All Publications

  • Single-Cell Proteomic Analysis Defines Metabolic Heterogeneity in Response to Venetoclax in AML Stuani, L., Jager, A., Sahal, A., Koladiya, A., Sarno, J., Domizi, P., Liu, Y., De Mas, V., Recher, C., Vergez, F., Sarry, J., Davis, K. L. AMER SOC HEMATOLOGY. 2022: 1028-1029
  • CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors. Nature communications Lo, Y., Keyes, T. J., Jager, A., Sarno, J., Domizi, P., Majeti, R., Sakamoto, K. M., Lacayo, N., Mullighan, C. G., Waters, J., Sahaf, B., Bendall, S. C., Davis, K. L. 2022; 13 (1): 934


    The increasing use of mass cytometry for analyzing clinical samples offers the possibility to perform comparative analyses across public datasets. However, challenges in batch normalization and data integration limit the comparison of datasets not intended to be analyzed together. Here, we present a data integration strategy, CytofIn, using generalized anchors to integrate mass cytometry datasets from the public domain. We show that low-variance controls, such as healthy samples and stable channels, are inherently homogeneous, robust against stimulation, and can serve as generalized anchors for batch correction. Single-cell quantification comparing mass cytometry data from 989 leukemia files pre- and post normalization with CytofIn demonstrates effective batch correction while recapitulating the gold-standard bead normalization. CytofIn integration of public cancer datasets enabled the comparison of immune features across histologies and treatments. We demonstrate the ability to integrate public datasets without necessitating identical control samples or bead standards for fast and robust analysis using CytofIn.

    View details for DOI 10.1038/s41467-022-28484-5

    View details for PubMedID 35177627

  • An instructive role for Interleukin-7 receptor alpha in the development of human B-cell precursor leukemia. Nature communications Geron, I., Savino, A. M., Fishman, H., Tal, N., Brown, J., Turati, V. A., James, C., Sarno, J., Hameiri-Grossman, M., Lee, Y. N., Rein, A., Maniriho, H., Birger, Y., Zemlyansky, A., Muler, I., Davis, K. L., Marcu-Malina, V., Mattson, N., Parnas, O., Wagener, R., Fischer, U., Barata, J. T., Jamieson, C. H., Muschen, M., Chen, C., Borkhardt, A., Kirsch, I. R., Nagler, A., Enver, T., Izraeli, S. 1800; 13 (1): 659


    Kinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis "ph-like" BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+ hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rgammanull mice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+ cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing of CDKN2A in primary human CD34+ cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.

    View details for DOI 10.1038/s41467-022-28218-7

    View details for PubMedID 35115489

  • Glucocorticoid-Resistant B-Cell Acute Lymphoblastic Leukemic Cells Can be Targeted By BCR-Signaling Inhibition Sarno, J., Domizi, P., Liu, Y., Merchant, M., Jedoui, D., Jager, A., Biondi, A., Gaipa, G., Bava, A., Davis, K. L. AMER SOC HEMATOLOGY. 2021
  • Ikaros Mediates Antigen Escape Following CD19 CAR T Cell Therapy in r/r B-ALL Domizi, P., Sarno, J., Jager, A., Baskar, R., Reynolds, W. D., Sahaf, B., Bendall, S., Mullighan, C. G., Leahy, A., Myers, R. M., Grupp, S. A., Sotillo, E., Barrett, D., Davis, K. L. AMER SOC HEMATOLOGY. 2021
  • Inhibition of Pre-BCR Signaling Mediates a Metabolic Switch in B-Cell Progenitor Acute Lymphoblastic Leukemia Liu, Y., Stuani, L., Jedoui, D., Merchant, M., Jager, A., Sarno, J., Mullighan, C. G., Hartmann, F. J., Bendall, S., Davis, K. L. AMER SOC HEMATOLOGY. 2021
  • Mass Cytometry of Hematopoietic Cells. Methods in molecular biology (Clifton, N.J.) Jager, A., Sarno, J., Davis, K. L. 2021; 2185: 65–76


    Mass cytometry is now a well-established method that enables the measurement of 40-50 markers (generally proteins but transcripts are also possible) in single cells. Analytes are detected via antibodies tagged with heavy metal and detected by using a time-of-flight mass spectrometer. Over the past decade, mass cytometry has proven to be a valuable method for immunophenotyping hematopoietic cells with remarkable precision in both healthy and malignant scenarios. This chapter explains in detail how to profile hematopoietic cells by using this high-dimensional multiplexed approach.

    View details for DOI 10.1007/978-1-0716-0810-4_5

    View details for PubMedID 33165843

  • Glucocorticoids-Resistant Leukemic B-Cells Undergo a Phenotypic Change That Increases Sensitivity to SRC/ABL Inhibition Sarno, J., Pedersen, C., Jager, A., Burns, T., Gaipa, G., Nolan, G. P., Bava, A., Davis, K. L. AMER SOC HEMATOLOGY. 2018
  • Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nature medicine Good, Z., Sarno, J., Jager, A., Samusik, N., Aghaeepour, N., Simonds, E. F., White, L., Lacayo, N. J., Fantl, W. J., Fazio, G., Gaipa, G., Biondi, A., Tibshirani, R., Bendall, S. C., Nolan, G. P., Davis, K. L. 2018; 24 (4): 474–83


    Insight into the cancer cell populations that are responsible for relapsed disease is needed to improve outcomes. Here we report a single-cell-based study of B cell precursor acute lymphoblastic leukemia at diagnosis that reveals hidden developmentally dependent cell signaling states that are uniquely associated with relapse. By using mass cytometry we simultaneously quantified 35 proteins involved in B cell development in 60 primary diagnostic samples. Each leukemia cell was then matched to its nearest healthy B cell population by a developmental classifier that operated at the single-cell level. Machine learning identified six features of expanded leukemic populations that were sufficient to predict patient relapse at diagnosis. These features implicated the pro-BII subpopulation of B cells with activated mTOR signaling, and the pre-BI subpopulation of B cells with activated and unresponsive pre-B cell receptor signaling, to be associated with relapse. This model, termed 'developmentally dependent predictor of relapse' (DDPR), significantly improves currently established risk stratification methods. DDPR features exist at diagnosis and persist at relapse. By leveraging a data-driven approach, we demonstrate the predictive value of single-cell 'omics' for patient stratification in a translational setting and provide a framework for its application to human cancer.

    View details for PubMedID 29505032

  • SRC/ABL inhibition disrupts CRLF2-driven signaling to induce cell death in B-cell acute lymphoblastic leukemia. Oncotarget Sarno, J., Savino, A. M., Buracchi, C., Palmi, C., Pinto, S., Bugarin, C., Jager, A., Bresolin, S., Barber, R. C., Silvestri, D., Israeli, S., Dyer, M. J., Cazzaniga, G., Nolan, G. P., Biondi, A., Davis, K. L., Gaipa, G. 2018; 9 (33): 22872–85


    Children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) overexpressing the CRLF2 gene (hiCRLF2) have poor prognosis. CRLF2 protein overexpression leads to activated JAK/STAT signaling and trials are underway using JAK inhibitors to overcome treatment failure. Pre-clinical studies indicated limited efficacy of single JAK inhibitors, thus additional pathways must be targeted in hiCRLF2 cells. To identify additional activated networks, we used single-cell mass cytometry to examine 15 BCP-ALL primary patient samples. We uncovered a coordinated signaling network downstream of CRLF2 characterized by co-activation of JAK/STAT, PI3K, and CREB pathways. This CRLF2-driven network could be more effectively disrupted by SRC/ABL inhibition than single-agent JAK or PI3K inhibition, and this could be demonstrated even in primary minimal residual disease (MRD) cells. Our study suggests SCR/ABL inhibition as effective in disrupting the cooperative functional networks present in hiCRLF2 BCP-ALL patients, supporting further investigation of this strategy in pre-clinical studies.

    View details for PubMedID 29796158

  • Single-cell mass cytometry and machine learning predict relapse in childhood leukemia. Molecular & cellular oncology Sarno, J., Davis, K. L. 2018; 5 (5): e1472057


    Improved insight into cancer cell populations responsible for treatment failure will lead to better outcomes for patients. We herein highlight a single-cell study of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) at diagnosis that revealed hidden developmentally dependent cell signaling states uniquely associated with relapse.

    View details for PubMedID 30263942

  • The histone deacetylase inhibitor givinostat (ITF2357) exhibits potent anti-tumor activity against CRLF2-rearranged BCP-ALL. Leukemia Savino, A. M., Sarno, J., Trentin, L., Vieri, M., Fazio, G., Bardini, M., Bugarin, C., Fossati, G., Davis, K. L., Gaipa, G., Izraeli, S., Meyer, L. H., Nolan, G. P., Biondi, A., te Kronnie, G., Palmi, C., Cazzaniga, G. 2017


    Leukemias bearing CRLF2 and JAK2 gene alterations are characterized by aberrant JAK/STAT signaling and poor prognosis. The HDAC inhibitor givinostat/ITF2357 has been shown to exert anti-neoplastic activity against both systemic juvenile idiopathic arthritis and myeloproliferative neoplasms through inhibition of the JAK/STAT pathway. These findings led us to hypothesize that givinostat might also act against CRLF2-rearranged BCP-ALL, which lack effective therapies. Here, we found that givinostat inhibited proliferation and induced apoptosis of BCP-ALL CRLF2-rearranged cell lines, positive for exon 16 JAK2 mutations. Likewise, givinostat killed primary cells, but not their normal hematopoietic counterparts, from patients carrying CRLF2 rearrangements. At low doses, givinostat downregulated the expression of genes belonging to the JAK/STAT pathway and inhibited STAT5 phosphorylation. In vivo, givinostat significantly reduced engraftment of human blasts in patient-derived xenograft models of CRLF2-positive BCP-ALL. Importantly, givinostat killed ruxolitinib-resistant cells and potentiated the effect of current chemotherapy. Thus, givinostat in combination with conventional chemotherapy may represent an effective therapeutic option for these difficult-to-treat subsets of ALL. Lastly, the selective killing of cancer cells by givinostat may allow the design of reduced intensity regimens in CRLF2-rearranged Down syndrome-associated BCP-ALL patients with an overall benefit in terms of both toxicity and related complications.Leukemia advance online publication, 21 April 2017; doi:10.1038/leu.2017.93.

    View details for DOI 10.1038/leu.2017.93

    View details for PubMedID 28331226

  • Peripheral blood cells from children with RASopathies show enhanced spontaneous colonies growth in vitro and hyperactive RAS signaling BLOOD CANCER JOURNAL Gaipa, G., Bugarin, C., Cianci, P., Sarno, J., Bonaccorso, P., Biondi, A., Selicorni, A. 2015; 5


    Germline mutations in genes coding for molecules involved in the RAS/RAF/MEK/ERK pathway are the hallmarks of a newly classified family of autosomal dominant syndromes termed RASopathies. Myeloproliferative disorders (MPDs), in particular, juvenile myelomonocytic leukemia, can lead to potentially severe complications in children with Noonan syndrome (NS). We studied 27 children with NS or other RASopathies and 35 age-matched children as control subjects. Peripheral blood (PB) cells from these patients were studied for in vitro colony-forming units (CFUs) activity, as well as for intracellular phosphosignaling. Higher spontaneous growth of both burst-forming units-erythroid (BFU-E) and CFU-granulocyte/macrophage (CFU-GM) colonies from RAS-mutated patients were observed as compared with control subjects. We also observed a significantly higher amount of GM-colony-stimulating factor-induced p-ERK in children with RASopathies. Our findings demonstrate for the first time that PB cells isolated from children suffering from NS or other RASopathies without MPD display enhanced BFU-E and CFU-GM colony formation in vitro. The biological significance of these findings clearly awaits further studies. Collectively, our data provide a basis for further investigating of only partially characterized hematological alterations present in children suffering from RASopathies, and may provide new markers for progression toward malignant MPD in these patients.

    View details for DOI 10.1038/bcj.2015.52

    View details for Web of Science ID 000358877500004

    View details for PubMedID 26186557

    View details for PubMedCentralID PMC4526778

  • Fine tuning of surface CRLF2 expression and its associated signaling profile in childhood B-cell precursor acute lymphoblastic leukemia HAEMATOLOGICA Bugarin, C., Sarno, J., Palmi, C., Savino, A. M., Te Kronnie, G., Dworzak, M., Shumich, A., Buldini, B., Maglia, O., Sala, S., Bronzini, I., Bourquin, J., Mejstrikova, E., Hrusak, O., Luria, D., Basso, G., Izraeli, S., Biondi, A., Cazzaniga, G., Gaipa, G. 2015; 100 (6): E229-E232

    View details for DOI 10.3324/haematol.2014.114447

    View details for Web of Science ID 000358577000005

    View details for PubMedID 25862705

    View details for PubMedCentralID PMC4450636