Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection

Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on short-read data from next-generation sequencing that aligns back to a reference genome to determine if and, if so, where a structural variant occurs. However, structural variant discovery by short-read sequencing is challenging, primarily because of the difficulty in mapping regions of repetitive sequences. Optical genome mapping (OGM) is a recent technology used for imaging and assembling long DNA strands to detect structural variations. To capture the structural variant landscape more thoroughly in the human genome, we developed an integrated pipeline that combines Bionano OGM and Illumina whole-genome sequencing and applied it to samples from 29 pediatric B-ALL patients. The addition of OGM allowed us to identify 511 deletions, 506 insertions, 93 duplications/gains, and 145 translocations that were otherwise missed in the short-read data. Moreover, we identified several novel gene fusions, the expression of which was confirmed by RNA sequencing. Our results highlight the benefit of integrating OGM and short-read detection methods to obtain a comprehensive analysis of genetic variation that can aid in clinical diagnosis, provide new therapeutic targets, and improve personalized medicine in cancers driven by structural variation.

Signaling pathways and regulation of gene expression in hematopoietic cells

Cellular functions are regulated by signal transduction pathway networks consisting of protein-modifying enzymes that control the activity of many downstream proteins. Protein kinases and phosphatases regulate gene expression by reversible phosphorylation of transcriptional factors, which are their direct substrates. Casein kinase II (CK2) is a serine/threonine kinase that phosphorylates a large number of proteins that have critical roles in cellular proliferation, metabolism and survival. Altered function of CK2 has been associated with malignant transformation, immunological disorders and other types of diseases. Protein phosphatase 1 (PP1) is a serine/threonine phosphatase, which regulates the phosphorylation status of many proteins that are essential for cellular functions. IKAROS is a DNA-binding protein, which functions as a regulator of gene transcription in hematopoietic cells. CK2 directly phosphorylates IKAROS at multiple phosphosites which determines IKAROS activity as a regulator of gene expression. PP1 binds to IKAROS via the PP1-consensus recognition site and dephosphorylates serine/threonine residues that are phosphorylated by CK2. Thus, the interplay between CK2 and PP1 signaling pathways have opposing effects on the phosphorylation status of their mutual substrate - IKAROS. This review summarizes the effects of CK2 and PP1 on IKAROS role in regulation of gene expression and its function as a tumor suppressor in leukemia.

Abstract 6052: Metabolic consequences of casein kinase 2α inhibition in lymphoid leukemia

Overexpression of casein kinase 2α (CK2α) is a common feature in lymphoid leukemias. Constitutively active CK2α can disable transcriptional activity of lymphoid transcription factors like IKAROS that act as metabolic gatekeeper and limit the energy supply needed for oncogenic transformation of B cells. Our studies have shown that pharmacological inhibition of CK2α can restore the transcriptional activity of IKAROS and ablate leukemia. However, the role of CK2α in glucose metabolism has not been fully studied in B and T acute lymphoblastic leukemia (ALL). Therefore, in the present study we explored the metabolic alterations induced by the pharmacological inhibition of CK2α in B and T ALL. We studied the effect of CK2α inhibition using a specific inhibitor - CX4945 on cell proliferation, glucose utilization, lactate production, and intracellular ATP levels using established methods in human B-ALL (NALM6) cell line. Effect of CX4945 on glycolysis was studied using the Seahorse cell analyzer in human B (NALM6 and 697) and T (MOLT4 and 697) ALL cell lines. Metabolomics study was undertaken to analyze differential metabolite profiling in NALM6 cells treated with CX4945 compared to vehicle using LC-MS/MS based methods. Results showed that CX4945 induced apoptotic cell death in ALL cell lines with IC50 concentrations ranging between 4-10 µM. CX4945 treatment significantly affected the glucose consumption in NALM6 cells. Similarly, substantial decrease in intracellular ATP and lactate levels compared to vehicle was recorded. CK2α inhibition significantly decreased the glycolytic activity in B- and T-ALL cell lines. It was observed that glycolytic reserves were significantly decreased in 697 (3-fold), MOLT4 (4-fold), CEM (3-fold) cells incubated with CX4945 in comparison to vehicle. The principal component analysis from metabolomics study showed a clear separation between CX4945 and vehicle-treated NAML6 cells. Sixty-four statistically significant, differentially expressed metabolites were recorded in the study. Analyte classes included TCA cycle intermediates, nucleic acids and their precursors as well as glycolysis intermediates that were significantly affected by CK2α inhibition. In conclusion, our study shows that selective inhibition of CK2α by CX4945 caused energy deficiency and cell death in ALL cell lines. CK2 inhibition targeted the key energy dependent pathway by rendering ALL cells inefficient in utilizing glucose and operating glycolysis for generation of cellular energy. These results offer a new mechanistic understanding of CK2α inhibition mediated ablation of ALL.

Citation Format: Diwakar Bastihalli Tukaramrao, Arati Sharma, Dhimant Desai, Sinisa Dovat. Metabolic consequences of casein kinase 2α inhibition in lymphoid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6052.

Abstract 3833: Leonurine derivatives as a potential novel therapeutic approach to acute lymphoblastic leukemias (ALL)

Background: Pre-B cell Acute lymphoblastic leukemia (B ALL) high risk (HR) subgroups continue to result in significant mortality and morbidity of pediatric oncology patients. T cell ALL is higher risk and therapy has made less improvement than B ALL with a higher rate of significant poor outcomes. Novel treatment strategies are required to overcome chemotherapy resistance and improve mortality/morbidity for HR B ALL. Leonurine is a bioactive alkaloid that is naturally occurring only in Herbra Leonuri which has been used in traditional herbal medicine. Traditionally, it has been used for menstrual disorders. Research has further described its ability to scavenge oxygen free radicals, anticoagulation properties, and other anti-inflammatory properties[1]. There are investigations in its role for myocardial infarction, stroke, chronic kidney disease, and other inflammatory disorders[2]. Our research data that suggests that leonurine and its derivatives have antileukemic effects.Methods/Results: We analyzed multiple derivatives of leonurine and selected a potent candidate based on cell viability assays use for further testing designated as investigational leonurine derivative (ILD). WST1 proliferation studies comparing ILD to vehicle were performed in cell lines Nalm6, 697, Molt4, CEM, and JM1 at multiple time points. The half maximal inhibitory concentration (IC50) values was variable depending on the treatment time and cell line although all values were consistently between 1.2-4.4 uM. Apoptosis activity was determined by flow cytometry Anexin/7AAD assays showed increased apoptosis in cell lines treated with ILD for Nalm6, Molt4, and 697 cell lines. Caspase 3/7 activity was increased in cells treated with ILD when compared to vehicle treatment. DNA damage assays were performed which revealed only an increased frequency in single strand breaks and not double strand breaks. Western blot was performed to determine levels of PI3K, p-AKT, BCL2/BCL-XL and caspases. The blots suggest that apoptosis may be a result of increased activation of PI3K/AKT signaling. We performed RNAseq on cells treated with ILD at the 24-hour time point and present gene ontology data for this analysis. Nalm6, 697, and Molt4 cell lines expressing GFP and Luciferase were injected into NRG mice as means for in vivo pharmacologic testing. NRG mice injected with these cell lines were treated with ILD five days a week for a total of 3 weeks. Nalm 6 leukemia cells showed minimal differences between treatment and control groups.Conclusion: In summary, leonurine derivatives have a promising impact on apoptosis and cell survival. Further investigation into mechanisms and pharmacokinetics/dynamics will be more revealing. Study of leonurine derivatives will result in further translational and therapeutic applications.

Citation Format: Joseph W. Schramm, Melanie Ehudin, Bing He, Chingakham Singh, Daniel Bogush, Jeremy Hengst, Diwakar Bastihalli Tukaramrao, Arati Sharma, Dhimant Desai, Sinisa Dovat. Leonurine derivatives as a potential novel therapeutic approach to acute lymphoblastic leukemias (ALL). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3833.

IND-2, a Quinoline Derivative, Inhibits the Proliferation of Prostate Cancer Cells by Inducing Oxidative Stress, Apoptosis and Inhibiting Topoisomerase II

In men, prostate cancer (PC) is the most frequently diagnosed cancer, causing an estimated 375,000 deaths globally. Currently, existing therapies for the treatment of PC, notably metastatic cases, have limited efficacy due to drug resistance and problematic adverse effects. Therefore, it is imperative to discover and develop novel drugs for treating PC that are efficacious and do not produce intolerable adverse or toxic effects. Condensed quinolines are naturally occurring anticancer compounds. In this study, we determined the in vitro efficacy of IND-2 (4-chloro-2-methylpyrimido[1″,2″:1,5]pyrazolo[3,4-b]quinolone) in the PC lines, PC-3 and DU-145. IND-2 significantly inhibited the proliferation of PC-3 and DU-145, with IC₅₀ values of 3 µM and 3.5 µM, respectively. The incubation of PC-3 cells with 5 and 10 µM of IND-2 caused the loss of the mitochondrial membrane potential in PC-3 cells. Furthermore, IND-2, at 5 µM, increased the expression of cleaved caspase-3, cleaved caspase-7 and cleaved poly (ADP-ribose) polymerase (PARP). The incubation of PC-3 cells with 5 µM of IND-2 significantly decreased the expression of the apoptotic protein, B-cell lymphoma 2 (Bcl-2). Furthermore, 5 and 10 µM of IND-2 produced morphological changes in PC-3 cells characteristic of apoptosis. Interestingly, IND-2 (2.5, 5 and 10 µM) also induced mitotic catastrophe in PC-3 cells, characterized by the accumulation of multinuclei. The incubation of DU-145 cells with 1.25 and 5 μM of IND-2 significantly increased the levels of reactive oxygen species (ROS). Finally, IND-2, at 10 μM, inhibited the catalytic activity of topoisomerase IIα. Overall, our findings suggest that IND-2 could be a potential lead compound for the development of more efficacious compounds for the treatment of PC.

DJ4 Targets the Rho-Associated Protein Kinase Pathway and Attenuates Disease Progression in Preclinical Murine Models of Acute Myeloid Leukemia

The poor prognosis of acute myeloid leukemia (AML) and the highly heterogenous nature of the disease motivates targeted gene therapeutic investigations. Rho-associated protein kinases (ROCKs) are crucial for various actin cytoskeletal changes, which have established malignant consequences in various cancers, yet are still not being successfully utilized clinically towards cancer treatment. This work establishes the therapeutic activity of ROCK inhibitor (5Z)-2-5-(1H-pyrrolo[2,3-b]pyridine-3-ylmethylene)-1,3-thiazol-4(5H)-one (DJ4) in both in vitro and in vivo preclinical models of AML to highlight the potential of this class of inhibitors. Herein, DJ4 induced cytotoxic and proapoptotic effects in a dose-dependent manner in human AML cell lines (IC50: 0.05-1.68 μM) and primary patient cells (IC50: 0.264-13.43 μM); however, normal hematopoietic cells were largely spared. ROCK inhibition by DJ4 disrupts the phosphorylation of downstream targets, myosin light chain (MLC2) and myosin-binding subunit of MLC phosphatase (MYPT), yielding a potent yet selective treatment response at micromolar concentrations, from 0.02 to 1 μM. Murine models injected with luciferase-expressing leukemia cell lines subcutaneously or intravenously and treated with DJ4 exhibited an increase in overall survival and reduction in disease progression relative to the vehicle-treated control mice. Overall, DJ4 is a promising candidate to utilize in future investigations to advance the current AML therapy.

A Novel Thienopyrimidine Analog, TPH104, Mediates Immunogenic Cell Death in Triple-Negative Breast Cancer Cells

Simple Summary

Triple-negative breast cancer (TNBC) is the most lethal and aggressive subtype of breast cancer that lacks an estrogen receptor, the progesterone receptor and the human epidermal growth factor receptor 2 (HER2), making it unsuitable for hormonal- or HER2-based therapy. TNBC is known for its higher relapse rate, poorer prognosis and higher rate of metastasis compared to non-TNBC because although patients initially respond to chemotherapy that kills cancer cells through a form of programmed cell death called apoptosis, they later develop chemoresistance and stop responding to the treatment, accounting for one fourth of all breast cancer deaths. In this study, we report a novel compound, TPH104, that elicits a unique, non-apoptotic cell death in TNBC cells. Upon treatment with TPH104, TNBC cells swell and burst, releasing immunogenic markers that alert and activate the immune system to further recognize and attack the neighboring breast cancer cells.

Abstract

Enhancing the tumor immunogenic microenvironment has been suggested to circumvent triple-negative breast cancer (TNBC) resistance and increase the efficacy of conventional chemotherapy. Here, we report a novel chemotherapeutic compound, TPH104, which induces immunogenic cell death in the TNBC cell line MDA-MB-231, by increasing the stimulatory capacity of dendritic cells (DCs), with an IC₅₀ value of 140 nM. TPH104 (5 µM) significantly increased ATP levels in the supernatant and mobilized intracellular calreticulin to the plasma membrane in MDA-MB-231 cells, compared to cells incubated with the vehicle. Incubating MDA-MB-231 cells for 12 h with TPH104 (1–5 µM) significantly increased TNF-α mRNA levels. The supernatants of dying MDAMB-231 cells incubated with TPH104 increased mouse bone marrow-derived DC maturation, the expression of MHC-II and CD86 and the mRNA expression of TNF-α, IL-6 and IL-12. Overall, these results indicate that TPH104 induces immunogenic cell death in TNBC cells, in part, by activating DCs.

Abstract 2406: Novel thienopyrimidine analog TPH104 induces immunogenic cell death in TNBC cells

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high propensity for metastasis and recurrence, accounting for one-fourth of all breast cancer deaths. Despite being chemo-sensitive to anthracyclines and taxanes, TNBCs have poor prognosis due to development of resistance often due to the overexpression of efflux transporters, increased DNA repair, and occurrence of genetic mutations that decrease the likelihood of apoptosis. Recently, we discovered a novel class of thieno-pyrimidin-hydrazinyl (TPH) compounds that in the nanomolar range, selectively elicited a unique, caspase-independent cell death in TNBC cells. The lead compound, TPH104, selectively activates receptor interacting protein kinase 1 (RIPK1), thus inducing a necroptosis like cell death. Since necroptosis is known to release endogenous immunogenic markers, we wanted to study whether TPH104 can promote immunogenic cell death (ICD) in TNBC cells and activate cells in the tumor immune milieu. ICD is characterized by presence of damage-associated molecular patterns (DAMPs) such as cell surface exposure of calreticulin (CRT), secretion of ATP, and release of high-mobility group box protein B1 (HMGB1) from dying tumor cells.

Methods: Human TNBC cell line MDA-MB-231 cells were treated with TPH104 and cell survival was examined by 3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide (MTT), clonogenic and live-cell imaging assays. Western blot analysis was used to assess death signal transducers. DAMPs were examined by ELISA, luminescence-based assay systems and immunofluorescence. Activation of mouse bone marrow derived dendritic cells (BMDCs) in response to conditioned media (CM) harvested after treatment of MDA-MB-231 cells with TPH104 (TPH104-CM) and/or mitoxantrone (MX, positive control) for 48h was evaluated using flow cytometry analysis of maturation markers (CD86, MHCII) expressed on CD11C+ BMDCs. Inflammatory gene expression was evaluated by q-PCR.

Results: The results demonstrated that TPH104 reduced cell survival and induced death of MDA-MB-231 cells in a dose-dependent pattern. TPH104 induced ICD, as evidenced by increased release of ATP, as well as surface exposure of CRT. Flow cytometric analysis revealed TPH104-CM treatment increased CD11C+CD86+MHC+ BMDCs as robustly as MX-CM. Further, TPH104 posed no toxicity to mice in a single dose toxicity study.

Conclusion: TPH104 induced selective ICD in MDA-MB-231 cells. TPH104 similar to MX primed cells to ICD and increased extracellular ATP levels and surface exposure of CRT. TPH104 promoted maturation of CD11C+ BMDCs and increased inflammatory gene expression. Our study demonstrated TPH104 as an ICD-inducer and immunomodulator in TNBC.

Citation Format: Diwakar Bastihalli Tukaramrao, Siddharth Saraiya, Ross A. Hanely, Saloni Malla, Amit K. Tiwari. Novel thienopyrimidine analog TPH104 induces immunogenic cell death in TNBC cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2406.

Abstract 4119: Necroptosis inducing thienopyridine analogs overcomes chemoresistance in TNBC

Triple-negative breast cancer (TNBC), defined by the lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2), is the most aggressive and lethal form of breast cancer. The treatment of chemo-resistant TNBC tumors is particularly challenging due to the overexpression of efflux transporters, increased DNA repair, and the occurrence of genetic mutations that decrease the likelihood of apoptosis. Lack of clear targets and development of drug resistance allows TNBC to advance to metastatic stage thus resulting in poor prognosis and survival outcome. Recently, we discovered thieno-pyrimidin-hydrazinyl (TPH) class of small molecules that causes necroptotic (i.e. programmed necrosis) cell death in TNBC cells. We found that the lead compound TPH104 has an IC50 value of 160-400 nm and has ~400-fold selectivity towards different TNBC cell lines compared to normal breast cells. TPH104 selectively induced receptor interacting protein kinase 1 (RIPK1) - mediated necroptosis, while promoting autophagy thus resulting in significant inhibition of TNBC cell proliferation. We characterized eighteen novel TPH analogs for their cytotoxic potential and structure activity relation (SAR) and learned that the subtle changes in TPH pharmacophore could enhance or decrease efficacy against TNBC cells. We observed that 2-OH group is required to exert cytotoxic potency. Two new hit analogs of TPH104, TPH104c and TPH104m were found to activate necroptotic cell death markers (RIP, MLKL) with IC50 values similar to TPH104 in TNBC cells. Both analogs decreased the TNBC cell proliferation, and rate of colony formation compared to controls. Mechanistically, similar to TPH104, these analogs did not produce significant apoptosis induction i.e. no loss of mitochondrial membrane potential and arrested the TNBC cells in S-phase of cell cycle. Interestingly, unlike TPH104, TPH104c and TPH104m activate executioner caspases 3 and 7 only at extremely high concentration. TPH104 and its analogs reversed resistance mediated by ABCB1 and ABCG2 transporters through collateral sensitivity. TPH analogs in combination with doxorubicin and paclitaxel synergistically inhibited TNBC and TNBC/resistant (R) cells and reduced the dose-reduction index. Further understanding SAR of TPH analogs and the biology of non-apoptotic, necroptosis cell death by this new class of small molecules will help define a multimodal, non-apoptotic approach to overcome chemoresistance in TNBC patients. This will lead to the development of more selective and efficacious compounds that kills TNBC cells through unique cell death mechanism.

Citation Format: Saloni Malla, Diwakar Bastihalli Tukaramrao, Divya L. Dayanidhi, Pia Vogel, Shikha Kumari, Amit K. Tiwari. Necroptosis inducing thienopyridine analogs overcomes chemoresistance in TNBC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4119.