Single-cell Proteomic Analysis Research Articles

Inhibition of ERK1/2 Reverses Venetoclax-Induced Autophagy to Overcome Resistance in Acute Myeloid Leukemia

Background: Activation of the RAS/MAPK pathway confers inherent/acquired resistance to the Bcl-2 inhibitor, venetoclax, in AML (Zhang et al., Signal Transduct Target Ther. 2022). Pro-survival Bcl-2 inhibits apoptosis as well as autophagy. Phosphorylation of Bcl-2 by ERK1/2 leads to dissociation of the autophagic protein Beclin 1 from Bcl-2 and promotes autophagy (Pattingre et al., Cell. 2005). Thus, while Bcl-2 inhibition can induce apoptosis, its inhibition leads to induction of autophagy (Pattingre et al., Cell. 2005) that can protect tumor cells from organelle damage and nutrient deprivation. Objective: We hypothesized that terminal MAPK pathway inhibition using an ERK1/2 inhibitor would reverse venetoclax-induced autophagy and synergistically lead to cell death/apoptosis. Methods: We inhibited ERK1/2 using Compound 27 (Heightman et al., J Med Chem. 2018), a close analog of ASTX029, which is a dual-mechanism ERK1/2 inhibitor currently under clinical investigation in solid tumors (NCT03520075). We studied the potential synergy of ERK1/2 and Bcl-2 inhibition in decreasing cell proliferation and inducing apoptosis and in overcoming venetoclax resistance in AML preclinical models and primary patient samples (n=8). We performed simultaneous analysis of cell proliferation, stress response and DNA damage using single cell proteomics analysis to understand the mechanism of synergy. Autophagy was measured by lipidated LC3 quantification (flow cytometry and immunoblotting). Colony formation assay using NRAS-mutant PDX was performed to analyze the effect on progenitor cells. For insights into the mechanisms of synergy, we conducted large-scale proteomics analyses by single cell mass cytometry (CyTOF) and simultaneously measured cell proliferation, stress response, DNA damage and Bcl-2 family proteins. Results: Inhibition of ERK1/2 sensitized OCI-AML3 (NRAS-mutant) cells (Combination Index [CI]: 0.008) and venetoclax-resistant OCI-AML2 cells (CI: 0.05) to venetoclax and shifted the cytostatic effect of the single agents to a cytotoxic effect. Combination treatment induced apoptosis in leukemia initiating progenitor cells (LICs, CD34+CD38-) in primary AML samples with 54% apoptosis in combination versus 10% with venetoclax alone (CI = 0.03-0.23), while sparing normal CD34+CD38- cells. Mechanistically, basal ERK1/2 phosphorylation and autophagy (LC3 lipidation), were higher in venetoclax-resistant OCI-AML2 cells versus parental cells (p=0.0008) and both were inhibited with ERK1/2 inhibition alone and in combination with venetoclax. Simultaneous analysis of cell proliferation, stress response and DNA damage showed downregulation of proliferation (Ki-67) and an increase in ATF4 in response to ERK1/2 inhibition. The combination of Compound 27 and venetoclax inhibited autophagy (lipidated LC3) and increased apoptosis (increased cleaved PARP and cleaved caspase 3, Fig 1a). Venetoclax-induced autophagy was also confirmed in OCI-AML3 cells at 24 h post treatment (p=0.03). ERK1/2 inhibition reversed venetoclax-induced autophagy in OCI-AML3 (p=0.0003) and OCI-AML2-venetoclax-resistant cells (p=0.0007). CyTOF analysis showed decreased p-AMPK in response to ERK1/2 inhibition in OCI-AML3 cells. As AMPK/FIS1-mediated mitochondrial autophagy is required for self-renewal of AML stem cells (Pie et al., Cell Stem Cell. 2018), we confirmed decreased clonogenic potential of AML progenitor cells by reduced colony formation in response to ERK1/2 inhibition using an NRAS-mutant AML PDX model (p=0.0002). Single cell proteomics (CyTOF) showed decreased p-AMPK in response to single agent ERK1/2 inhibition or the combination with venetoclax in LIC populations (CD34+CD38-) in the NRAS-mutant AML PDX model. In addition to p-AMPK the expression of cMyc and CD44 was also reduced in the combination treatment, indicating reduced stemness (Fig 1b). Conclusion: Mechanistically, our results indicate that pharmacological inhibition of ERK1/2 impairs autophagy and sensitizes venetoclax-resistant AML cells to apoptosis, thus overcoming primary and secondary resistance to venetoclax. In addition, combination treatment induced apoptosis of LICs and reduced clonogenic potential and markers of stem cell function. These data provide a strong rationale for the combination of ERK1/2 and Bcl-2 inhibitors in treatment of AML and warrant further investigation in the clinic. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Single-Cell Proteomic Analysis Defines Metabolic Heterogeneity in Response to Venetoclax in AML

Acute myeloid leukemia (AML) is among the deadliest blood cancers with over 10,000 patients dying annually in the U.S. Despite high rates of complete remission after conventional frontline genotoxic chemotherapy, patient prognosis remains poor with a 5-year overall survival of only 28%, which is largely attributable to frequent relapses. The standard chemotherapy for AML has changed little during the past 40 years. However, several new drugs have been approved by the FDA over the last 10 years including venetoclax (VEN), BH3 mimetic protein that selectively inhibits the anti-apoptotic function of BCL2. Combining VEN with the hypomethylating agent azacytidine (AZA) or with low-dose cytarabine (AraC) demonstrated promising results, leading to approval of these combinations by the FDA. However, durable response remains a challenge as resistance has emerged. Metabolic flexibility and intratumoral heterogeneity (both genetic and non-genetic) are key components of resistance. Resistance to VEN combination therapies has implicated alternative anti-apoptosis proteins such as MCL1, monocytic differentiation state, and remodeling of mitochondrial electron transport chain complex I. TP53 or RAS mutations are also associated with resistance. To better understand the interplay between differentiation state, metabolism, and signaling pathways in resistance to VEN and its combinations, we analyzed 36 primary AML samples (31 adult, 5 pediatric) and 2 healthy bone marrow controls using single-cell mass cytometry after ex vivo treatment for 24h with VEN, AraC, AZA and VEN+AraC and VEN+AZA. Across two antibody panels we measured myeloid phenotypic markers, key signaling pathways, transcription factors and metabolic proteins relevant to glycolysis, TCA cycle, fatty acid oxidation, amino acid transport, and mitochondrial dynamics, for a total of 76 unique markers. For more than 80% of the patients, we observe, at baseline, highly metabolic subpopulations with high expression of ATPA5, a subunit of mitochondrial ATP synthase, and glutathione synthetase (GSS), necessary for redox homeostasis as well as strong expression of mitochondrial proteins related to oxidative phosphorylation and TCA cycle. A small subset of these cells also highly express glycolytic enzymes, in particular enolase 1 (ENO1) and lactate dehydrogenase (LDHA) which converts pyruvate to lactate. This demonstrates the presence of cells with dual glycolytic and oxidative metabolism possibly reflecting a high demand for NAD+ to support oxidation reactions. These metabolic features do not correlate with specific phenotypic markers and is highly variable between patients. As expected, ex vivo treatment with VEN eradicates more immature subpopulations (CD34+ and/or CD117+) while sparing monocytic populations. In general, cells with the highest levels of BCL2 respond well to VEN (Panel A). However, defining populations solely with phenotypic proteins fails to adequately identify persistent and emerging populations after VEN or its combinations. Instead, clustering based on metabolic pathways identifies persistent or emerging populations. In several patients, expression of mitochondrial cristae-shaping protein (OPA1) and NADPH-producing enzymes isocitrate dehydrogenase (IDH1) or glucose-6-phosphate dehydrogenase (G6PD) defines BCL2+ subpopulations that persist through VEN treatment, likely through maintenance of mitochondrial integrity. In other patients, we observe selection of cells expressing monocarboxylate transporter 1 (MCT1), which facilitates lactate uptake, suggesting these cells undergo metabolic reprogramming to counteract the decrease in amino-acid uptakes following VEN. Interestingly, 4 of the 5 pediatric AML samples demonstrated VEN-resistant subpopulations characterized by co-expression of glucose transporter GLUT1, fatty acid transporter CD36, and alternative anti-apoptotic protein BCL-xL (Panel B). Very little is known about metabolic dependencies in pediatric AML and VEN is an emerging therapy in this patient group. Altogether, our data indicate that single-cell metabolic analysis may better organize intratumoral heterogeneity in AML and enables discovery of new pathways defining resistance or persistence to VEN and its combinations. Further analyses and integration of clinical data including mutational patterns are underway and will be presented. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Single-Cell Proteomic Interrogation of FLT3-ITD Leukemia Compartment Revealsdistinct Leukemia Cell Populations Resistant to Quizartinib, Decitabine and Venetoclax

Triplet therapy (TT) combining Quizartinib(Quiz), Decitabine(Dec) and Venetoclax(Ven) is highly effective against FLT3-ITD acute myeloid leukemia (AML) with high response rates (Yilmaz M, ASCO 2022).Signaling mutations, particularly those involving RAS/MAPK pathway, have emerged as key contributors to primary and secondary resistance to TT. Lack or loss of response to TT is not limited to presence or emergence of clones with signaling mutations and disease relapse occurs in FLT3-ITD AML patients with a variety of other mutations. We hypothesize that resistant leukemia clones have unique proteomic profiles that facilitate survival under therapy pressure and deciphering proteomic profiles at the single-cell level will delineate resistance mechanisms and adaptive responses driven by therapy pressure, and aid in identifying proteomic correlates of response and therapeutic vulnerabilities. To this end, we performed comprehensive single-cell proteomic analysis of serially collected samples (n:162) from patients treated with TT (n:14) and doublet (n:10, DEC+Quiz) therapy, using CyTOF and interrogated leukemia phenotypic profiles, apoptotic networks, signaling pathways, differentiation states and trajectories. First, we performed unsupervised analyses to identify leukemia cells and non-malignant cellular elements of the leukemia compartment in an unbiased manner, interrogated the leukemia proteomic landscape to identify leukemia associated proteomic features that may correlate with clinical response and assessed whether distinct mutation profiles are associated with specific proteomic profiles that may confer resistance to therapy. Since Ven targets BCL2 and FLT3i modulates the expression of anti-apoptotic molecules we assessed the expression of apoptosis regulators across leukemia landscapes and found that leukemia cells with immature phenotype, including those with leukemia stem cell(LSC) phenotype, almost always expressed moderate-high levels of BCL2. Monocytic cells(MC), generally situated in close proximity to leukemia cells in UMAPs, lacked BCL2 expression and had the highest levels of MCL1. Despite expressing moderate levels of MCL1 and BCL-XL, TT was effective in substantially eliminating CD34+ immature leukemia cells (Figure 1). Due to their contrasting apoptosis regulatory networks, we observed a relative enrichment of MCs, either benign or malignant, after TT. Since cells with MC phenotype were inherently resistant to TT we hypothesized that leukemia cell subsets having similar proteomic profiles to MCs will persist after TT. Of note, leukemia cell compartments harbor distinct differentiation hierarchies, the frequencies of which varied across patients. Phenotypic interrogation of leukemia cells (UMAP) revealed that LSCs generally clustered on the opposite pole distant from MCs and leukemia cells on poles facing MCs were more differentiated. Remarkably, FLT3-ITD mutation partners differentially altered and reshaped the proteomic landscape. NPM1 mutant FLT3-ITD AML cells displayed a less diverse leukemia architectural organization with differentiation block. Contrarily, signaling mutation diversified the leukemia landscape into a diverse continuum of differentiation states. Remarkably, we observed that RAS/MAPK mutations in FLT3-ITD AML overcame differentiation block and gave rise to a differentiation continuum encompassing less-differentiated, transitional and differentiated leukemia cells(Figure1). Importantly, we observed that transitional and CD34+ leukemia cells, mapped in close vicinity to MCs, and differentiated MCs preferentially persisted at D28, had active signaling pathways and expressed CD36, which indicates distinct metabolic programs could ensure survival under therapy pressure and also had lower levels of BCL2.The presence of CD34+ leukemia cells at D28, adapted under therapy pressure with persistent signaling at D28, both in CD34+ leukemia or MCs, was indicative of poor clinical outcomes. Conclusion: Single-cell proteomic assessment of FLT3-ITD AML treated with Quiz/Dec/Ven (TT) identifies a unique mode of resistance and proteomic features of surviving cells at D28, and elucidates how RAS/MAPK mutations diversify the leukemia proteomic landscape and modulate the architectural organization which eventually gives rise to emerging clones resistant to therapy. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Maximizing hydrophobic peptide recovery in proteomics and antibody development using a mass spectrometry compatible surfactant

Peptide loss due to surface absorption can happen at any step in a protein analysis workflow and is sometimes especially deleterious for hydrophobic peptides. In this study, we found the LC-MS compatible surfactant, n-Dodecyl-β-D-maltoside (DDM), can maximize hydrophobic peptide recovery in various samples including single cell digests, mAb clinical PK samples, and mAb peptide mapping samples. In HeLa single cell proteomics analysis, more than half of all unique peptides identified were found only in DDM prepared samples, most of which had significantly higher hydrophobicities compared to peptides in control samples. In clinical PK studies, DDM enhanced hydrophobic complementarity-determining region (CDR) peptide signals significantly. The fold change of CDR peptides’ intensity enhancement in DDM added samples compared to controls correlate with peptide retention time and hydrophobicity, providing guidance for surrogate peptide selection and peptide standard handling in PK studies. For peptide mapping analysis of mAbs, DDM can improve hydrophobic peptide signal and solution stability over 48 h in an autosampler at 4 °C, which can aid method qualification and transfer during drug development. Lastly, maximizing hydrophobic peptide recovery from samples dried in vacuo was achieved by DDM reconstitution, which provided higher signal for later eluting peaks and higher proteome coverage overall.

1714P Single-cell RNA sequencing and proteomic analysis reveals dedifferentiation-immunosuppression loop formed by malignant cell and macrophage in intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is an aggressive malignancy with highly heterogeneous cellular components that responds poorly to chemotherapy and immunotherapy. The complete elucidation of the ICC tumor ecosystem is essential for better prognosis and the development of novel treatments.

Single-Cell Quantitative Proteomic Analysis of Human Oocyte Maturation Revealed High Heterogeneity in InVitro-Matured Oocytes.

Oocyte maturation is pertinent to the success of in vitro maturation (IVM), which is used to overcome female infertility, and produced over 5000 live births worldwide. However, the quality of human IVM oocytes has not been investigated at single-cell proteome level. Here, we quantified 2094 proteins in human oocytes during in vitro and in vivo maturation (IVO) by single-cell proteomic analysis and identified 176 differential proteins between IVO and germinal vesicle oocytes and 45 between IVM and IVO oocytes including maternal effect proteins, with potential contribution to the clinically observed decreased fertilization, implantation, and birth rates using human IVM oocytes. IVM and IVO oocytes showed separate clusters in principal component analysis, with higher inter-cell variability among IVM oocytes, and have little correlation between mRNA and protein changes during maturation. The patients with the most aberrantly expressed proteins in IVM oocytes had the lowest level of estradiol per mature follicle on trigger day. Our data provide a rich resource to evaluate effect of IVM on oocyte quality and study mechanism of oocyte maturation.

Abstract 5337: Tolinapant (ASTX660) enhances the anti-leukemic activity of Venetoclax and Dexamethasone in T cell acute lymphoblastic leukemia (T-ALL)

Abstract Background: Inhibitors of apoptosis proteins (IAPs) are overexpressed in ALL leading to resistance to apoptosis and chemo-resistance. Tolinapant, a non-peptidomimetic antagonist of the cellular and X-linked inhibitors of apoptosis (cIAP1/2 and XIAP) being evaluated in Phase 1/2 clinical trial [NCT02503423] showed single-agent activity in T-cell lymphoma. Objectives: Herein, we analyzed the preclinical activity of tolinapant in combination with ABT199 and Dexamethasone (DEX) in T-ALL (in vitro and ex-vivo patient derived xenografts (PDX). Results: Using a panel of 8 T-ALL cell lines we analyzed the single agent activity of tolinapant. Loucy and SUP-T11 were most sensitive (IC50 = 190-309 nM). CCRF-CEM and ALL-SIL showed moderate sensitivity (IC50 = 10-18 µM) while Jurkat, MOLT16, MOLT4 and PF382 were resistant. Western blotting (WB) showed decreased levels of cIAP1and cIAP2 with no change in XIAP in response to tolinapant as a single agent. We next investigated the efficacy of tolinapant with Bcl2 inhibitor ABT199. The combination of ABT199 and ASTX660 was synergistic in Loucy cell line with combination index (CI) of 0.14. Cell death was increased to 64±3% in combination v/s 27±0.9% in ABT199. WB showed decreased cIAP2 and increased levels of cleaved caspase 7 and cleaved caspase 9 in combination compared to single agents, suggesting increased apoptosis. Treatment of PDX-derived cells with tolinapant and ABT199 was more effective than monotherapy in inducing apoptosis in CD45+ bulk (46±0.7% to 63±6%, p<0.0001) and leukemia initiating cells (LICs, CD45+ CD7+ CD19- CD34+) (39±3% to 54±8%, p=0.003). Next, we checked the effect of combination of DEX with tolinapant in T-ALL cell lines. CCRF-CEM cell line is from a relapsed patient and is resistant to DEX. The combination was synergistic with CI of 0.26 and cell death of 50±4% compared to 20±3% by DEX. A triple combination of DEX, ABT199 and tolinapant increased apoptotic response to 82.9±1%, compared to DEX+ABT199 dual combination where apoptosis was induced to 52.4±2%. Strong synergy in terms of both cytoreduction as well as apoptosis induction was observed in SUP-T11 cells. Tolinapant sensitized SUP-T11 cells to DEX with ED50 value of 542 nM in combination compared to ~2 µM with DEX treatment. Simultaneous analysis of cell proliferation, stress response and DNA damage using single-cell proteomics analysis showed downregulation of proliferation (Ki-67), stress response (ATF4, LC3B) and increased levels of cleaved PARP, cleaved caspase 3 suggesting increased apoptosis in combination of tolinapant with DEX. Treatment of PDX-derived cells with tolinapant enhanced the cytotoxic effect of DEX in CD45+ bulk (58±2% to 71±0.1%, p<0.0001) and LICs (62±2% to 78±0.9%, p<0.0001). Conclusion: Tolinapant synergizes with the anti-leukemic activity of ABT199 and DEX, establishing a therapeutic rationale for IAP antagonist in T-ALL. Citation Format: Priyanka Sharma, Sujan Piya, Huaxian Ma, Natalia Baran, Muharrem Muftuoglu, Mahesh Basyal, Vivian Ruvolo, George Ward, Tomoko Smyth, Martin J. Sims, Michael Andreeff, Gautam Borthakur. Tolinapant (ASTX660) enhances the anti-leukemic activity of Venetoclax and Dexamethasone in T cell acute lymphoblastic leukemia (T-ALL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5337.

Enrichment of high-risk innate immune cells in Hispanic and Black children with B-acute lymphoblastic leukemia.

7021 Background: Black and Hispanic children with B-acute lymphoblastic leukemia (B-ALL) experience worse outcomes compared to their non-Hispanic white (NHW) counterparts. Immune-based therapies have improved the outcomes of children with B-ALL, however, impact of racial/ethnic background on immune microenvironment is less studied. Methods: BM from 61 children with newly diagnosed B-ALL(Hispanic = 21, Black = 17, NHW = 23) was obtained via the Aflac Biorepository. High-dimensional analysis was performed utilizing single cell mass cytometry with 61 markers to characterize T, NK and myeloid cells. Data was analyzed using Cytobank and high-dimensional visualization platforms such as ViSNE. Clinical data including self-reported race/ethnicity and NCI-risk classification were obtained for all samples. Results: Multi-dimensional analysis was carried out for each cell population to dissect race/ethnicity-associated differences. ViSNE clustering of NK cells identified 3 different NK populations, including a distinct population of mature CD57+ NK cells with Tbethi, HLADRhi, granzymeBhi, CD27- phenotype. The distribution of NK subsets was highly impacted by race/ethnicity. Hispanic (H) patients had higher proportions of CD57+ mature NK cells when compared with other groups, (40 ± 4% vs 33 ± 2%; p = 0.03) with pronounced differences apparent within standard risk (SR) patients. H-SR had higher proportion of CD57+ NK cells compared to other SR patients (mean H-SR 43.4 ± 5.87% vs 26.3 ± 2.87% p = 0.0049). ViSNE clustering of myeloid cells identified 5 clusters based on patterns of cell surface markers, including a distinct CD11c+CD16+DRhi inflammatory/non-classical myeloid population. Further analysis showed that NHW-SR patients have significantly lower proportions of CD16+DR+ myeloid cells compared to Hispanic, Black and NHW-HR patients (mean NHW-SR 3.67 ± 2.56% vs Others 10.8 ± 7.87% p = 0.0394). Notably, a phenotypically similar population has recently been implicated in leukemic progression in preclinical models (Witkowski et al, Cancer Cell 2020). In contrast to innate cells, T cell clusters were broadly comparable between different racial/ethnic groups. Conclusions: These studies provide detailed single-cell proteomic analysis and highlight the impact of racial/ethnic background on immune microenvironment in pediatric B-ALL. Our data identify differences in innate immunity with enrichment of high-risk immune-populations in Hispanic and Black children and depletion of inflammatory myeloid populations in NHW-SR children with B-ALL. These variations may contribute to the observed differences in outcomes and may impact application of immune therapies in racial/ethnic groups.

Single-Cell Proteomics Analysis of Recurrent Low-Grade Serous Ovarian Carcinoma and Associated Brain Metastases.

Between 2% and 6% of epithelial ovarian cancer (EOC) patients develop brain metastases (brain mets), which are incurable and invariably result in death. This poor outcome is associated with a lack of established guidelines for the detection and treatment of brain mets in EOC patients. In this study, we characterize an unusual case of low-grade serous ovarian carcinoma (LGSOC) that metastasized to the brain. Using a spatially oriented single-cell proteomics platform, we compared sequential biopsies of a primary tumor with a peritoneal recurrence and brain mets. We identified several targetable oncogenic pathways and immunosuppressive mechanisms that are amplified in the brain mets and could be involved in the progression of LGSOC to the brain. Furthermore, we were able to identify cell populations that are shared between the primary tumor and the brain mets, suggesting that cells that have a propensity for metastasis to the brain could be identified early during the course of disease. Taken together, our findings further a path for personalized therapeutic decisions in LGSOC.

Bispecific targeting of CD20 and CD19 increases polyfunctionality of chimeric antigen receptor T-cell products in B-cell malignancies

Background aimsSelective immune pressure contributes to relapse due to target antigen downregulation in patients treated with anti-CD19 chimeric antigen receptor (CAR) T cells. Bispecific lentiviral anti-CD20/anti-CD19 (LV20.19) CAR T cells may prevent progression/relapse due to antigen escape. Highly polyfunctional T cells within a CAR T-cell product have been associated with response in single-antigen-targeted anti-CD19 CAR T cells. MethodsThe authors performed a single-cell proteomic analysis to assess polyfunctional cells in our LV20.19 CAR T-cell product. Analysis was limited to those treated at a fixed dose of 2.5 × 106 cells/kg (n = 16). Unused pre-infusion CAR T cells were thawed, sorted into CD4/CD8 subsets and stimulated with K562 cells transduced to express CD19 or CD20. Single-cell production of 32 individual analytes was measured and polyfunctionality and polyfunctional strength index (PSI) were calculated. ResultsFifteen patients had adequate leftover cells for analysis upon stimulation with CD19, and nine patients had adequate leftover cells for analysis upon stimulation with CD20. For LV20.19 CAR T cells, PSI was 866–1109 and polyfunctionality was 40–45%, which were higher than previously reported values for other CAR T-cell products. ConclusionsStimulation with either CD19 or CD20 antigens resulted in similar levels of analyte activation, suggesting that this product may have efficacy in CD19– patient populations.

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering.

SUMMARYSingle-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low-abundance proteins. Herein, we describe an ion-mobility-enhanced mass spectrometry acquisition and peptide identification method, transferring identification based on FAIMS filtering (TIFF), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells, with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes. A record of this paper’s transparent peer review process is included in the supplemental information.

Targeting the NOTCH1-MYC-CD44 axis in leukemia-initiating cells in T-ALL

The NOTCH1-MYC-CD44 axis integrates cell-intrinsic and extrinsic signaling to ensure the persistence of leukemia-initiating cells (LICs) in T-cell acute lymphoblastic leukemia (T-ALL) but a common pathway to target this circuit is poorly defined. Bromodomain-containing protein 4 (BRD4) is implicated to have a role in the transcriptional regulation of oncogenes MYC and targets downstream of NOTCH1, and here we demonstrate its role in transcriptional regulation of CD44. Hence, targeting BRD4 will dismantle the NOTCH1-MYC-CD44 axis. As a proof of concept, degrading BRD4 with proteolysis targeting chimera (PROTAC) ARV-825, prolonged the survival of mice in Notch1 mutated patient-derived xenograft (PDX) and genetic models (ΔPTEN) of T-ALL. Single-cell proteomics analysis from the PDX model, demonstrated quantitative reduction of LICs (CD34+ CD7+ CD19−) and downregulation of the NOTCH1-MYC-CD44 axis, along with cell cycle, apoptosis and PI3K/Akt pathways. Moreover, secondary transplantation from PDX and ΔPTEN models of T-ALL, confirmed delayed leukemia development and extended survival of mice engrafted with T-ALL from ARV-825 treated mice, providing functional confirmation of depletion of LICs. Hence, BRD4 degradation is a promising LIC-targeting therapy for T-ALL.

Cataloguing the proteome: Current developments in single-molecule protein sequencing.

The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.

Development of droplet microfluidics capable of quantitative estimation of single-cell multiplex proteins

This study presented constriction microchannel based droplet microfluidics realizing quantitative measurements of multiplex types of single-cell proteins with high throughput. Cell encapsulation with evenly distributed fluorescence labelled antibodies stripped from targeted proteins by proteinase K was injected into the constriction microchannel with the generated fluorescence signals captured and translated into protein numbers leveraging the equivalent detection volume formed by constriction microchannels in both droplet measurements and fluorescence calibration. In order to form the even distribution of fluorescence molecules within each droplet, the stripping effect of proteinase K to decouple binding forces between targeted proteins and fluorescence labelled antibodies was investigated and optimized. Using this microfluidic system, binding sites for beta-actin, alpha-tubulin, and beta-tubulin were measured as 1.15 ± 0.59 × 106, 2.49 ± 1.44 × 105, and 2.16 ± 1.01 × 105 per cell of CAL 27 (N cell = 15 486), 0.98 ± 0.58 × 106, 1.76 ± 1.34 × 105 and 0.74 ± 0.74 × 105 per cell of Hep G2 (N cell = 18 266). Neural net pattern recognition was used to differentiate CAL 27 and Hep G2 cells, producing successful rates of 59.4% (beta-actin), 64.9% (alpha-tubulin), 88.8% (beta-tubulin), and 93.0% in combination, validating the importance of quantifying multiple types of proteins. As a quantitative tool, this approach could provide a new perspective for single-cell proteomic analysis.

Scaling Up Single-Cell Proteomics

Single-cell tandem MS has enabled analyzing hundreds of single cells per day and quantifying thousands of proteins across the cells. The broad dissemination of these capabilities can empower the dissection of pathophysiological mechanisms in heterogeneous tissues. Key requirements for achieving this goal include robust protocols performed on widely accessible hardware, robust quality controls, community standards, and automated data analysis pipelines that can pinpoint analytical problems and facilitate their timely resolution. Toward meeting these requirements, this perspective outlines both existing resources and outstanding opportunities, such as parallelization, for catalyzing the wide dissemination of quantitative single-cell proteomics analysis that can be scaled up to tens of thousands of single cells. Indeed, simultaneous parallelization of the analysis of peptides and single cells is a promising approach for multiplicative increase in the speed of performing deep and quantitative single-cell proteomics. The community is ready to begin a virtuous cycle of increased adoption fueling the development of more technology and resources for single-cell proteomics that in turn drive broader adoption, scientific discoveries, and clinical applications.

Single-Cell Transcriptomic and Proteomic Analysis of Acute Myeloid Leukemia (AML) Patients with Abnormalities on Chromosome 7

Background:Chromosome 7 (chr7) abnormalities are commonly seen in patients with acute myeloid leukemia (AML) or myelodysplastic syndrome and are associated with poor prognosis. Flow cytometry (FCM) is typically used clinically to quantify residual malignancy during treatment but the relationship of cell surface immunophenotype with genetic features is incompletely defined. Single-cell RNA sequencing (scRNA-seq) with oligonucleotide-conjugated antibodies may be able to integrate cytogenetic genotypes found within leukemic clones with specific transcriptomic and immunophenotypic signatures.Methods:Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics and 3 healthy donors (HDs). We previously established a reference for normal immune cells where we assessed the BM of 20 HDs (PMID:30518681). HDs in present study were selected from this same cohort. Multi-parameter FCM was performed as previously described and scRNA-seq with 31 antibodies (10x Genomics, 3'v2) was performed on BM mononuclear cells. Data from 16 samples (including 1 patient replicate) were mapped onto the atlas with dimension reduction in gene expression (GEX) by principal component analysis and Uniform Manifold Approximation and Projection (UMAP). Cell clusters were constructed and surface proteins were utilized to determine cellular annotation.Patient GEX profiles were compared to those of HDs, and two algorithms were used to identify malignant cells with chromosomal abnormalities. Alterations of large chromosomal segments were identified by Hidden Markov Model. Clinical cytogenetics and expression matrices from the model output were combined to annotate individual cells as malignant or normal for all potential regions. Machine learning classifiers were applied to predict malignant cells using protein expression and important proteins were selected by models with measure for significant features.Results:After quality control, 132,658 cells were included, of which 43,441 and 12,572 cells from AML patients and HD respectively had additional cell surface immunophenotyping data. Samples were well-integrated by UMAP (Figure 1A) and cell annotation overlapped with previously reported annotations by GEX of HDs (Figure 1B), with 15,270 malignant cells identified (Figure 1C). Malignant groups were created if more than 20 cells shared the same chromosomal alterations. Among all 12 patients, 3 of them only had monosomy 7 as the sole genetic aberration, while 9 patients had abnormalities on other chromosomes.The correlation between cell types showed distinct features among patients, and cells in different groups had different protein expression profiles. For example, 22% of the cells (n = 432) from the myeloid population of patient 1 (n = 1957) were identified as normal and 77% had a loss of chr7 (Figure 2A). Clustering in lower resolution separated them into two groups: CD11b+CD33+ (n = 1026) and CD133+CD34+ (n = 931). The CD133+CD34+ group had a higher percentage of malignant cells overall (74% vs. 83%) while a subset of the CD11b+CD33+ group (CD16+CD13+) had the highest percentage of cells with losses on both chr2 and chr7 (60%). Data from patient 2 also suggested that cells with different immunophenotypes were estimated to have different chromosomal changes (Figure 2B). While 69% of the malignant cells had a loss on chr7, most of those without changes on chr7 were from CD45+CD11b+ group where 62% of the cells did not have a detectable change on chr7.The top significant proteins for distinguishing malignant from normal cells among all patients were CD117, CD33, CD34, CD44, and CD47. FCM intensity was compared with the scRNA-seq immunophenotyping data, confirming the similarity in distribution. The scRNA-seq data with immunophenotyping can capture and recapitulate the leukemic immunophenotype, further linking it with copy number changes to reveal potential subclonal structures.Conclusion:By comparing the expression profile of AML patients with abnormalities on chr7 to HDs, this study provides evidence that leukemic immunophenotype is correlated with chromosomal structural changes. The experiments on a single-cell level were able to identify clones in higher resolution and revealed potential cell surface protein markers that could be used clinically to identify specific malignant populations in patients with myeloid malignancies. [Display omitted] DisclosuresGhiaur: Syros Pharmaceuticals: Consultancy; Menarini Richerche: Research Funding. Hourigan: Sellas: Research Funding.

Glucocorticoid-Resistant B-Cell Acute Lymphoblastic Leukemic Cells Can be Targeted By BCR-Signaling Inhibition

Glucocorticoids (GCs) remain a backbone component of therapeutic regimens for childhood B-cell acute lymphoblastic leukemia (B-ALL). GCs resistance is a strong prognostic marker of relapse making its understanding an important challenge to be addressed to improve overall patients outcome.Healthy B-cell development is characterized by checkpoints where critical regulatory signaling influences the fate of developing B-cells. These stages are vulnerable for leukemic transformation and as we previously demonstrated, the developmental and functional state of B-ALL cells are of critical importance in treatment failure. Using this developmental framework, we examined the effect of GCs on healthy and malignant B-cells to better understand mediators of GC resistance and ways to overcome it.To define the dynamics of the transcriptional networks surrounding B-cell developmental checkpoints, we performed transcriptomic analysis of sorted pre-proB, pro-B and pre-B cells from 3 healthy donors. We found a coordinated upregulation of B cell receptor (BCR) and Glucocorticoid Receptor (GCR) pathways in healthy B cells during their development. Single cell proteomic analysis of these healthy populations confirmed the coordinated expression of GCR with early B-cell phenotypic markers. Furthermore, in vitro treatment of healthy B-cells with the GC dexamethasone (dex) demonstrated cycling pro-B/pre-B cells to be the most sensitive to GC-induced cell death.Given the importance of GCs in B-ALL treatment, we investigated GCs effects and resistance in NALM6 and REH cell lines. NALM6, expressing high levels of GCR, were significantly sensitive to dex treatment in terms of cell cycle arrest and cell death. By contrast, REH cells were resistant to dex treatment as they lack the GCR. Retroviral transfection of NR3C1 (GCR gene) in REH cells (REH GCR) resulted in acquired sensitivity to dex. To explore the potential crosstalk between GCR and BCR pathways, we also treated cells with BCR signaling inhibitor, dasatinib (das), alone or in combination with dex. While both cell lines survived to treatment with das, the combined treatment increased apoptosis compared to dex alone in NALM6 cells (p=0.0179) and REH GCR cells (p=ns). Whole transcriptome sequencing of dex-resistant cells revealed upregulation of BCR downstream signaling as one of the main pathways associated with resistance.The cell line data implicated active BCR signaling as a path to GCs resistance, so we next analyzed 19 B-ALL primary samples by mass cytometry, after in vitro exposure for 48 hrs to same treatments. Across the entire cohort, dex induced a significant reduction in viability (p=0.0007), compared to vehicle. Treatment with das and dex+das also decreased cell viability compared to vehicle (p=0.0038 and p=0.0002) although was not significant to dex alone. Interestingly dex-resistant cells showed a phenotypic modulation compatible with a late pre-B phenotype with increased CD45 and CD20 expression. In addition, surviving cells showed an activation of downstream targets of BCR signaling such as pSYK, pRPS6 and pCREB that was partially blunted by dasatinib treatment.To understand whether the phenotype and signaling modulation induced by dexamethasone also occurs in patients after treatment with GCs, we analyzed minimal residual disease (MRD) cells following 8 days of treatment with GCs from 9 B-ALL patients. This analysis confirmed our previous findings with MRD cells having same late pre-B cells phenotype and signaling profile as in vitro treated cells.Finally, we tested whether targeting of pre-BCR signaling via dasatinib, could overcome resistance in vivo. We evaluated engraftment of luciferase-expressing NALM6 cells at different timepoints after tail vein injection in mice treated with vehicle, dex, das or dex + das. Bioluminescence analysis revealed a significant reduction of early and late engraftment in the dex + das group compared to vehicle-treated mice. Furthermore, mice receiving the combined treatment also experienced a significant survival advantage as assessed by log rank test (p=0.0002).Taken together these data suggest a coordinated interplay between BCR and GCR pathways in healthy and leukemic B cells. GCs-resistant leukemic cells showed a mature pre-B phenotype that is vulnerable to BCR signaling inhibition in vitro and in vivo suggesting new therapeutic options to overcome GC resistance in childhood B-ALL. DisclosuresBiondi: Bluebird: Other: Advisory Board; Novartis: Honoraria; Incyte: Consultancy, Other: Advisory Board; Amgen: Honoraria; Colmmune: Honoraria. Bava: 10x Genomics: Current Employment. Davis: Jazz Pharmaceuticals: Research Funding; Novartis Pharmaceuticals: Honoraria.

Single-Cell Proteomics Identifies Leukemia Landscape Associated with Clinical Outcomes in R/R AML Treated with MDM2i (Milademetan) and FLT3i (Quizartinib): Putative Role of CD68 and Diversity Index

Single-Cell Proteomics Identifies Leukemia Landscape Associated with Clinical Outcomes in R/R AML Treated with MDM2i (Milademetan) and FLT3i (Quizartinib): Putative Role of CD68 and Diversity Index

In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment.

Cancer is a dynamic disease with heterogenic molecular signatures and constantly evolves during the course of the disease. Single cell proteomic analysis could offer a suitable pathway to monitor cancer cell heterogeneity and deliver critical information for the diagnosis, recurrence, and drug-resistant mechanisms in cancer. Current standard techniques for proteomic analysis such as ELISA, mass spectrometry, and Western blots are time-consuming, expensive, and often require fluorescence labeling that fails to provide accurate information about the multiple protein expression changes at the single cell level. Herein, we report a surface-enhanced Raman spectroscopy-based simple microfluidic device that enables the screening of single circulating tumor cells (CTC) in a dynamic state to precisely understand the heterogeneous expression of multiple protein biomarkers in response to therapy. It further enables identifying intercellular heterogeneous expression of CTC surface proteins which would be highly informative to identify the cancer cells surviving treatment and potentially responsible for drug resistance. Using a bead and cell line-based model system, we successfully detect single bead and single cell spectra when flowed through the device. Using SK-MEL-28 melanoma cells, we demonstrate that our system is capable of monitoring heterogeneous expressions of multiple surface protein markers (MCSP, MCAM, and LNGFR) before and during drug treatment. Integrating a label-free electrochemical system with the device, we also monitor the expression of an intracellular protein (here, BRAFV600E) under drug treatment. Finally, we perform a longitudinal study with 15 samples from five different melanoma patients who underwent therapy. We find that the average expression of receptor proteins in a patient fails to determine the therapy response particularly when the disease progresses. However, single CTC analysis with our device shows a high level of intercellular heterogeneity in the receptor expression profiles of patient-derived CTCs and identifies heterogeneity within CTCs. More importantly, we find that a fraction of CTCs still shows a high expression of these receptor proteins during and after therapy, indicating the presence of resistant CTCs which may evolve after a certain time and progress the disease. We believe this automated assay will have high clinical importance in disease diagnosis and monitoring treatment and will significantly advance the understanding of cancer heterogeneity on the single cell level.

Abstract CT182: Neoadjuvant cemiplimab demonstrates complete pathological responses in hepatocellular carcinoma

Abstract Introduction: Hepatic resection is the accepted treatment of early-stage hepatocellular carcinoma (HCC), however, the majority of tumors recur despite surgery and no perioperative intervention has demonstrated a survival advantage. Neoadjuvant immunotherapy has shown success in inducing pathological responses alongside induction of immune memory in multiple tumor types and is being evaluated to determine its potential in HCC. Methods: We recently completed accrual into a trial of perioperative cemiplimab (anti-PD-1) for resectable HCC (NCT03916627, Cohort B). This trial enrolled 21 patients to receive 2 cycles of neoadjuvant cemiplimab (350 mg Q3W) followed by surgical resection and an additional 8 adjuvant cycles. The primary endpoint was significant tumor necrosis, defined as >70% necrosis of the resected tumor. Secondary endpoints included delay of surgery, overall response rate, adverse events (AEs), and change in lymphocyte infiltration. Patients underwent pre-treatment biopsies and regular blood collection throughout treatment to enable exploratory analyses including multiplex IHC and single-cell proteomic and transcriptomic analysis. The final patient enrolled underwent resection on December 28, 2020. Results: Over the course of 18 months, 21 patients were enrolled. All patients received 2 cycles of preoperative cemiplimab, and all but 1 patient underwent successful resection; 1 patient was found to have metastatic disease at the time of surgery and resection was aborted. Cemiplimab demonstrated an acceptable risk-benefit profile: 90.5% of patients experienced any treatment-emergent AE (TEAE) of any grade during the neoadjuvant treatment period through the perioperative period; 28.6% of patients experienced any Grade 3 TEAE. One patient experienced Grade 3 pneumonitis during neoadjuvant therapy and surgery was delayed by 2 weeks past protocol defined surgical window. Of the 20 patients with resected tumors, 4 (20%) met the predefined endpoint of >70% tumor necrosis and 7 (35%) had ≥50% tumor necrosis. Three (15%) of the 4 patients with >70% tumor necrosis had a pathological complete response, defined as 100% tumor necrosis. We observed similar patterns of change in degree of necrosis on pathological assessment and 3D MRI at baseline and following completion of immunotherapy. Initial pathological assessment suggests an association between immune cell infiltration and tumor response. Tissue analysis is ongoing and multiplex IHC relating myeloid and lymphoid infiltration patterns with response to cemiplimab will be presented at the meeting. Conclusion: This is the largest trial reported to date of neoadjuvant PD-1 targeted monotherapy in HCC. Pathological response data support larger trials to identify optimal clinical endpoints that correlate with improvement in survival, and to establish the utility and safety of perioperative PD-1 blockade. Citation Format: Thomas Urban Marron, Ganesh Gunasekaran, Parissa Tabrizian, Edward Kim, Maria Isabel Fiel, Stephen Ward, Zhen Zhao, Deborah Doroshow, Meredith Legg, Ashley Hammad, Paul Kennedy, Guray Akturk, Pauline Hamon, Antoinette Bonaccorso, Daniel Labow, Sacha Gnjatic, Bachir Taouli, Elizabeth Miller, Pradeep Thanigaimani, Nathalie Fiaschi, Jennifer Sims, Jayakumar Mani, Nicola James, Sara Hamon, Vladimir Jankovic, Siyu Li, Hung Kam Cheung, Gavin Thurston, Israel Lowy, Myron Schwartz, Miriam Merad. Neoadjuvant cemiplimab demonstrates complete pathological responses in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT182.