTFT12-60Fail were independently associated with the worst outcome. Notably, the inclusion into the basic model of the time-to-therapy starts thresholds significantly increased the prognostic accuracy of the same risk model, achieving the best performance at the time-point of 18 months. Nevertheless, Harrell's C indices exceeded the 70% threshold in all the investigated TTFT intervals, underscoring the prognostic utility of the first therapy-free length in addition to the treatment itself. The clinical impact of TTFT18 on OS prompted us to design a novel scoring system incorporating this variable (SRSTTFT18) to predict mortality in CLL. Several measures of predictive performance were considered, all validating the SRSTTFT18. First, a significant improvement in fitness favoring the expanded model (with the TTFT18 variable) versus the reduced model (without the TTFT18 variable) was demonstrated. Second, Harrell's C index was higher for the model including TTFT18, although the accepted 70% threshold was exceeded in both cases. These data demonstrated that a risk prediction model that included TTFT18 had better prognostic accuracy than models without this new prognostic variable. Our SRSTTFT18 included both unchanging variables, that is, IGHV mutational status and TTFT18, along with a changing variable (age) and other variables that may change over time (i.e., β2M, 17p, and 11q deletions) thus ultimately modifying the initial risk class assignment. In this context, a reiterative model, similar to the CIRI score,10 that redefines the risk at different time points, including those of TTFT calculation, would be more meaningful for the patients. In conclusion, the results of this study may aid the identification of early-stage progressive cases who allegedly will fail from conventional therapies and can in turn benefit from risk-adapted treatment approaches with chemo-free regimens. However, this new prognosticator could be reconsidered in the setting of patients up-front treated with new drugs. Fortunato Morabito, Valter Gattei, and Massimo Gentile designed the study. Fortunato Morabito, Giovanni Tripepi, Massimo Gentile, Sabrina Mezzatesta, performed statistical analysis; Fortunato Morabito, Luca Laurenti, Gianluigi Reda, Iolanda Vincelli, Ernesto Vigna, Antonella Bruzzese, Antonella Zucchetto, Riccardo Bomben, Francesco Di Raimondo, Jacopo Olivieri, Giovanni Del Poeta, Massimo Gentile, Manlio Ferrarini, Giovanni Tripepi, Davide Rossi, Gianluca Gaidano, Enrica Antonia Martino, Gilberto Fronza, Adalgisa Condoluci, Giovanna Cutrona, Francesca Romana Mauro, Riccardo Moia, Francesco Di Raimondo, Fiorella Ilariucci, Antonino Neri, and Francesco Zaja analyzed and interpreted data. Fortunato Morabito, Massimo Gentile, Manlio Ferrarini, Antonino Neri, and Valter Gattei wrote the manuscript; all authors gave final approval with the only exclusion of Giovanni Del Poeta (deceased). Associazione Italiana Ricerca sul Cancro (AIRC) Grant 5× 1000 n. 9980 (to Fortunato Morabito, Manlio Ferrarini, Antonino Neri); AIRC, Special Program Metastases (n. 21198) 5× 1000 to Gianluca Gaidano; AIRC IG-5506 (to Gilberto Fronza), IG-14326 (to Manlio Ferrarini), IG-21687 (to Valter Gattei); AIRC and Fondazione CaRiCal co-financed Multi-Unit Regional Grant 2014 no. 16695 to Fortunato Morabito; Progetto Ricerca Finalizzata Italian Ministry of Health, Rome, RF-2018-12 365 790 (to Antonella Zucchetto and Giovanna Cutrona) and PE-2016-02362756 (to Valter Gattei); Italy Compagnia S. Paolo, Turin, Italy, Project 2017.0526 (to Gilberto Fronza); partially funded by Italian Ministry of Health (Project 5× 1000, 2015 and 2016) and Current Research 2016 and 2023 (to Gilberto Fronza, Giovanna Cutrona, and Antonino Neri); Swiss Cancer League, ID 3746, 4395, 4660, and 4705, Bern, Switzerland; European Research Council (ERC) Consolidator Grant CLLCLONE, ID: 772051 (to Davide Rossi); Swiss National Science Foundation, ID 320030_169670/1 and 310030_192439, Berne, Switzerland; The Leukemia & Lymphoma Society, Translational Research Program, ID 6594-20, New York. The authors declare no conflicts of interest. The data that support the findings of this study are available from the corresponding author upon reasonable request. Data S1. Supplementary appendix Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. 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Genes selection using deep learning and explainable artificial intelligence for chronic lymphocytic leukemia predicting the need and time to therapy Fortunato Morabito, Carlo Adornetto, Paola Monti, Adriana Amaro, Francesco Reggiani, Monica Colombo, Yissel Rodriguez-Aldana, Giovanni Tripepi, Graziella D’Arrigo, Claudia Vener, Federica Torricelli, Teresa Rossi, Antonino Neri, Manlio Ferrarini, Giovanna Cutrona, Massimo Gentile, Gianluigi Greco Frontiers in Oncology, 2023 Analyzing gene expression profiles (GEP) through artificial intelligence provides meaningful insight into cancer disease. This study introduces DeepSHAP Autoencoder Filter for Genes Selection (DSAF-GS), a novel deep learning and explainable artificial intelligence-based approach for feature selection in genomics-scale data. DSAF-GS exploits the autoencoder’s reconstruction capabilities without changing the original feature space, enhancing the interpretation of the results. Explainable artificial intelligence is then used to select the informative genes for chronic lymphocytic leukemia prognosis of 217 cases from a GEP database comprising roughly 20,000 genes. The model for prognosis prediction achieved an accuracy of 86.4%, a sensitivity of 85.0%, and a specificity of 87.5%. According to the proposed approach, predictions were strongly influenced by CEACAM19 and PIGP, moderately influenced by MKL1 and GNE, and poorly influenced by other genes. The 10 most influential genes were selected for further analysis. Among them, FADD, FIBP, FIBP, GNE, IGF1R, MKL1, PIGP, and SLC39A6 were identified in the Reactome pathway database as involved in signal transduction, transcription, protein metabolism, immune system, cell cycle, and apoptosis. Moreover, according to the network model of the 3D protein-protein interaction (PPI) explored using the NetworkAnalyst tool, FADD, FIBP, IGF1R, QTRT1, GNE, SLC39A6, and MKL1 appear coupled into a complex network. Finally, all 10 selected genes showed a predictive power on time to first treatment (TTFT) in univariate analyses on a basic prognostic model including IGHV mutational status, del(11q) and del(17p), NOTCH1 mutations, β2-microglobulin, Rai stage, and B-lymphocytosis known to predict TTFT in CLL. However, only IGF1R [hazard ratio (HR) 1.41, 95% CI 1.08-1.84, P=0.013), COL28A1 (HR 0.32, 95% CI 0.10-0.97, P=0.045), and QTRT1 (HR 7.73, 95% CI 2.48-24.04, P&lt;0.001) genes were significantly associated with TTFT in multivariable analyses when combined with the prognostic factors of the basic model, ultimately increasing the Harrell’s c-index and the explained variation to 78.6% (versus 76.5% of the basic prognostic model) and 52.6% (versus 42.2% of the basic prognostic model), respectively. Also, the goodness of model fit was enhanced (χ2 = 20.1, P=0.002), indicating its improved performance above the basic prognostic model. In conclusion, DSAF-GS identified a group of significant genes for CLL prognosis, suggesting future directions for bio-molecular research.
A High Percentage of CD16+ Monocytes Correlates with the Extent of Bone Erosion in Chronic Lymphocytic Leukemia Patients: The Impact of Leukemic B Cells in Monocyte Differentiation and Osteoclast Maturation Paolo Giannoni, Cecilia Marini, Giovanna Cutrona, Katia Todoerti, Antonino Neri, Adalberto Ibatici, Gianmario Sambuceti, Simona Pigozzi, Marco Mora, Manlio Ferrarini, Franco Fais, Daniela de Totero Cancers, 2022 Significant skeletal alterations are present in Chronic Lymphocytic Leukemia (CLL) patients; bone erosion, particularly evident in the long bone shaft, appeared increased in the progressive disease stage. Moreover, the partial colonization of the bone with reactive bone marrow we documented via PET-FDG imaging suggests that neoplastic cell overgrowth contributes to bone derangement. Indeed, cytokines released by leukemic B cells impair osteoblast differentiation and enhance osteoclast formation in vitro. CD16, Fcγ-RIIIa, has been previously indicated as a marker of osteoclast precursors. We demonstrate, here, that the percentage of circulating monocytes, CD16+, is significantly higher in CLL patients than in normal controls and directly correlated with the extent of bone erosion. When we assessed if healthy monocytes, treated with a CLL-conditioned medium, modulated RANK, RANKL and CD16, we observed that all these molecules were up-regulated and CD16 to a greater extent. Altogether, these findings suggest that leukemic cells facilitate osteoclast differentiation. Interestingly, the evidence that monocytes, polarized toward the M2 phenotype, were characterized by high CD16 expression and showed a striking propensity to differentiate toward osteoclasts may provide further explanations for the enhanced levels of bone erosion detected, in agreement with the high number of immunosuppressive-M2 cells present in these patients.
Lymphocyte Doubling Time As A Key Prognostic Factor To Predict Time To First Treatment In Early-Stage Chronic Lymphocytic Leukemia Fortunato Morabito, Giovanni Tripepi, Riccardo Moia, Anna Grazia Recchia, Paola Boggione, Francesca Romana Mauro, Sabrina Bossio, Graziella D’Arrigo, Enrica Antonia Martino, Ernesto Vigna, Francesca Storino, Gilberto Fronza, Francesco Di Raimondo, Davide Rossi, Adalgisa Condoluci, Monica Colombo, Franco Fais, Sonia Fabris, Robin Foa, Giovanna Cutrona, Massimo Gentile, Emili Montserrat, Gianluca Gaidano, Manlio Ferrarini, Antonino Neri Frontiers in Oncology, 2021
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Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia Sonia Fabris, Laura Mosca, Giovanna Cutrona, Marta Lionetti, Luca Agnelli, Gabriella Ciceri, Marzia Barbieri, Francesco Maura, Serena Matis, Monica Colombo, Massimo Gentile, Anna Grazia Recchia, Emanuela Anna Pesce, Francesco Di Raimondo, Caterina Musolino, Marco Gobbi, Nicola Di Renzo, Francesca Romana Mauro, Maura Brugiatelli, Fiorella Ilariucci, Maria Grazia Lipari, Francesco Angrilli, Ugo Consoli, Alberto Fragasso, Stefano Molica, Gianluca Festini, Iolanda Vincelli, Agostino Cortelezzi, Massimo Federico, Fortunato Morabito, Manlio Ferrarini, Antonino Neri American Journal of Hematology, 2013
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