William Matsui

Label-free approaches that capture both biochemical composition and physical state are needed to distinguish closely related cell populations without destructive assays. Here we present a multimodal screening framework that integrates two high-throughput, label-free techniques: broadband coherent anti-Stokes Raman scattering (BCARS) spectroscopy for molecular fingerprints and real-time deformability cytometry (RT-DC) for mechanical phenotyping. The RT-DC instrument incorporates a novel axicon-based darkfield illumination scheme that produces annular excitation to enhance optical contrast during microfluidic deformation while preserving measurement throughput. Mechanical features from RT-DC and broadband molecular signatures from BCARS were combined through offline data fusion to form a joint feature space. Across differentiated HL60/S4 myeloid lineages and breast cancer cells stratified by endothelial cell-selective adhesion molecule (ESAM) expression, integrating modalities improved discrimination relative to either alone, achieving >75% accuracy with linear models and ~90% with nonlinear classifiers. These results establish multimodal mechano-molecular screening as a scalable, label-free strategy for identifying closely related cellular phenotypes.

While therapies targeting CD19 by antibodies, chimeric antigen receptor T cells (CAR-T), and T cell engagers have improved the response rates in B cell malignancies, the emergence of resistant cell populations with low CD19 expression can lead to relapsed disease. We developed an in vitro model of adaptive resistance facilitated by chronic exposure of leukemia cells to a CD19 immunotoxin. Single-cell RNA-Seq (scRNA-Seq) showed an increase in transcriptionally distinct CD19 ^lo populations among resistant cells. Mass cytometry demonstrated that CD22 was also decreased in these CD19 ^lo -resistant cells. An assay for transposase-accessible chromatin with sequencing (ATAC-Seq) showed decreased chromatin accessibility at promoters of both CD19 and CD22 in the resistant cell populations. Combined loss of both CD19 and CD22 antigens was validated in samples from pediatric and young adult patients with B cell acute lymphoblastic leukemia (B-ALL) that relapsed after CD19 CAR-T–targeted therapy. Functionally, resistant cells were characterized by slower growth and lower basal levels of MEK activation. CD19 ^lo resistant cells exhibited preserved B cell receptor signaling and were more sensitive to both Bruton’s tyrosine kinase (BTK) and MEK inhibition. These data demonstrate that resistance to CD19 immunotherapies can result in decreased expression of both CD19 and CD22 and can result in dependency on BTK pathways.

An antibody–drug conjugate (ADC) targeting CD46 conjugated to monomethyl auristatin has a potent anti-myeloma effect in cell lines in vitro and in vivo, and patient samples treated ex vivo. Here, we tested if CD46–ADC may have the potential to target MM-initiating cells (MM-ICs). CD46 expression was measured on primary MM cells with a stem-like phenotype. A patient-derived xenograft (PDX) model was implemented utilizing implanted fetal bone fragments to provide a humanized microenvironment. Engraftment was monitored via serum human light chain ELISA, and at sacrifice via bone marrow and bone fragment flow cytometry. We then tested MM regeneration in PDX by treating mice with CD46–ADC or the nonbinding control–ADC. MM progenitor cells from patients that exhibit high aldehyde dehydrogenase activity also have a high expression of CD46. In PDX, newly diagnosed MM patient samples engrafted significantly more compared to relapsed/refractory samples. In mice transplanted with newly diagnosed samples, CD46–ADC treatment showed significantly decreased engraftment compared to control–ADC treatment. Our data further support the targeting of CD46 in MM. To our knowledge, this is the first study to show preclinical drug efficacy in a PDX model of MM. This is an important area for future study, as patient samples but not cell lines accurately represent intratumoral heterogeneity.

Tumor relapse and drug resistance are major factors that limit the curability of multiple myeloma (MM). New regimens have improved overall MM survival rates, but patients with high-risk features continue to have inferior outcomes. Chromosome 17p13 deletion (del17p) that includes the loss of the TP53 gene is a high-risk cytogenetic abnormality and is associated with poor clinical outcomes owing to relatively short remissions and the development of pan-drug resistant disease. Increased relapse rates suggest that del17p enhances clonogenic growth, and we found that the loss of p53 increased both the frequency and drug resistance of tumor-initiating MM cells (TICs). Subsequent RNA sequencing (RNA-seq) studies demonstrated significant activation of the Notch signaling pathway and upregulation of inhibitor of DNA binding (ID1/ID2) genes in p53–knock out (p53-KO) cells. We found that the loss of ID1 or HES-1 expression or treatment with a gamma-secretase inhibitor (GSI) significantly decreased the clonogenic growth of p53-KO but not p53 wild-type cells. GSI treatment in a small set of MM specimens also reduced the clonogenic growth in del17p samples but not in non-del17p samples. This effect was specific as overexpression of the Notch intracellular domain (NICD) rescued the effects of GSI treatment. Our study demonstrates that the Notch signaling and ID1 expression are required for TIC expansion in p53-KO MM cells. These findings also suggest that GSI may be specifically active in patients with p53 mutant MM.

SLC25A51 imports oxidized NAD⁺ into the mitochondrial matrix and is required for sustaining oxidative metabolism in human mitochondria. We observed that higher expression of SLC25A51 correlated with poorer survival in Acute Myeloid Leukemia (AML) patient data. Given AML’s dependency on oxidative cell metabolism, we sought to determine the role SLC25A51 may serve in this disease. We found that depleting SLC25A51 in AML cells led to increased apoptosis, as well as prolonged survival in a xenograft model. Metabolic flux analyses indicated that depletion of SLC25A51 shunted flux away from oxidative pathways and promoted glutamine utilization for reductive carboxylation to support aspartate production. Consequently, SLC25A51 loss sensitized AML cells to glutamine deprivation and glutaminase inhibitor CB-839. Together, the work highlights connections between SLC25A51 and oxidative mitochondrial flux in AML. We identified a rationale for targeting SLC25A51 in myeloid cancers with potential for a therapeutic window, especially when coupled with glutaminase inhibition. Citation Format: Mu-Jie Lu, Jonathan Busquets, Valeria Impedovo, Yu-Tai Chang, William Matsui, Stefano Tiziani, Xiaolu Cambronne. SLC25A51 impacts drug sensitivity in AML cells by sustaining mitochondrial oxidative flux [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A42.

XLSX file, 138K, Gene expression analysis for predictive signatures of response to MRK-003 plus GEM.

PDF file, 186K, Baseline gene expression profiles identify signatures of response to single agent MRK-003 and the combination of MRK-003 and GEM.

PDF file, 76K, FACS plots for ALDH and CD44 and CD24 controls.

PDF file, 209K, Representative H&E stained sections from Panc374 xenograft.