Assessing signaling pathways associated with in vitro resistance to cytotoxic agents in AML

Single-cell RNA Sequencing Contributes to the Treatment of Acute Myeloid Leukaemia With Hematopoietic Stem Cell Transplantation, Chemotherapy, and Immunotherapy

Acute myeloid leukemia (AML) is caused by altered maturation and differentiation of myeloid blasts, as well as transcriptional/epigenetic alterations and impaired apoptosis, all of which lead to excessive proliferation of malignant blood cells in the bone marrow. It is these mutations that cause tumor heterogeneity, which is linked to a higher risk of relapse and death and makes anti-AML treatments like HSCT, chemotherapy, and immunotherapy (ICI, CAR T-cell-based therapies, and cancer vaccines) less effective. Single-cell RNA sequencing (scRNA-seq) also makes it possible to find cellular subclones and profile tumors, which opens up new diagnostic and therapeutic targets for better AML management. The HSCT process works better when genetic and transcriptional information about the patient and donor stem cells is collected. This saves time and lowers the risk of harmful side effects happening in the body.

Single cell RNA sequencing improves the next generation of approaches to AML treatment: challenges and perspectives

Acute myeloid leukemia (AML) is caused by altered maturation and differentiation of myeloid blasts, as well as transcriptional/epigenetic alterations, all leading to excessive proliferation of malignant blood cells in the bone marrow. Tumor heterogeneity due to the acquisition of new somatic alterations leads to a high rate of resistance to current therapies or reduces the efficacy of hematopoietic stem cell transplantation (HSCT), thus increasing the risk of relapse and mortality. Single-cell RNA sequencing (scRNA-seq) will enable the classification of AML and guide treatment approaches by profiling patients with different facets of the same disease, stratifying risk, and identifying new potential therapeutic targets at the time of diagnosis or after treatment. ScRNA-seq allows the identification of quiescent stem-like cells, and leukemia stem cells responsible for resistance to therapeutic approaches and relapse after treatment. This method also introduces the factors and mechanisms that enhance the efficacy of the HSCT process. Generated data of the transcriptional profile of the AML could even allow the development of cancer vaccines and CAR T-cell therapies while saving valuable time and alleviating dangerous side effects of chemotherapy and HSCT in vivo. However, scRNA-seq applications face various challenges such as a large amount of data for high-dimensional analysis, technical noise, batch effects, and finding small biological patterns, which could be improved in combination with artificial intelligence models.

Combining Biology and Chemistry for a New Take on Chemotherapy: Antibody-Drug Conjugates in Hematologic Malignancies

PURPOSE OF REVIEW

This review is about the antibody-drug conjugate (ADC), a form of drug delivery consisting of a monoclonal antibody, linker, and cytotoxic payload. We summarize the history of ADC development, highlighting the three FDA-approved ADCs currently available.

RECENT FINDINGS

Gemtuzumab ozogamicin is a CD33-targeted ADC linked to calicheamicin. It is approved for CD33+ AML in the first line or the relapsed or refractory (R/R) setting. Brentuximab vedotin is a CD30-targeted ADC bound to MMAE. It is approved for the treatment of certain R/R CD30+ lymphomas. Recently, it has been approved for first line therapy with chemotherapy in advanced HL. Inotuzumab ozogamicin is a CD22-directed ADC attached to calicheamicin indicated for the treatment of adults with R/R B cell precursor ALL. Three ADCs have been approved for the treatment of various hematologic malignancies. We discuss the pertinent human trials that led to FDA approval. We include our perspectives about drug resistance, toxicities, and future development.

Novel single-cell technologies in acute myeloid leukemia research

Acute myeloid leukemia (AML) is a lethal malignancy because patients who initially respond to chemotherapy eventually relapse with treatment refractory disease. Relapse is caused by leukemia stem cells (LSCs) that reestablish the disease through self-renewal. Self-renewal is the ability of a stem cell to produce copies of itself and give rise to progeny cells. Therefore, therapeutic strategies eradicating LSCs are essential to prevent relapse and achieve long-term remission in AML. AML is a heterogeneous disease both at phenotypic and genotypic levels, and this heterogeneity extends to LSCs. Classical studies in AML have aimed at characterization of the bulk tumor population, thereby masking cellular heterogeneity. Single-cell approaches provide a novel opportunity to elucidate molecular mechanisms in heterogeneous diseases such as AML. In recent years, major advancements in single-cell measurement systems have revolutionized our understanding of the pathophysiology of AML and enabled the characterization of LSCs. Identifying the molecular mechanisms critical to AML LSCs will aid in the development of targeted therapeutic strategies to combat this deadly disease.

Quantitative measurement of alterations in DNA damage repair (DDR) pathways using single cell network profiling (SCNP)

Background

Homologous recombination repair (HRR) pathway deficiencies have significant implications for cancer predisposition and treatment strategies. Improved quantitative methods for functionally characterizing these deficiencies are required to accurately identify patients at risk of developing cancer and to identify mechanisms of drug resistance or sensitivity.

Methods

Flow cytometry-based single cell network profiling (SCNP) was used to measure drug-induced activation of DNA damage response (DDR) proteins in cell lines with defined HRR pathway mutations (including ATM-/-, ATM+/-, BRCA1+/-, BRCA2-/-) and in primary acute myeloid leukemia (AML) samples. Both non-homologous end joining (NHEJ) and HRR pathways were examined by measuring changes in intracellular readouts (including p-H2AX, p-ATM, p-DNA-PKcs, p-53BP1, p-RPA2/32, p-BRCA1, p-p53, and p21) in response to exposure to mechanistically distinct genotoxins. The cell cycle S/G2/M phase CyclinA2 marker was used to normalize for proliferation rates.

Results

Etoposide induced proliferation-independent DNA damage and activation of multiple DDR proteins in primary AML cells and ATM +/+but not ATM -/- cell lines. Treatment with the PARPi AZD2281 +/- temozolomide induced DNA damage in CyclinA2+ cells in both primary AML cells and cell lines and distngiushed cell lines deficient (BRCA2-/-) or impaired (BRCA1+/-) in HRR activity from BRCA1+/+ cell lines based on p-H2AX induction. Application of this assay to primary AML samples identified heterogeneous patterns of repair activity including muted or proficient activation of NHEJ and HRR pathways and predominant activation of NHEJ in a subset of samples.

Conclusions

SCNP identified functional DDR readouts in both NHEJ and HRR pathways, which can be applied to identify cells with BRCA1+/- haploinsuffiency and characterize differential DDR pathway functionality in primary clinical samples.

Immune system functional pathway analysis using single cell network profiling (SCNP): a novel tool in cancer immunotherapy

The development of cancer immunotherapies has been ongoing for many years and has shown limited success. Novel biomarkers are needed to identify patients most likely to respond to anticancer immune-therapeutic approaches. Moreover, a systems-level approach is required for comprehensive understanding of the interconnected components, pathways, and cell types associated with an immune response. In this chapter, we describe single cell network profiling (SCNP), a novel method for assessing and measuring immune function/dysfunction at a systems level. SCNP is a multiparametric flow-cytometry-based analysis that can simultaneously measure, at the single cell level, both extracellular surface markers and changes in intracellular signaling proteins in response to extracellular modulators. Measuring changes in signaling proteins following the application of an external modulation informs on the functional capacity of the signaling network which cannot be assessed by the measurement of basal signaling alone. In addition, the simultaneous analysis of multiple pathways in multiple cell subsets can provide insight into the connectivity of both cell signaling networks and immune cell subtypes. The experimental steps associated with an SCNP assay are (1) pre-analytical sample preparation; (2) modulation for functional analysis; (3) staining with antibody cocktail; (4) data acquisition on flow cytometer; and (5) data analysis and metrics. Important considerations for each step of the assay will be discussed, and data demonstrating the utility of SCNP for immune monitoring applications will be summarized.

Synergistic effect of 5-azacytidine and NF-κB inhibitor DHMEQ on apoptosis induction in myeloid leukemia cells

Constitutive NF-κB activation characterizes a subset of myeloid leukemia (ML) cells. Recent reports have indicated that DNA methyltransferase (DNMT) inhibitors are alternative candidates for the treatment of ML. However, the optimal use of DNMT as a chemotherapeutic agent against ML has yet to be established. In this report, we examined the effect of the NF-κB inhibitor dehydroxymethylepoxyquinomicin (DHMEQ) and its combinational use with the DNMT inhibitor 5-azacytidine (AZA) in ML cell lines. DHMEQ alone induced cell death in ML cell lines with NF-κB activation, although the response varied among the cell lines. The addition of DHMEQ enhanced the effect of AZA on the viability and apoptosis induction of ML cell lines. The treatment of ML cell lines with AZA marginally induced NF-κB binding activity, although the treatment induced NF-κB protein. These results indicate the potential usefulness of DHMEQ and its combinational use with AZA in the treatment of ML, although the molecular effect by AZA on the NF-κB pathway awaits further study.

AKT signaling as a novel factor associated with in vitro resistance of human AML to gemtuzumab ozogamicin

Gemtuzumab ozogamicin (GO), an immunoconjugate between an anti-CD33 antibody and a calicheamicin-γ₁ derivative, induces remissions and improves survival in a subset of patients with acute myeloid leukemia (AML). As the mechanisms underlying GO and calicheamicin-γ₁ resistance are incompletely understood, we herein used flow cytometry-based single cell network profiling (SCNP) assays to study cellular responses of primary human AML cells to GO. Our data indicate that the extent of DNA damage is quantitatively impacted by CD33 expression and drug efflux activity. However, although DNA damage is required for GO-induced cytotoxicity, it is not sufficient for effective cell kill, suggesting that downstream anti-apoptotic pathways may function as relevant resistance mechanisms. Supporting this notion, we found activated PI3K/AKT signaling to be associated with GO resistance in vitro in primary AML cells. Consistently, the investigational AKT inhibitor MK-2206 significantly sensitized various human AML cells to GO or free calicheamicin-γ₁ with particularly pronounced effects in otherwise GO or free calicheamicin-γ₁ -resistant cells. Likewise, MK-2206 also sensitized primary AML cells to calicheamicin-γ₁. Together, our findings illustrate the capacity of SCNP assays to discover chemotherapy-related biological pathways and signaling networks relevant to GO-induced genotoxic stress. The identification of AKT signaling as being associated with GO resistance in vitro may provide a novel approach to improve the in vivo efficacy of GO/calicheamicin-γ₁ and, by extrapolation, other DNA damage-based therapeutics.

A historical perspective on the development of the cytarabine (7days) and daunorubicin (3days) treatment regimen for acute myelogenous leukemia: 2013 the 40th anniversary of 7+3

This paper reviews the development of therapy for acute myelogenous leukemia that in 1973 led to the regimen of 7days of continuous intravenous arabinosylcytosine (cytarabine) and the first 3 concurrent days of intravenous daunorubicin, given the nickname "7+3." The state of leukemia treatment in the 1950s, 1960s and early 1970s is reviewed, the discovery of the two drugs in question described, and the introduction of clinical trials to reach an optimal regimen for their use delineated. During the 1950s, following World War Two and after a period of civil reconstitution, a national effort, facilitated by the U.S. Congress and federal investments in the National Cancer Institute, was initiated to enhance cancer therapy in the United States. The development of mouse models of leukemia and advances in understanding the structure and function of DNA and RNA and the process of cell proliferation provided new targets for drug development and new concepts for their use. The year, 2013, marks the 40th year that this protocol, 7+3, is the method of induction of remission for most patients with acute myelogenous leukemia. Its inadequacies also are made clear. Many patients with the disease die soon after diagnosis, and patients who have more unfavorable oncogenetic subtypes, intrinsically drug resistant cells, and greater intolerance to therapy make up the vast majority of the affected and few are cured. It is evident to all that new paradigms are needed if acute myelogenous leukemia is to be subdued in most patients with the disease.

From single cells to deep phenotypes in cancer

In recent years, major advances in single-cell measurement systems have included the introduction of high-throughput versions of traditional flow cytometry that are now capable of measuring intracellular network activity, the emergence of isotope labels that can enable the tracking of a greater variety of cell markers and the development of super-resolution microscopy techniques that allow measurement of RNA expression in single living cells. These technologies will facilitate our capacity to catalog and bring order to the inherent diversity present in cancer cell populations. Alongside these developments, new computational approaches that mine deep data sets are facilitating the visualization of the shape of the data and enabling the extraction of meaningful outputs. These applications have the potential to reveal new insights into cancer biology at the intersections of stem cell function, tumor-initiating cells and multilineage tumor development. In the clinic, they may also prove important not only in the development of new diagnostic modalities but also in understanding how the emergence of tumor cell clones harboring different sets of mutations predispose patients to relapse or disease progression.